diff --git a/isis/3rdParty/Makefile b/isis/3rdParty/Makefile index 576c3b44ec8586ba611694c09d3498ada7778325..967bd3e76ba62370f7b8b132b0f5c662fcc620c7 100644 --- a/isis/3rdParty/Makefile +++ b/isis/3rdParty/Makefile @@ -27,6 +27,21 @@ libs: done; \ fi; \ done; \ + for library in $(PATCHLIBS); do \ + $(INSTALL3P) $(INSTALL3POPTS) $$library $(ISISROOT)/3rdParty/lib/; \ + echo $(CURTIMESTAMP) " Installing [$$library]"; \ + if [ "$(HOST_ARCH)" == "Linux" ]; then \ + for file in $$library; do \ + localFile=$(ISISROOT)/3rdParty/lib/`basename $$file`; \ + if [ ! -L "$$localFile" ]; then \ + dollar='$$'; \ + newRpath=`echo "$${dollar}ORIGIN"`; \ + echo $(CURTIMESTAMP) " Patching [" `basename $$file` "]"; \ + $(PATCHELF) --set-rpath "$$newRpath" $$localFile; \ + fi; \ + done; \ + fi; \ + done; \ if [ "$(HOST_ARCH)" == "Darwin" ]; then \ chmod u+w $(ISISROOT)/3rdParty/lib/libcrypto.*.dylib; \ chmod u+w $(ISISROOT)/3rdParty/lib/libssl.*.dylib; \ diff --git a/isis/IsisPreferences b/isis/IsisPreferences index 4b7d3378bd609bfcf3363fa13cffc901c95abad6..81b062d6f4b719ce70bb490a1723c3507ee4c774 100644 --- a/isis/IsisPreferences +++ b/isis/IsisPreferences @@ -163,6 +163,7 @@ Group = DataDirectory Clementine1 = $ISIS3DATA/clementine1 Control = $ISIS3DATA/control Dawn = $ISIS3DATA/dawn + Tgo = $ISIS3DATA/tgo Galileo = $ISIS3DATA/galileo Hayabusa = $ISIS3DATA/hayabusa Kaguya = $ISIS3DATA/kaguya diff --git a/isis/Makefile b/isis/Makefile index 95bcaced2d69d8ac24d808a4584118fbe687b2f9..24fd4e1d5d0a9292b0bcfe214ece482bb1d370d5 100644 --- a/isis/Makefile +++ b/isis/Makefile @@ -22,7 +22,6 @@ help: echo "Isis Make System Commands" echo "------------------------ " echo "make all : Build and install the entire system (incs,api,apps,docs)" - echo "make config : Generate preliminary config parameters" echo "make thirdParty : Copy required 3rdParty libraries into distribution" echo "make incs : Install API include files" echo "make api : Build and install the Isis API" @@ -44,19 +43,7 @@ help: # After the API is created then the applications can be individually built # and installed. Finally create the web documentation for the entire system. #---------------------------------------------------------------------------- -all: config incs thirdParty api apps docs - -#---------------------------------------------------------------------------- -# Target = config -# Dependencies = none -# -# Set up any compile/link configuration dependancy files -#---------------------------------------------------------------------------- -config: FORCE - echo $(CURTIMESTAMP) "Creating config files" - $(MAKE) --directory=config -f config.mak config - echo $(CURTIMESTAMP) "Finished creating config files" - echo $(CURTIMESTAMP) " " +all: incs thirdParty api apps docs #---------------------------------------------------------------------------- # Target = incs @@ -67,7 +54,7 @@ config: FORCE # copy the include file from the individual object directory into the # system directory $(ISISROOT)/inc. #---------------------------------------------------------------------------- -incs: config +incs: echo $(CURTIMESTAMP) "Installing include files" mkdir -p inc $(MAKE) --directory=src includes @@ -94,6 +81,7 @@ incs: config # Finally after the API is completed the shared libraries will be # constructed from libisis.a #---------------------------------------------------------------------------- + api: echo $(CURTIMESTAMP) "Building Isis API" mkdir -p lib @@ -101,9 +89,29 @@ api: echo $(CURTIMESTAMP) "Finished building Isis API" echo $(CURTIMESTAMP) "" echo $(CURTIMESTAMP) "Adding API objects" - $(MAKE) --directory=src api + if [ "$(HOST_ARCH)" == "Linux" ]; then \ + $(MAKE) --directory=src api; \ + elif [ "$(HOST_ARCH)" == "Darwin" ]; then \ + $(MAKE) osx_static; \ + fi; echo $(CURTIMESTAMP) "Finished adding API objects" echo $(CURTIMESTAMP) " " + echo $(CURTIMESTAMP) "Creating Shared Libraries ..." + cp make/Makefile.libs lib/Makefile + $(MAKE) --directory=lib shared + echo $(CURTIMESTAMP) "Finished creating Shared Libraries ..." + echo $(CURTIMESTAMP) " " + +# Make the static library on Macos, faster then recursivly call make +osx_static: + $(eval UNIT_TESTS=$(wildcard src/*/objs/*/unitTest.o)) + $(eval PLUGIN_DIRS=$(dir $(wildcard src/*/objs/*/*.plugin))) + $(eval PLUGIN_FILES=$(foreach dir,$(PLUGIN_DIRS),$(wildcard $(dir)*.o))) + $(eval API_OBJS=$(filter-out $(PLUGIN_FILES),$(filter-out $(UNIT_TESTS),$(wildcard src/*/objs/*/*.o)))) + $(AR) -crs $(ISISROOT)/lib/libisis$(ISISLIBVERSION).a $(API_OBJS); + for i in $(PLUGIN_DIRS); do \ + $(MAKE) --directory=$$i plugin install; \ + done # echo "Building Isis API with debugging" # cd src; $(MAKE) objects MODE=DEBUG @@ -111,12 +119,6 @@ api: # echo "Finished building Isis API with debugging" # echo " " - echo $(CURTIMESTAMP) "Creating Shared Libraries ..." - cp make/Makefile.libs lib/Makefile - $(MAKE) --directory=lib shared - echo $(CURTIMESTAMP) "Finished creating Shared Libraries ..." - echo $(CURTIMESTAMP) " " - #---------------------------------------------------------------------------- # Target = apps # Dependencies = none @@ -152,7 +154,7 @@ docs: #---------------------------------------------------------------------------- -# Target = coverage +# Target = coverage # Dependencies = none # # This target builds a report on how much of Isis is tested in the automated @@ -224,7 +226,7 @@ coverage: # binary executables from the source tree. It also, clears the running # areas under $ISISROOT (inc, doc, bin, bin/xml, and lib) # -# Target = quickclean +# Target = quickclean # Dependencies = none # # This walks the src tree and removes ".o" files and binary files @@ -240,7 +242,6 @@ quickclean: rm -rf scopecoverage scopecoverage.html linecoverage linecoverage.html \ functioncoverage functioncoverage.html *.csmes *.csexe; \ $(MAKE) --directory=3rdParty clean; \ - $(MAKE) --directory=config -f config.mak clean; \ echo $(CURTIMESTAMP) "Finished cleaning Isis"; #---------------------------------------------------------------------------- @@ -267,7 +268,6 @@ clean: rm -rf scopecoverage scopecoverage.html linecoverage linecoverage.html \ functioncoverage functioncoverage.html *.csmes *.csexe; \ $(MAKE) --directory=3rdParty clean; \ - $(MAKE) --directory=config -f config.mak clean; \ echo $(CURTIMESTAMP) "Finished cleaning Isis"; cleansrc: @@ -321,7 +321,7 @@ catTest: HOST_ARCH ?= $(shell uname -s) HOST_MACH ?= $(shell uname -m) -thirdParty: config +thirdParty: echo $(CURTIMESTAMP) "Installing 3rdParty libraries" rm -f $(ISISROOT)/3rdParty/lib/lib* $(MAKE) -C $(ISISROOT)/3rdParty install @@ -347,4 +347,3 @@ FORCE: # Include the make file debugging targets #---------------------------------------------------------------------------- include $(ISISROOT)/make/isismake.print - diff --git a/isis/make/config.darwin-MacOSX10_10 b/isis/make/config.darwin-MacOSX10_10 index 37679c07379b6a565301d6689158c0d38dc89d2a..17e4f0ad1b7ff6165d812108b51561fa81956752 100644 --- a/isis/make/config.darwin-MacOSX10_10 +++ b/isis/make/config.darwin-MacOSX10_10 @@ -82,7 +82,6 @@ ISIS3PROP ?= $(IDK_ROOT)/proprietary # Set up paths to tools needed for doxygen DOXYGEN = $(ISIS3OPT)/bin/doxygen DOT_PATH = $(ISIS3OPT)/bin -LATEX = $(ISIS3OPT)/bin/latex #--------------------------------------------------------------------------- # Set up for cwd diff --git a/isis/make/config.darwin-MacOSX10_11 b/isis/make/config.darwin-MacOSX10_11 index d0e17a4d31c1660ff626501e4c894bf3d42bfe0c..5faabdb6a057bce7d2ae43aa2c6785680f4891f2 100644 --- a/isis/make/config.darwin-MacOSX10_11 +++ b/isis/make/config.darwin-MacOSX10_11 @@ -90,7 +90,6 @@ ISIS3PROP ?= $(IDK_ROOT)/proprietary # Set up paths to needed for doxygen DOXYGEN = $(ISIS3OPT)/bin/doxygen DOT_PATH = $(ISIS3OPT)/bin -LATEX = $(ISIS3OPT)/bin/latex GREP = $(ISIS3OPT)/bin/grep #--------------------------------------------------------------------------- @@ -339,8 +338,10 @@ HDF5LIB = -lhdf5 -lhdf5_hl -lhdf5_cpp -lhdf5_hl_cpp #--------------------------------------------------------------------------- #OPENCVINCDIR = -I$(ISIS3OPT)/include #OPENCVLIBDIR = -L$(ISIS3OPT)/lib # Redundant -OPENCVLIBS = -lopencv_calib3d -lopencv_core -lopencv_features2d \ - -lopencv_flann -lopencv_highgui -lopencv_imgproc \ +OPENCVLIBS = -lopencv_calib3d -lopencv_core \ + -lopencv_features2d -lopencv_xfeatures2d \ + -lopencv_flann -lopencv_highgui \ + -lopencv_imgproc -lopencv_imgcodecs \ -lopencv_ml -lopencv_objdetect \ -lopencv_photo -lopencv_stitching -lopencv_superres \ -lopencv_video -lopencv_videostab @@ -504,6 +505,17 @@ THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libglib-*.dylib" THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libp11-kit*.dylib" THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libffi*.dylib" +# OpenCV3 dependencies +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libavresample*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libxcb-shm*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libsoxr*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libopenjp2*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libOpenNI*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libswresample*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libidn*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libtasn1*.dylib" +THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libusb*.dylib" + # libxerces-c depends on these libraries THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libicui18n*.dylib" THIRDPARTYLIBS += "$(ISIS3OPT)/lib/libicuuc*.dylib" diff --git a/isis/make/config.darwin-MacOSX10_6 b/isis/make/config.darwin-MacOSX10_6 index 3f6a350479e8aead6ce2aab5bf41fd7aa5376df6..eac09ea0c9fae8255c281bd63d0cb216a0d0e432 100644 --- a/isis/make/config.darwin-MacOSX10_6 +++ b/isis/make/config.darwin-MacOSX10_6 @@ -79,7 +79,6 @@ ISIS3PROP ?= $(IDK_ROOT)/proprietary # Set up paths to needed for doxygen DOXYGEN = $(ISIS3OPT)/bin/doxygen DOT_PATH = $(ISIS3OPT)/bin -LATEX = $(ISIS3OPT)/bin/latex #--------------------------------------------------------------------------- # Set up for cwd diff --git a/isis/make/config.darwin-MacOSX10_8 b/isis/make/config.darwin-MacOSX10_8 index 03fd12f1acbe5ece16a5a39059a571bcd2f9ffe8..b7f693ccf3849b7ae46d7c445a43e9018d7adc29 100644 --- a/isis/make/config.darwin-MacOSX10_8 +++ b/isis/make/config.darwin-MacOSX10_8 @@ -82,7 +82,6 @@ ISIS3PROP ?= $(IDK_ROOT)/proprietary # Set up paths to needed for doxygen DOXYGEN = $(ISIS3OPT)/bin/doxygen DOT_PATH = $(ISIS3OPT)/bin -LATEX = $(ISIS3OPT)/bin/latex #--------------------------------------------------------------------------- # Set up for cwd diff --git a/isis/make/config.linux-x86_64 b/isis/make/config.linux-x86_64 index 724c4753652097e5fe3d6917e8a4559cb84f9bf8..ba58052189f53b0d191fcdba7df4113d44e39791 100644 --- a/isis/make/config.linux-x86_64 +++ b/isis/make/config.linux-x86_64 @@ -131,6 +131,8 @@ XERCESINCDIR = -I$(ISIS3LOCAL)/include/xercesc/xercesc-3.1.2 XERCESLIBDIR = -L$(ISIS3LOCAL)/lib XERCESLIB = -lxerces-c +XALAN = $(ISIS3LOCAL)/bin/Xalan + #--------------------------------------------------------------------------- # Set up for geotiff #--------------------------------------------------------------------------- @@ -274,8 +276,10 @@ HDF5LIB = -lhdf5 -lhdf5_hl -lhdf5_cpp -lhdf5_hl_cpp #--------------------------------------------------------------------------- OPENCVINCDIR = -I$(ISIS3LOCAL)/include OPENCVLIBDIR = -L$(ISIS3LOCAL)/lib -OPENCVLIBS = -lopencv_calib3d -lopencv_core -lopencv_features2d \ - -lopencv_flann -lopencv_highgui -lopencv_imgproc \ +OPENCVLIBS = -lopencv_calib3d -lopencv_core \ + -lopencv_features2d -lopencv_xfeatures2d \ + -lopencv_flann -lopencv_highgui \ + -lopencv_imgproc -lopencv_imgcodecs \ -lopencv_ml -l opencv_objdetect \ -lopencv_photo -lopencv_stitching -lopencv_superres \ -lopencv_video -lopencv_videostab \ diff --git a/isis/make/config.linux-x86_64_Debian8 b/isis/make/config.linux-x86_64_Debian8 new file mode 100644 index 0000000000000000000000000000000000000000..75deb91f17c2ef93ec7c6982ad9ec2dc4bf7d386 --- /dev/null +++ b/isis/make/config.linux-x86_64_Debian8 @@ -0,0 +1,455 @@ +#--------------------------------------------------------------------------- +# Compiler options +#--------------------------------------------------------------------------- + +ISISCPPFLAGS = -Wall +ISISCPPFLAGS += -ansi +ISISCPPFLAGS += -DISIS_LITTLE_ENDIAN=1 +ISISCPPFLAGS += -fPIC +ISISCPPFLAGS += -DGMM_USES_SUPERLU + +ifeq ($(findstring DEBUG, $(MODE)),DEBUG) + ISISCPPFLAGS += -g + ISISCPPFLAGS += -O0 + ISISCPPFLAGS += -DDEBUG + ifeq ($(findstring CWD, $(MODE)),CWD) + ISISCPPFLAGS += -DCWDEBUG -DLIBCWD_THREAD_SAFE -D_REENTRANT + ifeq (,$(findstring MEMCHECK, $(MODE))) + ISISCPPFLAGS += -DNOMEMCHECK + endif + endif +else + ISISCPPFLAGS += -O1 +endif + +ISISCFLAGS = + +#--------------------------------------------------------------------------- +# Linker options +#--------------------------------------------------------------------------- +RANLIB = /bin/true +SHAREDLIBEXT = so + +ISISLDFLAGS = -Wl,-E -Xlinker '-z' -Xlinker 'origin' +ISISLDFLAGS += -Xlinker "-rpath" -Xlinker "${ISISROOT}/lib:${ISISROOT}/3rdParty/lib" +ISISSYSLIBS = -pthread +ISISSTATIC = -Wl,-Bstatic +ISISDYNAMIC = -Wl,-Bdynamic + +ifeq ($(findstring DEBUG, $(MODE)),DEBUG) + ifeq ($(findstring CWD, $(MODE)),CWD) + ISISSYSLIBS += -lcwd_r + endif +endif + +#--------------------------------------------------------------------------- +# Shared library options +#--------------------------------------------------------------------------- +ISISSHAREDFLAGS = $(ISISLDFLAGS) -shared +ISISSHAREDON = -Wl,-whole-archive +ISISSHAREDOFF = -Wl,-no-whole-archive +ISISARFLAGS = + +#--------------------------------------------------------------------------- +# Set up for modifying the executable rpath +#--------------------------------------------------------------------------- +PATCHELF = $(ISIS3LOCAL)/bin/patchelf + +#--------------------------------------------------------------------------- +# Set up local library designations +#--------------------------------------------------------------------------- +ISIS3SYSINC := /usr/include +#ISIS3SYSLIB ?= /usr/lib64 +ISIS3SYSLIB := $(shell if [ -d /usr/lib64 ]; then echo "/usr/lib64"; else echo "/usr/lib"; fi;) +ISIS3ALTSYSLIB := $(shell if [ -f /usr/lib/x86_64-linux-gnu/libgfortran.so.3 ]; then \ + echo "/usr/lib/x86_64-linux-gnu"; else echo "/usr/lib64"; fi;) +ISIS3LOCAL := /usgs/pkgs/local/$(ISISLOCALVERSION) + +#--------------------------------------------------------------------------- +# Set up for cwd +#--------------------------------------------------------------------------- +#CWDINCDIR = +#CWDLIBDIR = +#CWDLIB = + +#ifeq ($(findstring DEBUG, $(MODE)),DEBUG) +# ifeq ($(findstring CWD, $(MODE)),CWD) +# CWDINCDIR = -I$(ISIS3LOCAL)/include/libcwd/libcwd-1.0.4 +# CWDLIBDIR = -L$(ISIS3LOCAL)/lib +# CWDLIB = -lcwd_r +# endif +#endif + +#--------------------------------------------------------------------------- +# Set up for Qt +#--------------------------------------------------------------------------- +QTINCDIR = -I$(ISIS3LOCAL)/include/qt/qt5.6.0 +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/Qt +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtCore +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtAssistant +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtConcurrent +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtDBus +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtGui +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtMultimedia +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtMultimediaWidgets +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtNetwork +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtOpenGL +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtPositioning +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtPrintSupport +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtQml +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtQuick +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtScript +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtScriptTools +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtSensors +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtSql +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtSvg +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtTest +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWebChannel +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWebEngine +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWebEngineWidgets +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWidgets +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtXml +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtXmlPatterns +QTLIBDIR = -L$(ISIS3LOCAL)/lib +QTLIB = -lQt5Core -lQt5Concurrent -lQt5XmlPatterns -lQt5Xml -lQt5Network -lQt5Sql -lQt5Gui -lQt5PrintSupport -lQt5Positioning -lQt5Qml -lQt5Quick -lQt5Sensors -lQt5Svg -lQt5Test -lQt5OpenGL -lQt5Widgets -lQt5Multimedia -lQt5MultimediaWidgets -lQt5WebChannel -lQt5WebEngine -lQt5WebEngineWidgets -lQt5DBus + +UIC = $(ISIS3LOCAL)/bin/uic +MOC = $(ISIS3LOCAL)/bin/moc +RCC = $(ISIS3LOCAL)/bin/rcc + +#--------------------------------------------------------------------------- +# Set up for Qwt +#--------------------------------------------------------------------------- +QWTINCDIR = -I$(ISIS3LOCAL)/include/qwt +QWTLIBDIR = -L$(ISIS3LOCAL)/lib +QWTLIB = -lqwt + +#--------------------------------------------------------------------------- +# Set up for Xerces +#--------------------------------------------------------------------------- +XERCESINCDIR = -I$(ISIS3LOCAL)/include/xercesc/xercesc-3.1.2 +XERCESLIBDIR = -L$(ISIS3LOCAL)/lib +XERCESLIB = -lxerces-c + +#--------------------------------------------------------------------------- +# Set up for geotiff +#--------------------------------------------------------------------------- +GEOTIFFINCDIR = -I$(ISIS3LOCAL)/include/geotiff +GEOTIFFLIBDIR = -L$(ISIS3LOCAL)/lib +GEOTIFFLIB = -lgeotiff + +#--------------------------------------------------------------------------- +# Set up for Tiff +#--------------------------------------------------------------------------- +TIFFINCDIR = -I$(ISIS3LOCAL)/include/tiff/tiff-4.0.5 +TIFFLIBDIR = -L$(ISIS3LOCAL)/lib +TIFFLIB = -ltiff + +#--------------------------------------------------------------------------- +# Set up for naif dsk and cspice libraries +#--------------------------------------------------------------------------- +NAIFINCDIR = -I$(ISIS3LOCAL)/include/naif +NAIFLIBDIR = -L$(ISIS3LOCAL)/lib +NAIFLIB = -ldsk -lcspice + +#--------------------------------------------------------------------------- +# Set up for TNT +#--------------------------------------------------------------------------- +TNTINCDIR = -I$(ISIS3LOCAL)/include/tnt/tnt126 -I$(ISIS3LOCAL)/include/tnt/tnt126/tnt +TNTLIBDIR = +TNTLIB = + +#--------------------------------------------------------------------------- +# Set up for JAMA +#--------------------------------------------------------------------------- +JAMAINCDIR = -I$(ISIS3LOCAL)/include/jama/jama125 +JAMALIBDIR = +JAMALIB = + +#--------------------------------------------------------------------------- +# Set up for GEOS +#--------------------------------------------------------------------------- +GEOSINCDIR = -I$(ISIS3LOCAL)/include/geos/geos3.5.0 +GEOSLIBDIR = -L$(ISIS3LOCAL)/lib +GEOSLIB = -lgeos-3.5.0 -lgeos_c + +#--------------------------------------------------------------------------- +# Set up for the GNU Scientific Library (GSL). Note that this setup +# suppports include patterns such as . With this +# format, any other include spec that points to the general include +# directory, such as GEOS, will suffice. Therefore, an explicit +# include directive is ommitted but provided as an empty reference +# in cases where it may be located elsewhere. This also goes for the +# library reference. +#--------------------------------------------------------------------------- +GSLINCDIR = -I$(ISIS3LOCAL)/include +GSLLIBDIR = -L$(ISIS3LOCAL)/lib +GSLLIB = -lgsl -lgslcblas + +#--------------------------------------------------------------------------- +# Set up for X11 +#--------------------------------------------------------------------------- +X11INCDIR = +X11LIBDIR = +X11LIB = -lX11 + +#--------------------------------------------------------------------------- +# Set up for GMM +#--------------------------------------------------------------------------- +GMMINCDIR = -I$(ISIS3LOCAL)/include/gmm/gmm-5.0 -I$(ISIS3LOCAL)/include/gmm/gmm-5.0/gmm +GMMLIBDIR = +GMMLIB = + +#--------------------------------------------------------------------------- +# Set up for SuperLU +#--------------------------------------------------------------------------- +SUPERLUINCDIR = -I$(ISIS3LOCAL)/include/superlu/superlu4.3 +SUPERLULIBDIR = -L$(ISIS3LOCAL)/lib +SUPERLULIB = -lsuperlu_4.3 -lblas -lgfortran + +#--------------------------------------------------------------------------- +# Set up for Google Protocol Buffers (ProtoBuf) +#--------------------------------------------------------------------------- +PROTOBUFINCDIR = -I$(ISIS3LOCAL)/include/google-protobuf/protobuf2.6.1 +PROTOBUFLIBDIR = -L$(ISIS3LOCAL)/lib +PROTOBUFLIB = -lprotobuf +PROTOC = $(ISIS3LOCAL)/bin/protoc + +#--------------------------------------------------------------------------- +# Set up for kakadu +# The Kakadu library is proprietary. The source files cannot be distributed +# with ISIS3. If you need to rebuild ISIS3 on your system, then you will +# need to modify the lines below that pertain to the location of the +# header files and library on your system. The compilation flag, ENABLEJP2K, +# should be set to true if you are building with the Kakadu library and +# you want to use the JPEG2000 specific code in the ISIS3 system. Otherwise, +# set the ENABLEJP2K flag to false. +# +# Added abililty to automatically detect the existance of the Kakadu include +# directory. One can set the environment variable JP2KFLAG with a 1 or 0 +# depending upon need. Developers can define appropriate enviroment variables +# for the complete JP2K environment. Just redefine them based upon the usage +# below (i.e., be sure to add -I, -L and -l to the variables for KAKADUINCDIR, +# KAKADULIBDIR and KAKADULIB, respectively). +#--------------------------------------------------------------------------- +KAKADUINCDIR := -I$(ISIS3LOCAL)/include/kakadu/v6_3-00967N +KAKADULIBDIR := -L$(ISIS3LOCAL)/lib +KAKADULIB := -lkdu_a63R +# Strip -I from Kakadu include directory macro and check for existance +JP2KFLAG := $(shell if [ -d $(subst -I,,$(KAKADUINCDIR)) ]; then echo "1"; else echo "0"; fi;) +ISISCPPFLAGS += -DENABLEJP2K=$(JP2KFLAG) + +#--------------------------------------------------------------------------- +# Set up for BOOST +#--------------------------------------------------------------------------- +BOOSTINCDIR = -I$(ISIS3LOCAL)/include/boost/boost1.59.0 +BOOSTLIBDIR = +BOOSTLIB = +#BOOSTLIBDIR = -L$(ISIS3LOCAL)/lib +#BOOSTLIB = -lboost_date_time -lboost_filesystem -lboost_graph -lboost_math_c99f \ +# -lboost_math_c99l -lboost_math_c99 -lboost_math_tr1f -lboost_math_tr1l \ +# -lboost_math_tr1 -lboost_prg_exec_monitor -lboost_program_options \ +# -lboost_regex -lboost_serialization -lboost_signals -lboost_system \ +# -lboost_thread -lboost_unit_test_framework -lboost_wave -lboost_wserialization + +#--------------------------------------------------------------------------- +# Set up for Cholmod libraries +#--------------------------------------------------------------------------- +CHOLMODINCDIR = -I$(ISIS3LOCAL)/include/SuiteSparse/SuiteSparse4.4.5/SuiteSparse +CHOLMODLIBDIR = -L$(ISIS3LOCAL)/lib +CHOLMODLIB = -lcholmod -lamd -lcamd -lccolamd -lcolamd -llapack -lsuitesparseconfig + +#--------------------------------------------------------------------------- +# Set up for HDF5 libraries +#--------------------------------------------------------------------------- +HDF5INCDIR = -I$(ISIS3LOCAL)/include/hdf5 +HDF5LIBDIR = -L$(ISIS3LOCAL)/lib +HDF5LIB = -lhdf5 -lhdf5_hl -lhdf5_cpp -lhdf5_hl_cpp + +#--------------------------------------------------------------------------- +# Set up for OpenCV libraries +# +# Add the following line to your app's Makefile (see the NN notes) +# ALLLIBS += $(OPENCVLIBS) +#--------------------------------------------------------------------------- +OPENCVINCDIR = -I$(ISIS3LOCAL)/include +OPENCVLIBDIR = -L$(ISIS3LOCAL)/lib +OPENCVLIBS = -lopencv_calib3d -lopencv_core \ + -lopencv_features2d -lopencv_xfeatures2d \ + -lopencv_flann -lopencv_highgui \ + -lopencv_imgproc -lopencv_imgcodecs \ + -lopencv_ml -l opencv_objdetect \ + -lopencv_photo -lopencv_stitching -lopencv_superres \ + -lopencv_video -lopencv_videostab \ + -lopencv_xfeatures2d + +#--------------------------------------------------------------------------- +# Set up for Natural Neigbor Library (NN) +# +# * Note that NNINCDIR is not added to ALLINCDIRS in isismake.os +# * and NNLIB is not added to ALLLIBDIRS in isismake.os +# +# For now, if you want to use this library, modify your app's Makefile. +# Add an empty line after the last line in the Makefile, then add +# ALLLIBS += $(NNLIB) +# on a new line. +#--------------------------------------------------------------------------- +NNINCDIR = -I$(ISIS3LOCAL)/include/nn +#NNLIBDIR = -L$(ISIS3LOCAL)/lib +NNLIB = -lnn + +#--------------------------------------------------------------------------- +# Final generic setup for includes at the top level +#--------------------------------------------------------------------------- +DEFAULTINCDIR = -I$(ISIS3LOCAL)/include + +#--------------------------------------------------------------------------- +# Define the third party distribution libraries (patterns) +#--------------------------------------------------------------------------- + +# Libraries +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Concurrent.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Concurrent.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Concurrent.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Core.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Core.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Core.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5DBus.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5DBus.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5DBus.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Gui.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Gui.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Gui.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Multimedia.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Multimedia.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Multimedia.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5MultimediaWidgets.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5MultimediaWidgets.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5MultimediaWidgets.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Network.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Network.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Network.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5OpenGL.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5OpenGL.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5OpenGL.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Positioning.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Positioning.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Positioning.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5PrintSupport.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5PrintSupport.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5PrintSupport.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Qml.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Qml.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Qml.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Quick.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Quick.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Quick.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sensors.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sensors.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sensors.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sql.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sql.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sql.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Svg.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Svg.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Svg.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Test.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Test.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Test.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebChannel.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebChannel.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebChannel.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineCore.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineCore.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineCore.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngine.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngine.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngine.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineWidgets.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineWidgets.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineWidgets.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Widgets.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Widgets.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Widgets.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XcbQpa.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XcbQpa.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XcbQpa.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Xml.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Xml.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Xml.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XmlPatterns.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XmlPatterns.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XmlPatterns.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libqwt.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libprotobuf.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgeos-*.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgeos_c.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libdsk.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcspice.so*" +#THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcwd_r.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcolamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libccolamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcholmod.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libsuperlu*.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libsuitesparseconfig.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/liblapack.so" +THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libblas/libblas*.so*" +THIRDPARTYLIBS += "$(ISIS3ALTSYSLIB)/libgfortran.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libxerces-c*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgeotiff*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libtiff*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgsl*.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libicuuc.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libicudata.so*" +#THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libpq.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libmysqlclient_r.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libssl.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libcrypto.so*" +#THIRDPARTYLIBS += "/lib64/libreadline.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libkdu_a63R.so*" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5_hl.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5_cpp.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5_hl_cpp.so*" + +# Add all the OpenCV libraries +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libopencv_*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libtbb.so*" +THIRDPARTYLIBS += $(wildcard $(ISIS3ALTSYSLIB)/libavcodec.so*) +THIRDPARTYLIBS += $(wildcard $(ISIS3ALTSYSLIB)/libavformat.so*) +THIRDPARTYLIBS += $(wildcard $(ISIS3ALTSYSLIB)/libavutil.so*) + +# Add system libraries that need their rpath's patched to $ORIGIN +PATCHLIBS += "$(ISIS3SYSLIB)/libsnappy.so*" # Qt5WebEngine dependency +PATCHLIBS += "$(ISIS3SYSLIB)/libsrtp.so*" # Qt5WebEngine dependency + + +# Plugins +THIRDPARTYPLUGINS += "$(ISIS3LOCAL)/plugins/" diff --git a/isis/make/config.linux-x86_64_Ubuntu14_04 b/isis/make/config.linux-x86_64_Ubuntu14_04 new file mode 100644 index 0000000000000000000000000000000000000000..75deb91f17c2ef93ec7c6982ad9ec2dc4bf7d386 --- /dev/null +++ b/isis/make/config.linux-x86_64_Ubuntu14_04 @@ -0,0 +1,455 @@ +#--------------------------------------------------------------------------- +# Compiler options +#--------------------------------------------------------------------------- + +ISISCPPFLAGS = -Wall +ISISCPPFLAGS += -ansi +ISISCPPFLAGS += -DISIS_LITTLE_ENDIAN=1 +ISISCPPFLAGS += -fPIC +ISISCPPFLAGS += -DGMM_USES_SUPERLU + +ifeq ($(findstring DEBUG, $(MODE)),DEBUG) + ISISCPPFLAGS += -g + ISISCPPFLAGS += -O0 + ISISCPPFLAGS += -DDEBUG + ifeq ($(findstring CWD, $(MODE)),CWD) + ISISCPPFLAGS += -DCWDEBUG -DLIBCWD_THREAD_SAFE -D_REENTRANT + ifeq (,$(findstring MEMCHECK, $(MODE))) + ISISCPPFLAGS += -DNOMEMCHECK + endif + endif +else + ISISCPPFLAGS += -O1 +endif + +ISISCFLAGS = + +#--------------------------------------------------------------------------- +# Linker options +#--------------------------------------------------------------------------- +RANLIB = /bin/true +SHAREDLIBEXT = so + +ISISLDFLAGS = -Wl,-E -Xlinker '-z' -Xlinker 'origin' +ISISLDFLAGS += -Xlinker "-rpath" -Xlinker "${ISISROOT}/lib:${ISISROOT}/3rdParty/lib" +ISISSYSLIBS = -pthread +ISISSTATIC = -Wl,-Bstatic +ISISDYNAMIC = -Wl,-Bdynamic + +ifeq ($(findstring DEBUG, $(MODE)),DEBUG) + ifeq ($(findstring CWD, $(MODE)),CWD) + ISISSYSLIBS += -lcwd_r + endif +endif + +#--------------------------------------------------------------------------- +# Shared library options +#--------------------------------------------------------------------------- +ISISSHAREDFLAGS = $(ISISLDFLAGS) -shared +ISISSHAREDON = -Wl,-whole-archive +ISISSHAREDOFF = -Wl,-no-whole-archive +ISISARFLAGS = + +#--------------------------------------------------------------------------- +# Set up for modifying the executable rpath +#--------------------------------------------------------------------------- +PATCHELF = $(ISIS3LOCAL)/bin/patchelf + +#--------------------------------------------------------------------------- +# Set up local library designations +#--------------------------------------------------------------------------- +ISIS3SYSINC := /usr/include +#ISIS3SYSLIB ?= /usr/lib64 +ISIS3SYSLIB := $(shell if [ -d /usr/lib64 ]; then echo "/usr/lib64"; else echo "/usr/lib"; fi;) +ISIS3ALTSYSLIB := $(shell if [ -f /usr/lib/x86_64-linux-gnu/libgfortran.so.3 ]; then \ + echo "/usr/lib/x86_64-linux-gnu"; else echo "/usr/lib64"; fi;) +ISIS3LOCAL := /usgs/pkgs/local/$(ISISLOCALVERSION) + +#--------------------------------------------------------------------------- +# Set up for cwd +#--------------------------------------------------------------------------- +#CWDINCDIR = +#CWDLIBDIR = +#CWDLIB = + +#ifeq ($(findstring DEBUG, $(MODE)),DEBUG) +# ifeq ($(findstring CWD, $(MODE)),CWD) +# CWDINCDIR = -I$(ISIS3LOCAL)/include/libcwd/libcwd-1.0.4 +# CWDLIBDIR = -L$(ISIS3LOCAL)/lib +# CWDLIB = -lcwd_r +# endif +#endif + +#--------------------------------------------------------------------------- +# Set up for Qt +#--------------------------------------------------------------------------- +QTINCDIR = -I$(ISIS3LOCAL)/include/qt/qt5.6.0 +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/Qt +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtCore +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtAssistant +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtConcurrent +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtDBus +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtGui +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtMultimedia +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtMultimediaWidgets +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtNetwork +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtOpenGL +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtPositioning +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtPrintSupport +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtQml +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtQuick +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtScript +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtScriptTools +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtSensors +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtSql +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtSvg +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtTest +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWebChannel +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWebEngine +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWebEngineWidgets +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtWidgets +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtXml +QTINCDIR += -I$(ISIS3LOCAL)/include/qt/qt5.6.0/QtXmlPatterns +QTLIBDIR = -L$(ISIS3LOCAL)/lib +QTLIB = -lQt5Core -lQt5Concurrent -lQt5XmlPatterns -lQt5Xml -lQt5Network -lQt5Sql -lQt5Gui -lQt5PrintSupport -lQt5Positioning -lQt5Qml -lQt5Quick -lQt5Sensors -lQt5Svg -lQt5Test -lQt5OpenGL -lQt5Widgets -lQt5Multimedia -lQt5MultimediaWidgets -lQt5WebChannel -lQt5WebEngine -lQt5WebEngineWidgets -lQt5DBus + +UIC = $(ISIS3LOCAL)/bin/uic +MOC = $(ISIS3LOCAL)/bin/moc +RCC = $(ISIS3LOCAL)/bin/rcc + +#--------------------------------------------------------------------------- +# Set up for Qwt +#--------------------------------------------------------------------------- +QWTINCDIR = -I$(ISIS3LOCAL)/include/qwt +QWTLIBDIR = -L$(ISIS3LOCAL)/lib +QWTLIB = -lqwt + +#--------------------------------------------------------------------------- +# Set up for Xerces +#--------------------------------------------------------------------------- +XERCESINCDIR = -I$(ISIS3LOCAL)/include/xercesc/xercesc-3.1.2 +XERCESLIBDIR = -L$(ISIS3LOCAL)/lib +XERCESLIB = -lxerces-c + +#--------------------------------------------------------------------------- +# Set up for geotiff +#--------------------------------------------------------------------------- +GEOTIFFINCDIR = -I$(ISIS3LOCAL)/include/geotiff +GEOTIFFLIBDIR = -L$(ISIS3LOCAL)/lib +GEOTIFFLIB = -lgeotiff + +#--------------------------------------------------------------------------- +# Set up for Tiff +#--------------------------------------------------------------------------- +TIFFINCDIR = -I$(ISIS3LOCAL)/include/tiff/tiff-4.0.5 +TIFFLIBDIR = -L$(ISIS3LOCAL)/lib +TIFFLIB = -ltiff + +#--------------------------------------------------------------------------- +# Set up for naif dsk and cspice libraries +#--------------------------------------------------------------------------- +NAIFINCDIR = -I$(ISIS3LOCAL)/include/naif +NAIFLIBDIR = -L$(ISIS3LOCAL)/lib +NAIFLIB = -ldsk -lcspice + +#--------------------------------------------------------------------------- +# Set up for TNT +#--------------------------------------------------------------------------- +TNTINCDIR = -I$(ISIS3LOCAL)/include/tnt/tnt126 -I$(ISIS3LOCAL)/include/tnt/tnt126/tnt +TNTLIBDIR = +TNTLIB = + +#--------------------------------------------------------------------------- +# Set up for JAMA +#--------------------------------------------------------------------------- +JAMAINCDIR = -I$(ISIS3LOCAL)/include/jama/jama125 +JAMALIBDIR = +JAMALIB = + +#--------------------------------------------------------------------------- +# Set up for GEOS +#--------------------------------------------------------------------------- +GEOSINCDIR = -I$(ISIS3LOCAL)/include/geos/geos3.5.0 +GEOSLIBDIR = -L$(ISIS3LOCAL)/lib +GEOSLIB = -lgeos-3.5.0 -lgeos_c + +#--------------------------------------------------------------------------- +# Set up for the GNU Scientific Library (GSL). Note that this setup +# suppports include patterns such as . With this +# format, any other include spec that points to the general include +# directory, such as GEOS, will suffice. Therefore, an explicit +# include directive is ommitted but provided as an empty reference +# in cases where it may be located elsewhere. This also goes for the +# library reference. +#--------------------------------------------------------------------------- +GSLINCDIR = -I$(ISIS3LOCAL)/include +GSLLIBDIR = -L$(ISIS3LOCAL)/lib +GSLLIB = -lgsl -lgslcblas + +#--------------------------------------------------------------------------- +# Set up for X11 +#--------------------------------------------------------------------------- +X11INCDIR = +X11LIBDIR = +X11LIB = -lX11 + +#--------------------------------------------------------------------------- +# Set up for GMM +#--------------------------------------------------------------------------- +GMMINCDIR = -I$(ISIS3LOCAL)/include/gmm/gmm-5.0 -I$(ISIS3LOCAL)/include/gmm/gmm-5.0/gmm +GMMLIBDIR = +GMMLIB = + +#--------------------------------------------------------------------------- +# Set up for SuperLU +#--------------------------------------------------------------------------- +SUPERLUINCDIR = -I$(ISIS3LOCAL)/include/superlu/superlu4.3 +SUPERLULIBDIR = -L$(ISIS3LOCAL)/lib +SUPERLULIB = -lsuperlu_4.3 -lblas -lgfortran + +#--------------------------------------------------------------------------- +# Set up for Google Protocol Buffers (ProtoBuf) +#--------------------------------------------------------------------------- +PROTOBUFINCDIR = -I$(ISIS3LOCAL)/include/google-protobuf/protobuf2.6.1 +PROTOBUFLIBDIR = -L$(ISIS3LOCAL)/lib +PROTOBUFLIB = -lprotobuf +PROTOC = $(ISIS3LOCAL)/bin/protoc + +#--------------------------------------------------------------------------- +# Set up for kakadu +# The Kakadu library is proprietary. The source files cannot be distributed +# with ISIS3. If you need to rebuild ISIS3 on your system, then you will +# need to modify the lines below that pertain to the location of the +# header files and library on your system. The compilation flag, ENABLEJP2K, +# should be set to true if you are building with the Kakadu library and +# you want to use the JPEG2000 specific code in the ISIS3 system. Otherwise, +# set the ENABLEJP2K flag to false. +# +# Added abililty to automatically detect the existance of the Kakadu include +# directory. One can set the environment variable JP2KFLAG with a 1 or 0 +# depending upon need. Developers can define appropriate enviroment variables +# for the complete JP2K environment. Just redefine them based upon the usage +# below (i.e., be sure to add -I, -L and -l to the variables for KAKADUINCDIR, +# KAKADULIBDIR and KAKADULIB, respectively). +#--------------------------------------------------------------------------- +KAKADUINCDIR := -I$(ISIS3LOCAL)/include/kakadu/v6_3-00967N +KAKADULIBDIR := -L$(ISIS3LOCAL)/lib +KAKADULIB := -lkdu_a63R +# Strip -I from Kakadu include directory macro and check for existance +JP2KFLAG := $(shell if [ -d $(subst -I,,$(KAKADUINCDIR)) ]; then echo "1"; else echo "0"; fi;) +ISISCPPFLAGS += -DENABLEJP2K=$(JP2KFLAG) + +#--------------------------------------------------------------------------- +# Set up for BOOST +#--------------------------------------------------------------------------- +BOOSTINCDIR = -I$(ISIS3LOCAL)/include/boost/boost1.59.0 +BOOSTLIBDIR = +BOOSTLIB = +#BOOSTLIBDIR = -L$(ISIS3LOCAL)/lib +#BOOSTLIB = -lboost_date_time -lboost_filesystem -lboost_graph -lboost_math_c99f \ +# -lboost_math_c99l -lboost_math_c99 -lboost_math_tr1f -lboost_math_tr1l \ +# -lboost_math_tr1 -lboost_prg_exec_monitor -lboost_program_options \ +# -lboost_regex -lboost_serialization -lboost_signals -lboost_system \ +# -lboost_thread -lboost_unit_test_framework -lboost_wave -lboost_wserialization + +#--------------------------------------------------------------------------- +# Set up for Cholmod libraries +#--------------------------------------------------------------------------- +CHOLMODINCDIR = -I$(ISIS3LOCAL)/include/SuiteSparse/SuiteSparse4.4.5/SuiteSparse +CHOLMODLIBDIR = -L$(ISIS3LOCAL)/lib +CHOLMODLIB = -lcholmod -lamd -lcamd -lccolamd -lcolamd -llapack -lsuitesparseconfig + +#--------------------------------------------------------------------------- +# Set up for HDF5 libraries +#--------------------------------------------------------------------------- +HDF5INCDIR = -I$(ISIS3LOCAL)/include/hdf5 +HDF5LIBDIR = -L$(ISIS3LOCAL)/lib +HDF5LIB = -lhdf5 -lhdf5_hl -lhdf5_cpp -lhdf5_hl_cpp + +#--------------------------------------------------------------------------- +# Set up for OpenCV libraries +# +# Add the following line to your app's Makefile (see the NN notes) +# ALLLIBS += $(OPENCVLIBS) +#--------------------------------------------------------------------------- +OPENCVINCDIR = -I$(ISIS3LOCAL)/include +OPENCVLIBDIR = -L$(ISIS3LOCAL)/lib +OPENCVLIBS = -lopencv_calib3d -lopencv_core \ + -lopencv_features2d -lopencv_xfeatures2d \ + -lopencv_flann -lopencv_highgui \ + -lopencv_imgproc -lopencv_imgcodecs \ + -lopencv_ml -l opencv_objdetect \ + -lopencv_photo -lopencv_stitching -lopencv_superres \ + -lopencv_video -lopencv_videostab \ + -lopencv_xfeatures2d + +#--------------------------------------------------------------------------- +# Set up for Natural Neigbor Library (NN) +# +# * Note that NNINCDIR is not added to ALLINCDIRS in isismake.os +# * and NNLIB is not added to ALLLIBDIRS in isismake.os +# +# For now, if you want to use this library, modify your app's Makefile. +# Add an empty line after the last line in the Makefile, then add +# ALLLIBS += $(NNLIB) +# on a new line. +#--------------------------------------------------------------------------- +NNINCDIR = -I$(ISIS3LOCAL)/include/nn +#NNLIBDIR = -L$(ISIS3LOCAL)/lib +NNLIB = -lnn + +#--------------------------------------------------------------------------- +# Final generic setup for includes at the top level +#--------------------------------------------------------------------------- +DEFAULTINCDIR = -I$(ISIS3LOCAL)/include + +#--------------------------------------------------------------------------- +# Define the third party distribution libraries (patterns) +#--------------------------------------------------------------------------- + +# Libraries +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Concurrent.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Concurrent.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Concurrent.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Core.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Core.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Core.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5DBus.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5DBus.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5DBus.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Gui.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Gui.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Gui.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Multimedia.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Multimedia.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Multimedia.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5MultimediaWidgets.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5MultimediaWidgets.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5MultimediaWidgets.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Network.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Network.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Network.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5OpenGL.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5OpenGL.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5OpenGL.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Positioning.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Positioning.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Positioning.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5PrintSupport.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5PrintSupport.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5PrintSupport.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Qml.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Qml.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Qml.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Quick.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Quick.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Quick.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sensors.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sensors.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sensors.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sql.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sql.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Sql.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Svg.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Svg.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Svg.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Test.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Test.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Test.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebChannel.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebChannel.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebChannel.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineCore.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineCore.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineCore.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngine.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngine.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngine.so.5.6.*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineWidgets.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineWidgets.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5WebEngineWidgets.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Widgets.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Widgets.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Widgets.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XcbQpa.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XcbQpa.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XcbQpa.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Xml.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Xml.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5Xml.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XmlPatterns.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XmlPatterns.so.5" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libQt5XmlPatterns.so.5.6*[^g]" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libqwt.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libprotobuf.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgeos-*.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgeos_c.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libdsk.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcspice.so*" +#THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcwd_r.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcolamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libccolamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcamd.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libcholmod.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libsuperlu*.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libsuitesparseconfig.so" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/liblapack.so" +THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libblas/libblas*.so*" +THIRDPARTYLIBS += "$(ISIS3ALTSYSLIB)/libgfortran.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libxerces-c*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgeotiff*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libtiff*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libgsl*.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libicuuc.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libicudata.so*" +#THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libpq.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libmysqlclient_r.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libssl.so*" +#THIRDPARTYLIBS += "$(ISIS3SYSLIB)/libcrypto.so*" +#THIRDPARTYLIBS += "/lib64/libreadline.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libkdu_a63R.so*" + +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5_hl.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5_cpp.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libhdf5_hl_cpp.so*" + +# Add all the OpenCV libraries +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libopencv_*.so*" +THIRDPARTYLIBS += "$(ISIS3LOCAL)/lib/libtbb.so*" +THIRDPARTYLIBS += $(wildcard $(ISIS3ALTSYSLIB)/libavcodec.so*) +THIRDPARTYLIBS += $(wildcard $(ISIS3ALTSYSLIB)/libavformat.so*) +THIRDPARTYLIBS += $(wildcard $(ISIS3ALTSYSLIB)/libavutil.so*) + +# Add system libraries that need their rpath's patched to $ORIGIN +PATCHLIBS += "$(ISIS3SYSLIB)/libsnappy.so*" # Qt5WebEngine dependency +PATCHLIBS += "$(ISIS3SYSLIB)/libsrtp.so*" # Qt5WebEngine dependency + + +# Plugins +THIRDPARTYPLUGINS += "$(ISIS3LOCAL)/plugins/" diff --git a/isis/make/isismake.init b/isis/make/isismake.init index d2d0929e39fdc0cb25758902997c687bbd265439..a7fc5e86ad041fb926abb1d1aad6097f7bb12ed7 100644 --- a/isis/make/isismake.init +++ b/isis/make/isismake.init @@ -1,7 +1,7 @@ SHELL=bash #--------------------------------------------------------------------------- -# This include is designed to be run before any others in the ISIS make +# This include is designed to be run before any others in the ISIS make # system. #--------------------------------------------------------------------------- @@ -22,7 +22,7 @@ HOST_PROC := $(shell uname -p) #--------------------------------------------------------------------------- -# Set up some basic shell commands OS specific includes can override +# Set up some basic shell commands OS specific includes can override # these later. These are often necessary to remove any user aliases #--------------------------------------------------------------------------- @@ -39,7 +39,6 @@ ECHO := /bin/echo EVAL := eval GREP := grep HEAD := head -LATEX := latex LN := ln -s LS := /bin/ls MKDIR := mkdir -p @@ -47,6 +46,7 @@ MOC := moc MV := mv PRINTF := /usr/bin/printf PROTOC := protoc +PYTHON := python3 RANLIB := /usr/bin/true RM := /bin/rm -f RMDIR := rmdir -p @@ -89,7 +89,6 @@ endif #--------------------------------------------------------------------------- # Set up the Isis include and library directories #--------------------------------------------------------------------------- -ISISINCDIR = -I$(ISISROOT)/inc -ISISLIBDIR = -L$(ISISROOT)/lib +ISISINCDIR = -I$(ISISROOT)/inc +ISISLIBDIR = -L$(ISISROOT)/lib ISISLIB = -lisis$(ISISLIBVERSION) - diff --git a/isis/make/isismake.objs b/isis/make/isismake.objs index b5bc3cafc8fc0b6a3a43eea6ec86888168a8660b..d1d5e868a3319be6d7044c29117b8cdf60f97dce 100644 --- a/isis/make/isismake.objs +++ b/isis/make/isismake.objs @@ -186,45 +186,9 @@ help: echo "make ostruthdata : Runs the unitTest and creates OS specific truth" echo "make protos : Builds the object of google protocol buffer(*.proto) files" +TEMPDIR:=${CURDIR} html: force - mkdir -p docbuild - cat $(ISISROOT)/src/docsys/Object/build//Programmer.conf > docbuild/ProgTester_temp.conf - echo "FILE_PATTERNS = *.h *.cpp *.doxydef" >> docbuild/ProgTester_temp.conf - echo "OUTPUT_DIRECTORY = $(CURDIR)/" >> docbuild/ProgTester_temp.conf - echo "STRIP_FROM_PATH = $(CURDIR)/" >> docbuild/ProgTester_temp.conf - echo "LATEX_OUTPUT = $(CURDIR)/html/latex" >> docbuild/ProgTester_temp.conf - echo "LATEX_CMD_NAME = $(LATEX)" >> docbuild/ProgTester_temp.conf - echo "INPUT = $(ISISROOT)/src/docsys/Object/build/isisDoxyDefs.doxydef $(CURDIR)/" >> docbuild/ProgTester_temp.conf - echo "HTML_HEADER = $(ISISROOT)/src/docsys/Object/build/IsisObjectHeaderProgTester.html" >> docbuild/ProgTester_temp.conf - echo "HTML_FOOTER = $(ISISROOT)/src/docsys/Object/build/IsisObjectFooterProgTester.html" >> docbuild/ProgTester_temp.conf - echo "HTML_OUTPUT = html" >> docbuild/ProgTester_temp.conf - echo "TAGFILES = " >> docbuild/ProgTester_temp.conf - echo "HTML_STYLESHEET = $(ISISROOT)/src/docsys/Object/build/doxygen.css" >> docbuild/ProgTester_temp.conf - echo "IMAGE_PATH = $(CURDIR)/" >> docbuild/ProgTester_temp.conf - - if [ "$(findstring LOUD,$(MODE))" = "LOUD" ]; \ - then \ - echo "QUIET = NO" >> docbuild/ProgTester_temp.conf; \ - echo "WARNINGS = YES" >> docbuild/ProgTester_temp.conf; \ - echo "WARN_IF_UNDOCUMENTED = YES" >> docbuild/ProgTester_temp.conf; \ - echo "WARN_IF_DOC_ERROR = YES" >> docbuild/ProgTester_temp.conf; \ - echo "WARN_NO_PARAMDOC = YES" >> docbuild/ProgTester_temp.conf; \ - else \ - echo "QUIET = YES" >> docbuild/ProgTester_temp.conf; \ - echo "WARNINGS = YES" >> docbuild/ProgTester_temp.conf; \ - echo "WARN_IF_UNDOCUMENTED = YES" >> docbuild/ProgTester_temp.conf; \ - echo "WARN_IF_DOC_ERROR = YES" >> docbuild/ProgTester_temp.conf; \ - echo "WARN_NO_PARAMDOC = YES" >> docbuild/ProgTester_temp.conf; \ - fi - - if [[ "$(DOT_PATH)" != "" ]]; \ - then \ - echo "DOT_PATH = $(DOT_PATH)" >> docbuild/ProgTester_temp.conf; \ - fi - - $(DOXYGEN) docbuild/ProgTester_temp.conf - -$(RM) -r docbuild - echo "View your documentation by opening the file html/index.html in a browser" + (cd $(ISISROOT)/src/docsys/Object/ ; make CURDIR=$(TEMPDIR) doProgTest ) clean: localclean $(RM) $(OBJS) $(PROTOSGEN) $(MOCGEN) unitTest.o unitTest print.prt \ @@ -323,34 +287,20 @@ unitTest: $(OBJS) unitTest.o -Xlinker "$${dollar}ORIGIN" $(ISISLDFLAGS) \ -o $@ unitTest.o $(ALLLIBS); \ else \ - $(AR) $(ISISARFLAGS) -crs $(LIBRARY).a *.o; \ - $(LDSHARED) $(ISISSHAREDFLAGS) $(ISISSHAREDON) \ - -o $(LIBRARY).$(SHAREDLIBEXT) $(LIBRARY).a \ - $(ISISSHAREDOFF); \ - $(RM) $(LIBRARY).a $(LIBRARY).a.csmes; \ - dollar='$$'; \ - $(CXX) $(ALLLIBDIRS) \ - -Xlinker "-rpath" \ - -Xlinker "$${dollar}ORIGIN" $(ISISLDFLAGS) \ - -o $@ unitTest.o -l:$(LIBRARY).$(SHAREDLIBEXT) $(ALLLIBS); \ + $(AR) $(ISISARFLAGS) -crs $(LIBRARY).a *.o; \ + $(LDSHARED) $(ISISSHAREDFLAGS) $(ISISSHAREDON) \ + -o $(LIBRARY).$(SHAREDLIBEXT) $(LIBRARY).a \ + $(ISISSHAREDOFF); \ + $(RM) $(LIBRARY).a $(LIBRARY).a.csmes; \ + dollar='$$'; \ + $(CXX) $(ALLLIBDIRS) \ + -Xlinker "-rpath" \ + -Xlinker "$${dollar}ORIGIN" $(ISISLDFLAGS) \ + -o $@ unitTest.o -l:$(LIBRARY).$(SHAREDLIBEXT) $(ALLLIBS); \ fi; \ - elif [ "$(HOST_ARCH)" == "Darwin" ]; then \ - $(MKDIR) .objs; \ - cd .objs; \ - cp $(ISISROOT)/lib/libisis$(ISISLIBVERSION).a .; \ - $(AR) x libisis$(ISISLIBVERSION).a; \ - $(RM) libisis$(ISISLIBVERSION).a; \ - cd ..; \ - if [ "$(OBJS)" != "" ]; then \ - $(CP) $(OBJS) .objs/; \ - fi; \ - $(LDSHARED) $(DYLIBFLAGS) $(ISISSHAREDON) \ - -o libisis$(ISISLIBVERSION).$(SHAREDLIBEXT) \ - -install_name $(CURDIR)/libisis$(ISISLIBVERSION).$(SHAREDLIBEXT) \ - $(DYLIBVERSION) .objs/*.o $(ISISSHAREDOFF); \ - $(CXX) $(ALLLIBDIRS) $(ISISLDFLAGS) \ - -o $@ unitTest.o $(ALLLIBS); \ - $(RM) -rd .objs; \ + elif [ "$(HOST_ARCH)" == "Darwin" ]; then \ + $(CXX) $(OBJS) $(ALLLIBDIRS) $(ISISLDFLAGS) \ + -o $@ unitTest.o $(ALLLIBS) ; \ fi; plugin: $(OBJS) diff --git a/isis/make/isismake.objstree b/isis/make/isismake.objstree index e104a20b82a872d18642f39995aaef85e7917586..c50a91df2d9536673811036a1da4235410baa2c5 100644 --- a/isis/make/isismake.objstree +++ b/isis/make/isismake.objstree @@ -30,7 +30,7 @@ cleanuplockfile: fi; # When we make appname-print it should print the app's log. This acquires the -# appropriate lock before printing. There is a 30s timeout on the lock before +# appropriate lock before printing. There is a 30s timeout on the lock before # breaking it. %-print: APPNAME=`$(ECHO) $@ | $(SED) 's/-print//'`; \ @@ -94,9 +94,9 @@ cleanuplockfile: api: if [ "$(OBJECTS)" != "" ]; \ then \ - for i in $(OBJECTS); do \ - echo $(CURTIMESTAMP) " Adding API object [$$i]"; \ - cd $$i; $(MAKE) install; cd ..; \ + for i in $(OBJECTS); do \ + echo $(CURTIMESTAMP) " Adding API object [$$i]"; \ + cd $$i; $(MAKE) install; cd ..; \ done \ fi diff --git a/isis/make/isismake.os b/isis/make/isismake.os index f816e965b90378375b54d463d5f77829eb5ac8f6..bdf5727ab15b75d4b91fdc291eb1c98b1cfc3de2 100644 --- a/isis/make/isismake.os +++ b/isis/make/isismake.os @@ -62,7 +62,6 @@ ifndef ISISCPPFLAGS $(error Unsupported platform, can not make for $(HOST_ARCH)) endif - # Set up Xalan's command-line option names. XALAN_VALIDATE_OPTION := -v XALAN_OUTFILE_OPTION := -o @@ -70,10 +69,6 @@ XALAN_PARAM_OPTION := -p XALAN_INFILE_OPTION := XALAN_XSL_OPTION := -ifneq "$(or $(findstring Fedora, $(HOST_OS)), $(findstring ScientificLinux, $(HOST_OS)))" "" - XALAN = $(ISIS3LOCAL)/bin/Xalan -endif - #--------------------------------------------------------------------------- # The BSD version of grep on 10.7-10.9 is reported to be broken so use GNU #--------------------------------------------------------------------------- diff --git a/isis/src/base/apps/ascii2isis/ascii2isis.cpp b/isis/src/base/apps/ascii2isis/ascii2isis.cpp index 7a5ec96728bbb754ea0f5037d21c3eab600cafd1..379c20b164dbd2379575309c97c6e393de42fa3c 100644 --- a/isis/src/base/apps/ascii2isis/ascii2isis.cpp +++ b/isis/src/base/apps/ascii2isis/ascii2isis.cpp @@ -116,11 +116,24 @@ void ascii2isis(Buffer &out) { } fin >> out[i]; + + // If we've reached the end of file and stream is bad, we didn't find enough numerical data if (!fin && fin.eof()) { QString msg = "End of file reached. There is not enough data in [" + from; msg += "] to fill the output cube."; throw IException(IException::User, msg, _FILEINFO_); } + + // Check if there was an issue extracting a double + if (!fin) { + // Clean stream to get the position and invalid data that broke the stream + fin.clear(); + QString msg = "Could not extract non-numerical data [" + QString(fin.peek()) + "] "; + msg += "at byte position [" + QString::number(fin.tellg()) + "]. "; + msg += "Please make sure to skip any header data in [" + from + "]."; + throw IException(IException::User, msg, _FILEINFO_); + } + out[i] = TestSpecial(out[i]); } } diff --git a/isis/src/base/apps/ascii2isis/ascii2isis.xml b/isis/src/base/apps/ascii2isis/ascii2isis.xml index 8dafed1a708b49fec9a4c6226329a82e66d9a1dd..139dbe56fc9ade2d0b9e7bd03158842cac517000 100644 --- a/isis/src/base/apps/ascii2isis/ascii2isis.xml +++ b/isis/src/base/apps/ascii2isis/ascii2isis.xml @@ -26,10 +26,14 @@ Added ability to change special pixel ranges. Added example. - - Fixed a problem with non-numeric cahracters in the file which resulted ascii2isis + + Fixed a problem with non-numeric characters in the file which resulted ascii2isis hanging. Fixes #2066. + + Added an error message when the reading fails if the file header isn't skipped. + Fixes #4596. + diff --git a/isis/src/base/apps/ascii2isis/tsts/errors/Makefile b/isis/src/base/apps/ascii2isis/tsts/errors/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..ff4c1e5a387754981eadb9b73e4c10168612f0ee --- /dev/null +++ b/isis/src/base/apps/ascii2isis/tsts/errors/Makefile @@ -0,0 +1,21 @@ +APPNAME = ascii2isis + +include $(ISISROOT)/make/isismake.tsts + +commands: +# TEST A: Broken stream when not skipping header. + echo -e "Error Test A: " > $(OUTPUT)/error_temp.txt; + if [[ `$(APPNAME) \ + from=$(INPUT)/input.txt \ + to=$(OUTPUT)/output.cub \ + lines=3 \ + samples=3 \ + 2>> $(OUTPUT)/error_temp.txt \ + > /dev/null` ]]; \ + then \ + true; \ + fi; + + $(SED) 's+\[/.*/input/+\[input/+' $(OUTPUT)/error_temp.txt > $(OUTPUT)/error.txt; + $(RM) $(OUTPUT)/error_temp.txt; + $(RM) $(OUTPUT)/output.cub; diff --git a/isis/src/base/apps/cam2map/tsts/errors/Makefile b/isis/src/base/apps/cam2map/tsts/errors/Makefile index b4d2c64dc8d145d416741d44a7dedd433eebbadb..b21ddca78b487632eda68f02ecd0b1828bd93b5d 100644 --- a/isis/src/base/apps/cam2map/tsts/errors/Makefile +++ b/isis/src/base/apps/cam2map/tsts/errors/Makefile @@ -1,10 +1,21 @@ -# This test will print errors thrown by the applicationName application. +# This test will print errors thrown by the cam2map application. APPNAME = cam2map include $(ISISROOT)/make/isismake.tsts commands: -# TEST A: Test that an exception is thrown when targetnames of cube and map do not match. +# TEST A: Testing for an error when list file is empty. + echo -e "Error Test A:" > $(OUTPUT)/error_temp.txt; + if [[ `$(APPNAME) \ + from=$(INPUT)/vesta.cub \ + to=$(OUTPUT)/output.cub \ + map=$(INPUT)/marsEquirectangular.map \ + 2>> $(OUTPUT)/error_temp.txt \ + > /dev/null` ]]; \ + then \ + true; \ + fi; +# TEST B: Test for an error if cube has instrument targetName as Sky. echo -e "Error Test A:" > $(OUTPUT)/error_temp.txt; if [[ `$(APPNAME) \ from=$(INPUT)/vesta.cub \ diff --git a/isis/src/base/apps/caminfo/caminfo.cpp b/isis/src/base/apps/caminfo/caminfo.cpp index f8367f82926202b1f90bef005bffb749c526bc3f..4fae60179473d0f5d02668fe665b67663beef571 100644 --- a/isis/src/base/apps/caminfo/caminfo.cpp +++ b/isis/src/base/apps/caminfo/caminfo.cpp @@ -424,8 +424,11 @@ void GenerateCSVOutput(Cube *incube, } } - keys.remove(QRegExp(delim + "$")); // Get rid of the extra delim char (",") + if (not appending) { + keys.remove(QRegExp(delim + "$")); // Get rid of the extra delim char (",") + outFile << keys << endl; + } values.remove(QRegExp(delim + "$")); // Get rid of the extra delim char (",") - outFile << keys << endl << values << endl; + outFile << values << endl; outFile.close(); } diff --git a/isis/src/base/apps/catoriglab/catoriglab.cpp b/isis/src/base/apps/catoriglab/catoriglab.cpp index c340ca6688725627f26dcbfd80cda5931b28efa3..96bde9302df7a03a61b965355e59c233035665cf 100644 --- a/isis/src/base/apps/catoriglab/catoriglab.cpp +++ b/isis/src/base/apps/catoriglab/catoriglab.cpp @@ -1,31 +1,83 @@ #include "Isis.h" + +#include +#include +#include + +#include "IException.h" #include "Pvl.h" #include "OriginalLabel.h" +#include "OriginalXmlLabel.h" using namespace Isis; using namespace std; void IsisMain() { + // QDomDocument makes use of QHashes to store attributes. + // This sets the QHash seed so that the attributes always come out in the + // same order. + qSetGlobalQHashSeed(1031); // Get user entered file name & mode UserInterface &ui = Application::GetUserInterface(); QString file = ui.GetFileName("FROM"); - // Extract history from file - OriginalLabel origLab(file); - Pvl pvl = origLab.ReturnLabels(); - if (ui.IsInteractive()) { - Application::GuiLog(pvl); + Pvl fromLabel(file); + if ( fromLabel.hasObject("OriginalLabel") ) { + OriginalLabel origLab(file); + Pvl pvl = origLab.ReturnLabels(); + if (ui.IsInteractive()) { + Application::GuiLog(pvl); + } + else if (ui.WasEntered("TO")) { + if (ui.GetBoolean("APPEND")) { + pvl.append(FileName(ui.GetFileName("TO")).expanded()); + } + else { + pvl.write(FileName(ui.GetFileName("TO")).expanded()); + } + } + else { + cout << pvl << endl; + } } - else if (ui.WasEntered("TO")) { - if (ui.GetBoolean("APPEND")) { - pvl.append(FileName(ui.GetFileName("TO")).expanded()); + else if ( fromLabel.hasObject("OriginalXmlLabel") ) { + OriginalXmlLabel origLab(file); + QDomDocument origXml = origLab.ReturnLabels(); + if ( ui.IsInteractive() ) { + Application::GuiLog( origXml.toString(2) ); + } + else if (ui.WasEntered("TO")) { + // Open the output file + QFile outFile( FileName( ui.GetFileName("TO") ).expanded() ); + QIODevice::OpenMode openMode; + if (ui.GetBoolean("APPEND")) { + openMode = QIODevice::WriteOnly | QIODevice::Append; + } + else { + openMode = QIODevice::WriteOnly | QIODevice::Truncate; + } + if ( !outFile.open(openMode) ) { + QString msg = "Unable to open output file [" + + FileName( ui.GetFileName("TO") ).expanded() + + "] with write permissions."; + throw IException(IException::Io, msg, _FILEINFO_); + } + + // Write to the output file + QTextStream outputStream(&outFile); + outputStream << origXml.toString(2); + + // Close the output file + outFile.close(); } else { - pvl.write(FileName(ui.GetFileName("TO")).expanded()); + cout << origXml.toString(2) << endl; } - } + } else { - cout << pvl << endl; + QString msg = "Could not find OriginalLabel or OriginalXmlLabel " + "in input file [" + file + "]."; + throw IException(IException::User, msg, _FILEINFO_); } } diff --git a/isis/src/base/apps/catoriglab/catoriglab.xml b/isis/src/base/apps/catoriglab/catoriglab.xml index ac3278604f0b3e90527d1a129fe2bdc5d9df358d..096c8300a9eac628b5fb49430429cd797290f21e 100644 --- a/isis/src/base/apps/catoriglab/catoriglab.xml +++ b/isis/src/base/apps/catoriglab/catoriglab.xml @@ -26,6 +26,9 @@ Documentation fixes + + Enabled output or OriginalXmlLabels. Fixes #4584. + diff --git a/isis/src/base/apps/catoriglab/tsts/XmlLabel/Makefile b/isis/src/base/apps/catoriglab/tsts/XmlLabel/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..13d8c87d2d7568c3bbcc10988c469a29ea912bad --- /dev/null +++ b/isis/src/base/apps/catoriglab/tsts/XmlLabel/Makefile @@ -0,0 +1,7 @@ +APPNAME = catoriglab + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(APPNAME) from= $(INPUT)/tgoCaSSISImage.cub \ + APPEND= false TO= $(OUTPUT)/XmlLabel.txt > /dev/null; diff --git a/isis/src/base/apps/ckwriter/tsts/messenger/Makefile b/isis/src/base/apps/ckwriter/tsts/messenger/Makefile index 269adc6f1f925696be9a32c1d23daae85d70a26d..6dbc9b10c1ed5185d8418ecfd3d11cd65a4d25f2 100644 --- a/isis/src/base/apps/ckwriter/tsts/messenger/Makefile +++ b/isis/src/base/apps/ckwriter/tsts/messenger/Makefile @@ -1,6 +1,6 @@ APPNAME = ckwriter BASES = $(basename $(notdir $(wildcard $(INPUT)/*.cub))) -EXTRA = $(shell ls -1t $(ISIS3DATA)/messenger/kernels/ck/*_mdis_pivot_pvtres.bc | head -1) +EXTRA = $(shell ls -1t $(ISIS3DATA)/messenger/kernels/ck/*_mdis_gm040819_150430v1.bc | head -1) include $(ISISROOT)/make/isismake.tsts diff --git a/isis/src/base/apps/cubeit/cubeit.xml b/isis/src/base/apps/cubeit/cubeit.xml index f0b232cf7e9cc8acb0ca549ae2ce7a6ac1f82940..c6f69f541bb634f1d27463f94c099ae049138429 100644 --- a/isis/src/base/apps/cubeit/cubeit.xml +++ b/isis/src/base/apps/cubeit/cubeit.xml @@ -7,25 +7,25 @@

- This program will stack a series of cubes into a single output cube. + This program will stack a series of cubes into a single output cube. You can use cubeit to combine individual color bands to create - a multi-band cube. + a multi-band cube.

A text-based file that contains a list of cubes to stack must be - entered in the FROMLIST. Each cube must have the same spatial dimensions - (e.g., samples and lines). The BandBin group, which is used to store information + entered in the FROMLIST. Each cube must have the same spatial dimensions + (e.g., samples and lines). The BandBin group, which is used to store information regarding each band in the cube, will be constructed.

- The order of the file is used to generate the stacking order. Cubes are automatically placed - down as cubeit reads the list from top-to-bottom. You can change the order to make certain - cubes appear in front of or behind other cubes by modifying the list order. + The order of the file is used to generate the stacking order. Cubes are automatically placed + down as cubeit reads the list from top-to-bottom. You can change the order to make certain + cubes appear in front of or behind other cubes by modifying the list order.

- By default, any tracking information stored within an input cube (for example, as generated by automos, mapmos, etc.) - is not propagated to the output cube, since, in most cases, this tracking information is no longer relevant to - the output cube. + By default, any tracking information stored within an input cube (for example, as generated by automos, mapmos, etc.) + is not propagated to the output cube, since, in most cases, this tracking information is no longer relevant to + the output cube.

@@ -57,24 +57,28 @@ Modified so that the cube list does not need to contain the full directory path for PROPLAB option - Removed references to CubeInfo + Removed references to CubeInfo Updated for changes in ProcessMosaic - Changed parameter LIST to FROMLIST + Changed parameter LIST to FROMLIST Fixed handling of band specifications in the list file. The band bin group is still incorrect, but the correct bands are now placed in the output cube. Fixes #964. - Fixed handing of input attributes so that the specified input band(s) are included in the output cube. + Fixed handing of input attributes so that the specified input band(s) are included in the output cube. Modified so that tracking information in the input cubes is not propagated to the output cube. + + Modified Makefile of badinputs app test to truncate paths before data directory. Allows tests + to pass when not using the default data area. Fixes #4783. + @@ -88,7 +92,7 @@ Each file in this list, one per line, will be added to the output cube in the order they appear. The last file - in the list must followed by a blank line. + in the list must followed by a blank line. *.lis diff --git a/isis/src/base/apps/cubeit/tsts/badinputs/Makefile b/isis/src/base/apps/cubeit/tsts/badinputs/Makefile index 8b7fa066ffdd5c0869259f43fad837fe6dc30ab1..b63017beaf6dc39f66c4e4bd167ccee091a11262 100644 --- a/isis/src/base/apps/cubeit/tsts/badinputs/Makefile +++ b/isis/src/base/apps/cubeit/tsts/badinputs/Makefile @@ -1,4 +1,4 @@ -#This test will print errors thrown by cubeit when given +#This test will print errors thrown by cubeit when given #input cubes of different sizes or nothing but TRAKCING bands APPNAME = cubeit @@ -35,13 +35,13 @@ commands: fi; # Remove Paths - $(SED) 's+\[/.*/input/+\[input/+' $(OUTPUT)/error_temp.txt > $(OUTPUT)/error_temp2.txt; - $(SED) 's+\[/.*/output/+\[output/+' $(OUTPUT)/error_temp2.txt > $(OUTPUT)/error.txt; + $(SED) "s/\/.*\/data/data/" $(OUTPUT)/error_temp.txt > $(OUTPUT)/error_temp2.txt; + $(SED) 's+\[/.*/input/+\[input/+' $(OUTPUT)/error_temp2.txt > $(OUTPUT)/error_temp3.txt; + $(SED) 's+\[/.*/output/+\[output/+' $(OUTPUT)/error_temp3.txt > $(OUTPUT)/error.txt; # Cleanup - $(RM) $(OUTPUT)/error_temp.txt; - $(RM) $(OUTPUT)/error_temp2.txt; - $(RM) $(OUTPUT)/tracking.lis; - $(RM) $(OUTPUT)/broken.lis; - - + $(RM) $(OUTPUT)/error_temp.txt; + $(RM) $(OUTPUT)/error_temp2.txt; + $(RM) $(OUTPUT)/error_temp3.txt; + $(RM) $(OUTPUT)/tracking.lis; + $(RM) $(OUTPUT)/broken.lis; diff --git a/isis/src/base/apps/cubenorm/staticStats.cpp b/isis/src/base/apps/cubenorm/staticStats.cpp index 4af097131ec01ca4b0bf6b4e329286e4fe94c207..edd43994568e1543484b48dcf7a0e8325a59c97b 100644 --- a/isis/src/base/apps/cubenorm/staticStats.cpp +++ b/isis/src/base/apps/cubenorm/staticStats.cpp @@ -1,4 +1,4 @@ -/* StaticStats +/* StaticStats PIRL CVS ID: $Id: staticStats.cpp,v 1.1 2007/01/11 20:59:17 kbecker Exp $ diff --git a/isis/src/base/apps/edrget/edrget.cpp b/isis/src/base/apps/edrget/edrget.cpp index fa268b3ab12649559550bba0bf1308a4e2e10402..231a4debdf354a8ed66e9bdbf9bbb9e98b2ee0b4 100644 --- a/isis/src/base/apps/edrget/edrget.cpp +++ b/isis/src/base/apps/edrget/edrget.cpp @@ -33,7 +33,8 @@ void IsisMain() { QUrl qurl(guiURL); //test if scheme is ftp or http - if (qurl.scheme().toLower() == "ftp" || qurl.scheme().toLower() == "http") { + if (qurl.scheme().toLower() == "ftp" || qurl.scheme().toLower() == "http" || + qurl.scheme().toLower() == "https") { if (ui.IsInteractive()) { QString parameters = "URL=" + guiURL; diff --git a/isis/src/base/apps/edrget/edrget.xml b/isis/src/base/apps/edrget/edrget.xml index a30eda1a8ae31e2c5da6d63dfbe696a2ca76ab80..70390108670b76398546724c27e49c70897d901f 100644 --- a/isis/src/base/apps/edrget/edrget.xml +++ b/isis/src/base/apps/edrget/edrget.xml @@ -41,6 +41,9 @@ xsi:noNamespaceSchemaLocation= Replaced httpget and ftpget classes with ResourceGet class for updating to Qt5. + + Added https to reflect changes in the server. + diff --git a/isis/src/base/apps/edrget/tsts/connectErrors/Makefile b/isis/src/base/apps/edrget/tsts/connectErrors/Makefile index 0254f7763303744f4050d0085c87434d52ca7444..8e12648156e28779ca71f396c254cdae6c5a475d 100644 --- a/isis/src/base/apps/edrget/tsts/connectErrors/Makefile +++ b/isis/src/base/apps/edrget/tsts/connectErrors/Makefile @@ -31,7 +31,7 @@ commands: true; \ fi; if [ `$(APPNAME) \ - url=http://pdsimage2.wr.usgs.gov/cdroms/Viking_Orbiter/vo_1004/f253sxx/f26.imq \ + url=https://pdsimage2.wr.usgs.gov/cdroms/Viking_Orbiter/vo_1004/f253sxx/f26.imq \ topath=$(OUTPUT) \ >& $(OUTPUT)/httpFileDNEtmp.txt` ]; then \ true; \ diff --git a/isis/src/base/apps/edrget/tsts/http/Makefile b/isis/src/base/apps/edrget/tsts/http/Makefile index 8c655e399087178c0d7dfa4b5939110c34c1202b..3bd1659788ea8d16a324683eaf6dba9d805f517c 100644 --- a/isis/src/base/apps/edrget/tsts/http/Makefile +++ b/isis/src/base/apps/edrget/tsts/http/Makefile @@ -3,6 +3,6 @@ APPNAME = edrget include $(ISISROOT)/make/isismake.tsts commands: - $(APPNAME) URL=http://pds-imaging.jpl.nasa.gov/data/mro/mars_reconnaissance_orbiter/marci/mrom_0209/calib/vis1flat.ddd TOPATH=$(OUTPUT) > /dev/null; + $(APPNAME) URL=https://pds-imaging.jpl.nasa.gov//data/mro/mars_reconnaissance_orbiter/marci/mrom_0209/calib/vis1flat.ddd TOPATH=$(OUTPUT) > /dev/null; ddd2isis from=$(OUTPUT)/vis1flat.ddd to=$(OUTPUT)/vis1flat.cub > /dev/null; $(RM) $(OUTPUT)/vis1flat.ddd > /dev/null; diff --git a/isis/src/base/apps/edrget/tsts/timeout/Makefile b/isis/src/base/apps/edrget/tsts/timeout/Makefile index 8b2625ba16cbf862f6bc5be719134aaf21549f99..7ec40e664853bb5de5720f3711fb98adcde15f4e 100644 --- a/isis/src/base/apps/edrget/tsts/timeout/Makefile +++ b/isis/src/base/apps/edrget/tsts/timeout/Makefile @@ -6,7 +6,7 @@ commands: $(APPNAME) URL=ftp://pdsimage2.wr.usgs.gov/cdroms/Viking_Orbiter/vo_1004/f253sxx/f253s05.imq TOPATH=$(OUTPUT) TIMEOUT=6 >& $(OUTPUT)/temp.txt; $(SED) 's/.*Timeout/Timeout/' < $(OUTPUT)/temp.txt > $(OUTPUT)/temp1.txt; $(TAIL) '-2' < $(OUTPUT)/temp1.txt > $(OUTPUT)/ftperror.txt; - $(APPNAME) URL=http://pdsimage2.wr.usgs.gov/cdroms/Viking_Orbiter/vo_1004/f253sxx/f253s05.imq TOPATH=$(OUTPUT) TIMEOUT=6 >& $(OUTPUT)/temp.txt; + $(APPNAME) URL=https://pdsimage2.wr.usgs.gov/cdroms/Viking_Orbiter/vo_1004/f253sxx/f253s05.imq TOPATH=$(OUTPUT) TIMEOUT=6 >& $(OUTPUT)/temp.txt; $(SED) 's/.*Timeout/Timeout/' < $(OUTPUT)/temp.txt > $(OUTPUT)/temp1.txt; $(TAIL) '-2' < $(OUTPUT)/temp1.txt > $(OUTPUT)/httperror.txt; $(RM) $(OUTPUT)/temp.txt; diff --git a/isis/src/base/apps/equalizer/equalizer.xml b/isis/src/base/apps/equalizer/equalizer.xml index 24ad67a84b573682488b799ab677a425d81eda36..d2dee5aefd62fe2ba0513be62b379e362665a580 100644 --- a/isis/src/base/apps/equalizer/equalizer.xml +++ b/isis/src/base/apps/equalizer/equalizer.xml @@ -16,8 +16,8 @@

Statistic gathering is done on a band-by-band basis. The statistics are used in a least squares solution to determine multiplicative (GAIN or MULT) and additive - (OFFSET or BASE) corrections for each image. In addition to simply calculating corrective - factors and applying said factors to each image (BOTH), the user has the option to only + (OFFSET or BASE) corrections for each image. In addition to simply calculating corrective + factors and applying said factors to each image (BOTH), the user has the option to only calculate statistics (CALCULATE) and then examine these gathered statistics in a text file (OUTSTATS). Then, equalizer can be run again using that statistics file as input (INSTATS) to apply correction to any or all of the images without the need to calculate corrective @@ -31,7 +31,7 @@

When corrective factors are undetermined, the user can use the RECALCULATE process option to try to solve them. To do this, images can be added to the input list to try to create - more overlaps or images without overlaps can be removed. An input statistics file (INSTATS) + more overlaps or images without overlaps can be removed. An input statistics file (INSTATS) containing previously calculated image statistics must be provided. These statistics will be reloaded so overlap statistics will only be recalculated for new images in the modified input list. If all the images have overlaps and sufficient valid overlaps exist, corrective factors @@ -42,19 +42,19 @@ Additionally, the RETRYBOTH process option may be used to recalculate statistics and then apply corrective factors. This requires the user to provide an INSTATS file containing previously calculated statistics. It is also suggested that the user provide an OUTSTATS file - in case corrective factors cannot be determined. If the corrective factors are determined, + in case corrective factors cannot be determined. If the corrective factors are determined, they will then be applied to the input images.

The addition of these RETRYBOTH and RECALCULATE parameters has modified the content of the output statistics. Additional information is included in the output statistics so that previously calculated overlap statistics can be reloaded when using these parameters. - Note that statistics files created with previous versions of ISIS 3 can still be used as + Note that statistics files created with previous versions of ISIS 3 can still be used as input statistics.

The actual equation to be used for equalization, for ADJUST=BRIGHTNESS, CONTRAST or BOTH, on - each band in each cube is as follows: + each band in each cube is as follows: 

         newdn(s,l,b)   =   (olddn(s,l,b) - avg(b)) * GAIN(b) + (avg(b) + OFFSET(b))
@@ -231,7 +231,7 @@ in the QRD description. References #962. - Added the option "ADJUST=GAIN" based on a prototype developed by Jeff + Added the option "ADJUST=GAIN" based on a prototype developed by Jeff Anderson. Fixes #911. @@ -242,6 +242,10 @@ in the input image list and recalculate statistics for any new images in the input list, reusing previously calculated statistics for the rest of the images. Fixes #2282. + + Changed pvl.DIFF of input for app tests nonOverlapRecalculate and nonOverlapRetryBoth to + ignore file names. Allows test to pass when not using default data area. Fixes #4738. + @@ -359,7 +363,7 @@ Calculate statistics and apply correction - This option will calculate image statistics and then apply + This option will calculate image statistics and then apply corrections from the results. @@ -391,7 +395,7 @@ Calculate statistics only - This option will calculate image statistics and write them to an + This option will calculate image statistics and write them to an output PVL file. Image corrections will not be applied. @@ -520,7 +524,7 @@ Algorithm type used to adjust the pixel values - This option allows the user to select the algorithm that will be + This option allows the user to select the algorithm that will be used to adjust the pixel values. The BRIGHTNESS mode will equalize using only an offset (the gain will be set to 1.0), and the CONTRAST mode will equalize using only a gain (the offset will @@ -835,7 +839,7 @@ subset of the images used to produce a specified input statistics file. - @@ -905,7 +909,7 @@ In addition to specifying a fromlist, we must also specify the previously calculated statistics PVL file (instats), specify a location to write the output statistics PVL file - (outstats), and set the process type to "recalculate." Since no output images will be + (outstats), and set the process type to "recalculate." Since no output images will be created, we do not (and cannot), specify a tolist. All other options are at default values. @@ -921,7 +925,7 @@ Screenshot of the GUI with parameters set to initially calculate statistics for a set of images with non-overlapping images. - @@ -989,12 +993,12 @@ - Click here to see the output text file containing the statistics needed for + Click here to see the output text file containing the statistics needed for recalculating This PVL file contains equalization-related statistics where corrective factors have not - been determined (since there were images without overlaps). This can be used to + been determined (since there were images without overlaps). This can be used to recalculate statistics for a corrected input image list. Overlap statistics will only be calculated for new overlaps. (INSTATS) @@ -1005,7 +1009,7 @@ used for equalizing - This PVL file contains equalization-related statistics that were recalculated from a + This PVL file contains equalization-related statistics that were recalculated from a previous run of equalizer. This can be used for applying correction to any or all images used to generate this file. (OUTSTATS) @@ -1021,7 +1025,7 @@ - fromlist=fixedFromlist.lis tolist=tolist.lis outstats=retryBothStats.pvl + fromlist=fixedFromlist.lis tolist=tolist.lis outstats=retryBothStats.pvl instats=nonOverlapStats.pvl process=retryboth @@ -1039,7 +1043,7 @@ Example GUI - Screenshot of the GUI with parameters set to calculate statistics and apply + Screenshot of the GUI with parameters set to calculate statistics and apply corrections (BOTH). This fails because some of the images do not have any overlaps (see the application log at the bottom of the screenshot). @@ -1056,7 +1060,7 @@ Screenshot of the GUI with parameters set to recalculate statistics from previously calculated statistics and apply corrections (RETRYBOTH) to the input images. - @@ -1113,7 +1117,7 @@ - Click here to see the output text file containing the statistics needed for + Click here to see the output text file containing the statistics needed for recalculating and then applying. @@ -1128,7 +1132,7 @@ Click here to see the output text file containing the recalculated statistics. - This PVL file contains equalization-related statistics that were recalculated from a + This PVL file contains equalization-related statistics that were recalculated from a previous run of equalizer. (OUTSTATS) diff --git a/isis/src/base/apps/findimageoverlaps/findimageoverlaps.xml b/isis/src/base/apps/findimageoverlaps/findimageoverlaps.xml index 833223eab8a7bf3eba1644a93694d125aaedc8ec..f3f20fc6b4fab76e51bacdce14d6fc104a8cd902 100644 --- a/isis/src/base/apps/findimageoverlaps/findimageoverlaps.xml +++ b/isis/src/base/apps/findimageoverlaps/findimageoverlaps.xml @@ -127,6 +127,9 @@ Added an exception for giving findimageoverlaps a cube list of only one cube. Fixes #4200. + + Added a tryLock to avoid a segfault that could occur on OSX. Fixes #4810. + diff --git a/isis/src/base/apps/footprintinit/footprintinit.xml b/isis/src/base/apps/footprintinit/footprintinit.xml index cae7fcfdf6c66e4486ba203afa5c12cd85414e87..2ede9c6a53f7668fae5542a01e5b2c47a64876bb 100644 --- a/isis/src/base/apps/footprintinit/footprintinit.xml +++ b/isis/src/base/apps/footprintinit/footprintinit.xml @@ -4,7 +4,7 @@ Creates a lat/lon polygon and writes it to the image - +

This applications creates a geometric polygon ("footprint") of the input @@ -33,7 +33,7 @@ must be run prior to running this application.

- + Control Networks @@ -44,10 +44,10 @@ cnetadd - + - Original version + Original version Changed input from a list of cube files to a single cube and added appTest. @@ -74,11 +74,11 @@ Updated to work with Geos3.0.0 - Deletes old footprint (generated off cubes serial number) if its found. + Deletes old footprint (generated off cubes serial number) if its found. New name for blob is just Footprint. - PIXINC parameter was removed, ImagePolygon now uses a new method of + PIXINC parameter was removed, ImagePolygon now uses a new method of finding footprints @@ -154,12 +154,15 @@ Modified code to get TargetRadii using the cube label and mapping group rather than just the TargetName. References #3892 + + Removed terminal output from poleMultiBoundary apptest. Fixes #4548. + - + - + - + cube input @@ -167,17 +170,17 @@ Input cube - The cube to initialize polygons. + The cube to initialize polygons. *.cub - + - + - + boolean FALSE @@ -188,12 +191,12 @@ invalid polygon. In addition, a results group will be created with the keywords SINC/LINC which reveal what SINC/LINC values were actually used for the creation of the footprint. - + NOTE: This parameter can result in a drastic increase in running time as well as a change to user input values. - + string LINCSINC @@ -244,11 +247,11 @@ accurate) - This is approximately how many lines in the input image + This is approximately how many lines in the input image to skip for every point stored in the footprint. - + integer 1 @@ -258,11 +261,11 @@ accurate) - This is approximately how many samples in the input image + This is approximately how many samples in the input image to skip for every point stored in the footprint. - + integer 40 @@ -290,12 +293,12 @@ When this value is provided, footprintinit will only consider points with an emission angle less than or equal to the provided value. - + There should never be an emission angle above 90. However, planet features can cause abnormalities. - + double 0.0 @@ -307,16 +310,16 @@ When this value is provided, footprintinit will only consider points with an incidence angle less than or equal to the provided value. - + There should never be an incidence angle above 90. However, planet features can cause abnormalities. - + - + - + string ELLIPSOID @@ -335,17 +338,17 @@ - + - + - + boolean FALSE @@ -389,9 +392,9 @@ *.map *.cub - + - + - + diff --git a/isis/src/base/apps/footprintinit/tsts/poleMultiBoundary/Makefile b/isis/src/base/apps/footprintinit/tsts/poleMultiBoundary/Makefile index e2df283254cc80f6160c45211e1d119a06443fd2..0d1ed208437398e82794e347fc77a09e083c4f97 100644 --- a/isis/src/base/apps/footprintinit/tsts/poleMultiBoundary/Makefile +++ b/isis/src/base/apps/footprintinit/tsts/poleMultiBoundary/Makefile @@ -12,7 +12,7 @@ commands: $$ISISROOT/bin/blobdump from=$(OUTPUT)/e1202081.cub \ to=$(OUTPUT)/e1202081.txt \ name=footprint \ - type=Polygon + type=Polygon \ >& /dev/null; $(CAT) $(OUTPUT)/e1202081.txt \ | $(SED) 's/\([0-9]\.[0-9]\{3\}\)\([0-9]*\)/\1/g' \ diff --git a/isis/src/base/apps/grid/grid.cpp b/isis/src/base/apps/grid/grid.cpp index 4e52983555df24a0b438126536dbdc1484695d86..ebb7238699b9569003d9df88e81e75d1b40dd33f 100644 --- a/isis/src/base/apps/grid/grid.cpp +++ b/isis/src/base/apps/grid/grid.cpp @@ -121,8 +121,11 @@ void IsisMain() { //if > 1 input band and IsBandIndependent = false, need to regenerate grid for // each band - if ( (inputBands >= 2) && !(icube->camera()->IsBandIndependent()) ) { - recalculateForEachBand = true; + + if (icube->hasGroup("Instrument")) { + if ((inputBands >= 2) && !(icube->camera()->IsBandIndependent())) { + recalculateForEachBand = true; + } } gmap = new UniversalGroundMap(*icube, UniversalGroundMap::ProjectionFirst); diff --git a/isis/src/base/apps/grid/grid.xml b/isis/src/base/apps/grid/grid.xml index a0508615862a74f92d560a6db488cd212853de1e..9d8f91c3e90f292abbdc7cb6c6a0f1b573f1e100 100644 --- a/isis/src/base/apps/grid/grid.xml +++ b/isis/src/base/apps/grid/grid.xml @@ -166,6 +166,10 @@ when MODE="GROUND" on a Cube with a band-dependent camera model, the grid will be re-calculated for each band. Fixes #2191. + + Fixed error introduced in last change which caused grid to no longer work on multi-band + cubes without camera models (for example: a mosaic will not have a camera model.) Fixes #4586. + diff --git a/isis/src/base/apps/grid/tsts/mosaic/Makefile b/isis/src/base/apps/grid/tsts/mosaic/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..3e76e531642c45231b1b250b0aa83a03384ea979 --- /dev/null +++ b/isis/src/base/apps/grid/tsts/mosaic/Makefile @@ -0,0 +1,10 @@ +APPNAME = grid + +# Added to test that grid works on mosaics, which notably will not have camera models. + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(APPNAME) from=$(INPUT)/lroMosaicOntop.cub \ + to=$(OUTPUT)/lroMosaicOntop.cub > /dev/null; + diff --git a/isis/src/base/apps/isis2pds/isis2pds.cpp b/isis/src/base/apps/isis2pds/isis2pds.cpp index 85e16770d7b41cf7d9bca59c1bc27fee78560c62..3db6011a6b6e4a85239ae870f6c778e7deb6ce72 100644 --- a/isis/src/base/apps/isis2pds/isis2pds.cpp +++ b/isis/src/base/apps/isis2pds/isis2pds.cpp @@ -63,6 +63,10 @@ void IsisMain() { if(ui.GetString("LABTYPE") == "FIXED") p.SetExportType(ProcessExportPds::Fixed); + if (ui.GetBoolean("CHECKSUM")) { + p.setCanGenerateChecksum(true); + } + //Set the resolution to Kilometers p.SetPdsResolution(ProcessExportPds::Kilometer); @@ -73,6 +77,9 @@ void IsisMain() { ofstream oCube(outFileName.toLatin1().data()); p.OutputLabel(oCube); p.StartProcess(oCube); + if (ui.GetBoolean("CHECKSUM")) { + p.updateChecksumInLabel(oCube); + } oCube.close(); p.EndProcess(); diff --git a/isis/src/base/apps/isis2pds/isis2pds.xml b/isis/src/base/apps/isis2pds/isis2pds.xml index 86a2bc8040272ad6d16389e326642e562aa4d053..2817c09c5ae6e1f8bcbac456c2baad4d31d1747d 100644 --- a/isis/src/base/apps/isis2pds/isis2pds.xml +++ b/isis/src/base/apps/isis2pds/isis2pds.xml @@ -22,7 +22,11 @@ Added the Label Type capability (param) - Changed to assume that radii without units in the input Isis cube are in meters, map scales without units are in meters/pixel, and map resolutions without units are in pixels/degree. + Changed to assume that radii without units in the input Isis cube are in meters, map scales without units are in meters/pixel, and map resolutions without units are in pixels/degree. + + + Added CHECKSUM parameter to optionally generate and attach an MD5 checksum to the exported + image label. This checksum is generated from the image data. Fixes #1013. @@ -142,7 +146,7 @@ true Dedicates the minimum DN value for null pixels. - If set to true, the minimum value of the raw output data will be + If set to true, the minimum value of the raw output data will be reserved for null pixels. The actual value used for null pixels will be denoted in the print.prt file as well as displayed onscreen. @@ -187,6 +191,15 @@ file as well as displayed onscreen. + + boolean + false + Generates and attaches an MD5 checksum to the labels. + + If set to true, then an MD5 checksum will be generated from the image data and + attached to the output image labels. + + @@ -327,7 +340,7 @@ - + @@ -342,7 +355,7 @@ from=ab102401.lev2.cub to=ab102401.lev2.img - In this example isis2pds will convert a cube to a pds + In this example isis2pds will convert a cube to a pds format image. @@ -364,12 +377,12 @@ Output pds image - This is the exact same image with exact same DNs, but in + This is the exact same image with exact same DNs, but in the pds format. TO - + diff --git a/isis/src/base/apps/isis2pds/tsts/checksum/Makefile b/isis/src/base/apps/isis2pds/tsts/checksum/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..bcbfaf48279f97af05419073609dab566c9fb6d7 --- /dev/null +++ b/isis/src/base/apps/isis2pds/tsts/checksum/Makefile @@ -0,0 +1,27 @@ +# Checks the MD5 checksum (CHECKSUM=yes) functionality. +# Note that the md5sum.txt is generated by md5sum and should match labels.pvl's CHECKSUM value. +APPNAME = isis2pds + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(APPNAME) from=$(INPUT)/ab102401.cub \ + to=$(OUTPUT)/ab102401.img \ + bittype=u16bit \ + checksum=yes \ + > /dev/null; + catlab from=$(OUTPUT)/ab102401.img to=$(OUTPUT)/labels.pvl > /dev/null; + pds2isis from=$(OUTPUT)/ab102401.img to=$(OUTPUT)/ab102401.cub > /dev/null; + dd if=$(OUTPUT)/ab102401.img \ + bs=`getkey from=$(OUTPUT)/ab102401.img keyword=^IMAGE` \ + count=1 >& $(OUTPUT)/TEMP.txt > $(OUTPUT)/labelsEOL.txt; + # do a cubeit to extract only data and perform md5sum on it to compare + $(LS) -1 $(INPUT)/*.cub > $(OUTPUT)/cube.lis; + cubeit from=$(OUTPUT)/cube.lis \ + to=$(OUTPUT)/cubeit.cub+Lsb+BandSequential+Detached \ + > /dev/null; + #md5sum $(OUTPUT)/cubeit.cub > $(OUTPUT)/md5sum.txt; + $(RM) $(OUTPUT)/cube.lis > /dev/null; + $(RM) $(OUTPUT)/cubeit* > /dev/null; + $(RM) $(OUTPUT)/ab102401.img > /dev/null; + $(RM) $(OUTPUT)/TEMP.txt > /dev/null; diff --git a/isis/src/base/apps/isis2pds/tsts/offsetTest/Makefile b/isis/src/base/apps/isis2pds/tsts/offsetTest/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..ec2eb475af9268205eef51cc38f54bcdf83c85bb --- /dev/null +++ b/isis/src/base/apps/isis2pds/tsts/offsetTest/Makefile @@ -0,0 +1,10 @@ +APPNAME = isis2pds + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(APPNAME) from=$(INPUT)/ldem_4.cub \ + to=$(OUTPUT)/ldem_4_isis2pds.img > /dev/null; + catlab from=$(OUTPUT)/ldem_4_isis2pds.img to=$(OUTPUT)/ldem_4truth.pvl > /dev/null; + $(RM) $(OUTPUT)/ldem_4_isis2pds.img > /dev/null; + diff --git a/isis/src/base/apps/isisminer/GisOverlapStrategy.cpp b/isis/src/base/apps/isisminer/GisOverlapStrategy.cpp index 52064a82c6597014f2ea699d2c3b54aeba593cb1..3cf9d753ce604294d000d1c4d0acd70f68784c7c 100644 --- a/isis/src/base/apps/isisminer/GisOverlapStrategy.cpp +++ b/isis/src/base/apps/isisminer/GisOverlapStrategy.cpp @@ -202,7 +202,9 @@ namespace Isis { // Build the RTree geometry int ngeoms = qMax(goodones.size(), 2); - cout << "Total Geoms: " << ngeoms << "\n"; + if ( isDebug() ) { + cout << "Total Geoms: " << ngeoms << "\n"; + } GEOSSTRtree *rtree = GEOSSTRtree_create(ngeoms); if ( !rtree ) { cout << "Address: " << rtree << "\n"; diff --git a/isis/src/base/apps/isisminer/GisOverlapStrategy.h b/isis/src/base/apps/isisminer/GisOverlapStrategy.h index 93283260b6297e7cd7e0211139103cf217e2619f..c828f251acf7eec46a89ba4bacb348ec4ce1cbab 100644 --- a/isis/src/base/apps/isisminer/GisOverlapStrategy.h +++ b/isis/src/base/apps/isisminer/GisOverlapStrategy.h @@ -64,6 +64,8 @@ namespace Isis { * a global resource list. * @history 2015-06-15 Kris Becker - Ensure at least 2 entries are allocated * for GOES RTree allocations (required by GEOS) + * @history 2017-01-06 Jesse Mapel - Made the "Total Geoms" output a debug + * statement. Fixes #4581. */ class GisOverlapStrategy : public Strategy { diff --git a/isis/src/base/apps/isisminer/isisminer.xml b/isis/src/base/apps/isisminer/isisminer.xml index a2948432ac4ed7d0750aa94d0f201034c8370fbc..5da3f9cf44989657767c71a0a701edfa035d96a9 100644 --- a/isis/src/base/apps/isisminer/isisminer.xml +++ b/isis/src/base/apps/isisminer/isisminer.xml @@ -895,6 +895,18 @@ EndObject Bitwise or x | y + + 6 + && + Logical and + x && y + + + 6 + || + Logical or + x || y + 6 % @@ -1206,6 +1218,25 @@ EndObject True. + + Header + Optional + + The list of keywords that the values in each column will be stored + in. The column values will be associated with keywords from left to + right unless Index is used. + + + + Index + Optional + + The column indices in the CSV file that the keywords in + Header will use for their values. The first entry will be + the value for the first keyword in Header, the second entry + will be the value for the second keyword, etc. + + SkipLines Optional @@ -1532,11 +1563,11 @@ EndObject The following is an example of a CsvWriter strategy: 
 Object = Strategy
-  Type = CsvWriter
-  Name = mdismla
-  Filename = "mdis_mla_ridelong.lis"
-  Mode = Create
-  Header = True
+  Type     = CsvWriter
+  Name     = mdismla
+  CSVFile  = "mdis_mla_ridelong.lis"
+  Mode     = Create
+  Header   = True
   Keywords = (YearDoy, SourceProductId, StartTime, EtStartTime, 
               ExposureDuration, CenterLongitude, CenterLatitude,
               PixelResolution, MeanGroundResolution,
@@ -2169,7 +2200,7 @@ EndObject
        of the primary Resource. Keywords from both Resources are combined into a 
        single Resource by renaming each keyword from both Resources and 
        propagating them to the merged Asset Resource. An A is appended to the 
-       source Resource keywords and aA is appended to the candidate Resource 
+       source Resource keywords and a B is appended to the candidate Resource 
        keywords before they are merged to distinguish keywords. The suffix of 
        keyword sources can be specified by the user using the                                                         
        MergeSuffixA and MergeSuffixB keywords, respectively. 
@@ -2289,7 +2320,7 @@ EndObject
               Description
             
             
-               Intersect 
+               Intersection 
               
                   Combines the two GIS footprints as an intersection. This will 
                   result in a GIS geometry that contains the area of common 
@@ -3928,7 +3959,7 @@ Result = StereoPairRank
       keyword suffixes for each image as they are merged. MergeSuffixA 
       is used to identify the primary stereo image, MergeSuffixB the 
       secondary or matched stereo image. Defaults for merge suffix keywords are 
-      A and A respectively.
+      A and B respectively.
     

     

        If data is provided by caminfo, then the values required by this Strategy 
diff --git a/isis/src/base/apps/pds2isis/tsts/offsetTest/Makefile b/isis/src/base/apps/pds2isis/tsts/offsetTest/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..ed1e3e7f0032e2cf2838d9e1f780056f46d28d63
--- /dev/null
+++ b/isis/src/base/apps/pds2isis/tsts/offsetTest/Makefile
@@ -0,0 +1,9 @@
+APPNAME = pds2isis
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	$(APPNAME) from=$(INPUT)/ldem_4.lbl \
+	to=$(OUTPUT)/ldem_4.cub > /dev/null;
+	catlab from=$(OUTPUT)/ldem_4.cub to=$(OUTPUT)/ldem_4truth.pvl > /dev/null;
+
diff --git a/isis/src/base/apps/pixel2map/pixel2map.cpp b/isis/src/base/apps/pixel2map/pixel2map.cpp
index b84f7f6e60f77ac0b4860b8930c170bfc2cf1346..9862ebee7f00ce26045c500db6735b3234e60bfd 100755
--- a/isis/src/base/apps/pixel2map/pixel2map.cpp
+++ b/isis/src/base/apps/pixel2map/pixel2map.cpp
@@ -42,9 +42,7 @@ int g_numIFOVs = 0;
 
 void IsisMain() {
 
-  ProcessRubberSheet processRubberSheet;
   g_incam = NULL;
-  Cube *icube;
 
   // Get the map projection file provided by the user
   UserInterface &ui = Application::GetUserInterface();
@@ -58,18 +56,19 @@ void IsisMain() {
     list.push_back(FileName(ui.GetAsString("FROM")));
   }
   else {
-    list.read(ui.GetFileName("FROMLIST"));
-  }
-  if (list.size() < 1) {
-    QString msg = "The list file [" + ui.GetFileName("FROMLIST") +
-                  "does not contain any data";
-    throw IException(IException::User, msg, _FILEINFO_);
+    try {
+      list.read(ui.GetFileName("FROMLIST"));
+    }
+    catch (IException &e) {
+      throw IException(e);
+    }
   }
+
   if (ui.GetString("FOVRANGE") == "INSTANTANEOUS") {
     g_numIFOVs = 1;
   }
   else {
-    g_numIFOVs = 3;
+    g_numIFOVs = ui.GetInteger("NUMIFOV");
   }
 
   double newminlat, newmaxlat, newminlon, newmaxlon;
@@ -83,11 +82,17 @@ void IsisMain() {
   // Get the combined lat/lon range for all input cubes
   int bands = 1;
   for (int i = 0; i < list.size(); i++) {
+
     // Open the input cube and get the camera
     CubeAttributeInput atts0(list[i]);
-    icube = processRubberSheet.SetInputCube(list[i].toString(), atts0);
-    bands = icube->bandCount();
-    g_incam = icube->camera();
+    Cube icube;
+    if(atts0.bands().size() != 0) {
+      vector lame = atts0.bands();
+      icube.setVirtualBands(lame);
+    }
+    icube.open( list[i].toString() );
+    bands = icube.bandCount();
+    g_incam = icube.camera();
 
     // Make sure it is not the sky
     if (g_incam->target()->isSky()) {
@@ -97,7 +102,7 @@ void IsisMain() {
     }
 
     // Make sure all the bands for all the files match
-    if (i > 1 && atts0.bandsString() != lastBandString) {
+    if (i >= 1 && atts0.bandsString() != lastBandString) {
       QString msg = "The Band numbers for all the files do not match.";
       throw IException(IException::User, msg, _FILEINFO_);
     }
@@ -126,6 +131,9 @@ void IsisMain() {
     if (newmaxlon > maxlon) {
       maxlon = newmaxlon;
     }
+
+    // The camera will be deleted when the Cube is deleted so NULL g_incam
+    g_incam = NULL;
   } //end for list.size
 
   camGrp.addKeyword(PvlKeyword("MinimumLatitude", toString(minlat)), Pvl::Replace);
@@ -225,7 +233,17 @@ void IsisMain() {
 
   // See if the user want us to handle the longitude seam
   if (ui.GetString("DEFAULTRANGE") == "CAMERA" || ui.GetString("DEFAULTRANGE") == "MINIMIZE") {
-  // TODO: the g_incam below is left over from the for loop above. This must be fixed
+
+    // Open the last cube and use its camera
+    CubeAttributeInput atts0( list.back() );
+    Cube icube;
+    if(atts0.bands().size() != 0) {
+      vector lame = atts0.bands();
+      icube.setVirtualBands(lame);
+    }
+    icube.open( list.back().toString() );
+    g_incam = icube.camera();
+
     if (g_incam->IntersectsLongitudeDomain(userMap)) {
       if (ui.GetString("LONSEAM") == "AUTO") {
         if ((int) userGrp["LongitudeDomain"] == 360) {
@@ -271,6 +289,9 @@ void IsisMain() {
         throw IException(IException::User, msg, _FILEINFO_);
       }
     }
+
+    // The camera will be deleted when the Cube is deleted so NULL g_incam
+    g_incam = NULL;
   }
 
 
@@ -315,7 +336,7 @@ void IsisMain() {
     processBrick.SetBrickSize(1, 1, bands);
     // Recall list[f] is a FileName, which stores the attributes
     CubeAttributeInput atts0(list[f]);
-    icube = processBrick.SetInputCube(list[f].toString(), atts0, 0);
+    Cube *icube = processBrick.SetInputCube(list[f].toString(), atts0, 0);
     g_incam = icube->camera();
 
     processBrick.StartProcess(rasterizePixel);
diff --git a/isis/src/base/apps/pixel2map/pixel2map.xml b/isis/src/base/apps/pixel2map/pixel2map.xml
index 34df479fc3a5e1c0190afaf78e815655b1481a7f..1b9c79b043d0b1cf1c479eb3b6dde4894ad44992 100755
--- a/isis/src/base/apps/pixel2map/pixel2map.xml
+++ b/isis/src/base/apps/pixel2map/pixel2map.xml
@@ -6,65 +6,110 @@
   
 
   
-    This specialized program projects an ISIS level0 or 
-    level1 cube to a 
-    map projected (ISIS level2) cube.  
+    The pixel2map program projects an ISIS level0 or
+    level1 cube to a
+    map-projected, ISIS level2
+    cube. Please note that pixels that fall
+    in either polar region (i.e. latitude of 90.0 degrees or -90.0 degrees)
+    cannot currently be processed and are assigned as NULL pixels (i.e. this is currently
+    unsupported).
     

-      The program, cam2map also projects a cube, and is recommended for most mapping 
-      applications. Use pixel2map to project cubes where pixels do not overlap.
-      For instance, this program is used to project Cassini VIMS, a point instrument. It is
-      also used for line scan instruments whose lines may not overlap, such as 
-      Mars Reconnaissance Orbiter CRISM and Dawn VIR.
-      
+      In order for pixel2map to run successfully, input cubes must have SPICE data. The
+      program spiceinit should be used to attach the appropriate SPICE data to input cubes.
+      If a shape model is provided (or added in spiceinit by default), orthorectification is
+      supported through the determination of the field-of-view (FOV) latitude/longitude coordinates
+      as they map onto the digital elevation map (DEM). The pixel2map program also
+      requires a map projection specification. The map projection is defined
+      using a PVL file specified with the MAP parameter. The maptemplate
+      program can be used to create a map projection file.
     

     

-    Note: pixel2map cannot currently process the input pixel which contains either pole
-    (i.e. latitude of 90.0 degrees or -90.0 degrees), which will cause a NULL pixel in your output map projected
-    cube where the pole is located.
+      The cam2map program also projects a cube and is recommended
+      for most mapping applications. The cam2map program assumes contiguous pixels and will
+      interpolate to fill any gaps that occur in the output image during projection.
+      The pixel2map program will preserve these gaps where the pixels are not contiguous.
+      This program is designed to project cubes for the following cases:
+      
    
+        
  • pixels do not overlap spatially
    • 
+        
  • data is smeared from long exposure times and drifting (see FOVRANGE=FULLEXPOSURE)
    • 
+        
  • data is captured from spectrometers
    • 
+        
      
+          
    • CRISM
      • 
+          
    • DAWN VIR
      • 
+          
    • NEARS MSI
      • 
+          
    • VIMS
      • 
+        
    
+      

+      It is important to note that when projecting multiple spectrometer images within a single run
+      of pixel2map, the hyperspectral information present in the input may be compromised in
+      the output projection because individual overlapping pixels are averaged in the output pixel.
+      With a single observation as input, the hyperspectral information will be preserved.
+      With multiple observations as input (by using FROMTYPE=FROMLIST
+      and FROMLIST), each observation may have different geometry depending on the timeframe the
+      observations were acquired. Input pixels from each input observation mapped to an overlapping
+      output surface pixel will be averaged.
     

+
+    The following table indicates how pixel2map and cam2map differ:
+
+    
+      
+        
+        
+      
+
+      
+        
+        
+      
+
+      
+        
+        
+      
+
+      
+        
+        
+      
+
+      
+        
+        
+      
+    
pixel2mapcam2map
Uses a forward driven algorithm for projection.Uses a reverse driven algorithm for projection.
Each input pixel is converted to a FOV polygon, typically using the latitude/longitude of
+            the pixel corners, and rasterized into the output projected image by calculating output
+            pixels that fall in the boundary of the input pixel.Each input pixel is not converted to a polygon to be rasterized. Up to 16 input
+            pixels are interpolated around the center latitude and longitude of the output map
+            pixel.
The space between pixels is retained in the output projected cube.The space between pixels are interpolated thus gaps are filled in the output projected cube.
The output cube will be spatially accurate for non-continuous pixels.The output cube may not be spatially accurate as output pixels are interpolated.

+
     

-    How pixel2map and cam2map differ
+    The examples below are Mars Reconnaissance Orbiter/CRISM cubes where scan lines do not overlap
+    in their original state. The major difference is in the output of the application used to
+    project the cube. Both applications will project the cube,
+    but will also result in a different spatial outcome.
     

+     
+     
     

-    
    
-    
  • The pixel2map application uses a forward driven algorithm.
    • 
-    
  • Each input pixel is converted to a polygon and rasterized into the output projected image by calculating output
-     pixels that fall in the boundary of the input pixel.
    • 
-    
  • The space between pixels is retained in the output projected cube.
    • 
-    

-    Versus
-    
    
-    
  • The cam2map application uses a reverse driven algorithm.
    • 
-    
  • Each input pixel is not converted to a polygon and rasterized into the output projected image. The input pixels
-    are calculated by pixels situated at the same latitude and longitude.
    • 
-    
  • The space between pixels are interpolated thus gaps are filled in the output projected cube.
    • 
-    

+    Left Cube: cam2map was chosen to project the cube. Notice the scan lines have been
+    interpolated/filled.  If you want to preserve gaps, cam2map will not achieve this result (but
+    nearest-neighbor interpolation will be more accurate). In addition, the cube is no longer accurate
+    (traceable for this type of instrument).
     

     

-    The examples below are Mars Reconnaissance Orbiter/CRISM cubes where scan lines do not overlap in their original state.
-    The major difference is in the output of the application used to project the cube. Both applications will project the cube,
-    but also result in a different spatial outcome. 
-    Left Cube: cam2map was chosen to project the cube. Notice the scan lines have been interpolated thus filled.  If you want to
-    preserve gaps, cam2map will not achieve this result. In addition, the cube is no longer spatially correct. 
-    Right Cube: pixel2map was chosen to project the cube. Notice how the gaps are retained in the output. The cube is spatially
-    correct.   
+    Right Cube: pixel2map was chosen to project the cube. Notice the gaps are retained in the output and the cube is spatially
+    correct.
     

-     
-     
+
     

-    The input cube requires SPICE data and therefore the program spiceinit should be run on it 
-    prior to pixel2map.  The map projection is defined using a 
-    PVL file specified with the MAP parameter.  The default projection is the system Sinusoidal projection 
-    ($ISIS3DATA/base/templates/maps/sinusoidal.map).  To learn more about using map projections in ISIS, 
-    refer to the ISIS Workshop 
-    
-    "Learning About Map Projections".
+      Mapping Parameterization
     

     

-      If you need to generate your own map file you can use the maptemplate program or alternatively, 
-    hand create a file using your favorite editor.  The file need only specify the ProjectionName 
-    as defaults will be computed for the remaining map file parameters.  The following table indicates 
-    how the defaults are established:
+      Several parameters of the map projection have default values when not
+      specified in the map projection file. The default projection is the
+      system sinusoidal projection. The following table indicates how the
+      defaults are established:
     

 
     
@@ -80,7 +125,7 @@
 
       
-        
 
@@ -101,9 +146,9 @@
 
       
-        
+        
@@ -114,7 +159,7 @@
     

         EquatorialRadius
PolarRadius		Read from SPICE pck file set during spiceinit.  The pck file is defined in the Kernels 
+        Read from SPICE PCK file set during spiceinit.  The PCK file is defined in the Kernels
         group via the TargetAttitudeShape keyword
       

         MinimumLatitude
MaximumLatitude
MinimumLongitude
MaximumLongitude		Computed from the input cube or read from the map file.   However, any combination of the 
-        four values can then be overridden by the user.  The values the user specifies are expected 
-        to be in the coodinate system of the projection.Computed from the input cube or read from the map file.   However, any combination of the
+        four values can then be overridden by the user.  The values the user specifies are expected
+        to be in the coordinate system of the projection.
       

 
       

 
     

-      If you only entered the input cube (FROM) and output cube (TO) and changed no other parameters the 
+      If you only entered the input cube (FROM) and output cube (TO) and changed no other parameters, the
       following is the default Mapping group:
     

     
@@ -138,24 +183,25 @@
   EndGroup
     

 
-   The map file can be an existing map projected (level2) cube.  A level2 cube has PVL labels 
-   and contains the Mapping group.  Depending on the values of the input parameters, the output 
-   cube can use some or all of the keyword values of the map file.  For instance, setting 
-   MATCHMAP=true causes all of the mapping parameters to come from the map file, resulting 
-   in an output cube having the same number of lines and 
-   samples as the map file.  If MATCHMAP=true and the map file is missing 
-   a keyword like PixelResolution, the application will fail with a PVL error.  Setting 
-   MATCHMAP=false allows for some of the mapping components to be overridden by the user or 
+   The map file can be an existing map projected (level2) cube.  A level2 cube has PVL labels
+   with a Mapping group that is used to determine the default output map geometric extents and
+   resolution.  Depending on the values of the input parameters, the output
+   cube can use some or all of the keyword values of the map file.  For instance, setting
+   MATCHMAP=true causes all of the mapping parameters to come from the map file, resulting
+   in an output cube having the same number of lines and
+   samples as the map file.  If MATCHMAP=true and the map file is missing
+   a keyword like PixelResolution, the application will fail with a PVL error.  Setting
+   MATCHMAP=false allows for some of the mapping components to be overridden by the user or
    computed from the FROM cube.
-   
 
-   
If you are attempting to construct a mosaic, it is important that the PixelResolution, EquatorialRadius, 
-   PolarRadius, LatitudeType, LongitudeDirection, LongitudeDomain, ProjectionName, and projection 
-   specific parameters (e.g., CenterLongitude, CenterLatitude) are the same for all cubes.  That is, 
-   you should create one map file and use it as input for all the cubes in your mosaic.  By letting the 
-   minimum and maximum latitude and longitude values default, the application will determine the coverage of each image.  
-   However, if the mosaic Latiude and Longitude range is entered, each output image will be projected to the full 
-   size of the mosaic resulting in large file sizes and images with many NULL pixels.  
+
+   
If you are attempting to construct a mosaic, it is important that the PixelResolution, EquatorialRadius,
+   PolarRadius, LatitudeType, LongitudeDirection, LongitudeDomain, ProjectionName, and projection
+   specific parameters (e.g., CenterLongitude, CenterLatitude) are the same for all cubes.  That is,
+   you should create one map file and use it as input for all the cubes in your mosaic.  By letting the
+   minimum and maximum latitude and longitude values default, the application will determine the coverage of each image.
+   However, if the mosaic Latitude and Longitude range is entered, each output image will be projected to the full
+   size of the mosaic resulting in large file sizes and images with many NULL pixels.
 
    The following Mapping group could be used for mosaicking:
    

@@ -168,25 +214,51 @@

- Finally, depending on the projection, problems can occur with cubes that fall on the projection - longitude seam. For example, if you are making a mosaic with LongitudeDomain = 360 and your - cube crosses 0/360 seam, this program would compute the default longitude range of the cube to - MinimumLongitude = 0 and MaximumLongitude = 360. A very large output image could be created - depending on the pixel resolution. The LONSEAM parameter allows you to selectively handle this case. + Finally, depending on the projection, problems can occur with cubes that fall on the projection + longitude seam. For example, if you are making a mosaic with LongitudeDomain = 360 and your + cube crosses the 0/360 seam, this program would compute the default longitude range of the cube to + MinimumLongitude = 0 and MaximumLongitude = 360. A very large output image could be created + depending on the pixel resolution. The LONSEAM parameter allows you to selectively handle this case. If you are making mosaics near the seam you will need to understand and alter the default for this parameter. - Section 14 of The ISIS Workshop "Learning About Map Projections" includes an example to help + Section 14 of The ISIS Workshop "Learning About Map Projections" includes an example to help illustrate the problem.

- Output of pixel2map + Output of pixel2map

- A single input file produces a projected level2 cube. A list of files (filelist) produces an averaged mosaic as output. - A count cube that contains the number of input pixels averaged into each output pixel is created along with the output + A single input file (FROM) produces a projected level2 cube. A list of files (FILELIST) produces + an averaged mosaic as output. An additional count cube with one band that contains the number of + input pixels averaged into each output pixel is created along with the output cube or mosaic.

+ +

+ Instantaneous FOV (IFOV) vs. Full FOV +

+

+ As mentioned above, pixel2map uses a forward-driven mapping algorithm to create a + projection. In short, this means that pixel2map determines a polygon (footprint) FOV for each + input pixel and rasterizes it into the output image space. Depending on what the METHOD + parameter has been set to, the input pixel DN value is included in the average of any output + pixels that fall within the polygon. +

+

+ The default behavior of pixel2map is FOVRANGE=INSTANTANEOUS. This means that the IFOV + at the center time of the exposure is being used to determine + each pixel's footprint. For spectrometers that have longer exposure times, this method does + not adequately address any smearing that can occur due to drifting during the exposure. + In order to account for smearing, FOVRANGE=FULLEXPOSURE can be used. This method determines + a pixel's polygon by finding the IFOV polygons at the start time, middle time, and + end time of the exposure and then drawing an envelope around these polygons. The images + below visually demonstrate the differences between the two FOVRANGE parameter values. +

+ +

+ For more details, see the parameter description for FOVRANGE or examples 3 and 4. +

@@ -199,11 +271,11 @@ - + Original version - Removed references to CubeInfo + Removed references to CubeInfo Fixed parameter names @@ -235,6 +307,22 @@ IsisCube labels and tables are now attached to the output cubes if there is a single input image. Fixes #4433. Removed unused UniveralGroundMap instance. References #4495. + + Added tests to for all errors. Fixed a check so now all files in a list have to have the + same number of bands selected. References #4535. + + + Added the NUMIFOV parameter to determine how many IFOVs are used when creating a full FOV. + References #4576. + + + Modified to no longer keep all cubes in the fromlist open. This resulted in crashing due to + reaching the maximum number of open files when the fromlist was large. Cubes will now be + opened one at a time and then closed before opening the next cube. Fixes #4761. + + + Updated documentation and added examples. Fixes #4537. + @@ -253,17 +341,21 @@ The specification of the input cube to be projected. The cube must have been initialized using the spiceinit program. - This option allows a single input cube to be processed. + This option allows a single input cube to be processed. Processing a single cube at a + time is recommended to avoid averaging output pixels with other observations not + acquired close in time. FROMLIST @@ -287,9 +379,9 @@ *.lis Input list of cubes to be projected - This option allows a list to be used to process multiple input cubes. All cubes + This option allows a list to be used to process multiple input cubes. All cubes contained in this list will be projected to the same output cube given in the 'TO' - parameter. This effictively projects and mosaics all input cubes given in the list + parameter. This effectively projects and mosaics all input cubes given in the list to the same output map projected file. FROM @@ -456,10 +548,11 @@ MINIMIZE This parameter is used to specify how the default latitude/longitude ground range for the output map projected image - is obtained. The ground range can be obtained from the camera or map file. Note the user can overide the default + is obtained. The ground range can be obtained from the camera or map file. Note the user can override the default using the MINLAT, MAXLAT, MINLON, MAXLON parameters. The purpose of the ground range is to define the coverage of the map projected image. Essentially, the ground range and pixel resolution are used to compute the - size (samples and line) of the output image. + size (samples and line) of the output image. Recall that any pixels that fall within the + polar regions (-90 and 90 degrees latitude) will be assigned NULL values in the output. @@ -480,9 +573,9 @@ + + + + + Default settings with MRO CRISM + + In this example, we demonstrate projecting a CRISM image using the default pixel2map + parameters. Note that the output retains the gaps in the data, indicating that the input + pixels do not overlap spatially. + + + + from=crism.cub + to=crism_default.cub + + + Project the CRISM cube using default pixel2map settings. + + + + + + CRISM input image + + A CRISM image is being used for the input. + + + FROM + + + + + Output projected image + + Project output image using default settings. Note the gaps in the projection. + + + TO + + + Output count image + + The count cube generated by pixel2map. Pixel values indicate how many input + pixels were used to generate the average value for the respective output pixel. + + + + + + + + + LONSEAM=CONTINUE with Cassini VIMS + + In this example, we project a VIMS-IR image using the LONSEAM=CONTINUE parameter setting. + This means when we cross the longitude boundary in the image, the longitude domain + is not automatically reset. The output image is split at the longitude boundary + that it crosses; therefore the entire range of the target body is included in the output, + a full 360 degree longitude. Note that a count cube is still created when running the + commands below, it is just ignored in this example. + + + + from=C1621694254_1.ir.band248.cub + map=/usgs/cpkgs/isis3/data/base/templates/maps/equirectangular.map + to=default.cub + lonseam=continue + + + Project a VIMS-IR cube into an equirectangular mapping. When the longitude boundary is + reached, continue to project pixels into the cube's longitude domain. The image is split + at the longitude boundary that it crosses, the entire range of the target body is included + in the output. + + + + + + Ingested VIMS-IR cube + + A VIMS-IR cube ingested with vims2isis. + + + FROM + + + + + Map projected VIMS-IR cube across the longitude seam + + The output cube is projected across the longitude seam. When using LONSEAM=CONTINUE, + the output cube longitude domain will not be reset when the data crosses the + longitude seam. For this image, a large gap of NULL pixels shows up in the output + because the entire longitude range of the target body is included. + + + TO + + + + + + Instantaneous FOV with Dawn VIR + + In this example, we project a DAWN VIR image using an instantaneous + field of view and a full field of view to determine the output pixels. This demonstrates + FOVRANGE=INSTANTANEOUS (default setting for FOVRANGE). Note that + a count cube is still created when running the commands below, it is just ignored in this + example. Compare this with FOVRANGE=FULLEXPOSURE in Example 4. + + + + from=VIR_IR_1B_1_506266095_refl_1.b75.l1.cub + map=/usgs/cpkgs/isis3/data/base/templates/maps/equirectangular.map + to=dawn_vir_instantaneous_fov.cub + + + Project the DAWN VIR image into an equirectangular projection using the default + instantaneous field of view (FOVRANGE=INSTANTANEOUS) to determine the output pixel + projections. + + + + + + Input image for pixel2map + + This is the input DAWN VIR (IR) image for this example. Note the output "strips" and + compare these with the output image in Example 4. + + + FROM + + + + + Output image using FOVRANGE=INSTANTANEOUS + + This is the output image for the first run (FOVRANGE=INSTANTANEOUS). + + + TO + + + + + FULL FOV with Dawn VIR + + In this example, we project a DAWN VIR image and use each pixel's full field of view to + determine the output pixels. This example demonstrates FOVRANGE=FULLEXPOSURE. Note that + a count cube is still created when running the commands below, it is just ignored in this + example. + + + + from=VIR_IR_1B_1_506266095_refl_1.b75.l1.cub + map=/usgs/cpkgs/isis3/data/base/templates/maps/equirectangular.map + to=dawn_vir_full_fov.cub + fovrange=fullexposure + + + Project the DAWN VIR image into an equirectangular projection using the full field of + view of each pixel to determine the output pixel projections. This accounts for any smear + that occurs with the long exposure times of the pixels. + + + + + + Input image for pixel2map + + This is the input DAWN VIR (IR) image for this example. + + + FROM + + + + + Output image using FOVRANGE=FULLEXPOSURE + + This is the output image for FOVRANGE=FULLEXPOSURE. When comparing to the previous + example, note that the output image data accommodates drift (the "strips" are wider). + + + TO + + + + diff --git a/isis/src/base/apps/pixel2map/tsts/errors/Makefile b/isis/src/base/apps/pixel2map/tsts/errors/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..8511b9bcf5baa3b95e24cd7e85dedee2b3758280 --- /dev/null +++ b/isis/src/base/apps/pixel2map/tsts/errors/Makefile @@ -0,0 +1,60 @@ +# This test will print errors thrown by the pixel2map application. +# @internal +# @history 2016-12-09 Curtis Rose - Original Version. +# References #4535. + +APPNAME = pixel2map + +include $(ISISROOT)/make/isismake.tsts + +commands: +# TEST A: Test that an exception is thrown when the cube list is empty. + echo -e "Error Test A:" > $(OUTPUT)/error_temp.txt; + touch $(OUTPUT)/emptyList.lis; + if [[ ` $(APPNAME) fromtype=fromlist \ + fromlist=$(OUTPUT)/emptyList.lis \ + to=$(OUTPUT)/output.cub \ + 2>> $(OUTPUT)/error_temp.txt \ + > /dev/null` ]]; \ + then \ + true; \ + fi; + $(RM) $(OUTPUT)/emptyList.lis; +# TEST B: Test that an exception is thrown when the cube has an Instrument targetName is the Sky. + echo -e "Error Test B:" >> $(OUTPUT)/error_temp.txt; + if [[ ` $(APPNAME) from=$(INPUT)/targetsky.cub \ + to=$(OUTPUT)/output.cub \ + 2>> $(OUTPUT)/error_temp.txt \ + > /dev/null` ]]; \ + then \ + true; \ + fi; +# TEST C: Test that an exception is thrown when cubes in the list have different band dimensions. + echo -e "Error Test C:" >> $(OUTPUT)/error_temp.txt; + $(LS) $(INPUT)/CM_1540484927_1_001.ir.cub | xargs -I "{}" echo "{}+2" > $(OUTPUT)/files.lis; + $(LS) $(INPUT)/CM_1540484927_1_002.ir.cub >> $(OUTPUT)/files.lis; + $(LS) $(INPUT)/CM_1540484927_1_003.ir.cub >> $(OUTPUT)/files.lis; + if [[ ` $(APPNAME) fromtype=fromlist \ + fromlist=$(OUTPUT)/files.lis \ + to=$(OUTPUT)/output.cub \ + 2>> $(OUTPUT)/error_temp.txt \ + > /dev/null` ]]; \ + then \ + true; \ + fi; + $(RM) $(OUTPUT)/files.lis; + $(RM) $(OUTPUT)/output-count-.cub; + $(RM) $(OUTPUT)/output.cub; +# TEST D: Test that an exception is thrown when an image spans the 0-360 longitude seam. + echo -e "Error Test D:" >> $(OUTPUT)/error_temp.txt; + if [[ ` $(APPNAME) from=$(INPUT)/VIR_b75_lv1.cub \ + to=$(OUTPUT)/output.cub \ + lonseam=error \ + 2>> $(OUTPUT)/error_temp.txt \ + > /dev/null` ]]; \ + then \ + true; \ + fi; + + $(SED) 's+\[/.*/input/+\[input/+' $(OUTPUT)/error_temp.txt > $(OUTPUT)/error.txt; + $(RM) $(OUTPUT)/error_temp.txt; \ No newline at end of file diff --git a/isis/src/base/apps/pixel2map/tsts/multipleInputCubes/Makefile b/isis/src/base/apps/pixel2map/tsts/multipleInputCubes/Makefile index 45bf23561a6aef828a19fe45fa09e5c9441e289a..833b872f3d198d4884b6edda79f1b0a5fa58b69a 100755 --- a/isis/src/base/apps/pixel2map/tsts/multipleInputCubes/Makefile +++ b/isis/src/base/apps/pixel2map/tsts/multipleInputCubes/Makefile @@ -3,8 +3,11 @@ # The send test ensures that band selection works within a fromlist, and that it creates the # expected output (output identical to band 2 of the first test's output). # -# @history 2016-11-18 Ian Humphrey - Added documentation to Makefile. Added TEST 2. -# References #4520. +# @internal +# @history 2016-11-18 Ian Humphrey - Added documentation to Makefile. Added TEST 2. +# References #4520. +# @history 2016-12-01 Ian Humphrey - Replaced xargs deprecated -i with -I. The -i +# option was unrecognized on prog17. APPNAME = pixel2map include $(ISISROOT)/make/isismake.tsts @@ -20,7 +23,7 @@ commands: # TEST 2 # Test the fromlist with band selection (band 2). # Note the command below is adding +2 to each of the input cube listings, then redirecting. - $(LS) $(INPUT)/*.cub | xargs -i echo "{}+2" > $(OUTPUT)/files.lis; + $(LS) $(INPUT)/*.cub | xargs -I "{}" echo "{}+2" > $(OUTPUT)/files.lis; $(APPNAME) fromtype=fromlist \ fromlist=$(OUTPUT)/files.lis \ to=$(OUTPUT)/combinedCubesBand2.sinu.cub \ diff --git a/isis/src/base/apps/pixel2map/tsts/numifov/Makefile b/isis/src/base/apps/pixel2map/tsts/numifov/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..b49f16fda5206ef76735f3ed3a484a19a070c05a --- /dev/null +++ b/isis/src/base/apps/pixel2map/tsts/numifov/Makefile @@ -0,0 +1,13 @@ +APPNAME = pixel2map + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(APPNAME) from=$(INPUT)/VIR_IR_1B_1_506266095_refl_1.b75.l1.cub \ + to=$(OUTPUT)/p2m-VIR_IR_1B_1_506266095_refl_1.b75.l2.full.cub \ + map=$(INPUT)/equirectangular.map \ + pixres=mpp \ + resolution=100 \ + fovrange=fullexp \ + numifov=5 \ + > /dev/null; diff --git a/isis/src/base/apps/shadow/tsts/moon/Makefile b/isis/src/base/apps/shadow/tsts/moon/Makefile index 59f7ca541d576c36fd931d19453916e9e053d162..82c57ec6eb2c9bc9ce1efb7f0bbaf7d9556bc865 100644 --- a/isis/src/base/apps/shadow/tsts/moon/Makefile +++ b/isis/src/base/apps/shadow/tsts/moon/Makefile @@ -7,6 +7,7 @@ A15.lowprec2.subtracted.cub.TOLERANCE = 0.00001 A15.noshadow.subtracted.cub.TOLERANCE = 0.00001 # Added tolerance for OS X 10.11 A15.accurate.shadow.subtracted.cub.TOLERANCE = 0.00001 +A15.shadow.subtracted.cub.TOLERANCE = 0.00001 commands: A15 M1104295651RE diff --git a/isis/src/base/apps/spechighpass/spechighpass.cpp b/isis/src/base/apps/spechighpass/spechighpass.cpp index 91185ffa4ec6b189f9d4427eee3ac2e9a43e7611..17b3493168c90b29b43c934aed9e66897ecf3566 100644 --- a/isis/src/base/apps/spechighpass/spechighpass.cpp +++ b/isis/src/base/apps/spechighpass/spechighpass.cpp @@ -28,9 +28,9 @@ void IsisMain() { //Check for cases of too many bands if(bands >= (2 * cubeBands)) { - QString msg = "Parameter bands [" + QString(bands) + "] " + QString msg = "Parameter bands [" + QString::number(bands) + "] " "exceeds maximum allowable size of [" - + QString((cubeBands * 2) - 1) + "] for cube [" + + QString::number((cubeBands * 2) - 1) + "] for cube [" + icube->fileName() + "]"; throw IException(IException::User, msg, _FILEINFO_); } diff --git a/isis/src/base/apps/spiceinit/spiceinit.xml b/isis/src/base/apps/spiceinit/spiceinit.xml index f466c308ca03f14d8a87f4aabfc0a16f5c27a8ed..e55470f754a6abc563e673064c2935037ba69248 100644 --- a/isis/src/base/apps/spiceinit/spiceinit.xml +++ b/isis/src/base/apps/spiceinit/spiceinit.xml @@ -261,6 +261,12 @@ Added assets directory for web example. Updated Documentation. Fixes #1849. + + Changed the URL for the spice server to https://services.isis.astrogeology.usgs.gov/cgi-bin/spiceinit.cgi + and the default port to 443 (it was originally 80). This is due to the recent https migration implementation + from within the Department of the Interior, which was causing people on the outside of the DOI network + to get an unrecognized server response error when attempting to download spice data. Fixes #4552. + @@ -807,16 +813,15 @@ This is where a request for SPICE data is sent. The default is the USGS SPICE server. - http://services.isis.astrogeology.usgs.gov/cgi-bin/spiceinit.cgi + https://services.isis.astrogeology.usgs.gov/cgi-bin/spiceinit.cgi integer The Spice Service Port - This is the port on which a request for SPICE data is sent. The USGS server works on - port 80. + This is the port on which a request for SPICE data is sent. - 80 + 443 0 @@ -1222,4 +1227,4 @@ - \ No newline at end of file + diff --git a/isis/src/base/apps/spkwriter/Commentor.h b/isis/src/base/apps/spkwriter/Commentor.h index f812b925dad07eef40979c029133b76451911242..6715f53130a4f92ac4292d2b6131ca99b4d32646 100644 --- a/isis/src/base/apps/spkwriter/Commentor.h +++ b/isis/src/base/apps/spkwriter/Commentor.h @@ -2,8 +2,8 @@ #define Commentor_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 5850 $ + * $Date: 2014-05-27 15:22:24 -0700 (Tue, 27 May 2014) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -22,7 +22,7 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. * - * $Id$ + * $Id: Commentor.h 5850 2014-05-27 22:22:24Z jwbacker@GS.DOI.NET $ */ #include #include "TextFile.h" diff --git a/isis/src/base/apps/spkwriter/KernelWriter.h b/isis/src/base/apps/spkwriter/KernelWriter.h index 4756a6fd6d6aa97224fea61d7290a95882a7dd6d..4b46e3ce67b877d09f51000f87a9c7fcce4b83aa 100644 --- a/isis/src/base/apps/spkwriter/KernelWriter.h +++ b/isis/src/base/apps/spkwriter/KernelWriter.h @@ -2,8 +2,8 @@ #define KernelWriter_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -22,7 +22,7 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. * - * $Id$ + * $Id: KernelWriter.h 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ */ #include diff --git a/isis/src/base/apps/spkwriter/SpiceKernel.h b/isis/src/base/apps/spkwriter/SpiceKernel.h index a2237265affa6b8012547fca567605cdc5890df4..fb01d7ebe8ba82c28311e815e6c4eb9e6831f8e2 100644 --- a/isis/src/base/apps/spkwriter/SpiceKernel.h +++ b/isis/src/base/apps/spkwriter/SpiceKernel.h @@ -2,8 +2,8 @@ #define SpiceKernel_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 5850 $ + * $Date: 2014-05-27 15:22:24 -0700 (Tue, 27 May 2014) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -22,7 +22,7 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. * - * $Id$ + * $Id: SpiceKernel.h 5850 2014-05-27 22:22:24Z jwbacker@GS.DOI.NET $ */ #include diff --git a/isis/src/base/apps/spkwriter/SpiceSegment.cpp b/isis/src/base/apps/spkwriter/SpiceSegment.cpp index c28b5e81179e27b69d7503036df2a20d6b6fb5ab..3d01f716afe0c3fb5d8d2c45c827d53749c49a6d 100644 --- a/isis/src/base/apps/spkwriter/SpiceSegment.cpp +++ b/isis/src/base/apps/spkwriter/SpiceSegment.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ + * $Id: SpiceSegment.cpp 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/base/apps/spkwriter/SpiceSegment.h b/isis/src/base/apps/spkwriter/SpiceSegment.h index 1c7b2a1d8019fc6e281ba84bfe5025a685af7f78..e6c74c63ab020c6a89f0ac78a7278bb8e86264e7 100644 --- a/isis/src/base/apps/spkwriter/SpiceSegment.h +++ b/isis/src/base/apps/spkwriter/SpiceSegment.h @@ -2,8 +2,8 @@ #define SpiceSegment_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6314 $ + * $Date: 2015-08-12 15:30:27 -0700 (Wed, 12 Aug 2015) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -22,7 +22,7 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. * - * $Id$ + * $Id: SpiceSegment.h 6314 2015-08-12 22:30:27Z jwbacker@GS.DOI.NET $ */ #include diff --git a/isis/src/base/apps/spkwriter/SpkKernelWriter.cpp b/isis/src/base/apps/spkwriter/SpkKernelWriter.cpp index f82edf3f5830ffea68382363c9d25daf8caa3701..9ced2e0b7d635d0f46b793cc8525966541c9cbf2 100644 --- a/isis/src/base/apps/spkwriter/SpkKernelWriter.cpp +++ b/isis/src/base/apps/spkwriter/SpkKernelWriter.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 5850 $ + * $Date: 2014-05-27 15:22:24 -0700 (Tue, 27 May 2014) $ + * $Id: SpkKernelWriter.cpp 5850 2014-05-27 22:22:24Z jwbacker@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/base/apps/spkwriter/SpkKernelWriter.h b/isis/src/base/apps/spkwriter/SpkKernelWriter.h index 50cf8eb35eceebdc225e03d0316e62856d7a31ae..1dfb86e76c6f2c6607e2c9c66eab62f5a17147d5 100644 --- a/isis/src/base/apps/spkwriter/SpkKernelWriter.h +++ b/isis/src/base/apps/spkwriter/SpkKernelWriter.h @@ -2,8 +2,8 @@ #define SpkKernelWriter_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -22,7 +22,7 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. * - * $Id$ + * $Id: SpkKernelWriter.h 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ */ #include #include "SpiceKernel.h" diff --git a/isis/src/base/apps/spkwriter/SpkSegment.cpp b/isis/src/base/apps/spkwriter/SpkSegment.cpp index 7323356ddc6f6128389182adb5bdfc32d575414b..a1b923bef78421c7adc350ae1e847ec607554884 100644 --- a/isis/src/base/apps/spkwriter/SpkSegment.cpp +++ b/isis/src/base/apps/spkwriter/SpkSegment.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ + * $Id: SpkSegment.cpp 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/base/apps/spkwriter/SpkSegment.h b/isis/src/base/apps/spkwriter/SpkSegment.h index 95db2c58f31dacaf0d244553ed4c35152f90c459..a98f254cc81a3448858987a2e1fc0eb3b2d45139 100644 --- a/isis/src/base/apps/spkwriter/SpkSegment.h +++ b/isis/src/base/apps/spkwriter/SpkSegment.h @@ -2,8 +2,8 @@ #define SpkSegment_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6314 $ + * $Date: 2015-08-12 15:30:27 -0700 (Wed, 12 Aug 2015) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -22,7 +22,7 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. * - * $Id$ + * $Id: SpkSegment.h 6314 2015-08-12 22:30:27Z jwbacker@GS.DOI.NET $ */ #include diff --git a/isis/src/base/apps/uncrop/assets/image/insert.jpg b/isis/src/base/apps/uncrop/assets/image/insert.jpg new file mode 100644 index 0000000000000000000000000000000000000000..a625273baca12e72464d99190ee7723ef2d28212 Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/image/insert.jpg differ diff --git a/isis/src/base/apps/uncrop/assets/image/parent.jpg b/isis/src/base/apps/uncrop/assets/image/parent.jpg new file mode 100644 index 0000000000000000000000000000000000000000..8e5cc3fed3c103e07cd393171750341bbfdcccc1 Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/image/parent.jpg differ diff --git a/isis/src/base/apps/uncrop/assets/image/result.jpg b/isis/src/base/apps/uncrop/assets/image/result.jpg new file mode 100644 index 0000000000000000000000000000000000000000..83fedf2a0754b0aa2ba2c1ed95125e940930671e Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/image/result.jpg differ diff --git a/isis/src/base/apps/uncrop/assets/image/uncropGUI.jpg b/isis/src/base/apps/uncrop/assets/image/uncropGUI.jpg new file mode 100644 index 0000000000000000000000000000000000000000..a5e82a6a40551acf69a9584898654b0eb4baec6b Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/image/uncropGUI.jpg differ diff --git a/isis/src/base/apps/uncrop/assets/thumb/insertThumb.jpg b/isis/src/base/apps/uncrop/assets/thumb/insertThumb.jpg new file mode 100644 index 0000000000000000000000000000000000000000..ddf108d6759ecceeb2bb9455f10742bc99202698 Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/thumb/insertThumb.jpg differ diff --git a/isis/src/base/apps/uncrop/assets/thumb/parentThumb.jpg b/isis/src/base/apps/uncrop/assets/thumb/parentThumb.jpg new file mode 100644 index 0000000000000000000000000000000000000000..c644df1d7bc7f6824d1e6f5e8f50d0782ed30655 Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/thumb/parentThumb.jpg differ diff --git a/isis/src/base/apps/uncrop/assets/thumb/resultThumb.jpg b/isis/src/base/apps/uncrop/assets/thumb/resultThumb.jpg new file mode 100644 index 0000000000000000000000000000000000000000..bcd3b520d6d95cb4f8cf3caf7e18518dcfce3bbf Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/thumb/resultThumb.jpg differ diff --git a/isis/src/base/apps/uncrop/assets/thumb/uncropGUIThumb.jpg b/isis/src/base/apps/uncrop/assets/thumb/uncropGUIThumb.jpg new file mode 100644 index 0000000000000000000000000000000000000000..00ddfbe9d2e8af3aebe5e7f539b92475baf1b2d1 Binary files /dev/null and b/isis/src/base/apps/uncrop/assets/thumb/uncropGUIThumb.jpg differ diff --git a/isis/src/base/apps/uncrop/uncrop.xml b/isis/src/base/apps/uncrop/uncrop.xml index 859a33bd2a2ded2cbc7a39e25f7a82d0317add57..99762de7ceea470030544a92c17d20fb9bd19093 100644 --- a/isis/src/base/apps/uncrop/uncrop.xml +++ b/isis/src/base/apps/uncrop/uncrop.xml @@ -7,7 +7,7 @@ This program reverses the effect of crop. That is, it puts a cropped cube back - into a parent cube. The sub or child cube must have an AlphaCube label. + into a parent cube. The sub- or child- cube must have an AlphaCube label. Note: The filename and size of the parent cube is not checked for correctness. @@ -40,12 +40,11 @@ Updated documentation; fixes #458 + + Added example in documentation + - - mosaic - - @@ -105,7 +104,7 @@ Parent cube takes priority When the parent pixel is not NULL, the parent - pixel value will be left unchanged. If the parent pixel is NULL + pixel value will be left unchanged. If the parent pixel is NULL, the cropped pixel will be written to the output cube. @@ -113,4 +112,57 @@ + + + Insert a sub-cube into a parent cube + + Insert a cube of 200 samples by 300 lines into a parent cube. + + + FROM=crop.cub PARENT=pcrp.cub COMBINE=CROP + + + In this example, uncrop will insert a 200x300 sub-area into the parent cube. + + + + + + Parent image + This is the full size input image. The area (200x300) + to be "uncropped" is grey. + + + PARENT + + + Sub-cube image + This is the sub-cube to be inserted into the parent image. + + + FROM + + + + + + Parent with inserted sub-cube + This is the parent image with the sub-cube inserted using the "crop" combine mode. + + + PARENT + + + + + + + Example GUI + This is a screenshot of uncrop. The GUI shows the parameters filled to insert a 200x300 pixel sub-area into the parent image. + + + + + + diff --git a/isis/src/base/objs/AdaptiveGruen/AdaptiveGruen.truth b/isis/src/base/objs/AdaptiveGruen/AdaptiveGruen.truth index db970f9cca4a1a1d1180324ec1232a21c5258f5b..c240173f392ef9fa7ed4d22cf45dbc9b08f20500 100644 --- a/isis/src/base/objs/AdaptiveGruen/AdaptiveGruen.truth +++ b/isis/src/base/objs/AdaptiveGruen/AdaptiveGruen.truth @@ -19,5 +19,5 @@ Object = AutoRegistration End_Object End Register = 1 -Goodness = 0.000831 -Position = 512.683 511.704 +Goodness = 0.00451 +Position = 512.592 511.628 diff --git a/isis/src/base/objs/Camera/Camera.cpp b/isis/src/base/objs/Camera/Camera.cpp index 3b4e553708a2204fa8a6de01c28d68e91bc3a700..6f361f09d42d437f5e57e609f1f2f19e9e57a2bc 100644 --- a/isis/src/base/objs/Camera/Camera.cpp +++ b/isis/src/base/objs/Camera/Camera.cpp @@ -1,7 +1,7 @@ /** * @file - * $Revision$ - * $Date$ + * $Revision: 7229 $ + * $Date: 2016-11-10 21:04:46 -0700 (Thu, 10 Nov 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -568,74 +568,28 @@ namespace Isis { /** - * @description This function provides an improved estimate of the detector resolution (in meters) - * when the target is near the limb. It does this by calculating the determinant of an affine - * transformation. The area element of one pixel projected onto the surface at Nadir looks - * like a square with sides of length = Detector Resolution. The detector resolution is the - * value returned by the original function. An affine projective transformation of this - * area element as one would see if it was on the limb instead of looking straight down, appears - * like a skewed parallelogram. + * @brief This method returns the Oblique Detector Resolution + * if the Look Vector intersects the target and if the emission angle is greater than or equal + * to 0, and less than 90 degrees. Otherwise, it returns -1.0. This formula provides an + * improved estimate to the detector resolution for images near the limb: * - * The determinant of the transformation matrix taking the Nadir-area element into - * some parallelogram near the limb of a planet measures the change in area for the - * transformation when we are off-Nadir. The sqare-root of the area of this parallelogram - * gives us the resolution. * - *The calculation is straightforward. Any affine transformation with a strictly positive - *determinant that is not a similarity transformation has a unique decomposition - *(See Theorem 2.1 in Reference #1): + * @f[ \text{Oblique\;\;Detector\;\; Resolution} = \frac{n}{cos(\theta)} @f] * * + * The equation is derived two separate ways. A geometric argument is presented in + * Reference 2, while a matrix algebra based argument is presented in Theorem 2.1 of + * Reference 1. * * - * @f{eqnarray*} - * - * A = \[\left[\begin{array}{cc} a & b \\ - * c & d \end{array} \right]\] = - * - * H_{\lambda}R_1(\psi)T_tR_2(\phi) = \lambda - * \[ \left[\begin{array}{cc} cos(\psi) & -sin(\psi) \\ - * sin(\psi) & cos(\psi) \end{array} \right]\] - * \[ \left[\begin{array}{cc} t & 0 \\ - * 0 & 1 \end{array} \right]\] - * \[ \left[\begin{array}{cc} cos(\phi) & -sin(\phi) \\ - * sin(\phi) & cos(\phi) \end{array} \right]\] - * - * @f} - * - * Where: - * - * @f$ t = \frac{1}{cos(\theta)}},\;\;\theta = \text{Emmission\;\; Angle}@f$ - * and @f$\lambda = \text{zoom\;\;factor} = 1@f$ - * - * The determinant of A is: - * - * @f[ |A| = \lambda t = \frac{\lambda}{cos(\theta)} = \frac{1}{\cos(\theta)} @f] - * - * This is because the two rotation matrices in this decomposition have determinants equal to 1. - * - * Let @f$ n = \text{Detector\;\;Resolution} @f$ - * - * Then: - * - * @f[ Area = n^2 |A| =\frac{n^2}{cos(\theta)}@f] - * - * And: - * - * @f[ \text{Local\;\;Detector\;\; Resolution} = \frac{n}{\sqrt{cos(\theta)}} @f] - * - * - * This method returns the Local Detector Resolution if the Look Vector intersects the target - * and if @f$ 0 \leq \theta < \frac{\pi}{2} @f$ and -1.0 otherwise. - * - * - * - * - * Reference 1: J-M Morel and G. Yu, "Asift: A new framework for fully affine + * Reference 1: J-M Morel and G. Yu, "Asift: A new framework for fully affine * invariant image comparison," SIAM Journal on Imaging Sciences * 2(2), pp. 438-469, 2009 * * + * Reference 2: Handwritten notes by Orrin Thomas which can be found in the + * Glossary under the entry for Oblique Detector Resolution. + * * @return @b double */ double Camera::ObliqueDetectorResolution(){ @@ -643,26 +597,14 @@ namespace Isis { if(HasSurfaceIntersection()){ - - double thetaRad; - double sB[3]; - instrumentPosition(sB); - double pB[3]; - Coordinate(pB); - double a = sB[0] - pB[0]; - double b = sB[1] - pB[1]; - double c = sB[2] - pB[2]; - double rho = sqrt(a * a + b * b + c * c) * 1000.0; - + double thetaRad; thetaRad = EmissionAngle()*DEG2RAD; - if (thetaRad < HALFPI) { - - double nadirResolution = rho/(p_focalLength/p_pixelPitch); - return nadirResolution/sqrt(cos(thetaRad)); + if (thetaRad < HALFPI) { + return DetectorResolution()/cos(thetaRad); } - return Isis::Null; + return Isis::Null; } @@ -1595,9 +1537,9 @@ namespace Isis { // order of points in vector is top, bottom, left, right QList< QPair< double, double > > surroundingPoints; surroundingPoints.append(qMakePair(samp, line - 0.5)); - surroundingPoints.append(qMakePair(samp, line + 0.5)); + surroundingPoints.append(qMakePair(samp, line + 0.5 - DBL_MIN)); surroundingPoints.append(qMakePair(samp - 0.5, line)); - surroundingPoints.append(qMakePair(samp + 0.5, line)); + surroundingPoints.append(qMakePair(samp + 0.5 - DBL_MIN, line)); // save input state to be restored on return double originalSample = samp; diff --git a/isis/src/base/objs/Camera/Camera.h b/isis/src/base/objs/Camera/Camera.h index cb48f6a75842b550804585ce5f7ad411e2ffaff8..eabde3a63c9c21aaa60d134d6f7350daa33a8e8d 100644 --- a/isis/src/base/objs/Camera/Camera.h +++ b/isis/src/base/objs/Camera/Camera.h @@ -2,8 +2,8 @@ #define Camera_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 7234 $ + * $Date: 2016-11-12 14:04:38 -0700 (Sat, 12 Nov 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -232,6 +232,12 @@ namespace Isis { * to using the band the camera is set to. References #4476. * @history 2016-10-21 Jeannie Backer - Reorder method signatures and member variable * declarations to fit ISIS coding standards. References #4476. + * @history 2016-12-02 Victor Silva - Made changes to GetLocalNormal to calculate local normal + * accurately for LRO by changing 4 corner surrounding points from adding + * 0.5 to adding 0.5 - DBL_MIN. Fixes #4560. + * @history 2017-03-03 Tyler Wilson - Updated the oblique detector resolution function to correct + * an error in the original formula, and updated the documention for this + * function. Fixes #4614. */ class Camera : public Sensor { diff --git a/isis/src/base/objs/Camera/Camera.truth b/isis/src/base/objs/Camera/Camera.truth index 64d6a5ad5474f94515333da50a218de1f7599802..0e3fd12cf1e14d5fcd769cc487041ba2cf64dbb7 100644 --- a/isis/src/base/objs/Camera/Camera.truth +++ b/isis/src/base/objs/Camera/Camera.truth @@ -20,7 +20,7 @@ SetImage (sample, line): Yes NorthAzimuth: 269.544 SunAzimuth: 168.17 SpacecraftAzimuth: 184.591 -OffNadirAngle: 44.4225 +OffNadirAngle: 44.4012 CelestialNorthClockAngle: 186.19 RaDecResolution: 0.0216226 @@ -84,13 +84,13 @@ GroundRange: 0 IntersectsLongitudeDomain: 0 PixelResolution: 628 ExposureDuration: 0.4 -ObliquePixelResolution: 685 +ObliquePixelResolution: 748 LineResolution: 628 -ObliqueLineResolution: 685 +ObliqueLineResolution: 748 SampleResolution: 628 -ObliqueSampleResolution: 685 +ObliqueSampleResolution: 748 DetectorResolution: 157 -ObliqueDetectorResolution: 171 +ObliqueDetectorResolution: 187 LowestImageResolution: 2047 HighestImageResolution: 430 Calling BasicMapping (pvl)... diff --git a/isis/src/base/objs/CameraPointInfo/CameraPointInfo.truth b/isis/src/base/objs/CameraPointInfo/CameraPointInfo.truth index 11c5dfed9067881b2cbda0515cc86bcc6b2eb5f6..2ff1dc289ef774e441d171c147a45efa6d900cf6 100644 --- a/isis/src/base/objs/CameraPointInfo/CameraPointInfo.truth +++ b/isis/src/base/objs/CameraPointInfo/CameraPointInfo.truth @@ -15,10 +15,10 @@ Group = GroundPoint LocalRadius = 1737400.0 SampleResolution = 187.48511798825 LineResolution = 187.48511798825 - ObliqueDetectorResolution = 187.48933248321 - ObliquePixelResolution = 187.48933248321 - ObliqueLineResolution = 187.48933248321 - ObliqueSampleResolution = 187.48933248321 + ObliqueDetectorResolution = 187.49354707291 + ObliquePixelResolution = 187.49354707291 + ObliqueLineResolution = 187.49354707291 + ObliqueSampleResolution = 187.49354707291 # Spacecraft Information SpacecraftPosition = (216.76438021037, 54.256829538645, @@ -77,10 +77,10 @@ Group = GroundPoint LocalRadius = 1737400.0 SampleResolution = 187.50339379912 LineResolution = 187.50339379912 - ObliqueDetectorResolution = 187.52061363579 - ObliquePixelResolution = 187.52061363579 - ObliqueLineResolution = 187.52061363579 - ObliqueSampleResolution = 187.52061363579 + ObliqueDetectorResolution = 187.53783505388 + ObliquePixelResolution = 187.53783505388 + ObliqueLineResolution = 187.53783505388 + ObliqueSampleResolution = 187.53783505388 # Spacecraft Information SpacecraftPosition = (216.76438021037, 54.256829538645, diff --git a/isis/src/base/objs/CameraStatistics/CameraStatistics.truth b/isis/src/base/objs/CameraStatistics/CameraStatistics.truth index 413624756888abfbca8b5e9e06cce57a2e1113a5..3d16a81c1db6fae6d3c6c19aeb35d3e18af1a1a4 100644 --- a/isis/src/base/objs/CameraStatistics/CameraStatistics.truth +++ b/isis/src/base/objs/CameraStatistics/CameraStatistics.truth @@ -38,21 +38,21 @@ Resolution: ObliqueSampleResolution: ObliqueSampleResolutionMinimum = 244.735 - ObliqueSampleResolutionMaximum = 246.319 - ObliqueSampleResolutionAverage = 245.205 - ObliqueSampleResolutionStandardDeviation = 0.304432 + ObliqueSampleResolutionMaximum = 246.963 + ObliqueSampleResolutionAverage = 245.396 + ObliqueSampleResolutionStandardDeviation = 0.428052 ObliqueLineResolution: ObliqueLineResolutionMinimum = 244.735 - ObliqueLineResolutionMaximum = 246.319 - ObliqueLineResolutionAverage = 245.205 - ObliqueLineResolutionStandardDeviation = 0.304432 + ObliqueLineResolutionMaximum = 246.963 + ObliqueLineResolutionAverage = 245.396 + ObliqueLineResolutionStandardDeviation = 0.428052 ObliqueResolution: ObliqueResolutionMinimum = 244.735 - ObliqueResolutionMaximum = 246.319 - ObliqueResolutionAverage = 245.205 - ObliqueResolutionStandardDeviation = 0.304432 + ObliqueResolutionMaximum = 246.963 + ObliqueResolutionAverage = 245.396 + ObliqueResolutionStandardDeviation = 0.428052 AspectRatio: AspectRatioMinimum = 1 diff --git a/isis/src/base/objs/CubeAttribute/CubeAttribute.h b/isis/src/base/objs/CubeAttribute/CubeAttribute.h index 01ad8a387462397e1df3c882c36a2f1b1bc16d66..d4eecbaea2794f2f958c123b6264b9a5be82a0e3 100644 --- a/isis/src/base/objs/CubeAttribute/CubeAttribute.h +++ b/isis/src/base/objs/CubeAttribute/CubeAttribute.h @@ -70,7 +70,7 @@ namespace Isis { if(labelType == DetachedLabel) return "Detached"; if(labelType == ExternalLabel) return "External"; - QString msg = "Invalid label attachment type [" + QString(labelType) + "]"; + QString msg = "Invalid label attachment type [" + QString::number(labelType) + "]"; throw IException(IException::Programmer, msg, _FILEINFO_); } diff --git a/isis/src/base/objs/DemShape/DemShape.cpp b/isis/src/base/objs/DemShape/DemShape.cpp index 7ff16f2af7d692e0c703b806b57d6c5038f568e9..2a699f251b14f2e527167e58cc13d7dd4a0c983c 100644 --- a/isis/src/base/objs/DemShape/DemShape.cpp +++ b/isis/src/base/objs/DemShape/DemShape.cpp @@ -295,11 +295,39 @@ namespace Isis { * This method calculates the default normal (Ellipsoid for backwards * compatability) for the DemShape. */ + void DemShape::calculateDefaultNormal() { - calculateEllipsoidalSurfaceNormal(); + + if (!surfaceIntersection()->Valid() || !hasIntersection() ) { + IString msg = "A valid intersection must be defined before computing the surface normal"; + throw IException(IException::Programmer, msg, _FILEINFO_); + } + + // Get the coordinates of the current surface point + SpiceDouble pB[3]; + pB[0] = surfaceIntersection()->GetX().kilometers(); + pB[1] = surfaceIntersection()->GetY().kilometers(); + pB[2] = surfaceIntersection()->GetZ().kilometers(); + + // Get the radii of the ellipsoid + vector radii = targetRadii(); + double a = radii[0].kilometers(); + double b = radii[1].kilometers(); + double c = radii[2].kilometers(); + + vector normal(3,0.); + + NaifStatus::CheckErrors(); + surfnm_c(a, b, c, pB, (SpiceDouble *) &normal[0]); + NaifStatus::CheckErrors(); + + setNormal(normal); + setHasNormal(true); + } + /** * Returns the DEM Cube object. * @@ -385,7 +413,7 @@ namespace Isis { * point. */ void DemShape::calculateSurfaceNormal() { - calculateEllipsoidalSurfaceNormal(); + calculateDefaultNormal(); } diff --git a/isis/src/base/objs/DemShape/DemShape.h b/isis/src/base/objs/DemShape/DemShape.h index 661df4f918779af3051ac19770fcffd03d861f2a..231bd919b0685716c683af56e7b4e8640b9376d2 100644 --- a/isis/src/base/objs/DemShape/DemShape.h +++ b/isis/src/base/objs/DemShape/DemShape.h @@ -53,6 +53,14 @@ namespace Isis { * closer to ISIS coding standards. References #1438 * @history 2016-06-13 Kelvin Rodriguez - Removed redundant contructor PlaneShape(Target, Pvl). * References #2214 + * @history 2017-05-19 Tyler Wilson - calculateDefaultNormal() and calculateSurfaceNormal() + * now return the normal vector to an ellipsoid. All references + * to ShapeModel::calculateEllipsoidalSurfaceNormal have been + * removed. References #1028. + * @history 2017-05-19 Christopher Combs - Modified unitTest.cpp: Removed path of output in + * testDemCube() to allow the test to pass when not using the standard + * data areas. Fixes #4738. + * */ class DemShape : public ShapeModel { public: diff --git a/isis/src/base/objs/DemShape/DemShape.truth b/isis/src/base/objs/DemShape/DemShape.truth index 521658bffa9a95826b3ae688e6f10aacaaa301ef..616462ba05bea8b1cff5da863e4069e7d6ed86cd 100644 --- a/isis/src/base/objs/DemShape/DemShape.truth +++ b/isis/src/base/objs/DemShape/DemShape.truth @@ -18,10 +18,10 @@ Begin testing Dem Shape Model class.... local normal = (-0.58374, -0.701835, 0.408259 Testing class method calculateSurfaceNormal... - surface normal = (-0.623384, -0.698838, 0.350738 + surface normal = (-0.62247, -0.697813, 0.354383 Testing class method calculateDefaultNormal... - default normal = (-0.623384, -0.698838, 0.350738 + default normal = (-0.62247, -0.697813, 0.354383 Testing localRadius method with good lat/lon values... Local radius = 3406.18 @@ -40,7 +40,7 @@ Begin testing Dem Shape Model class.... The map scale of the dem file is 128 pixels/degree Testing protected methods demCube ... - Using dem cube file = /usgs/cpkgs/isis3/data/base/dems/molaMarsPlanetaryRadius0004.cub + Using dem cube file = molaMarsPlanetaryRadius0004.cub Testing input of dem file with keyword ElevationModel diff --git a/isis/src/base/objs/DemShape/unitTest.cpp b/isis/src/base/objs/DemShape/unitTest.cpp index 706649f18754f9152c00ed5fc1ce5424f902dfb1..84578391762f3983c4cfcc88f8bd3e3905c2ea30 100644 --- a/isis/src/base/objs/DemShape/unitTest.cpp +++ b/isis/src/base/objs/DemShape/unitTest.cpp @@ -28,6 +28,7 @@ #include "Cube.h" #include "DemShape.h" #include "EllipsoidShape.h" +#include "FileName.h" #include "IException.h" #include "IString.h" #include "Latitude.h" @@ -39,7 +40,7 @@ using namespace std; using namespace Isis; - + /** * This application tests the DemShape base class * @@ -49,7 +50,7 @@ using namespace Isis; * @internal * @history 2015-04-30 Jeannie Backer - Added a test for calculateLocalNormal() with * empty neighbor points and a test for isDEM(). References #2243. - * + * * testcoverage 2015-04-30 - 78.571% scope, 94.309% line, 100% function */ class MyShape : public DemShape { @@ -61,7 +62,7 @@ class MyShape : public DemShape { void testDemCube() { // Cube *demCube(); IString fileName = demCube()->fileName(); - cout << " Using dem cube file = " << demCube()->fileName() << endl; + cout << " Using dem cube file = " << FileName(demCube()->fileName()).name() << endl; } }; @@ -88,7 +89,7 @@ int main() { cout << " Shape name is " << defaultShape.name() << endl; cout << " Shape is DEM type? " << toString(shape.isDEM()) << endl; - cout << endl << " Testing method intersectSurface..." << endl; + cout << endl << " Testing method intersectSurface..." << endl; cout << " Do we have an intersection? " << shape.hasIntersection() << endl; cout << " Set a pixel in the image and check again." << endl; double line = 453.0; @@ -108,13 +109,13 @@ int main() { Incidence = 85.341094499768 Emission = 46.966269013795 */ - if (!shape.intersectSurface(sB, lookB)) { + if (!shape.intersectSurface(sB, lookB)) { cout << " ... intersectSurface method failed" << endl; return -1; } cout << " Do we have an intersection? " << shape.hasIntersection() << endl; SurfacePoint *sp = shape.surfaceIntersection(); - cout << " surface point = (" << sp->GetX().kilometers() << ", " << + cout << " surface point = (" << sp->GetX().kilometers() << ", " << sp->GetY().kilometers() << ", " << sp->GetZ().kilometers() << endl; cout << endl << " Testing class method calculateLocalNormal " @@ -153,7 +154,7 @@ int main() { cout << " local normal = (" << myNormal[0] << ", " << myNormal[1] << ", " << myNormal[2] << endl; cout << endl << " Testing class method calculateSurfaceNormal..." << endl; - shape.calculateSurfaceNormal(); + shape.calculateSurfaceNormal(); myNormal = shape.normal(); cout << " surface normal = (" << myNormal[0] << ", " << myNormal[1] << ", " << myNormal[2] << endl; @@ -178,7 +179,7 @@ int main() { cout << endl << " Testing setSurfacePoint method ..." << endl; shape.setSurfacePoint(*sp); cout << " Do we have an intersection? " << shape.hasIntersection() << endl; - cout << " surface point = (" << sp->GetX().kilometers() << ", " << + cout << " surface point = (" << sp->GetX().kilometers() << ", " << sp->GetY().kilometers() << ", " << sp->GetZ().kilometers() << endl; cout << endl << " Testing demScale method..." << endl; diff --git a/isis/src/base/objs/EllipsoidShape/EllipsoidShape.cpp b/isis/src/base/objs/EllipsoidShape/EllipsoidShape.cpp index 5a88f01988c91d48af174205411551c03cf1e44e..a350e65f69d49ff9e7d87244ef6f2f28039f5ccc 100644 --- a/isis/src/base/objs/EllipsoidShape/EllipsoidShape.cpp +++ b/isis/src/base/objs/EllipsoidShape/EllipsoidShape.cpp @@ -2,6 +2,7 @@ #include + #include #include #include @@ -53,7 +54,8 @@ namespace Isis { * */ void EllipsoidShape::calculateDefaultNormal() { - calculateEllipsoidalSurfaceNormal(); + QVector points; + calculateLocalNormal(points); } @@ -61,7 +63,8 @@ namespace Isis { * */ void EllipsoidShape::calculateSurfaceNormal() { - calculateEllipsoidalSurfaceNormal(); + QVector points; + calculateLocalNormal(points); } @@ -77,17 +80,33 @@ namespace Isis { } - /** Calculate local normal + /** + * Calculates the unit normal to an ellipsoid at the point of intersection. + * In the event that the three axial radii of the body are equal, this + * method returns the normal vector for a sphere. + * + * The implicit equation for an ellipsoid is: + * U(x,y,z) = x^2/a^2 + y^2/b^2 + z^2/c^2 -1 =0 + * + * + * The normal to U(x,y,z) is given by: * + * n = grad(U)/norm(U) + * + * i.e. as: + * + * n = /sqrt(ux^2,+uy^2+uz^2) + * + * @param cornerNeighborPoints */ void EllipsoidShape::calculateLocalNormal(QVector cornerNeighborPoints) { if (!surfaceIntersection()->Valid() || !hasIntersection()) { IString msg = "A valid intersection must be defined before computing the surface normal"; throw IException(IException::Programmer, msg, _FILEINFO_); - } + } - // Get the coordinates of the current surface point + // Get the coordinates of the current surface point SpiceDouble pB[3]; pB[0] = surfaceIntersection()->GetX().kilometers(); pB[1] = surfaceIntersection()->GetY().kilometers(); @@ -98,8 +117,8 @@ namespace Isis { double a = radii[0].kilometers(); double b = radii[1].kilometers(); double c = radii[2].kilometers(); - vector normal(3,0.); + vector normal(3,0.); NaifStatus::CheckErrors(); surfnm_c(a, b, c, pB, (SpiceDouble *) &normal[0]); NaifStatus::CheckErrors(); diff --git a/isis/src/base/objs/EllipsoidShape/EllipsoidShape.h b/isis/src/base/objs/EllipsoidShape/EllipsoidShape.h index 562dcf971722b1346cccc7e7824fb21d5721da07..18793f92f1b60d40c93392406002d866e27d0600 100644 --- a/isis/src/base/objs/EllipsoidShape/EllipsoidShape.h +++ b/isis/src/base/objs/EllipsoidShape/EllipsoidShape.h @@ -48,6 +48,12 @@ namespace Isis { * were signaled. References #2248. * @history 2016-06-13 Kelvin Rodriguez - Removed redundant contructor * EllipsoidShape(Target, Pvl). References #2214 + * @history 2017-05-19 Tyler Wilson - calculateSurfaceNormal() and calculateDefaultNormal() + * now call calculateLocalNormal(), which calculates the normal + * vector to an ellipsoid. Prior to this, they were calling + * ShapeModel::calculateEllipsoidalSurfaceNormal() function + * which was incorrectly returning the normal vector to a + * sphere and not an ellipsoid. Fixes #1028. */ class EllipsoidShape : public Isis::ShapeModel { public: diff --git a/isis/src/base/objs/EllipsoidShape/EllipsoidShape.truth b/isis/src/base/objs/EllipsoidShape/EllipsoidShape.truth index 0974e8eaa1b692f850630f60f160ba0da5c2c2f4..4cae352f248c535da63e50ae850e0f360894c511 100644 --- a/isis/src/base/objs/EllipsoidShape/EllipsoidShape.truth +++ b/isis/src/base/objs/EllipsoidShape/EllipsoidShape.truth @@ -1,3 +1,4 @@ +Radii=[3396.19,3396.19,3376.2] Begin testing Ellipsoid Shape Model class.... Testing constructors... @@ -16,23 +17,23 @@ Testing method intersectSurface... Do we have an intersection? 0 Set a pixel in the image and check again. Do we have an intersection? 1 - surface point = (-2105.83, -2380.77, 1189.41 + surface point = (-2105.830811, -2380.77411, 1189.409824) Testing class method calculateLocalNormal... - local normal = (-0.6196, -0.700497, 0.354117 + local normal = (-0.6196003462, -0.7004971413, 0.3541174467 Testing class method calculateSurfaceNormal... - surface normal = (-0.620509, -0.701524, 0.350474 + surface normal = (-0.6196003462, -0.7004971413, 0.3541174467 Testing class method calculateDefaultNormal... - default normal = (-0.620509, -0.701524, 0.350474 + default normal = (-0.6196003462, -0.7004971413, 0.3541174467 Testing localRadius method ... - Local radius = 3393.71 + Local radius = 3393.711719 Testing setHasIntersection method Do we have an intersection? 0 Testing setSurfacePoint method ... Do we have an intersection? 1 - surface point = (-2105.83, -2380.77, 1189.41 + surface point = (-2105.830811, -2380.77411, 1189.409824 diff --git a/isis/src/base/objs/EllipsoidShape/unitTest.cpp b/isis/src/base/objs/EllipsoidShape/unitTest.cpp index ebea906ce28d11ff3e84d77a7e322ba6ad981c12..49d78229e340598798900bda6e1cf75bd1c2cc86 100644 --- a/isis/src/base/objs/EllipsoidShape/unitTest.cpp +++ b/isis/src/base/objs/EllipsoidShape/unitTest.cpp @@ -10,7 +10,7 @@ * and related material nor shall the fact of distribution constitute any such * warranty, and no responsibility is assumed by the USGS in connection * therewith. - * + *i * For additional information, launch * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see * the Privacy & Disclaimers page on the Isis website, @@ -26,6 +26,7 @@ #include "Camera.h" #include "CameraFactory.h" #include "Cube.h" +#include "Distance.h" #include "EllipsoidShape.h" #include "IException.h" #include "Latitude.h" @@ -51,17 +52,24 @@ using namespace Isis; */ int main() { try { + + + + + Preference::Preferences(true); QString inputFile = "$mgs/testData/ab102401.cub"; Cube cube; cube.open(inputFile); Camera *c = cube.camera(); - std::vector radii = c->target()->radii(); + vector radii = c->target()->radii(); + cout << setprecision(10)<< "Radii=["< uB(3); c->sunPosition((double *) &uB[0]); c->SpacecraftSurfaceVector((double *) &lookB[0]); - /* - Sample/Line = 534/453 - surface normal = -0.623384, -0.698838, 0.350738 - Local normal = -0.581842, -0.703663, 0.407823 - Phase = 40.787328112158 - Incidence = 85.341094499768 - Emission = 46.966269013795 - */ + if (!shape.intersectSurface(sB, lookB)) { cout << " ... intersectSurface method failed" << endl; return -1; @@ -117,7 +118,7 @@ int main() { cout << " Do we have an intersection? " << shape.hasIntersection() << endl; SurfacePoint *sp = shape.surfaceIntersection(); cout << " surface point = (" << sp->GetX().kilometers() << ", " << - sp->GetY().kilometers() << ", " << sp->GetZ().kilometers() << endl; + sp->GetY().kilometers() << ", " << sp->GetZ().kilometers() << ")" << endl; cout << endl << " Testing class method calculateLocalNormal..." << endl; QVector notUsed(4); @@ -128,11 +129,18 @@ int main() { shape.calculateLocalNormal(notUsed); vector myNormal(3); myNormal = shape.normal(); + + //Hand-calculated truth value: [-0.6196003462957385, -0.7004971412244801, 0.3541174466282787] + + cout << " local normal = (" << myNormal[0] << ", " << myNormal[1] << ", " << myNormal[2] << endl; cout << endl << " Testing class method calculateSurfaceNormal..." << endl; shape.calculateSurfaceNormal(); myNormal = shape.normal(); + + + cout << " surface normal = (" << myNormal[0] << ", " << myNormal[1] << ", " << myNormal[2] << endl; cout << endl << " Testing class method calculateDefaultNormal..." << endl; @@ -143,7 +151,7 @@ int main() { cout << endl << " Testing localRadius method ..." << endl; cout << " Local radius = " << shape.localRadius(Latitude(20.532461495381, Angle::Degrees), Longitude(228.26609149754, Angle::Degrees)).kilometers() << endl; - // Mars radii = 3397. 3397. 3375. + cout << endl << " Testing setHasIntersection method" << endl; shape.setHasIntersection(false); diff --git a/isis/src/base/objs/Equalization/Equalization.h b/isis/src/base/objs/Equalization/Equalization.h index 926a30c6dfdb74a87eb81f15952b6b98921b3aeb..b2a55b68ff3117ff5ac5fca4427f3dd5191486e4 100644 --- a/isis/src/base/objs/Equalization/Equalization.h +++ b/isis/src/base/objs/Equalization/Equalization.h @@ -120,16 +120,20 @@ namespace Isis { * formula in evaluate() instead of just modifying how statistics * are computed. Implemented the GainsWithoutNormalization solution * type. References #911. - * @history 2016-07-15 Ian Humphrey - Added recalculateStatistics() method to allow for + * @history 2016-07-15 Ian Humphrey - Added recalculateStatistics() method to allow for * statistics to be calculated only for new input images, using * previously calculated statistics for the rest of the input images. * Added fromPvl() method to unserialize Equalization data from a pvl * object. Refactored calculateStatistics() to separate functionality - * and allow for statistics recalculation. Added methods to properly - * free some of the vector members. Added new members to help with + * and allow for statistics recalculation. Added methods to properly + * free some of the vector members. Added new members to help with * unserialization via the fromPvl() method and help with recalulating * overlap statistics. Added API documentation. Updated unit test. * Fixes #2282. + * @history 2017-05-19 Christopher Combs - Modified uniTest.cpp: truncated paths of NonOverlaps + * in output PVL on lines 100 and 123 to allow the test to pass when + * not using the standard data areas. Added ReportError method to + * remove paths when outputting errors. Fixes #4738. */ class Equalization { public: @@ -138,8 +142,8 @@ namespace Isis { void addHolds(QString holdListName); - void calculateStatistics(double samplingPercent, - int mincnt, + void calculateStatistics(double samplingPercent, + int mincnt, bool wtopt, LeastSquares::SolveMethod methodType); void recalculateStatistics(QString inStatsFileName); @@ -212,7 +216,7 @@ namespace Isis { OverlapNormalization::SolutionType m_sType; }; - /** + /** * This class is used as a functor calculate image statistics * * @author ????-??-?? Unknown @@ -225,7 +229,7 @@ namespace Isis { * Constructs a CalculateFunctor * * @param stats Pointer to a Statistics object to add data to - * @param percent Sampling percentage of the image, used to calculate a line increment, + * @param percent Sampling percentage of the image, used to calculate a line increment, * when calculating statistics */ CalculateFunctor(Statistics *stats, double percent) { @@ -246,7 +250,7 @@ namespace Isis { }; /** - * This class is used as a functor to apply adjustments (equalize) to an image + * This class is used as a functor to apply adjustments (equalize) to an image * * @author ????-??-?? Unknown * @@ -329,7 +333,7 @@ namespace Isis { //! The normalization solution type for solving normalizations (offsets, gains, or both) OverlapNormalization::SolutionType m_sType; //! Least squares method for solving normalization correcitve factors - LeastSquares::SolveMethod m_lsqMethod; + LeastSquares::SolveMethod m_lsqMethod; Pvl *m_results; //!< Calculation results and normalization corrective factors (if solved) }; diff --git a/isis/src/base/objs/Equalization/Equalization.truth b/isis/src/base/objs/Equalization/Equalization.truth index 63b241f90515754f2559c87ef7309e01fecf68ca..46fdb4417ac4ca6affea1493aefd213a25e85659 100644 --- a/isis/src/base/objs/Equalization/Equalization.truth +++ b/isis/src/base/objs/Equalization/Equalization.truth @@ -53,10 +53,8 @@ Group = General Weighted = false SolutionType = 2 SolveMethod = 1 - NonOverlaps = (/usgs/cpkgs/isis3/data/odyssey/testData/I00824006RDR.lev- - 2.cub, - /usgs/cpkgs/isis3/data/odyssey/testData/I02609002RDR.lev2- - .cub) + NonOverlaps = (data/odyssey/testData/I00824006RDR.lev2.cub, + data/odyssey/testData/I02609002RDR.lev2.cub) HasCorrections = false End_Group Write results to file... @@ -140,8 +138,7 @@ Group = General SolveMethod = 1 NonOverlaps = Null HasCorrections = true - FileName = /usgs/cpkgs/isis3/data/odyssey/testData/I00824006RDR.lev2- - .cub + FileName = data/odyssey/testData/I00824006RDR.lev2.cub Band1 = (0.80247733802282, -6.41865351231352e-05, 3.75633639030183e-04) Band2 = (0.79065929400895, -6.36729218508168e-05, @@ -162,8 +159,7 @@ Group = General 5.26586798911814e-04) Band10 = (1.1365072636781, -6.00857909632202e-05, 1.68162009248859e-04) - FileName = /usgs/cpkgs/isis3/data/odyssey/testData/I01523019RDR.lev2- - .cub + FileName = data/odyssey/testData/I01523019RDR.lev2.cub Band1 = (1.0, -1.25221260739074e-35, 3.09460986870763e-04) Band2 = (1.0, 1.2328347713385e-35, 3.08373709744676e-04) Band3 = (1.0, -2.48556416128503e-36, 3.91940207887308e-04) @@ -174,8 +170,7 @@ Group = General Band8 = (1.0, -5.96696530716469e-36, 4.90828757009813e-04) Band9 = (1.0, 1.0677794001636e-35, 4.84059968314066e-04) Band10 = (1.0, 1.6178149252362e-36, 1.12636583098266e-04) - FileName = /usgs/cpkgs/isis3/data/odyssey/testData/I02609002RDR.lev2- - .cub + FileName = data/odyssey/testData/I02609002RDR.lev2.cub Band1 = (1.9316157478611, 1.59619509035933e-04, 1.42658743858439e-04) Band2 = (1.932336336529, 1.57588763433619e-04, @@ -8677,13 +8672,13 @@ Testing loadInputs exception ... **USER ERROR** The input file [HoldList.lst] must contain at least 2 file names. Testing errorCheck exception (1)... -**USER ERROR** Number of bands do not match between cubes [/usgs/cpkgs/isis3/data/odyssey/testData/I00824006RDR.lev2.cub] and [/usgs/cpkgs/isis3/data/base/testData/isisTruth.cub]. +**USER ERROR** Number of bands do not match between cubes [data/odyssey/testData/I00824006RDR.lev2.cub] and [data/base/testData/isisTruth.cub]. Testing errorCheck exception (2)... -**USER ERROR** Mapping groups do not match between cubes [/usgs/cpkgs/isis3/data/odyssey/testData/I00824006RDR.lev2.cub] and [/usgs/cpkgs/isis3/data/odyssey/testData/I56632006EDR.lev2.cub]. +**USER ERROR** Mapping groups do not match between cubes [data/odyssey/testData/I00824006RDR.lev2.cub] and [data/odyssey/testData/I56632006EDR.lev2.cub]. Testing validateInputStatistics exception (1)... **USER ERROR** Each input file in the FROM LIST must have a corresponding input file in the INPUT STATISTICS. Testing validateInputStatistics exception (2)... -**USER ERROR** The from list file [/usgs/cpkgs/isis3/data/odyssey/testData/I00824006RDR.lev2.cub] does not have any corresponding file in the stats list. +**USER ERROR** The from list file [data/odyssey/testData/I00824006RDR.lev2.cub] does not have any corresponding file in the stats list. diff --git a/isis/src/base/objs/Equalization/unitTest.cpp b/isis/src/base/objs/Equalization/unitTest.cpp index 0364a8e517d6ab0fceb5aa971984fc66cdf110f2..33792c68cb21c6f5bcedd76c6e22e5a5ec064131 100644 --- a/isis/src/base/objs/Equalization/unitTest.cpp +++ b/isis/src/base/objs/Equalization/unitTest.cpp @@ -11,10 +11,14 @@ #include "Preference.h" #include "ProcessByLine.h" #include "PvlGroup.h" +#include "QRegularExpression" using namespace std; using namespace Isis; +void ReportError(QString err) { + cout << err.replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data") << endl; +} class TestFunctor { public: @@ -46,7 +50,6 @@ class TestFunctor { int m_lineCount; }; - int main(int argc, char *argv[]) { Preference::Preferences(true); cout << setprecision(9); @@ -93,6 +96,9 @@ int main(int argc, char *argv[]) { results = equalizer.getResults(); cout << "Results:" << endl; + for (int i = 0; i < results["NonOverlaps"].size(); i++) { + results["NonOverlaps"][i].replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data"); + } cout << results << endl; cout << " Write results to file..." << endl; @@ -112,6 +118,11 @@ int main(int argc, char *argv[]) { results = equalizerFixed.getResults(); cout << "Results:" << endl; + for (int i = 0; i < results.keywords(); i++) { + if (results[i].isNamed("FileName")) { + results[i].setValue(QString(results[i]).replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data")); + } + } cout << results << endl; cout << " Write results to file..." << endl; @@ -214,7 +225,7 @@ int main(int argc, char *argv[]) { Equalization equalizer(OverlapNormalization::Both, tmpList); } catch (IException &e) { - e.print(); + ReportError(e.toString()); } try { @@ -227,7 +238,7 @@ int main(int argc, char *argv[]) { Equalization equalizer(OverlapNormalization::Both, tmpList); } catch (IException &e) { - e.print(); + ReportError(e.toString()); } // Testing loadOutputs exceptions TODO @@ -239,7 +250,7 @@ int main(int argc, char *argv[]) { equalizer.importStatistics(nonOverlapStats); } catch (IException &e) { - e.print(); + ReportError(e.toString()); } try { @@ -248,7 +259,7 @@ int main(int argc, char *argv[]) { equalizer.importStatistics(allOverlapStats); } catch (IException &e) { - e.print(); + ReportError(e.toString()); } // Remove all the temporary files diff --git a/isis/src/base/objs/GisBlob/GisBlob.truth b/isis/src/base/objs/GisBlob/GisBlob.truth index dee42e2436c379786b7a5ddd50e51389cf534ab5..ee75776376542b8794e0fa288b876e126390f399 100644 --- a/isis/src/base/objs/GisBlob/GisBlob.truth +++ b/isis/src/base/objs/GisBlob/GisBlob.truth @@ -1,9 +1,9 @@ Testing GisBlob's constructor from cube... 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Polygon = "" Adding WKT polygon to GisBlob... - Polygon = "MULTIPOLYGON (((291.7259256919469976 54.0783959422994158, 291.7789445157497425 54.0310967038859431, 291.8309303561991328 53.9846043685970542, 291.8827969013699999 53.9381053149077445, 291.9345449075967167 53.8915993651327767, 291.9861751261867084 53.8450863412012524, 292.0376883034713273 53.7985660646532082, 292.0890851808566708 53.7520383566360920, 292.1403664948735468 53.7055030379012450, 292.1915329772272685 53.6589599288003782, 292.2425853548462555 53.6124088492817705, 292.2935243499310900 53.5658496188866877, 292.3443506800020941 53.5192820567455598, 292.3950650579470789 53.4727059815742223, 292.4456681920681831 53.4261212116699369, 292.4961607861285984 53.3795275649076260, 292.5465435393983284 53.3329248587357512, 292.5968171467000616 53.2863129101723203, 292.6469822984541906 53.2396915358008727, 292.6970396807230372 53.1930605517662158, 292.7469899752558717 53.1464197737703117, 292.7968338595316595 53.0997690170679846, 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48.8535006122709063, 286.3831420753027146 48.8974063618426840, 286.3313949286018101 48.9412186275038579, 286.2794287606336638 48.9849733476629297, 286.2271237527501171 49.0286407173921361, 286.1747934942748657 49.0723176450905072, 286.1226207794685479 49.1160491477687486, 286.0705778239361052 49.1598179149401204, 286.0185387849462586 49.2035851470715215, 285.9663555293917057 49.2473136664860647, 285.9139828228739475 49.2909956681908312, 285.8615048751227050 49.3346515723928292, 285.8089409308830682 49.3782853448059882, 285.7561709971500932 49.4218750455458391, 285.7033744198886325 49.4654544937027154, 285.6505294182767898 49.5090178755621935, 285.5977727123407135 49.5525837744106425, 285.5447446092979362 49.5960970702829229, 285.4914875549942508 49.6395684556400170, 285.4379846370865152 49.6829997262990304, 285.3843843052756597 49.7264110256648948, 285.3308342690713175 49.7698167182288245, 285.2773646050080174 49.8132152409817408, 285.2239238309639404 49.8565975374196668, 285.1703158928399375 49.8999460743720107, 285.1164481902447960 49.9432567010531869, 285.0625323547681660 49.9865451770147544, 285.0082665476087413 50.0297957865672416, 284.9537084881674787 50.0730166730696595, 284.8991894805907918 50.1162226853946606, 284.8446182125073278 50.1594081318238167, 284.7898601929547908 50.2025694147422996, 284.7349043728681863 50.2457080812009522, 284.6799771552385323 50.2888265780296280, 284.6248540494665917 50.3319228431918049, 284.5695238923811416 50.3749986845891300, 284.5144490571994993 50.4180478736866817, 284.4593856466942725 50.4610690021459973, 284.4040790806055838 50.5040674495806385, 284.3484586308211988 50.5470482927714784, 284.2935341408388581 50.5899723488597601, 284.2391049473005182 50.6328348676932407, 284.1837853403296208 50.6757005534934777, 284.1663273815096318 50.6919534014300766, 284.2345597693270065 50.7277015503154161, 284.3020640473581579 50.7628777224099892, 284.3702656899958470 50.7979746069000484, 284.4387418467628663 50.8330150873104074, 284.5071713340328188 50.8680245376072975, 284.5755687379514143 50.9030045092247363, 284.6443164345435548 50.9379171054902500, 284.7135533824027220 50.9727405217829670, 284.7829461739408430 51.0075059628211491, 284.8521768237749825 51.0422529775025851, 284.9213779308003609 51.0769691887487411, 284.9906032701824756 51.1116495917477351, 285.0598819033065183 51.1462913063788349, 285.1294270280205865 51.1808602737040772, 285.1992202696198433 51.2153549031564808, 285.2689486693911363 51.2498278200912978, 285.3385407699790335 51.2842969395446175, 285.4080991362617965 51.3187480716453166, 285.4778056611060606 51.3531464893620608, 285.5483833920509369 51.3873301698831071, 285.6193015406489053 51.4213979996852473, 285.6897321570879740 51.4555427015166273, 285.7594982587881987 51.4898277189353308, 285.8295266909508996 51.5240324011132174, 285.8995795188444049 51.5582171669147584, 285.9694603052748789 51.5924415814695649, 286.0394555568004762 51.6266293964584264, 286.1098454748561153 51.6606923298506473, 286.1806846868420280 51.6946012555894825, 286.2515634685805139 51.7284818757417852, 286.3217610437835106 51.7625925450240558, 286.3918947636801136 51.7967386371245837, 286.4624479942411881 51.8307423644522842, 286.5336661467025579 51.8644918118881932, 286.6050516772942274 51.8981677383684854, 286.6765569414309311 51.9317872895232000, 286.7481309225292421 51.9653721726498503, 286.8199530521117708 51.9988397589956506, 286.8920127214390163 52.0321867072350770, 286.9640676739491596 52.0655270933311627, 287.0361337373960282 52.0988579772036928, 287.1084521342681342 52.1320521938549248, 287.1808429436290453 52.1652016017904359, 287.2528037265199146 52.1986044777616200, 287.3251766498365214 52.2317791050783669, 287.3976852881675086 52.2648798818484437, 287.4697242670244464 52.2983072795676875, 287.5421226029587842 52.3315320485897573, 287.6148867344307405 52.3645289209294447, 287.6877004396365578 52.3975127478532059, 287.7605440724607888 52.4305033881260840, 287.8332983279560722 52.4636054057247634, 287.9057493954031202 52.4970217668427779, 287.9780316068848265 52.5306795409256608, 288.0504439921309086 52.5643367368246146, 288.1234401644522904 52.5975550143054207, 288.1976382829452064 52.6296474297664219, 288.2721681013861144 52.6613877226737159, 288.3463897438006143 52.6934494034029157, 288.4202322563753569 52.7259736328181674, 288.4939397938130696 52.7587388913465958, 288.5678468760376063 52.7913568215394164, 288.6419218814429541 52.8238536973012103, 288.7165029135949794 52.8557306608363362, 288.7912456624506490 52.8874137480644535, 288.8656727128577586 52.9196471844023790, 288.9400718311589458 52.9520515232037781, 289.0145695908635162 52.9844388557765029, 289.0890412533441349 53.0170554947797967, 289.1635635592601830 53.0497993040304365, 289.2382911325804002 53.0823639878877032, 289.3132195813146836 53.1147272726123987, 289.3882373382535889 53.1471368006245015, 289.4633522768713192 53.1795932616528120, 289.5386395897923535 53.2118916057759463, 289.6140551665824887 53.2441442933252560, 289.6895157143202368 53.2766587857948153, 289.7651099666896926 53.3091747733643402, 289.8409073665112601 53.3413820299417480, 289.9168235491238192 53.3736136015565563, 289.9928758081005071 53.4057942992804442, 290.0690425949051701 53.4380804602550015, 290.1453574173241918 53.4702653414589975, 290.2218095760875372 53.5024220046409624, 290.2983878999274339 53.5347670501741035, 290.3751182413015499 53.5670164502047257, 290.4519987557255263 53.5988030640775577, 290.5290061844957563 53.6305483723634140, 290.6061466002392422 53.6623930165058809, 290.6834140633079642 53.6940874221143645, 290.7608043693315949 53.7256675476979808, 290.8382970713091709 53.7569901973408975, 290.9159587660024044 53.7886645754515271, 290.9938283926157396 53.8207705659212365, 291.0717891428241728 53.8524693735371756, 291.1498394700072367 53.8838731934801629, 291.2279334662110841 53.9148453185582071, 291.3061172279390689 53.9456783680282825, 291.3844357241167131 53.9765654329084370, 291.4627282140606894 54.0069110349376871, 291.5408564454050975 54.0363542888421122, 291.6190588029043624 54.0657945141910190, 291.6482444065063646 54.0748894594413585)))" diff --git a/isis/src/base/objs/GisGeometry/GisGeometry.truth b/isis/src/base/objs/GisGeometry/GisGeometry.truth index 1cadb00600552ee344c65d460cd39969b175c61e..b300df2829dd511a869bcacf9773685a40db1244 100644 --- a/isis/src/base/objs/GisGeometry/GisGeometry.truth +++ b/isis/src/base/objs/GisGeometry/GisGeometry.truth @@ -29,8 +29,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "IsisCube" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Construct Geometry from WKT GIS source" @@ -39,8 +39,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "WKT" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Construct Geometry from WKB GIS source" @@ -49,8 +49,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "WKB" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Construct Geometry from IsisCube GIS source" @@ -59,8 +59,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "IsisCube" - area? 4.05913 - length? 8.38034 + area? 4.09421 + length? 8.41585 points? 209 "Construct Geometry from GEOSGeometry" @@ -69,8 +69,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "GeosGis" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Construct Empty Default Geometry" @@ -89,8 +89,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "IsisCube" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Construct Copy Geometry from Undefined Geometry" @@ -109,8 +109,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "IsisCube" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Construct Equal Geometry from Equal Geometry" @@ -119,8 +119,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "IsisCube" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Construct Equal Geometry from Undefined Geometry" @@ -139,8 +139,8 @@ GisGeometry::Types: isValidReason? "Valid Geometry" isEmpty? false type? "IsisCube" - area? 50.218 - length? 29.6669 + area? 50.3519 + length? 29.6976 points? 413 "Clone Geometry from Undefined Geometry" @@ -178,7 +178,7 @@ GisGeometry::Types: disjoint? "No" overlaps? "Yes" equals? "No" - intersect ratio? "0.95216803927449" + intersect ratio? "0.95030561790462" "Source: WKT Geometry, Target: WKB Geometry (equal geometries)" distance? "0.0" @@ -190,7 +190,7 @@ GisGeometry::Types: intersect ratio? "1.0" "Source: WKT Geometry, Target: Lat/Lon Geometry" - distance? "288.73577074892" + distance? "288.65234410472" intersects? "No" contains? "No" disjoint? "Yes" @@ -206,8 +206,8 @@ Intersect Ratio of WKT Geometry with Lat/Lon (single point) Geometry: 0 isValidReason? "Valid Geometry" isEmpty? false type? "GeosGis" - area? 97.1265 - length? 40.3919 + area? 97.31 + length? 40.4313 points? 5 "Envelope Geometry from Invalid Geometry" @@ -226,9 +226,9 @@ Intersect Ratio of WKT Geometry with Lat/Lon (single point) Geometry: 0 isValidReason? "Valid Geometry" isEmpty? false type? "GeosGis" - area? 51.236 - length? 29.6587 - points? 211 + area? 51.3562 + length? 29.6897 + points? 108 "Convex Hull Geometry from Invalid Geometry" isDefined? false @@ -246,8 +246,8 @@ Intersect Ratio of WKT Geometry with Lat/Lon (single point) Geometry: 0 isValidReason? "Valid Geometry" isEmpty? false type? "GeosGis" - area? 50.2148 - length? 29.6512 + area? 50.3126 + length? 29.6816 points? 5 Simplified Geometry from Invalid Geometry is NULL. @@ -278,9 +278,9 @@ Simplified Geometry from Invalid Geometry is NULL. isValidReason? "Valid Geometry" isEmpty? false type? "GeosGis" - area? 3.86497 - length? 8.20245 - points? 188 + area? 3.89075 + length? 8.23376 + points? 187 "Union Geometry of Invalid Geometry with WKT Geometry as target" isDefined? false @@ -308,9 +308,9 @@ Simplified Geometry from Invalid Geometry is NULL. isValidReason? "Valid Geometry" isEmpty? false type? "GeosGis" - area? 50.4122 - length? 29.8448 - points? 438 + area? 50.5554 + length? 29.8797 + points? 439 "Centroid Geometry of Invalid Geometry" isDefined? false @@ -335,8 +335,8 @@ Simplified Geometry from Invalid Geometry is NULL. Centroid found for Invalid Geometry? false Centroid found for WKT Geometry? true - Longitude: 290.491 - Latitude: 50.1643 + Longitude: 290.412 + Latitude: 50.1576 Testing Errors... **PROGRAMMER ERROR** Unknown GIS type given [None]. diff --git a/isis/src/base/objs/GisTopology/GisTopology.truth b/isis/src/base/objs/GisTopology/GisTopology.truth index c22f80079931b1c19d40cd17798b4b6c7667cb40..89ae4e96cbf6ceb9511d4c1cd0f84a310bec88e8 100644 --- a/isis/src/base/objs/GisTopology/GisTopology.truth +++ b/isis/src/base/objs/GisTopology/GisTopology.truth @@ -1,13 +1,13 @@ Testing GisTopology... -wkt from cube: "MULTIPOLYGON (((291.7259256919469976 54.0783959422994158, 291.7789445157497425 54.0310967038859431, 291.8309303561991328 53.9846043685970542, 291.8827969013699999 53.9381053149077445, 291.9345449075967167 53.8915993651327767, 291.9861751261867084 53.8450863412012524, 292.0376883034713273 53.7985660646532082, 292.0890851808566708 53.7520383566360920, 292.1403664948735468 53.7055030379012450, 292.1915329772272685 53.6589599288003782, 292.2425853548462555 53.6124088492817705, 292.2935243499310900 53.5658496188866877, 292.3443506800020941 53.5192820567455598, 292.3950650579470789 53.4727059815742223, 292.4456681920681831 53.4261212116699369, 292.4961607861285984 53.3795275649076260, 292.5465435393983284 53.3329248587357512, 292.5968171467000616 53.2863129101723203, 292.6469822984541906 53.2396915358008727, 292.6970396807230372 53.1930605517662158, 292.7469899752558717 53.1464197737703117, 292.7968338595316595 53.0997690170679846, 292.8465720068031146 53.0531080964626298, 292.8962050861391617 53.0064368263018437, 292.9457337624675120 52.9597550204730041, 292.9951586966164996 52.9130624923988080, 293.0444805453568051 52.8663590550327100, 293.0936999614425531 52.8196445208543821, 293.1428175936520120 52.7729187018650165, 293.1918340868279529 52.7261814095827219, 293.2407500819177812 52.6794324550376345, 293.2895662160128154 52.6326716487672641, 293.3382831223876224 52.5858988008115062, 293.3869014305387282 52.5391137207077890, 293.4354217662231576 52.4923162174860352, 293.4838447514963491 52.4455060996637386, 293.5321710047498982 52.3986831752407198, 293.5804011407487906 52.3518472516941102, 293.6285357706685772 52.3049981359730793, 293.6765755021316977 52.2581356344935699, 293.7245209392440302 52.2112595531329902, 293.7723726826305324 52.1643696972248065, 293.8201313294711667 52.1174658715531862, 293.8677974735358589 52.0705478803473483, 293.9153717052195134 52.0236155272761778, 293.9628546115767449 51.9766686154424349, 294.0102467763561549 51.9297069473772197, 294.0575487800339829 51.8827303250341316, 294.1047611998483262 51.8357385497835139, 294.1518846098321092 51.7887314224066131, 294.1989195808462227 51.7417087430895748, 294.2458666806123233 51.6946703114175392, 294.2927264737454607 51.6476159263685659, 294.3394995217858536 51.6005453863074663, 294.3861863832314043 51.5534584889797571, 294.4327876135686779 51.5063550315052439, 294.4793037653049055 51.4592348103718678, 294.5257353879982816 51.4120976214292682, 294.5720830282896259 51.3649432598823523, 294.6183472299323967 51.3177715202848077, 294.6645285338229314 51.2705821965325086, 294.7106274780308581 51.2233750818569220, 294.7566445978286538 51.1761499688183790, 294.8025804257210893 51.1289066492992674, 294.8484354914746746 51.0816449144973035, 294.8942103221465345 51.0343645549184757, 294.9399054421134565 50.9870653603702024, 294.9855213731003118 50.9397471199542196, 295.0310586342081933 50.8924096220593967, 295.0765177419429506 50.8450526543546744, 295.1218992102427592 50.7976760037817314, 295.1672035505058602 50.7502794565476307, 295.2124312716179020 50.7028627981173869, 295.2575828799796227 50.6554258132066337, 295.3026588795331122 50.6079682857738291, 295.3476597717893810 50.5604899990128018, 295.3925860558544514 50.5129907353449354, 295.4374382284559601 50.4654702764114234, 295.4822167839693066 50.4179284030653818, 295.5269222144437435 50.3703648953638989, 295.5715550096281845 50.3227795325600127, 295.6161156569966124 50.2751720930945964, 295.6606046417739435 50.2275423545881452, 295.7050224469607542 50.1798900938325190, 295.7493695533589175 50.1322150867825869, 295.7936464395958751 50.0845171085478071, 295.8378535821501600 50.0367959333836225, 295.8819914553751005 49.9890513346829408, 295.9260605315237740 49.9412830849673455, 295.9700612807729385 49.8934909558783701, 296.0139941712473046 49.8456747181686026, 296.0578596690432960 49.7978341416927250, 296.1016582382526394 49.7499689953983903, 296.1453903409863528 49.7020790473171488, 296.1890564373977099 49.6541640645552107, 296.2326569857058303 49.6062238132840321, 296.2761924422186439 49.5582580587309423, 296.3196632613559132 49.5102665651695801, 296.3630698956721972 49.4622490959102805, 296.4064127958794188 49.4142054132903823, 296.4496924108693747 49.3661352786643306, 296.4929091877363021 49.3180384523938002, 296.5360635717991045 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53.5024220046409624, 290.2983878999274339 53.5347670501741035, 290.3751182413015499 53.5670164502047257, 290.4519987557255263 53.5988030640775577, 290.5290061844957563 53.6305483723634140, 290.6061466002392422 53.6623930165058809, 290.6834140633079642 53.6940874221143645, 290.7608043693315949 53.7256675476979808, 290.8382970713091709 53.7569901973408975, 290.9159587660024044 53.7886645754515271, 290.9938283926157396 53.8207705659212365, 291.0717891428241728 53.8524693735371756, 291.1498394700072367 53.8838731934801629, 291.2279334662110841 53.9148453185582071, 291.3061172279390689 53.9456783680282825, 291.3844357241167131 53.9765654329084370, 291.4627282140606894 54.0069110349376871, 291.5408564454050975 54.0363542888421122, 291.6190588029043624 54.0657945141910190, 291.6482444065063646 54.0748894594413585)))" wkt from cube == wkt from geometry? true GEOSGeometry from cube is preserved. ============================================================================== -WKB: 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wkt from cube == wkb from geometry? false wkb from original geometry == wkb from new geometry? true diff --git a/isis/src/base/objs/GroundGrid/GroundGrid.cpp b/isis/src/base/objs/GroundGrid/GroundGrid.cpp index 7249e13226edf963c7952ae21fd4d763b207989c..44e92955e0c7d0e815498ea8acaf86b8b37099a7 100644 --- a/isis/src/base/objs/GroundGrid/GroundGrid.cpp +++ b/isis/src/base/objs/GroundGrid/GroundGrid.cpp @@ -325,7 +325,11 @@ namespace Isis { progress->CheckStatus(); } - for (Latitude lat = startLat; lat <= endLat + latInc / 2; lat += latInc) { + // Ensure that the Latitude being incremented does not throw an exception + // if incremented past -90 or 90 degrees. + Latitude latStep = startLat; + latStep.setErrorChecking(Latitude::AllowPastPole); + for (; latStep <= endLat + latInc / 2; latStep += latInc) { unsigned int previousX = 0; unsigned int previousY = 0; bool havePrevious = false; @@ -333,7 +337,7 @@ namespace Isis { for (Longitude lon = *p_minLon; lon <= *p_maxLon; lon += latRes) { unsigned int x = 0; unsigned int y = 0; - bool valid = GetXY(lat, lon, x, y); + bool valid = GetXY(latStep, lon, x, y); if (valid && havePrevious) { if (previousX != x || previousY != y) { @@ -356,11 +360,15 @@ namespace Isis { unsigned int previousY = 0; bool havePrevious = false; - for (Latitude lat = *p_minLat; lat <= *p_maxLat; lat += lonRes) { + // Ensure that the Latitude being incremented does not throw an exception + // if incremented past -90 or 90 degrees. + latStep = *p_minLat; + latStep.setErrorChecking(Latitude::AllowPastPole); + for (; latStep <= *p_maxLat; latStep += lonRes) { unsigned int x = 0; unsigned int y = 0; - bool valid = GetXY(lat, lon, x, y); + bool valid = GetXY(latStep, lon, x, y); if (valid && havePrevious) { if (previousX == x && previousY == y) { @@ -423,7 +431,11 @@ namespace Isis { const Longitude &maxLon = *p_maxLon; // Walk the minLat/maxLat lines - for (Latitude lat = minLat; lat <= maxLat; lat += (maxLat - minLat)) { + // Ensure that the Latitude being incremented does not throw an exception + // if incremented past -90 or 90 degrees. + Latitude latStep = minLat; + latStep.setErrorChecking(Latitude::AllowPastPole); + for (; latStep <= maxLat; latStep += (maxLat - minLat)) { unsigned int previousX = 0; unsigned int previousY = 0; bool havePrevious = false; @@ -431,7 +443,7 @@ namespace Isis { for (Longitude lon = minLon; lon <= maxLon; lon += latRes) { unsigned int x = 0; unsigned int y = 0; - bool valid = GetXY(lat, lon, x, y); + bool valid = GetXY(latStep, lon, x, y); if (valid && havePrevious) { if (previousX != x || previousY != y) { @@ -451,10 +463,14 @@ namespace Isis { unsigned int previousY = 0; bool havePrevious = false; - for (Latitude lat = minLat; lat <= maxLat; lat += lonRes) { + // Ensure that the Latitude being incremented does not throw an exception + // if incremented past -90 or 90 degrees. + latStep = minLat; + latStep.setErrorChecking(Latitude::AllowPastPole); + for (; latStep <= maxLat; latStep += lonRes) { unsigned int x = 0; unsigned int y = 0; - bool valid = GetXY(lat, lon, x, y); + bool valid = GetXY(latStep, lon, x, y); if (valid && havePrevious) { if (previousX != x || previousY != y) { diff --git a/isis/src/base/objs/GroundGrid/GroundGrid.h b/isis/src/base/objs/GroundGrid/GroundGrid.h index c150ef203f1134d11bb0af12b8d4bb6be7834eb7..f276b3ad980d9306731e128fb94fbe70cceda6bb 100644 --- a/isis/src/base/objs/GroundGrid/GroundGrid.h +++ b/isis/src/base/objs/GroundGrid/GroundGrid.h @@ -65,6 +65,8 @@ namespace Isis { * method was fixed to match the signature of the parent method. * Moved implementation of GroundMap() and GetMappingGroup() to the * cpp file per ISIS coding standards. + * @history 2017-04-10 Jesse mapel - Modified to not throw an exception when calculating + * longitude lines close to 90 or -90 latitude. Fixes #4766. */ class GroundGrid { public: diff --git a/isis/src/base/objs/Gruen/Gruen.truth b/isis/src/base/objs/Gruen/Gruen.truth index 4691a4fb06aeaa394debc5664b7e2b914696864e..bd3788e740054ef78cb27253aa02439654ac69ef 100644 --- a/isis/src/base/objs/Gruen/Gruen.truth +++ b/isis/src/base/objs/Gruen/Gruen.truth @@ -19,4 +19,4 @@ Object = AutoRegistration End_Object End Register = 1 -Position = 512.684 511.703 +Position = 512.604 511.63 diff --git a/isis/src/base/objs/Gui/Gui.cpp b/isis/src/base/objs/Gui/Gui.cpp index 6a313fd5312849a70b1ffc0bd03703c57267e7d8..2e1d3aa8342d79c5ccdc8e007a7c3e0b857aec36 100644 --- a/isis/src/base/objs/Gui/Gui.cpp +++ b/isis/src/base/objs/Gui/Gui.cpp @@ -8,6 +8,7 @@ #include #include #include +#include #include #include #include @@ -70,21 +71,20 @@ namespace Isis { #endif } - Gui *Gui::Create(Isis::UserInterface &ui, int &argc, char *argv[]) { // Don't recreate if(p_gui != NULL) return p_gui; // Get preferences PvlGroup &uiPref = Preference::Preferences().findGroup("UserInterface"); - // Create the application new QApplication(argc, argv); // When QApplication is initialized, it will reset the locale to the shells locale. As a result // the locale needs to be reset after QApplications initialization. setlocale(LC_ALL, "en_US"); - QCoreApplication::setApplicationName(FileName(argv[0]).baseName()); + QApplication::setQuitOnLastWindowClosed(true); + QApplication::setApplicationName(FileName(argv[0]).baseName()); // Qt is smart enough to use the style of the system running the program. @@ -94,7 +94,21 @@ namespace Isis { QString style = uiPref["GuiStyle"]; QApplication::setStyle(style); } - + + + if (uiPref.hasKeyword("GuiFontName")) { + QString fontString = uiPref["GuiFontName"]; + QFont font = QFont(fontString); + + if (uiPref.hasKeyword("GuiFontSize")) { + int pointSize = uiPref["GuiFontSize"]; + font.setPointSize(pointSize); + } + + QApplication::setFont(font); + } + + // Create the main window p_gui = new Gui(ui); p_gui->show(); @@ -107,6 +121,9 @@ namespace Isis { // Create the toolbar and menu and populate them with actions CreateAreas(); + // Set title + QWidget::setWindowTitle(QApplication::applicationName()); + // Add parameters to the main area for(int group = 0; group < ui.NumGroups(); group++) { for(int param = 0; param < ui.NumParams(group); param++) { @@ -141,6 +158,7 @@ namespace Isis { // Setup the current history pointer p_historyEntry = -1; + } //! Destructor @@ -261,12 +279,14 @@ namespace Isis { helpMenu->addAction(whatsThisAction); QAction *aboutProgram = new QAction(this); + aboutProgram->setMenuRole(QAction::AboutRole); aboutProgram->setText("About this program"); aboutProgram->setShortcut(Qt::CTRL + Qt::Key_H); helpMenu->addAction(aboutProgram); connect(aboutProgram, SIGNAL(triggered(bool)), this, SLOT(AboutProgram())); QAction *aboutIsis = new QAction(this); + aboutIsis->setMenuRole(QAction::NoRole); aboutIsis->setText("About Isis"); aboutIsis->setShortcut(Qt::CTRL + Qt::Key_I); helpMenu->addAction(aboutIsis); diff --git a/isis/src/base/objs/Gui/Gui.h b/isis/src/base/objs/Gui/Gui.h index 44f38b51d15adce74a0dcf39b800be2b18c65438..6f3ce1c3179bc1ed87ba430653273624a68b7735 100644 --- a/isis/src/base/objs/Gui/Gui.h +++ b/isis/src/base/objs/Gui/Gui.h @@ -70,7 +70,7 @@ namespace Isis { * GuiFileNameParameter.cpp and removed SelectFile() * from GuiCubeParameter. Cube and File customization * preferences are now being handled in Cube's - * CubeIoHandler and IsisAml classes. + * CubeIoHandler and IsisAml classes. * @history 2012-11-08 Janet Barrett - Modified the AddParameter method to * only update exclusions for list and combobox widgets. * Fixes #624. @@ -79,8 +79,12 @@ namespace Isis { * #1452. * @history 2016-06-28 Adam Paquette - Modified UpdateHistory to appropriately * retrieve lists from the history pvl. - * @history 2016-08-15 Adam Paquette - Reset locale after QApplication is + * @history 2016-08-15 Adam Paquette - Reset locale after QApplication is * instantiated. Fixes #3908. + * @history 2017-05-16 Cole Neubauer - Fixed Title not showing in Putty/Xming + * setup. Fixes #4731. + * @history 2017-05-19 Marjorie Hahn - Applied font style and font size from the + * IsisPreferences file. Fixes #198. */ class Gui : public QMainWindow { @@ -88,7 +92,7 @@ namespace Isis { public: static void checkX11(); - + static Gui *Create(Isis::UserInterface &ui, int &argc, char *argv[]); void ProgressText(const QString &text); diff --git a/isis/src/base/objs/Histogram/Histogram.h b/isis/src/base/objs/Histogram/Histogram.h index 346b1e0fc14a901fdefaa0019b46d92a3e36b963..ce6fc470e1b04ddd07f42682bdc0fc97b2fd0283 100644 --- a/isis/src/base/objs/Histogram/Histogram.h +++ b/isis/src/base/objs/Histogram/Histogram.h @@ -68,13 +68,16 @@ namespace Isis { * @history 2012-04-10 Orrin Thomas - Added constructor parameters to read * from ControlNets automatically (For control measure * data.) - * @history 2015-09-03 Tyler Wilson - Overrode Statistics::SetValidRange to - * set the bin range as well as the statistical range + * @history 2015-09-03 Tyler Wilson - Overrode Statistics::SetValidRange to + * set the bin range as well as the statistical range * for the data. The function Histogram::SetBinRange - * has been removed from this class. + * has been removed from this class. * @history 2016-04-20 Makayla Shepherd - Added UnsignedWord pixel type handling. + * @history 2017-05-19 Christopher Combs - Modified unitTest.cpp: Removed path of output file + * name in output PVL to allow the test to pass when not using the + * standard data areas. Fixes #4738. */ - + class Histogram : public Statistics { public: Histogram(double minimum, double maximum, @@ -84,7 +87,7 @@ namespace Isis { double endSample = Null, double endLine = Null, int bins = 0, bool addCubeData = false); - //constuctors that use ControlNetworks to build histograms of ControlMeasure data + //constuctors that use ControlNetworks to build histograms of ControlMeasure data Histogram(ControlNet &net, double(ControlMeasure::*statFunc)() const, int bins); Histogram(ControlNet &net, double(ControlMeasure::*statFunc)() const, double binWidth); diff --git a/isis/src/base/objs/Histogram/Histogram.truth b/isis/src/base/objs/Histogram/Histogram.truth index 2001932e99b9c6a4edbd6371b2611aaaca42d9ee..f4de0263ca1568289ce365e87916b8a59c2165df 100644 --- a/isis/src/base/objs/Histogram/Histogram.truth +++ b/isis/src/base/objs/Histogram/Histogram.truth @@ -33,7 +33,7 @@ BinCount(20): 0 **PROGRAMMER ERROR** Array subscript [1024] is out of array bounds. End old unit test. -/usgs/cpkgs/isis3/data/base/testData/enceladus_sp-Jig.net +data/base/testData/enceladus_sp-Jig.net Loading Control Points... 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed diff --git a/isis/src/base/objs/Histogram/unitTest.cpp b/isis/src/base/objs/Histogram/unitTest.cpp index 2a6db22c707264926565ab74408df5fa0e03a5c4..060e15e78ded4602fda16dbbc87e38ef7d92af3d 100644 --- a/isis/src/base/objs/Histogram/unitTest.cpp +++ b/isis/src/base/objs/Histogram/unitTest.cpp @@ -1,5 +1,6 @@ #include #include +#include "QRegularExpression" #include "Histogram.h" #include "IException.h" #include "Preference.h" @@ -159,8 +160,7 @@ int main(int argc, char *argv[]) { Isis::Progress progress; Isis::FileName netName("$base/testData/enceladus_sp-Jig.net"); flist.append(netName.expanded()); - cout << netName.expanded().toStdString() << endl; - + cout << netName.toString().replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data").toStdString() << endl; Isis::ControlNet net(flist[0], &progress); diff --git a/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.cpp b/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.cpp index c915b26b474e209abd08e38803fd33dede674f30..5e1826cf1208df83d195d47fdbdd6f7244a9bbea 100644 --- a/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.cpp +++ b/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.cpp @@ -444,7 +444,7 @@ namespace Isis { * @param filename The file to write the image overlaps to */ void ImageOverlapSet::WriteImageOverlaps(const QString &filename) { - + QString file = FileName(filename).expanded(); bool failed = false; bool noOverlaps = false; @@ -493,7 +493,6 @@ namespace Isis { p_writtenSoFar ++; } } - p_lonLatOverlapsMutex.unlock(); } @@ -505,23 +504,26 @@ namespace Isis { catch (...) { failed = true; } - + /** * Don't wait for an unlock from FindImageOverlaps(...) if we're done * calculating. */ if (p_calculatedSoFar == p_lonLatOverlaps.size()) { - if (p_threadedCalculate) { + if (p_threadedCalculate && !noOverlaps) { + p_calculatePolygonMutex.tryLock(); p_calculatePolygonMutex.unlock(); } } if (failed) { + p_calculatePolygonMutex.tryLock(); p_calculatePolygonMutex.unlock(); QString msg = "Unable to write the image overlap list to [" + filename + "]"; throw IException(IException::Io, msg, _FILEINFO_); } else if (noOverlaps) { + p_calculatePolygonMutex.tryLock(); p_calculatePolygonMutex.unlock(); QString msg = "No overlaps were found."; throw IException(IException::User, msg, _FILEINFO_); @@ -554,6 +556,7 @@ namespace Isis { // unblock the writing process after every 10 polygons if we need to write if (p_calculatedSoFar % 10 == 0 && (!snlist || (p_lonLatOverlaps.size() > snlist->size()))) { if (p_threadedCalculate) { + p_calculatePolygonMutex.tryLock(); p_calculatePolygonMutex.unlock(); } } diff --git a/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.h b/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.h index 8be86964f65cf55f21974b0b650ddb9f4b7f0b4f..2d03f455f37f8dac86601e8dc2610c3203e032e1 100644 --- a/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.h +++ b/isis/src/base/objs/ImageOverlapSet/ImageOverlapSet.h @@ -93,6 +93,11 @@ namespace Isis { * @history 2016-09-28 Jeannie Backer - Replaced deprecated IStrings with QStrings. Added mutex * unlock() calls immediately before exception calls to prevent warning * message by latest Qt library 5.7. + * @history 2016-12-09 Marjorie Hahn - Added mutex tryLock() calls before unlocking to prevent + * undefined behavior caused by unlocking an unlocked mutex. + * @history 2017-05-23 Ian Humphrey - Added a tryLock() to FindAllOverlaps to prevent a + * segfault from occuring on OSX with certain data. Fixes #4810. + * */ class ImageOverlapSet : private QThread { public: diff --git a/isis/src/base/objs/InfixToPostfix/InfixToPostfix.cpp b/isis/src/base/objs/InfixToPostfix/InfixToPostfix.cpp index 3593587e580fbec424ec36d0dedfe3fbd0ec3bb4..d8c22feceff687ea2bc021b6a8e8496b18d8e67f 100644 --- a/isis/src/base/objs/InfixToPostfix/InfixToPostfix.cpp +++ b/isis/src/base/objs/InfixToPostfix/InfixToPostfix.cpp @@ -388,7 +388,8 @@ namespace Isis { // parenthesis for(int i = 0; i < equation.size(); i++) { // Ensure there is whitespace in the equation - if(!equation[i].isLetterOrNumber() && !equation[i].isSpace() && equation[i] != '.') { + if(!equation[i].isLetterOrNumber() && !equation[i].isSpace() && + equation[i] != '.' && equation[i] != '_') { // Convert all braces to parens if(equation[i] == '[' || equation[i] == '{') { output += " ( "; @@ -425,6 +426,14 @@ namespace Isis { output += " != "; i++; } + else if(i < equation.size() - 1 && equation[i] == '|' && equation[i+1] == '|') { + output += " || "; + i++; + } + else if(i < equation.size() - 1 && equation[i] == '&' && equation[i+1] == '&') { + output += " && "; + i++; + } // Take care of scientific notiation where the exponent is negative else if((i > 1) && equation[i] == '-' && equation[i-1].toLower() == 'e' && equation[i-2].isLetterOrNumber()) { output += equation[i].toLatin1(); diff --git a/isis/src/base/objs/InfixToPostfix/InfixToPostfix.h b/isis/src/base/objs/InfixToPostfix/InfixToPostfix.h index 6e11478c9528b5dbcc9685a29b3d2765bd0c3139..b221b9dc9c2a2404bd4d670b77765a3bfaa2c723 100644 --- a/isis/src/base/objs/InfixToPostfix/InfixToPostfix.h +++ b/isis/src/base/objs/InfixToPostfix/InfixToPostfix.h @@ -53,6 +53,10 @@ namespace Isis { * @history 2010-04-08 Steven Lambright - Min, max functions expanded upon * @history 2012-01-09 Jeff Anderson - Modified to conform * ISIS programming standards + * @history 2017-01-09 Jesse Mapel - Modified to allow for "_" in variables. + * Fixes #4581. + * @history 2017-01-09 Jesse Mapel - Added logical and, or operators. + * Fixes #4581. */ class InfixToPostfix { public: diff --git a/isis/src/base/objs/InlineCalculator/InlineCalculator.cpp b/isis/src/base/objs/InlineCalculator/InlineCalculator.cpp index e89ad1f3ae5659bd0615065d4fec620a4a3eafc5..1e2e38eeee23ffe90b6c869d248d432c54121fd3 100644 --- a/isis/src/base/objs/InlineCalculator/InlineCalculator.cpp +++ b/isis/src/base/objs/InlineCalculator/InlineCalculator.cpp @@ -398,6 +398,54 @@ namespace Isis { Push(result); return; } + + + /** + * Pops the top two vectors off the current stack and performs a logical or + * on each pair. + * + * @throws IException::Unknown "Failed performing logical or operation, " + * "input vectors are of differnet lengths." + */ + void InlineCalculator::logicalOr() { + QVector inputA = Pop(); + QVector inputB = Pop(); + QVector results; + if ( inputA.size() != inputB.size() ) { + QString msg = "Failed performing logical or operation, " + "input vectors are of differnet lengths."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + for (int i = 0; i < inputA.size(); i++) { + results.push_back( inputA[i] || inputB[i] ); + } + Push(results); + return; + } + + + /** + * Pops the top two vectors off the current stack and performs a logical and + * on each pair. + * + * @throws IException::Unknown "Failed performing logical and operation, " + * "input vectors are of differnet lengths." + */ + void InlineCalculator::logicalAnd() { + QVector inputA = Pop(); + QVector inputB = Pop(); + QVector results; + if ( inputA.size() != inputB.size() ) { + QString msg = "Failed performing logical and operation, " + "input vectors are of differnet lengths."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + for (int i = 0; i < inputA.size(); i++) { + results.push_back( inputA[i] && inputB[i] ); + } + Push(results); + return; + } /** @@ -597,6 +645,8 @@ namespace Isis { addFunction(new InlineVoidFx("degs", &InlineCalculator::degrees, this)); addFunction(new InlineVoidFx("rads", &InlineCalculator::radians, this)); addFunction(new InlineVoidFx("e", &InlineCalculator::eConstant, this)); + addFunction(new InlineVoidFx("||", &InlineCalculator::logicalOr, this)); + addFunction(new InlineVoidFx("&&", &InlineCalculator::logicalAnd, this)); // Add new functions available for inlining // m_variablePoolList = defaultVariables(); diff --git a/isis/src/base/objs/InlineCalculator/InlineCalculator.h b/isis/src/base/objs/InlineCalculator/InlineCalculator.h index 907409992453daa0502b8a54da1fd93987affcac..3f16fcbdf58ac609c9ed50391cf2de85bf77fc80 100644 --- a/isis/src/base/objs/InlineCalculator/InlineCalculator.h +++ b/isis/src/base/objs/InlineCalculator/InlineCalculator.h @@ -62,6 +62,7 @@ namespace Isis { * @history 2015-03-24 Jeffrey Covington and Jeannie Backer - Improved documentation. * @history 2016-02-21 Kristin Berry - Added unit test and minor coding standard updates. * Fixes #2401. + * @history 2017-01-09 Jesse Mapel - Added logical and, or operators. Fixes #4581. */ class InlineCalculator : public Calculator { @@ -90,6 +91,8 @@ namespace Isis { void floatModulus(); void radians(); void degrees(); + void logicalOr(); + void logicalAnd(); void pi(); void eConstant(); diff --git a/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.cpp b/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.cpp index db864ac1e5b697926b557cc3f6f27fd7c5c394b5..bd08a20f0e4081fa758860d31e06fd4c2130dc2c 100644 --- a/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.cpp +++ b/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.cpp @@ -129,9 +129,13 @@ namespace Isis { p_operators.push_back(new InfixOperator(1, "&")); p_operators.push_back(new InfixOperator(1, "and")); + + p_operators.push_back(new InfixOperator(1, "&&")); p_operators.push_back(new InfixOperator(1, "|")); p_operators.push_back(new InfixOperator(1, "or")); + + p_operators.push_back(new InfixOperator(1, "||")); return; } diff --git a/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.h b/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.h index 83c2651721beb0b95b5414e0bde35e031f421174..f9f7c80a45dbb7354a87ac4049c45dda45e9a233 100644 --- a/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.h +++ b/isis/src/base/objs/InlineInfixToPostfix/InlineInfixToPostfix.h @@ -46,6 +46,7 @@ namespace Isis { * @history 2015-03-24 Jeannie Backer - Changed m_variables from a QVector * to QStringList * @history 2016-02-21 Kristin Berry - Added unitTest. + * @history 2017-01-09 Jesse Mapel - Added logical and, or operators. Fixes #4581. */ class InlineInfixToPostfix : public InfixToPostfix { diff --git a/isis/src/base/objs/Isis/Isis.h b/isis/src/base/objs/Isis/Isis.h index eb0cd853d063c5d6d7029259605b9457a5e92a29..df6889d3e23bc4f64fde2b2f67a5cfaf2bf9cce3 100644 --- a/isis/src/base/objs/Isis/Isis.h +++ b/isis/src/base/objs/Isis/Isis.h @@ -120,6 +120,10 @@ int main(int argc, char *argv[]) { Isis::Application::p_applicationForceGuiApp = true; #endif + // Add the plugin directory so QT looks at the Isis plugin dir + Isis::FileName qtpluginpath("$ISISROOT/3rdParty/plugins"); + QCoreApplication::addLibraryPath(qtpluginpath.expanded()); + Isis::Application *app = new Isis::Application(argc, argv); app->RegisterGuiHelpers(GuiHelpers()); int status = app->Run(APPLICATION); diff --git a/isis/src/base/objs/Kernels/Kernels.cpp b/isis/src/base/objs/Kernels/Kernels.cpp index 27dbd9588bdbe6269cfdde9e41df2ad7bdbaf1de..42bc2bb4beeee6b8133e75d0601da2d6d5452fb1 100644 --- a/isis/src/base/objs/Kernels/Kernels.cpp +++ b/isis/src/base/objs/Kernels/Kernels.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ + * $Id: Kernels.cpp 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/base/objs/Kernels/Kernels.h b/isis/src/base/objs/Kernels/Kernels.h index ffc70871c90a36fa96cb05d1efd91bb3ace0279a..58bb65426ce3ac553048dc0370439dd9224970e9 100644 --- a/isis/src/base/objs/Kernels/Kernels.h +++ b/isis/src/base/objs/Kernels/Kernels.h @@ -2,9 +2,9 @@ #define Kernels_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 6314 $ + * $Date: 2015-08-12 15:30:27 -0700 (Wed, 12 Aug 2015) $ + * $Id: Kernels.h 6314 2015-08-12 22:30:27Z jwbacker@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.cpp b/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.cpp new file mode 100644 index 0000000000000000000000000000000000000000..22d2edc1983eb7c359058b2ebcc858f7606e9b98 --- /dev/null +++ b/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.cpp @@ -0,0 +1,163 @@ +/** + * @file + * $Revision: 1.10 $ + * $Date: 2010/01/04 18:01:31 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include "PvlTranslationTable.h" + +#include "IException.h" +#include "IString.h" +#include "LabelTranslationManager.h" +#include "Message.h" +#include "Pvl.h" +#include "PvlContainer.h" +#include "PvlGroup.h" +#include "PvlKeyword.h" +#include "PvlObject.h" + +using namespace std; +namespace Isis { + + /** + * Constructs a default LabelTranslationManager. + */ + LabelTranslationManager::LabelTranslationManager() + : PvlTranslationTable() { + } + + + /** + * Constructs a LabelTranslationManager with a given translation table. + * + * @param transfile The translation table file. + */ + LabelTranslationManager::LabelTranslationManager(const QString &transFile) + : PvlTranslationTable() { + AddTable(transFile); + } + + + /** + * Constructs and initializes a LabelTranslationManager object + * + * @param transStrm A stream containing the tranlation table to be used to + * tranlate keywords in the input label. + */ + LabelTranslationManager::LabelTranslationManager(std::istream &transStrm) + : PvlTranslationTable() { + AddTable(transStrm); + } + + + /** + * Destroys the LabelTranslationManager object. + */ + LabelTranslationManager::~LabelTranslationManager() { + } + + + /** + * Automatically translate all the output names tagged as Auto in the + * translation table If a output name does not translate an error will be + * thrown by one of the support members. + * + * The results of the translations will be stored in the outputLabel PVL + * based on the OutputPosition keywords in the translation table. + * + * @param outputLabel The PVL to add the translated keywords to. + */ + void LabelTranslationManager::Auto(Pvl &outputLabel) { + // Attempt to translate every group in the translation table + for(int i = 0; i < TranslationTable().groups(); i++) { + PvlGroup &g = TranslationTable().group(i); + if(IsAuto(g.name())) { + try { + PvlContainer *con = CreateContainer(g.name(), outputLabel); + (*con) += DoTranslation(g.name()); + } + catch(IException &e) { + if(!IsOptional(g.name())) { + throw; + } + } + } + } + } + + + /** + * Creates all parent PVL containers for an output keyword. If any parent + * containers already exist then they will not be recreated. + * + * @param nName The name of the output keyword. The OutputPosition keyword + * in the translation group for nName will be used to determine + * which containers are made. + * @param pvl The PVL file to create the containers in. + * + * @return @b PvlContainer The immediate parent container for nName. + */ + PvlContainer *LabelTranslationManager::CreateContainer(const QString nName, + Pvl &pvl) { + + // Get the array of Objects/Groups from the OutputName keyword + PvlKeyword np = OutputPosition(nName); + + PvlObject *obj = &pvl; + + // Look at every pair in the output position + for(int c = 0; c < np.size(); c += 2) { + // If this pair is an object + if(np[c].toUpper() == "OBJECT") { + // If the object doesn't exist create it + if(!obj->hasObject(np[c+1])) { + obj->addObject(np[c+1]); + } + obj = &(obj->findObject(np[c+1])); + } + // If this pair is a group + else if(np[c].toUpper() == "GROUP") { + // If the group doesn't exist create it + if(!obj->hasGroup(np[c+1])) { + obj->addGroup(np[c+1]); + } + return (PvlContainer *) & (obj->findGroup(np[c+1])); + + } + } + + return (PvlContainer *) obj; + } + + + /** + * Translate the requested output name to output values using the input name + * and values or default value + * + * @param outputName The output name used to identify the input keyword to be + * translated. + * + * @return @b PvlKeyword A keyword containing the output name and output value. + * + * @TODO output units + */ + PvlKeyword LabelTranslationManager::DoTranslation(const QString outputName) { + PvlKeyword outputKeyword( outputName, Translate(outputName) ); + return outputKeyword; + } +} // end namespace isis diff --git a/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.h b/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.h new file mode 100644 index 0000000000000000000000000000000000000000..bf66c2947ced6ca6612307ca319b75dde5a22bdd --- /dev/null +++ b/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.h @@ -0,0 +1,78 @@ +#ifndef LabelTranslationManager_h +#define LabelTranslationManager_h +/** + * @file + * $Revision: 1.6 $ + * $Date: 2010/01/04 18:01:31 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include + +#include "FileName.h" +#include "PvlTokenizer.h" +#include "PvlTranslationTable.h" + +namespace Isis { + class Pvl; + class PvlContainer; + class PvlKeyword; + /** + * @brief Allows applications to translate simple text files + * + * This class allows the translation of text files which can be parsed by the + * Pvl class. + * + * @ingroup Parsing + * + * @author 2017-01-11 Jeannie Backer + * + * @internal + * @history 2017-01-11 Jeannie Backer - Original Version. Code moved out of + * PvlTranslationManager to make a generic parent + * class. Fixes #4584. + * @history 2017-01-20 Jesse Mapel - Updated documentation and unit test. Fixes #4584. + */ + class LabelTranslationManager : public PvlTranslationTable { + public: + LabelTranslationManager(); + + LabelTranslationManager(const QString &transFile); + + LabelTranslationManager(std::istream &transStrm); + + virtual ~LabelTranslationManager(); + + // Attempt to translate the requested output name to output value + // using the input name and value/default value + virtual QString Translate(QString nName, int findex = 0) = 0; + + // Translate all translation table groups which contain "Auto" + virtual void Auto(Pvl &outputLabel); + + protected: + + virtual PvlKeyword DoTranslation(const QString nName); + virtual PvlContainer *CreateContainer(const QString nName, Pvl &pvl); + }; +}; + +#endif + + diff --git a/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.truth b/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.truth new file mode 100644 index 0000000000000000000000000000000000000000..66e912f8f6f897e2749ef5111ef22da2b4a01217 --- /dev/null +++ b/isis/src/base/objs/LabelTranslationManager/LabelTranslationManager.truth @@ -0,0 +1,23 @@ +Testing LabelTranslationManager object + +Testing Translate method: + +Translating Extra: Test Input, Index 0 + +Testing Auto method: + +Object = IsisCube + Object = BandBin + BandName = "Test Input, Index 0" + End_Object + + Group = Dimensions + NumberOfLines = "Test Input, Index 0" + NumberOfBands = "Test Input, Index 0" + End_Group +End_Object + +Group = Mapping + CenterLongitude = "Test Input, Index 0" +End_Group +End diff --git a/isis/src/hayabusa/objs/AmicaCamera/Makefile b/isis/src/base/objs/LabelTranslationManager/Makefile similarity index 100% rename from isis/src/hayabusa/objs/AmicaCamera/Makefile rename to isis/src/base/objs/LabelTranslationManager/Makefile diff --git a/isis/src/base/objs/LabelTranslationManager/unitTest.cpp b/isis/src/base/objs/LabelTranslationManager/unitTest.cpp new file mode 100644 index 0000000000000000000000000000000000000000..1c8a5b291ff116174e56bab492086b4c0d288125 --- /dev/null +++ b/isis/src/base/objs/LabelTranslationManager/unitTest.cpp @@ -0,0 +1,124 @@ +#include +#include "LabelTranslationManager.h" +#include "Preference.h" +#include "IException.h" +#include "IString.h" +#include "Preference.h" + +using namespace Isis; +using namespace std; +/** + * Child class of LabelTranslationManager to implement pure virtual methods. + * + * @author 2017-01-11 Jeannie Backer + * + * @internal + * @history 2017-01-11 Jeannie Backer - Original Version. Fixes #4584. + */ +class TestTranslationManager : public LabelTranslationManager { + public: + + TestTranslationManager(const QString &transFile) : LabelTranslationManager() { + AddTable(transFile); + } + + TestTranslationManager(std::istream &transStrm) : LabelTranslationManager() { + AddTable(transStrm); + } + + ~TestTranslationManager() { + } + + virtual QString Translate(QString nName, int findex = 0) { + QString inputValue = "Test Input, Index " + toString(findex); + return PvlTranslationTable::Translate(nName, inputValue); + } +}; + +int main(void) { + Preference::Preferences(true); + + try { + + stringstream trnsStrm; + trnsStrm << "Group = NumberOfLines" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " OutputName = Lines" << endl; + trnsStrm << " OutputPosition = (\"Object\",\"IsisCube\","; + trnsStrm << "\"Group\",\"Dimensions\")" << endl; + trnsStrm << " InputPosition = (Image,Size)" << endl; + trnsStrm << " InputKey = NL" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = NumberOfBands" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Optional" << endl; + trnsStrm << " OutputName = Bands" << endl; + trnsStrm << " OutputPosition = (\"Object\",\"IsisCube\","; + trnsStrm << "\"Group\",\"Dimensions\")" << endl; + trnsStrm << " InputPosition = (Image,Size)" << endl; + trnsStrm << " InputKey = Nb" << endl; + trnsStrm << " InputDefault = 1" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = Bonus" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Optional" << endl; + trnsStrm << " InputPosition = (Image,Pixel)" << endl; + trnsStrm << " InputKey = Bonus" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = Extra" << endl; + trnsStrm << " Optional" << endl; + trnsStrm << " InputPosition = (Image,Bogus)" << endl; + trnsStrm << " InputKey = Extra" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = PixelResolution" << endl; + trnsStrm << " InputPosition = (Image,Pixel)" << endl; + trnsStrm << " InputKey = Resolution" << endl; + trnsStrm << " InputDefault = 1" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = BandName" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " OutputName = Band" << endl; + trnsStrm << " OutputPosition = (\"Object\",\"IsisCube\","; + trnsStrm << "\"Object\",\"BandBin\")" << endl; + trnsStrm << " InputPosition = (Image,BandInfo)" << endl; + trnsStrm << " InputKey = Band" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = CenterLongitude" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " OutputPosition = (\"Group\",\"Mapping\")" << endl; + trnsStrm << " OutputName = CenterLongitude" << endl; + trnsStrm << " InputPosition = IMAGE_MAP_PROJECTION" << endl; + trnsStrm << " InputPosition = (QUBE,IMAGE_MAP_PROJECTION)" << endl; + trnsStrm << " InputPosition = (SPECTRAL_QUBE,IMAGE_MAP_PROJECTION)" << endl; + trnsStrm << " InputKey = CENTER_LONGITUDE" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + + trnsStrm << "End" << endl; + + TestTranslationManager transMgr(trnsStrm); + + cout << "Testing LabelTranslationManager object" << endl; + + cout << endl << "Testing Translate method:" << endl; + cout << endl << "Translating Extra: "; + cout << transMgr.Translate("Extra") << endl; + + cout << endl << "Testing Auto method:" << endl; + Pvl translatedLabel; + transMgr.Auto(translatedLabel); + cout << endl << translatedLabel << endl; + + } + catch(IException &e) { + e.print(); + } + + return 0; +} diff --git a/isis/src/base/objs/Latitude/Latitude.cpp b/isis/src/base/objs/Latitude/Latitude.cpp index 8621a1d4f480d164d32e1fe8f9fccd838484d722..475f253e39604aa7004986a436c655684915869e 100644 --- a/isis/src/base/objs/Latitude/Latitude.cpp +++ b/isis/src/base/objs/Latitude/Latitude.cpp @@ -407,6 +407,31 @@ namespace Isis { } + /** + * Get the error checking status. This indicates if the Latitude object will + * throw an error when set to an angle less than -90 degrees or greater than + * 90 degrees. + * + * @return @b ErrorChecking The error checking status. + */ + Latitude::ErrorChecking Latitude::errorChecking() const { + return m_errors; + } + + + /** + * Set the error checking status. If set to ThrowAllErrors, then an exception + * will be thrown if the Latitude object is set to an angle less than -90 + * degrees or greater than 90 degrees. If set to AllowPastPole, then no + * exception will be thrown. + * + * @param error The new error checking status. + */ + void Latitude::setErrorChecking(ErrorChecking errors) { + m_errors = errors; + } + + /** * Checks if this latitude value is within the given range. Defines the * range as the change from the minimum latitude to the maximum latitude (an diff --git a/isis/src/base/objs/Latitude/Latitude.h b/isis/src/base/objs/Latitude/Latitude.h index 49fe58af7825836692e261ea641073d62fb62786..96fcaf35f68ced9289d2e46800ef5dab8a3dca77 100644 --- a/isis/src/base/objs/Latitude/Latitude.h +++ b/isis/src/base/objs/Latitude/Latitude.h @@ -55,6 +55,8 @@ namespace Isis { * documentation for all exceptions thrown. Fixes #3907 * @history 2016-09-29 Jeannie Backer - Changed strings in error message to use Angle::toString * instead of the Isis::toString(double) method. + * @history 2017-04-10 Jesse Mapel - Added an accessor and mutator for ErrorChecking member. + * Fixes #4766. */ class Latitude : public Angle { public: @@ -144,6 +146,9 @@ namespace Isis { void setPlanetographic(double latitude, Angle::Units units = Angle::Radians); + ErrorChecking errorChecking() const; + void setErrorChecking(ErrorChecking errors); + bool inRange(Latitude min, Latitude max) const; Latitude& operator=(const Latitude & latitudeToCopy); diff --git a/isis/src/base/objs/Mollweide/Mollweide.cpp b/isis/src/base/objs/Mollweide/Mollweide.cpp index c33dbf477e7c889fe535b50132f111c420baf290..6c66906cce546fbeed256a1570f422660c21a5f5 100644 --- a/isis/src/base/objs/Mollweide/Mollweide.cpp +++ b/isis/src/base/objs/Mollweide/Mollweide.cpp @@ -176,8 +176,10 @@ namespace Isis { /** - * @description This method is used to set the latitude/longitude (assumed to be of the - * correct LatitudeType, LongitudeDirection, and LongitudeDomain. The Set + * @brief Set lat/lon and attempt to calculate x/y values + * + * This method is used to set the latitude/longitude (assumed to be of the + * correct LatitudeType, LongitudeDirection, and LongitudeDomain). The Set * forces an attempted calculation of the projection X/Y values. This may or * may not be successful and a status is returned as such. * @@ -284,7 +286,9 @@ namespace Isis { /** - * @description This method is used to determine the x/y range which completely covers the + * @brief Find x/y range from lat/lon range + * + * This method is used to determine the x/y range which completely covers the * area of interest specified by the lat/lon range. The latitude/longitude * range may be obtained from the labels. The purpose of this method is to * return the x/y range so it can be used to compute how large a map may need diff --git a/isis/src/base/objs/Mollweide/Mollweide.h b/isis/src/base/objs/Mollweide/Mollweide.h index 5457d26148542efd2721a7111373a0d2163496b0..71e72c57701f244afe4e23a03fb2760fd3886a44 100644 --- a/isis/src/base/objs/Mollweide/Mollweide.h +++ b/isis/src/base/objs/Mollweide/Mollweide.h @@ -28,7 +28,7 @@ namespace Isis { class Pvl; class PvlGroup; /** - * @description Mollweide Map Projection + * @brief Mollweide Map Projection * * This class provides methods for the forward and inverse equations of a * Mollweide Equal-Area map projection (for a sphere). diff --git a/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.h b/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.h index 613768e6a05ae372e66b9f26be828ca00c592590..22d8ced40201b7a417d1cff975535b05d8500922 100755 --- a/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.h +++ b/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.h @@ -35,95 +35,98 @@ namespace Isis { class Latitude; class Longitude; class SurfacePoint; - + /** - * @brief Implementation interface API for NAIF's DSK plate model - * - * This class implements a thread safe version of the NAIF DSK plate model API. - * This version is coded using the "alpha" version of the DSK library toolkit as - * release in 2010. - * - * Part of the design of this implementation is the abilty to efficiently clone - * the object so that it is suitable for use in a threaded environment. Note - * that files is only closed when the last reference is released. - * - * It is recommended that a shared or scoped pointer that provides the necessary - * elements for efficient safe thread computing. - * - * @author 2013-12-05 Kris Becker - * @internal - * @history 2013-12-05 Kris Becker Original Version + * @brief Implementation interface API for NAIF's DSK plate model + * + * This class implements a thread safe version of the NAIF DSK plate model API. + * This version is coded using the "alpha" version of the DSK library toolkit as + * release in 2010. + * + * Part of the design of this implementation is the abilty to efficiently clone + * the object so that it is suitable for use in a threaded environment. Note + * that files is only closed when the last reference is released. + * + * It is recommended that a shared or scoped pointer that provides the necessary + * elements for efficient safe thread computing. + * + * @author 2013-12-05 Kris Becker + * @internal + * @history 2013-12-05 Kris Becker Original Version * @history 2015-03-08 Jeannie Backer - Added documentation and test. Added class to ISIS trunk. * References #2035 + * @history 2017-05-19 Christopher Combs - Modified unitTest.cpp: added ReportError method to + * truncate paths before data directory. Allows test to pass when not + * using the default data area. Fixes #4738. */ class NaifDskPlateModel { - + public: NaifDskPlateModel(); NaifDskPlateModel(const QString &dskfile); virtual ~NaifDskPlateModel(); - + bool isValid() const; QString filename() const; - + int size() const; SpiceInt numberPlates() const; SpiceInt numberVertices() const; - + SurfacePoint *point(const Latitude &lat, const Longitude &lon) const; Intercept *intercept(const NaifVertex &vertex, const NaifVector &raydir) const; // Intercept *intercept(const SurfacePoint &pnt) const; - + // Lower level I/O bool isPlateIdValid(const SpiceInt plateid) const; - SpiceInt plateIdOfIntercept(const NaifVertex &vertex, + SpiceInt plateIdOfIntercept(const NaifVertex &vertex, const NaifVector &raydir, NaifVertex &xpoint) const; NaifTriangle plate(SpiceInt plateid) const; - + NaifDskPlateModel *clone() const; - + private: - /** - * Enumeration to indicate whether to throw an exception if an error - * occurs. - */ + /** + * Enumeration to indicate whether to throw an exception if an error + * occurs. + */ enum ErrAction { Throw, //!< Throw an exception if an error occurs. NoThrow //!< Do not throw an exception if an error occurs. }; - + /** - * @brief NAIF DSK file descriptor - * - * This local class is designed to make the plate model object copyable, thread - * safe and inherently extensible. The file remains open as long as the - * original NaifDskDescriptor has a reference. - * - * @author 2013-12-05 Kris Becker - * @internal - * @history 2013-12-05 Kris Becker Original Version + * @brief NAIF DSK file descriptor + * + * This local class is designed to make the plate model object copyable, thread + * safe and inherently extensible. The file remains open as long as the + * original NaifDskDescriptor has a reference. + * + * @author 2013-12-05 Kris Becker + * @internal + * @history 2013-12-05 Kris Becker Original Version */ class NaifDskDescriptor { public: NaifDskDescriptor(); ~NaifDskDescriptor(); - + QString m_dskfile; //!< The NAIF DSK file representing this plate's shape model. SpiceInt m_handle; //!< The DAS file handle of the DSK file. - SpiceDLADescr m_dladsc; /**< The DLA descriptor of the DSK segment representing the + SpiceDLADescr m_dladsc; /**< The DLA descriptor of the DSK segment representing the target surface.*/ SpiceDSKDescr m_dskdsc; //!< The DSK descriptor. SpiceInt m_plates; //!< Number of Plates in the model. SpiceInt m_vertices; //!< Number of vertices defining the plate. QMutex m_mutex; //!< Mutex for thread saftey }; - + // Shared file descriptor supports copying of object typedef QSharedPointer SharedNaifDskDescriptor; - SharedNaifDskDescriptor m_dsk; //!< Shared pointer to the NaifDskDescriptor for this plate. - + SharedNaifDskDescriptor m_dsk; //!< Shared pointer to the NaifDskDescriptor for this plate. + NaifDskDescriptor *openDSK(const QString &dskfile); - bool verify(const bool &test, const QString &errmsg, + bool verify(const bool &test, const QString &errmsg, const ErrAction &action = Throw) const; SurfacePoint *makePoint(const NaifVertex &v) const; }; @@ -131,4 +134,3 @@ namespace Isis { } // namespace Isis #endif - diff --git a/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.truth b/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.truth index 220ec81be458419686ca31e9b55cdb94a952e42c..6cf306835abd8986e76af678fb0d844882038c27 100644 --- a/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.truth +++ b/isis/src/base/objs/NaifDskPlateModel/NaifDskPlateModel.truth @@ -53,4 +53,5 @@ Thrown from openDSK(): Open DSK file that doesn't exist. **USER ERROR** NAIF DSK file [./junk.bds] does not exist. ~NaifDskDescriptor(): Unknown NAIF error has occured. -**ERROR** An unknown NAIF error has been encountered. The short explanation provided by NAIF is [SPICE(FILARCHMISMATCH)]. The Naif error is [A request to load the DAF file, /usgs/cpkgs/isis3/data/base/kernels/spk/de405.bsp, has been made by the DAS system. This operation is not permitted.]. +"**ERROR** An unknown NAIF error has been encountered. The short explanation provided by NAIF is [SPICE(FILARCHMISMATCH)]. The Naif error is [A request to load the DAF file, data/base/kernels/spk/de405.bsp, has been made by the DAS system. This operation is not permitted.]." + diff --git a/isis/src/base/objs/NaifDskPlateModel/unitTest.cpp b/isis/src/base/objs/NaifDskPlateModel/unitTest.cpp index fba5d2958659fd65917576e087a5125942f5e97e..2d35b0339ab704aec55a1fdc2eb3f3a1e556ba61 100755 --- a/isis/src/base/objs/NaifDskPlateModel/unitTest.cpp +++ b/isis/src/base/objs/NaifDskPlateModel/unitTest.cpp @@ -29,20 +29,31 @@ #include "NaifDskPlateModel.h" #include "Preference.h" #include "SurfacePoint.h" +#include "QRegularExpression" using namespace Isis; -/** - * - * @internal +/** + * + * @internal * @history 2015-02-25 Jeannie Backer - Original version. * Code coverage: 91.667% scope, 95.960% line, and 100% function. * Unable to create circumstances for missing coverage. - * + * * @todo - Test coverage - Constructor error throw - get dsk file openDSK returns NULL * @todo - Test coverage - openDSK error throw - get dsk file with no segments * + * + * @history 2017-05-19 Christopher Combs - Added ReportError method to remove paths that would + * cause the test to fail when not using the standard data area. + * Fixes #4738. + * */ + + void ReportError(QString err) { + qDebug() << err.replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data") << endl; + } + int main(int argc, char *argv[]) { try { Preference::Preferences(true); @@ -90,7 +101,7 @@ int main(int argc, char *argv[]) { qDebug() << "Ray Dir: " << rayDir; qDebug() << "Observer: " << obsPos; qDebug() << "Intercept is null? " << toString(intercept == NULL); - qDebug() << "intercept plateID? " + qDebug() << "intercept plateID? " << naifPlateModelFromDSK.plateIdOfIntercept(obsPos, rayDir, xpoint); // Find obs/rayDir with valid intercept @@ -108,14 +119,14 @@ int main(int argc, char *argv[]) { xpoint[1] = xp.GetY().meters(); xpoint[2] = xp.GetZ().meters(); qDebug() << "intercept surface point (location) = " << xpoint << " meters"; - qDebug() << "intercept plateID = " + qDebug() << "intercept plateID = " << naifPlateModelFromDSK.plateIdOfIntercept(obsPos, rayDir, xpoint); qDebug() << ""; qDebug() << "Get plate info from id:"; qDebug() << "Is plate ID = 0 valid? " << naifPlateModelFromDSK.isPlateIdValid(0); qDebug() << "Is plate ID = 1 valid? " << naifPlateModelFromDSK.isPlateIdValid(1); - qDebug() << "Is plate ID = 1 valid for invalid NaifDskPlateModel? " + qDebug() << "Is plate ID = 1 valid for invalid NaifDskPlateModel? " << naifPlateModel.isPlateIdValid(1); qDebug() << "Triangular Plate for ID = 1:"; qDebug() << naifPlateModelFromDSK.plate(1); @@ -136,7 +147,7 @@ int main(int argc, char *argv[]) { // try { // FileName junkFile(""); // NaifDskPlateModel naifPlateModelFromDSK(junkFile.expanded()); -// } +// } // catch (IException &e) { // e.print(); // } @@ -146,7 +157,7 @@ int main(int argc, char *argv[]) { NaifVertex badObs(2); badObs[0] = 0.0; badObs[1] = 0.0; naifPlateModelFromDSK.plateIdOfIntercept(badObs, rayDir, xpoint); - } + } catch (IException &e) { e.print(); } @@ -154,7 +165,7 @@ int main(int argc, char *argv[]) { qDebug() << "Thrown from plate(): Get plate from invalid plate ID."; try { naifPlateModelFromDSK.plate(0); - } + } catch (IException &e) { e.print(); } @@ -163,7 +174,7 @@ int main(int argc, char *argv[]) { try { FileName junkFile("./junk.bds"); NaifDskPlateModel naifPlateModelFromDSK(junkFile.expanded()); - } + } catch (IException &e) { e.print(); } @@ -172,7 +183,7 @@ int main(int argc, char *argv[]) { // try { // FileName noSegmentsFile(""); // NaifDskPlateModel junkmodel(noSegmentsFile.expanded()); -// } +// } // catch (IException &e) { // e.print(); // } @@ -180,12 +191,12 @@ int main(int argc, char *argv[]) { qDebug() << "~NaifDskDescriptor(): Unknown NAIF error has occured."; try { FileName junkFile("$base/kernels/spk/de405.bsp"); - NaifDskPlateModel naifPlateModelFromDSK(junkFile.expanded()); - } + NaifDskPlateModel naifPlateModelFromDSK(junkFile.toString()); + } catch (IException &e) { - e.print(); + ReportError(e.toString()); } - + } catch (IException &e) { qDebug() << ""; diff --git a/isis/src/base/objs/ObservationNumberList/ObservationNumberList.h b/isis/src/base/objs/ObservationNumberList/ObservationNumberList.h index 048e85dca92c1fb10fb86e1a8df3aca64fdf9897..798b42e23c666ebc892ccbb0ca17c63f9f3e0b8f 100644 --- a/isis/src/base/objs/ObservationNumberList/ObservationNumberList.h +++ b/isis/src/base/objs/ObservationNumberList/ObservationNumberList.h @@ -36,7 +36,7 @@ namespace Isis { /** * @brief Create a list of observation numbers from a file or serial number list * - * @description This class allows for creating observation numbers from a provided file or + * This class allows for creating observation numbers from a provided file or * and existing non-empty SerialNumberList. Internally, it will map the observation numbers * that are created to the corresponding serial number for a given observation. * diff --git a/isis/src/base/objs/OriginalXmlLabel/Makefile b/isis/src/base/objs/OriginalXmlLabel/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..f122bc88227c5c7ebd108dea5d339d1d2e074d82 --- /dev/null +++ b/isis/src/base/objs/OriginalXmlLabel/Makefile @@ -0,0 +1,7 @@ +ifeq ($(ISISROOT), $(BLANK)) +.SILENT: +error: + echo "Please set ISISROOT"; +else + include $(ISISROOT)/make/isismake.objs +endif \ No newline at end of file diff --git a/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.cpp b/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.cpp new file mode 100644 index 0000000000000000000000000000000000000000..c466003682c71aa7eed5a88dd719477cb2fec949 --- /dev/null +++ b/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.cpp @@ -0,0 +1,160 @@ +/** + * @file + * $Revision: 1.5 $ + * $Date: 2010/05/14 19:20:28 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are + * public domain. See individual third-party library and package descriptions + * for intellectual property information, user agreements, and related + * information. + * + * Although Isis has been used by the USGS, no warranty, expressed or + * implied, is made by the USGS as to the accuracy and functioning of such + * software and related material nor shall the fact of distribution + * constitute any such warranty, and no responsibility is assumed by the + * USGS in connection therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html + * in a browser or see the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include +#include +#include + +#include +#include + +#include "OriginalXmlLabel.h" +#include "Application.h" +#include "PvlObject.h" + +using namespace std; +namespace Isis { + /** + * Constructors a default OriginalXmlLabel with an empty label. + */ + OriginalXmlLabel::OriginalXmlLabel() : Isis::Blob("IsisCube", "OriginalXmlLabel") { + p_blobPvl += Isis::PvlKeyword("ByteOrder", "NULL"); + } + + + /** + * Constructs an OriginalXmlLabel from a cube label file. + * + * @param file Xml file to read labels from + */ + OriginalXmlLabel::OriginalXmlLabel(const QString &file) : + Isis::Blob("IsisCube", "OriginalXmlLabel") { + p_blobPvl += Isis::PvlKeyword("ByteOrder", "NULL"); + Blob::Read(file); + } + + + /** + * Destructor + */ + OriginalXmlLabel::~OriginalXmlLabel() { + } + + + /** + * Read the original label from an Xml file. + * + * @param FileName The Xml file containing the original label. + * + * @throws IException::Io "Could not open label file." + * @throws IException::Unknown "XML read/parse error in file." + */ + void OriginalXmlLabel::readFromXmlFile(const FileName &xmlFileName) { + QFile xmlFile(xmlFileName.expanded()); + if ( !xmlFile.open(QIODevice::ReadOnly) ) { + QString msg = "Could not open label file [" + xmlFileName.expanded() + + "]."; + throw IException(IException::Io, msg, _FILEINFO_); + } + + QString errmsg; + int errline, errcol; + if ( !m_originalLabel.setContent(&xmlFile, false, &errmsg, &errline, &errcol) ) { + xmlFile.close(); + QString msg = "XML read/parse error in file [" + xmlFileName.expanded() + + "] at line [" + toString(errline) + "], column [" + toString(errcol) + + "], message: " + errmsg; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + + xmlFile.close(); + } + + + /** + * Read the xml file data from an input stream. + * + * @param stream The input stream to read from. + * + * @throws IException::Unknown "XML read/parse error when parsing original label." + * + * @see Blob::Read(const Pvl &pvl, std::istream &is) + */ + void OriginalXmlLabel::ReadData(std::istream &stream) { + // Use Blob's ReadData to fill p_buffer + Blob::ReadData(stream); + + // Setup variables for error reproting in QT's xml parser + QString errorMessage; + int errorLine; + int errorColumn; + + // Attempt to use QT's xml parser to internalize the label + if ( !m_originalLabel.setContent( QByteArray(p_buffer, p_nbytes) ) ) { + QString msg = "XML read/parse error when parsing original label. " + "Error at line [" + toString(errorLine) + + "], column [" + toString(errorColumn) + + "]. Error message: " + errorMessage; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + } + + + /** + * Prepare to write the label out. + * + * @see Blob::Write + */ + void OriginalXmlLabel::WriteInit() { + p_nbytes = m_originalLabel.toByteArray(0).size(); + + if (Isis::IsLsb()) { + p_blobPvl["ByteOrder"] = Isis::ByteOrderName(Isis::Lsb); + } + else { + p_blobPvl["ByteOrder"] = Isis::ByteOrderName(Isis::Msb); + } + } + + + /** + * Write the label out to a stream. + * + * @param os The stream to write the label out to. + * + * @see Blob::Write + */ + void OriginalXmlLabel::WriteData(std::fstream &os) { + QByteArray labelByteArray = m_originalLabel.toByteArray(0); + os.write( labelByteArray.data(), labelByteArray.size() ); + } + + + /** + * Returns the original Xml label. + * + * @return @b QDomDocument The parsed original label + */ + const QDomDocument &OriginalXmlLabel::ReturnLabels() const { + return m_originalLabel; + } +} diff --git a/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.h b/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.h new file mode 100644 index 0000000000000000000000000000000000000000..878d873b41dadd55a8f8ea2704579102a8ca7ffe --- /dev/null +++ b/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.h @@ -0,0 +1,68 @@ +#ifndef OriginalXmlLabel_h +#define OriginalXmlLabel_h + +/** + * @file + * $Revision: 1.5 $ + * $Date: 2010/05/14 19:20:28 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are + * public domain. See individual third-party library and package descriptions + * for intellectual property information, user agreements, and related + * information. + * + * Although Isis has been used by the USGS, no warranty, expressed or + * implied, is made by the USGS as to the accuracy and functioning of such + * software and related material nor shall the fact of distribution + * constitute any such warranty, and no responsibility is assumed by the + * USGS in connection therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html + * in a browser or see the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include + +#include "Blob.h" +#include "FileName.h" + +namespace Isis { + /** + * @brief Read and store original Xml labels. + * + * This class provides a means to read and store the Xml labels from the + * original source. + * + * @ingroup LowLevelCubeIO + * + * @author 2017-01-30 Jesse Mapel + * + * @internal + * @history 2017-01-30 Jesse Mapel - Original version, adapted from + * OriginalLabel. Fixes #4584. + * + */ + class OriginalXmlLabel : public Isis::Blob { + public: + OriginalXmlLabel(); + OriginalXmlLabel(const QString &file); + ~OriginalXmlLabel(); + + void readFromXmlFile(const FileName &xmlFileName); + const QDomDocument &ReturnLabels() const; + + protected: + void ReadData(std::istream &stream); + void WriteData(std::fstream &os); + void WriteInit(); + + private: + QDomDocument m_originalLabel; //!< Original Xml Label. + }; +}; + +#endif + diff --git a/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.truth b/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.truth new file mode 100644 index 0000000000000000000000000000000000000000..06aec0c5735da30d5017ed2cef7c180239e2a8b6 --- /dev/null +++ b/isis/src/base/objs/OriginalXmlLabel/OriginalXmlLabel.truth @@ -0,0 +1,7 @@ +Ingesting label file into check object. + +Ingesting label file into OriginalXmlLabel object: + +Testing accessor: + Xml is the same?: Yes. + diff --git a/isis/src/base/objs/OriginalXmlLabel/unitTest.cpp b/isis/src/base/objs/OriginalXmlLabel/unitTest.cpp new file mode 100644 index 0000000000000000000000000000000000000000..15758fab19a02e6fdf2bad89fcbb54631034b0cf --- /dev/null +++ b/isis/src/base/objs/OriginalXmlLabel/unitTest.cpp @@ -0,0 +1,79 @@ +/** + * Unit Test for OriginalXmlLabel class. + */ + + +#include +#include + +#include +#include + +#include "Blob.h" +#include "Cube.h" +#include "FileName.h" +#include "IException.h" +#include "OriginalXmlLabel.h" +#include "Preference.h" +#include "Pvl.h" + +using namespace Isis; +using namespace std; + +QDomDocument parseXmlFile(const FileName &xmlFileName); + +int main(int argc, char *argv[]) { + + Isis::Preference::Preferences(true); + + OriginalXmlLabel testLabel; + FileName labelFileName("$base/testData/xmlTestLabel.xml"); + + cout << "Ingesting label file into check object." << endl << endl; + QDomDocument checkDoc = parseXmlFile(labelFileName); + + cout << "Ingesting label file into OriginalXmlLabel object:" << endl << endl; + testLabel.readFromXmlFile(labelFileName); + + cout << "Testing accessor:" << endl; + cout << " Xml is the same?: "; + if ( testLabel.ReturnLabels().toString() == checkDoc.toString() ) { + cout << "Yes." << endl << endl; + } + else { + cout << "No." << endl << endl; + } +} + +/** + * Read the original label from an Xml file. + * + * @param FileName The Xml file containing the original label. + * + * @throws IException::Io "Could not open label file." + * @throws IException::Unknown "XML read/parse error in file." + */ +QDomDocument parseXmlFile(const FileName &xmlFileName) { + QDomDocument parsedXmlFile; + + QFile xmlFile(xmlFileName.expanded()); + if ( !xmlFile.open(QIODevice::ReadOnly) ) { + QString msg = "Could not open label file [" + xmlFileName.expanded() + + "]."; + throw IException(IException::Io, msg, _FILEINFO_); + } + + QString errmsg; + int errline, errcol; + if ( !parsedXmlFile.setContent(&xmlFile, false, &errmsg, &errline, &errcol) ) { + xmlFile.close(); + QString msg = "XML read/parse error in file [" + xmlFileName.expanded() + + "] at line [" + toString(errline) + "], column [" + toString(errcol) + + "], message: " + errmsg; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + + xmlFile.close(); + + return parsedXmlFile; +} diff --git a/isis/src/base/objs/PointPerspective/PointPerspective.cpp b/isis/src/base/objs/PointPerspective/PointPerspective.cpp index 5965fc38459f6c92c3b5d0f7de4bff4abc838bb8..39f0d4429dc6c3c58a15c8e4b3b70dc7c23708f9 100644 --- a/isis/src/base/objs/PointPerspective/PointPerspective.cpp +++ b/isis/src/base/objs/PointPerspective/PointPerspective.cpp @@ -22,17 +22,19 @@ #include "PointPerspective.h" -#include #include +#include +#include #include "Constants.h" #include "IException.h" -#include "TProjection.h" #include "Pvl.h" #include "PvlGroup.h" #include "PvlKeyword.h" +#include "TProjection.h" using namespace std; + namespace Isis { /** * Constructs an PointPerspective object @@ -90,8 +92,8 @@ namespace Isis { // the center of planet), and calculate P m_distance = mapGroup["Distance"]; m_distance *= 1000.; - m_P = 1.0 + (m_distance / m_equatorialRadius); + m_P = 1.0 + (m_distance / m_equatorialRadius); } catch(IException &e) { QString message = "Invalid label group [Mapping]"; @@ -155,6 +157,14 @@ namespace Isis { * correct LatitudeType, LongitudeDirection, and LongitudeDomain. The Set * forces an attempted calculation of the projection X/Y values. This may or * may not be successful and a status is returned as such. + * @internal + * @history 2016-11-22 Tyler Wilson The call to SetGround now fails + * if the x,y values fall outside of the circle + * with center at (centerLat,centerLong) and + * radius = R/sqrt(P+1)/(P-1). See: + * P.173 of Map Projections - A Working Manual + * USGS Professional Paper 1395, by John P. Snyer. + * for details. Fixes #3879. * * @param lat Latitude value to project * @@ -164,6 +174,8 @@ namespace Isis { */ bool PointPerspective::SetGround(const double lat, const double lon) { // Convert longitude to radians & clean up + double projectionRadius = m_equatorialRadius*sqrt((m_P+1)/(m_P+1)); + m_longitude = lon; double lonRadians = lon * PI / 180.0; if (m_longitudeDirection == PositiveWest) lonRadians *= -1.0; @@ -186,15 +198,23 @@ namespace Isis { m_good = false; return m_good; } - // Compute the coordinates double ksp = (m_P - 1.0) / (m_P - g); + double x = m_equatorialRadius * ksp * cosphi * sin(deltaLon); double y = m_equatorialRadius * ksp * (m_cosph0 * sinphi - m_sinph0 * cosphi * coslon); - SetComputedXY(x, y); - m_good = true; - return m_good; + + if (sqrt(x*x+y*y)> projectionRadius) { + + m_good =false; + + return m_good; + } + + SetComputedXY(x,y); + m_good = true; + return m_good; } /** @@ -211,6 +231,8 @@ namespace Isis { * @return bool */ bool PointPerspective::SetCoordinate(const double x, const double y) { + + // Save the coordinate SetXY(x, y); @@ -278,6 +300,7 @@ namespace Isis { // Cleanup the latitude if (IsPlanetocentric()) m_latitude = ToPlanetocentric(m_latitude); + m_good = true; return m_good; } @@ -290,6 +313,15 @@ namespace Isis { * to be. For example, how big a piece of paper is needed or how large of an * image needs to be created. The method may fail as indicated by its return * value. + * @internal + * @history 2016-11-22 Tyler Wilson Deleted the original XYRange() function + * and replaced it with a version whose details can be found on P. 173 + * of Map Projections - A Working Manual, USGS Professional Paper 1395 + * by John P. Snyder. Basically the limit of the map is a circle + * of radius = projectionRadius centered at the center of the projection. + * Fixes #3879. + * + * * * @param minX Minimum x projection coordinate which covers the latitude * longitude range specified in the labels. @@ -306,55 +338,17 @@ namespace Isis { * @return bool */ bool PointPerspective::XYRange(double &minX, double &maxX, double &minY, double &maxY) { - double lat, lon; - - // Check the corners of the lat/lon range - XYRangeCheck(m_minimumLatitude, m_minimumLongitude); - XYRangeCheck(m_maximumLatitude, m_minimumLongitude); - XYRangeCheck(m_minimumLatitude, m_maximumLongitude); - XYRangeCheck(m_maximumLatitude, m_maximumLongitude); - // Walk top and bottom edges - for (lat = m_minimumLatitude; lat <= m_maximumLatitude; lat += 0.01) { - lon = m_minimumLongitude; - XYRangeCheck(lat, lon); - - lon = m_maximumLongitude; - XYRangeCheck(lat, lon); - } + double projectionRadius = m_equatorialRadius*sqrt((m_P-1.0)/(m_P+1.0)); - // Walk left and right edges - for (lon = m_minimumLongitude; lon <= m_maximumLongitude; lon += 0.01) { - lat = m_minimumLatitude; - XYRangeCheck(lat, lon); + SetCoordinate(0.0,0.0); + minX = XCoord() - projectionRadius; + maxX = XCoord() + projectionRadius; + minY = YCoord() - projectionRadius; + maxY = YCoord() + projectionRadius; - lat = m_maximumLatitude; - XYRangeCheck(lat, lon); - } - - // Walk the limb - for (double angle = 0.0; angle <= 360.0; angle += 0.01) { - double x = m_equatorialRadius * cos(angle * PI / 180.0); - double y = m_equatorialRadius * sin(angle * PI / 180.0); - if (SetCoordinate(x, y) == 0) { - if (m_latitude > m_maximumLatitude) continue; - if (m_longitude > m_maximumLongitude) continue; - if (m_latitude < m_minimumLatitude) continue; - if (m_longitude < m_minimumLongitude) continue; - XYRangeCheck(m_latitude, m_longitude); - } - } - - // Make sure everything is ordered - if (m_minimumX >= m_maximumX) return false; - if (m_minimumY >= m_maximumY) return false; - - // Return X/Y min/maxs - minX = m_minimumX; - maxX = m_maximumX; - minY = m_minimumY; - maxY = m_maximumY; return true; + } diff --git a/isis/src/base/objs/PointPerspective/PointPerspective.h b/isis/src/base/objs/PointPerspective/PointPerspective.h index fd3a88f8ea8a7848477208017caf6bccfb96a4b6..a102712c4e153081000726a4fce04aae5b78816c 100644 --- a/isis/src/base/objs/PointPerspective/PointPerspective.h +++ b/isis/src/base/objs/PointPerspective/PointPerspective.h @@ -58,6 +58,10 @@ namespace Isis { * References #775. * @history 2016-08-28 Kelvin Rodriguez - Removed useless var=var lines causing warnigns in * clang. Part of Porting to OSX 10.11 + * @history 2016-11-22 Tyler Wilson - Modified the XYRange() and SetGround() functions to eliminate + * clipping in the output map. Also added new tests to + * the unit test to excercise the forward/reverse projection + * equations. Fixes #3879. */ class PointPerspective : public TProjection { public: diff --git a/isis/src/base/objs/PointPerspective/PointPerspective.truth b/isis/src/base/objs/PointPerspective/PointPerspective.truth index f4ea3e4ee96139f8c7a3e2e8bda8da022194e311..6de58456d13ed1a33adf0c55706c6dfe9ad52b00 100644 --- a/isis/src/base/objs/PointPerspective/PointPerspective.truth +++ b/isis/src/base/objs/PointPerspective/PointPerspective.truth @@ -13,14 +13,14 @@ Test missing distance keyword... **ERROR** PVL Keyword [Distance] does not exist in [Group = Mapping]. Test TrueScaleLatitude method... -TrueScaleLatitude = 39 +TrueScaleLatitude = 0 Test SetGround method ... Setting ground to (41,-74) Latitude: 41 Longitude: -74 -XCoord: 251640.079 -YCoord: 226487.551 +XCoord: -0.635866687 +YCoord: 0.575026011 Test SetCoordinate method ... Setting coordinate to (251640.079, 226487.551) @@ -30,10 +30,10 @@ XCoord: 251640.079 YCoord: 226487.551 Test XYRange method ... -Minimum X: -5874155.27 -Maximum X: 3.88277327e-10 -Minimum Y: 2252833.7 -Maximum Y: 5006411.82 +Minimum X: -0.858797303 +Maximum X: 0.858797303 +Minimum Y: -0.858797303 +Maximum Y: 0.858797303 Test Name and comparision method ... Name: PointPerspective @@ -41,57 +41,148 @@ operator== 1 Test default computation ... Group = Mapping - EquatorialRadius = 6371000.0 - PolarRadius = 6371000.0 + EquatorialRadius = 1.0 + PolarRadius = 1.0 LatitudeType = Planetographic LongitudeDirection = PositiveEast LongitudeDomain = 180 - MinimumLatitude = -90.0 - MaximumLatitude = 90.0 - MinimumLongitude = -180.0 - MaximumLongitude = 180.0 + MinimumLatitude = 0.0 + MaximumLatitude = 80.0 + MinimumLongitude = 0.0 + MaximumLongitude = 80.0 ProjectionName = PointPerspective - Distance = 500000.0 - CenterLongitude = 0.0 - CenterLatitude = 0.0 + Distance = 0.00562 + CenterLongitude = 40.0 + CenterLatitude = 40.0 End_Group End Testing Mapping() methods ... +This test outputs Table 27 (p.174) of Map Projections - A Working Manual +USGS Professional Paper 1395 +Author: John P. Snyder + Mapping() = Group = Mapping ProjectionName = PointPerspective - EquatorialRadius = 6371000.0 - PolarRadius = 6371000.0 + EquatorialRadius = 1.0 + PolarRadius = 1.0 LatitudeType = Planetographic LongitudeDirection = PositiveEast LongitudeDomain = 180 - MinimumLatitude = -90.0 - MaximumLatitude = 90.0 - MinimumLongitude = -180.0 - MaximumLongitude = 180.0 - CenterLatitude = 39.0 - CenterLongitude = -77.0 - Distance = 500000.0 + MinimumLatitude = 0.0 + MaximumLatitude = 80.0 + MinimumLongitude = 0.0 + MaximumLongitude = 80.0 + CenterLatitude = 0.0 + CenterLongitude = 0.0 + Distance = 0.00562 End_Group End MappingLatitudes() = Group = Mapping - MinimumLatitude = -90.0 - MaximumLatitude = 90.0 - CenterLatitude = 39.0 + MinimumLatitude = 0.0 + MaximumLatitude = 80.0 + CenterLatitude = 0.0 End_Group End MappingLongitudes() = Group = Mapping - MinimumLongitude = -180.0 - MaximumLongitude = 180.0 - CenterLongitude = -77.0 + MinimumLongitude = 0.0 + MaximumLongitude = 80.0 + CenterLongitude = 0.0 End_Group End -Unit test was obtained from: +Testing SetGround... +<80.0000,80.0000> = <0.0000,0.0000> +<80.0000,70.0000> = <0.0000,0.0000> +<80.0000,60.0000> = <0.0000,0.0000> +<80.0000,50.0000> = <0.0000,0.0000> +<80.0000,40.0000> = <0.0000,0.0000> +<80.0000,30.0000> = <0.0000,0.0000> +<80.0000,20.0000> = <0.0517,0.8572> +<80.0000,10.0000> = <0.0263,0.8582> +<80.0000,0.0000> = <0.0000,0.8586> +<70.0000,80.0000> = <0.0000,0.8586> +<70.0000,70.0000> = <0.0000,0.8586> +<70.0000,60.0000> = <0.2581,0.8189> +<70.0000,50.0000> = <0.2301,0.8251> +<70.0000,40.0000> = <0.1943,0.8306> +<70.0000,30.0000> = <0.1520,0.8351> +<70.0000,20.0000> = <0.1044,0.8385> +<70.0000,10.0000> = <0.0531,0.8405> +<70.0000,0.0000> = <0.0000,0.8412> +<60.0000,80.0000> = <0.0000,0.8412> +<60.0000,70.0000> = <0.4094,0.7547> +<60.0000,60.0000> = <0.3820,0.7641> +<60.0000,50.0000> = <0.3418,0.7727> +<60.0000,40.0000> = <0.2896,0.7804> +<60.0000,30.0000> = <0.2271,0.7867> +<60.0000,20.0000> = <0.1563,0.7914> +<60.0000,10.0000> = <0.0796,0.7943> +<60.0000,0.0000> = <0.0000,0.7953> +<50.0000,80.0000> = <0.0000,0.7953> +<50.0000,70.0000> = <0.5304,0.6727> +<50.0000,60.0000> = <0.4967,0.6835> +<50.0000,50.0000> = <0.4458,0.6936> +<50.0000,40.0000> = <0.3789,0.7026> +<50.0000,30.0000> = <0.2979,0.7100> +<50.0000,20.0000> = <0.2054,0.7156> +<50.0000,10.0000> = <0.1048,0.7191> +<50.0000,0.0000> = <0.0000,0.7203> +<40.0000,80.0000> = <0.0000,0.7203> +<40.0000,70.0000> = <0.6363,0.5682> +<40.0000,60.0000> = <0.5978,0.5792> +<40.0000,50.0000> = <0.5382,0.5895> +<40.0000,40.0000> = <0.4587,0.5988> +<40.0000,30.0000> = <0.3614,0.6065> +<40.0000,20.0000> = <0.2496,0.6123> +<40.0000,10.0000> = <0.1275,0.6159> +<40.0000,0.0000> = <0.0000,0.6171> +<30.0000,80.0000> = <0.0000,0.6171> +<30.0000,70.0000> = <0.7232,0.4444> +<30.0000,60.0000> = <0.6813,0.4542> +<30.0000,50.0000> = <0.6149,0.4634> +<30.0000,40.0000> = <0.5252,0.4717> +<30.0000,30.0000> = <0.4146,0.4787> +<30.0000,20.0000> = <0.2867,0.4840> +<30.0000,10.0000> = <0.1465,0.4872> +<30.0000,0.0000> = <0.0000,0.4884> +<20.0000,80.0000> = <0.8055,0.2977> +<20.0000,70.0000> = <0.7879,0.3052> +<20.0000,60.0000> = <0.7436,0.3125> +<20.0000,50.0000> = <0.6725,0.3195> +<20.0000,40.0000> = <0.5753,0.3258> +<20.0000,30.0000> = <0.4548,0.3311> +<20.0000,20.0000> = <0.3148,0.3350> +<20.0000,10.0000> = <0.1610,0.3375> +<20.0000,0.0000> = <0.0000,0.3384> +<10.0000,80.0000> = <0.8452,0.1513> +<10.0000,70.0000> = <0.8277,0.1553> +<10.0000,60.0000> = <0.7822,0.1593> +<10.0000,50.0000> = <0.7082,0.1630> +<10.0000,40.0000> = <0.6065,0.1664> +<10.0000,30.0000> = <0.4798,0.1692> +<10.0000,20.0000> = <0.3324,0.1714> +<10.0000,10.0000> = <0.1701,0.1727> +<10.0000,0.0000> = <0.0000,0.1732> +<0.0000,80.0000> = <0.8586,0.0000> +<0.0000,70.0000> = <0.8412,0.0000> +<0.0000,60.0000> = <0.7953,0.0000> +<0.0000,50.0000> = <0.7203,0.0000> +<0.0000,40.0000> = <0.6171,0.0000> +<0.0000,30.0000> = <0.4884,0.0000> +<0.0000,20.0000> = <0.3384,0.0000> +<0.0000,10.0000> = <0.1732,0.0000> +<0.0000,0.0000> = <0.0000,0.0000> + +Testing SetCoordinate... +This is taken from the numerical example given on p. 321 of Map Projections - A Working Manual +USGS Professional Paper 1395 +Author: John P. Snyder - Map Projections - A Working Manual - USGS Professional Paper 1395 by John P. Snyder - Pages 320-321 +Latitude: 40.9653 +Longitude: -74.0546 +XCoord: 247194.0900 +YCoord: 222485.9600 diff --git a/isis/src/base/objs/PointPerspective/unitTest.cpp b/isis/src/base/objs/PointPerspective/unitTest.cpp index 997b5344adb2f245605d431ded54a66837077f35..3a7cc5840133b38e5e6838b2f80e5736d38ca719 100644 --- a/isis/src/base/objs/PointPerspective/unitTest.cpp +++ b/isis/src/base/objs/PointPerspective/unitTest.cpp @@ -17,15 +17,15 @@ int main(int argc, char *argv[]) { Pvl lab; lab.addGroup(PvlGroup("Mapping")); PvlGroup &mapGroup = lab.findGroup("Mapping"); - mapGroup += PvlKeyword("EquatorialRadius", toString(6371000.)); - mapGroup += PvlKeyword("PolarRadius", toString(6371000.)); + mapGroup += PvlKeyword("EquatorialRadius", toString(1.0)); + mapGroup += PvlKeyword("PolarRadius", toString(1.0)); mapGroup += PvlKeyword("LatitudeType", "Planetographic"); mapGroup += PvlKeyword("LongitudeDirection", "PositiveEast"); mapGroup += PvlKeyword("LongitudeDomain", toString(180)); - mapGroup += PvlKeyword("MinimumLatitude", toString(-90.0)); - mapGroup += PvlKeyword("MaximumLatitude", toString(90.0)); - mapGroup += PvlKeyword("MinimumLongitude", toString(-180.0)); - mapGroup += PvlKeyword("MaximumLongitude", toString(180.0)); + mapGroup += PvlKeyword("MinimumLatitude", toString(0.0)); + mapGroup += PvlKeyword("MaximumLatitude", toString(80.0)); + mapGroup += PvlKeyword("MinimumLongitude", toString(0.0)); + mapGroup += PvlKeyword("MaximumLongitude", toString(80.0)); mapGroup += PvlKeyword("ProjectionName", "PointPerspective"); cout << "Test missing center longitude keyword ..." << endl; @@ -37,7 +37,7 @@ int main(int argc, char *argv[]) { } cout << endl; - mapGroup += PvlKeyword("CenterLongitude", toString(-77.0)); + mapGroup += PvlKeyword("CenterLongitude", toString(0.0)); cout << "Test missing center latitude keyword..." << endl; try { @@ -48,7 +48,7 @@ int main(int argc, char *argv[]) { } cout << endl; - mapGroup += PvlKeyword("CenterLatitude", toString(39.0)); + mapGroup += PvlKeyword("CenterLatitude", toString(0.0)); cout << "Test missing distance keyword..." << endl; try { @@ -59,7 +59,7 @@ int main(int argc, char *argv[]) { } cout << endl; - mapGroup += PvlKeyword("Distance", toString(500000.0)); + mapGroup += PvlKeyword("Distance", toString(.00562)); try { TProjection *p = (TProjection *) ProjectionFactory::Create(lab); @@ -112,7 +112,10 @@ int main(int argc, char *argv[]) { cout << endl; cout << "Testing Mapping() methods ... " << endl; - + cout <<"This test outputs Table 27 (p.174) of Map Projections - A Working Manual" << endl; + cout << "USGS Professional Paper 1395" << endl; + cout << "Author: John P. Snyder" << endl; + cout << endl; Pvl tmp1; Pvl tmp2; Pvl tmp3; @@ -128,10 +131,58 @@ int main(int argc, char *argv[]) { cout << tmp3 << endl; cout << endl; - cout << "Unit test was obtained from:" << endl << endl; - cout << " Map Projections - A Working Manual" << endl; - cout << " USGS Professional Paper 1395 by John P. Snyder" << endl; - cout << " Pages 320-321" << endl; + cout<< "Testing SetGround..." <= 0) { + lon = 80.0; + while (lon >=0.0) { + p->SetGround(lat,lon); + cout << "<" << setprecision(4) << fixed << lat << "," << lon <<"> = "; + cout << setprecision(4) << fixed << "<" << p->XCoord(); + cout << setprecision(4) << fixed << "," << p->YCoord() << ">" << endl; + lon -= 10.0; + } + lat -=10.0; + } + + cout << endl; + cout << "Testing SetCoordinate..." << endl; + cout <<"This is taken from the numerical example given on p. 321"; + cout << " of Map Projections - A Working Manual" << endl; + cout << "USGS Professional Paper 1395" << endl; + cout << "Author: John P. Snyder" << endl; + cout << endl; + + double x = 247194.09; + double y = 222485.96; + + Pvl lab1; + lab1.addGroup(PvlGroup("Mapping")); + PvlGroup &mapGroup = lab1.findGroup("Mapping"); + mapGroup += PvlKeyword("EquatorialRadius", toString(6371000)); + mapGroup+= PvlKeyword("PolarRadius",toString(6371000)); + mapGroup += PvlKeyword("LatitudeType", "Planetographic"); + mapGroup += PvlKeyword("LongitudeDirection", "PositiveEast"); + mapGroup += PvlKeyword("LongitudeDomain", toString(180)); + mapGroup += PvlKeyword("MinimumLatitude", toString(-90.0)); + mapGroup += PvlKeyword("MaximumLatitude", toString(90.0)); + mapGroup += PvlKeyword("MinimumLongitude", toString(-180.0)); + mapGroup += PvlKeyword("MaximumLongitude", toString(180.0)); + mapGroup += PvlKeyword("CenterLongitude", toString(-77.0)); + mapGroup += PvlKeyword("CenterLatitude", toString(39.0)); + mapGroup += PvlKeyword("Distance", toString(500000)); + mapGroup += PvlKeyword("ProjectionName", "PointPerspective"); + + TProjection *p1 = (TProjection *) ProjectionFactory::Create(lab1); + + p1->SetCoordinate(x,y); + cout << "Latitude: " << p1->Latitude() << endl; + cout << "Longitude: " << p1->Longitude() << endl; + cout << "XCoord: " << p1->XCoord() << endl; + cout << "YCoord: " << p1->YCoord() << endl; } catch(IException &e) { e.print(); diff --git a/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.cpp b/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.cpp index 18922df1bc42006efede0d0bf504d7a85d7d195b..550fad5b1ca2828306028e6c3525152f3e3ea063 100644 --- a/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.cpp +++ b/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.cpp @@ -39,7 +39,21 @@ namespace Isis { p_degree = degree; } + /** + * Create a PolynomialUnivariate object + * + * @param degree The order/degree of the polynomial + * @param coeffs a list of the coefficients + */ + PolynomialUnivariate::PolynomialUnivariate(int degree, std::vector coeffs) : + Isis::Basis1VariableFunction("PolynomialUnivariate", (degree + 1)) { + p_degree = degree; + SetCoefficients(coeffs); + } + + + /** * This is the the overriding virtual function that provides the expansion of * the two input variables into the polynomial equation. * See BasisFunction for more information. diff --git a/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.h b/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.h index 9666161018eafd4b9d6d846c080dcc53133b7b0d..6054b8d87d6d0efeb0021e587d48855f58336f54 100644 --- a/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.h +++ b/isis/src/base/objs/PolynomialUnivariate/PolynomialUnivariate.h @@ -46,11 +46,14 @@ namespace Isis { * @history 2008-01-11 Tracie Sucharski - Renamed from Poly1D, add derivative methods. * @history 2008-02-05 Jeannie Walldren - Renamed from Polynomial1Variable. * @history 2015-02-20 Jeannie Backer - Improved error messages. + * @history 2016-11-10 Kristin Berry - Added additional convenience constructor which + * accepts a vector of coeffs. References #3888. */ class PolynomialUnivariate : public Isis::Basis1VariableFunction { public: PolynomialUnivariate(int degree); + PolynomialUnivariate(int degree, std::vector coeffs); //! Destroys the PolynomialUnivariate object ~PolynomialUnivariate() {}; diff --git a/isis/src/base/objs/Preference/TestPreferences b/isis/src/base/objs/Preference/TestPreferences index 7c5ccca77e38dc65aec4e9e5afa159213354272f..26d1492e1aead191fdcc495b84ed03526f3898d4 100644 --- a/isis/src/base/objs/Preference/TestPreferences +++ b/isis/src/base/objs/Preference/TestPreferences @@ -165,6 +165,7 @@ Group = DataDirectory Clementine1 = $ISIS3DATA/clementine1 Control = $ISIS3DATA/control Dawn = $ISIS3DATA/dawn + Tgo = $ISIS3DATA/tgo Galileo = $ISIS3DATA/galileo Hayabusa = $ISIS3DATA/hayabusa Kaguya = $ISIS3DATA/kaguya diff --git a/isis/src/base/objs/ProcessByBrick/ProcessByBrick.cpp b/isis/src/base/objs/ProcessByBrick/ProcessByBrick.cpp index 234d07f2450518d09051ead0142dd15a644693a4..3668baa7cd4c2a40a11f5dd6fcefdef74e12ed33 100644 --- a/isis/src/base/objs/ProcessByBrick/ProcessByBrick.cpp +++ b/isis/src/base/objs/ProcessByBrick/ProcessByBrick.cpp @@ -132,12 +132,7 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { * * @throws iException::Message */ - - - - - void ProcessByBrick::VerifyCubes(IOCubes cn){ - + void ProcessByBrick::VerifyCubes(IOCubes cn){ switch(cn){ @@ -152,7 +147,6 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { string m = "You haven't specified an input or output cube"; throw IException(IException::Programmer, m, _FILEINFO_); - } break; @@ -170,8 +164,6 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { } // The lines in the input and output must match - - if(InputCubes[0]->lineCount() != OutputCubes[0]->lineCount()) { string m = "The number of lines in the input and output cubes "; m += "must match"; @@ -201,8 +193,6 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { break; - - case InputOutputList: // Make sure we had an image @@ -247,9 +237,7 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { * * @param nb Number of bands */ - - - void ProcessByBrick::SetBrickSize(int ns, int nl, int nb) { + void ProcessByBrick::SetBrickSize(int ns, int nl, int nb) { SetInputBrickSize(ns, nl, nb); SetOutputBrickSize(ns, nl, nb); return; @@ -730,6 +718,8 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { bool haveInput; if (InputCubes.size() == 1) { + + SetBricks(InPlace); // Make sure the brick size has been set if (!p_inputBrickSizeSet) { string m = "Use the SetBrickSize() or SetInputBrickSize() method to set" @@ -748,6 +738,7 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { p_inputBrickLines[1], p_inputBrickBands[1], p_reverse); } else { + SetBricks(InPlace); // Make sure the brick size has been set if (!p_outputBrickSizeSet) { string m = "Use the SetBrickSize() or SetOutputBrickSize() method to " @@ -795,7 +786,7 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { string m = "You must specify exactly one output cube"; throw IException(IException::Programmer, m, _FILEINFO_); } - + SetBricks(InputOutput); // Make sure the brick size has been set if (!p_inputBrickSizeSet || !p_outputBrickSizeSet) { string m = "Use the SetBrickSize(), SetInputBrickSize(), or " @@ -887,6 +878,8 @@ void ProcessByBrick::SetOutputRequirements(int outputRequirements) { throw IException(IException::Programmer, m, _FILEINFO_); } + SetBricks(InputOutputList); + // Make sure the brick size has been set if(!p_inputBrickSizeSet && InputCubes.size() > 0) { string m = "Use the SetBrickSize() or SetInputBrick() method to set the " diff --git a/isis/src/base/objs/ProcessByBrick/ProcessByBrick.h b/isis/src/base/objs/ProcessByBrick/ProcessByBrick.h index 2c7a77cd30175dcd3543e9689166a9359008f422..1bbb30223f7c0bcb08db31e616c5000e44eae92e 100644 --- a/isis/src/base/objs/ProcessByBrick/ProcessByBrick.h +++ b/isis/src/base/objs/ProcessByBrick/ProcessByBrick.h @@ -90,6 +90,9 @@ namespace Isis { * @history 2016-04-26 Ian Humphrey - Modified BlockingReportProgress() so that it unlocks * the local QMutex before it goes out of scope (Qt5 issues a warning * if a locked QMutex is destroyed). + * @history 2017-05-08 Tyler Wilson - Added a call to the virtual method SetBricks inside + * the functions PreProcessCubeInPlace/PreProcessCube/PreProcessCubes. + * Fixes #4698. */ class ProcessByBrick : public Process { public: diff --git a/isis/src/base/objs/ProcessByLine/ProcessByLine.cpp b/isis/src/base/objs/ProcessByLine/ProcessByLine.cpp index 676948a77e8e0fe7131d1e9b3eb6c9a42cf1a9d5..f4fc966c34084c1509830cb054fccb35ac125c5d 100644 --- a/isis/src/base/objs/ProcessByLine/ProcessByLine.cpp +++ b/isis/src/base/objs/ProcessByLine/ProcessByLine.cpp @@ -61,6 +61,7 @@ namespace Isis { return Process::SetInputCube(parameter, allRequirements); } + /** * Opens an input cube file specified by the user with cube attributes and * requirements. For more information see Process::SetInputCube @@ -93,20 +94,18 @@ namespace Isis { * * @param inCube - Pointer to input Cube */ - void ProcessByLine::SetInputCube(Isis::Cube *inCube) - { + void ProcessByLine::SetInputCube(Isis::Cube *inCube) { Process::SetInputCube(inCube); } - - void ProcessByLine::SetBricks(IOCubes cn){ + void ProcessByLine::SetBricks(IOCubes cn) { switch(cn){ case InPlace: - if(InputCubes.size() == 1) { + if (InputCubes.size() == 1) { SetBrickSize(InputCubes[0]->sampleCount(), 1, 1); } @@ -116,7 +115,6 @@ namespace Isis { break; - case InputOutput: SetInputBrickSize(InputCubes[0]->sampleCount(), 1, 1); @@ -124,24 +122,17 @@ namespace Isis { break; - case InputOutputList: - for(unsigned int i = 0; i < InputCubes.size(); i++) { + for (unsigned int i = 0; i < InputCubes.size(); i++) { SetInputBrickSize(InputCubes[i]->sampleCount(), 1, 1, i + 1); } - for(unsigned int i = 0; i < OutputCubes.size(); i++) { + for (unsigned int i = 0; i < OutputCubes.size(); i++) { SetOutputBrickSize(OutputCubes[i]->sampleCount(), 1, 1, i + 1); } - break; - - } - - - } @@ -166,15 +157,12 @@ namespace Isis { * written. */ void ProcessByLine::StartProcess(void funct(Isis::Buffer &inout)) { - - VerifyCubes(InPlace); SetBricks(InPlace); ProcessByBrick::StartProcess(funct); } - /** * This method invokes the process by line operation over exactly one input * and one output cube. Typically, this method is used for simple operations @@ -188,15 +176,12 @@ namespace Isis { * @throws Isis::IException::Message */ void ProcessByLine::StartProcess(void funct(Isis::Buffer &in, Isis::Buffer &out)) { - VerifyCubes(InputOutput); SetBricks(InputOutput); ProcessByBrick::StartProcess(funct); } - - /** * This method invokes the process by line operation over multiple input and * output cubes. Typically, this method is used when two input cubes are @@ -208,9 +193,8 @@ namespace Isis { * * @throws Isis::iException::Message */ - void ProcessByLine::StartProcess( void funct(std::vector &in, + void ProcessByLine::StartProcess(void funct(std::vector &in, std::vector &out)) { - VerifyCubes(InputOutputList); SetBricks(InputOutputList); ProcessByBrick::StartProcess(funct); diff --git a/isis/src/base/objs/ProcessByLine/ProcessByLine.h b/isis/src/base/objs/ProcessByLine/ProcessByLine.h index ca6328213b1ef55c197ef094a712ccf84deabf99..3c64b1e26e059925b4223366f5e401070419954f 100644 --- a/isis/src/base/objs/ProcessByLine/ProcessByLine.h +++ b/isis/src/base/objs/ProcessByLine/ProcessByLine.h @@ -45,8 +45,8 @@ namespace Isis { * #include "SpecialPixel.h" * void mirror (Buffer &in, Buffer &out); * void IsisMain() { - * // We will be processing by line ProcessByLine p; - * // Setup the input and output cubes + * // We will be processing by line + * ProcessByLine p; // Setup the input and output cubes * p.SetInputCube("FROM"); * p.SetOutputCube ("TO"); * // Start the processing @@ -93,12 +93,22 @@ namespace Isis { * $temporary variable instead of /tmp directory. * Added some documentation to methods. * @history 2015-09-25 Tyler Wilson - Combined SetBrickSizesForProcessCube, - * SetBrickSizesForProcessCubeInPlace, and SetBrickSizesForProcessCubes into one - * function: SetBricks(CubeNum) which takes in the enumerated date type enum - * as an argument (CubeNum = {InPlace, InputOutput, InputOutputList}). Also moved - * the verification of cubes out of the SetBrick functions and into - * ProcessByBrick:: VerifyCubes(CubeNum) in parent class. - * + * SetBrickSizesForProcessCubeInPlace, + * and SetBrickSizesForProcessCubes + * into one + * function:SetBricks(CubeNum) which + * takes in the enumerated date type + * enum as an argument (CubeNum = + * {InPlace, InputOutput, + * InputOutputList}). Also moved the + * verification of cubes out of the + * SetBrick functions and into + * ProcessByBrick:: + * VerifyCubes(CubeNum) in parent + * class. + * @history 2017-04-13 Kaj Williams - Fixed a minor typo in + * the API documentation. Fixed a few + * source code formatting issues. */ class ProcessByLine : public Isis::ProcessByBrick { @@ -116,18 +126,14 @@ namespace Isis { void SetInputCube(Isis::Cube *inCube); - void StartProcess(void funct(Isis::Buffer &inout)); void StartProcess(void funct(Isis::Buffer &in, Isis::Buffer &out)); void StartProcess(void funct(std::vector &in, std::vector &out)); - void SetBricks(IOCubes cn); - //void VerifyCubes(IOCubes cn); - - + /** * Same functionality as StartProcess(void funct(Isis::Buffer &inout)) * using Functors. The Functor operator(), takes the parameter @@ -138,17 +144,14 @@ namespace Isis { * @param funct - Functor with overloaded operator()(Isis::Buffer &) * @param threaded @see ProcessByBrick::ProcessCubeInPlace() */ - template void ProcessCubeInPlace(const Functor & funct, bool threaded = true) { - VerifyCubes(InPlace); SetBricks(InPlace); ProcessByBrick::ProcessCubeInPlace(funct, threaded); } - /** * Same functionality as * StartProcess(void funct(Isis::Buffer &in, Isis::Buffer &out)) using @@ -163,7 +166,6 @@ namespace Isis { */ template void ProcessCube(const Functor & funct, bool threaded = true) { - VerifyCubes(InputOutput); SetBricks(InputOutput); ProcessByBrick::ProcessCube(funct, threaded); @@ -185,7 +187,6 @@ namespace Isis { */ template void ProcessCubes(const Functor & funct, bool threaded = true) { - VerifyCubes(InputOutputList); SetBricks(InputOutputList); ProcessByBrick::ProcessCubes(funct, threaded); diff --git a/isis/src/base/objs/ProcessBySample/ProcessBySample.cpp b/isis/src/base/objs/ProcessBySample/ProcessBySample.cpp index 3aaa1279158f9c26e16f906b226d95d41c0c8f8e..a04bbbb2ba5d3b0c4f9d09da6649cacf60c0513e 100644 --- a/isis/src/base/objs/ProcessBySample/ProcessBySample.cpp +++ b/isis/src/base/objs/ProcessBySample/ProcessBySample.cpp @@ -20,7 +20,6 @@ * http://www.usgs.gov/privacy.html. */ - #include "ProcessBySample.h" #include "Buffer.h" @@ -50,11 +49,9 @@ namespace Isis { * * @param requirements See Process::SetInputCube for more information. * Defaults to 0 - * - * @throws Isis::iException::Message */ Isis::Cube *ProcessBySample::SetInputCube(const QString ¶meter, - int requirements) { + int requirements) { int allRequirements = Isis::SpatialMatch | Isis::BandMatchOrOne; allRequirements |= requirements; return Process::SetInputCube(parameter, allRequirements); @@ -74,8 +71,8 @@ namespace Isis { * */ Isis::Cube *ProcessBySample::SetInputCube(const QString &file, - Isis::CubeAttributeInput &att, - int requirements) { + Isis::CubeAttributeInput &att, + int requirements) { int allRequirements = Isis::SpatialMatch | Isis::BandMatchOrOne; allRequirements |= requirements; return Process::SetInputCube(file, att, allRequirements); @@ -92,16 +89,11 @@ namespace Isis { * * @deprecated Please use ProcessCubeInPlace() * @param funct (Isis::Buffer &b) Name of your processing function - * - * @throws Isis::iException::Message - * */ - void ProcessBySample::StartProcess(void funct(Isis::Buffer &inout)) { - VerifyCubes(InPlace); - SetBricks(InPlace); - //SetBrickSizesForProcessCubeInPlace(); - ProcessByBrick::StartProcess(funct); + VerifyCubes(InPlace); + SetBricks(InPlace); + ProcessByBrick::StartProcess(funct); } @@ -114,17 +106,12 @@ namespace Isis { * @deprecated Please use ProcessCube() * @param funct (Isis::Buffer &in, Isis::Buffer &out) Name of your processing * function - * - * @throws Isis::iException::Message - */ - - void ProcessBySample::StartProcess(void - funct(Isis::Buffer &in, Isis::Buffer &out)) { - - VerifyCubes(InputOutput); - SetBricks(InputOutput); - //SetBrickSizesForProcessCube(); - ProcessByBrick::StartProcess(funct); + */ + void ProcessBySample::StartProcess(void funct(Isis::Buffer &in, + Isis::Buffer &out)) { + VerifyCubes(InputOutput); + SetBricks(InputOutput); + ProcessByBrick::StartProcess(funct); } @@ -136,58 +123,39 @@ namespace Isis { * @deprecated Please use ProcessCubes() * @param funct (vector &in, vector &out) Name * of your processing function - * - * @throws Isis::iException::Message */ - void ProcessBySample::StartProcess(void funct(std::vector &in, - std::vector &out)) { - - VerifyCubes(InputOutputList) ; - SetBricks(InputOutputList); - //SetBrickSizesForProcessCubes(); + std::vector &out)) { + VerifyCubes(InputOutputList) ; + SetBricks(InputOutputList); ProcessByBrick::StartProcess(funct); } - void ProcessBySample::SetBricks(IOCubes cn){ - - switch(cn){ - - case InPlace: - if(InputCubes.size() == 1) SetBrickSize(1, InputCubes[0]->lineCount(), 1); - else SetBrickSize(1, OutputCubes[0]->lineCount(), 1); - - break; - - case InputOutput: - - SetInputBrickSize(1, InputCubes[0]->lineCount(), 1); - SetOutputBrickSize(1, OutputCubes[0]->lineCount(), 1); - - - - - break; - - case InputOutputList: - - for(unsigned int i = 0; i < InputCubes.size(); i++) { - SetInputBrickSize(1, InputCubes[i]->lineCount(), 1, i + 1); - } - for(unsigned int i = 0; i < OutputCubes.size(); i++) { - SetOutputBrickSize(1, OutputCubes[i]->lineCount(), 1, i + 1); - } - - break; - - - - } - + void ProcessBySample::SetBricks(IOCubes cn){ + switch(cn){ + case InPlace: + if (InputCubes.size() == 1) { + SetBrickSize(1, InputCubes[0]->lineCount(), 1); + } + else { + SetBrickSize(1, OutputCubes[0]->lineCount(), 1); + } + break; + + case InputOutput: + SetInputBrickSize(1, InputCubes[0]->lineCount(), 1); + SetOutputBrickSize(1, OutputCubes[0]->lineCount(), 1); + break; + + case InputOutputList: + for(unsigned int i = 0; i < InputCubes.size(); i++) { + SetInputBrickSize(1, InputCubes[i]->lineCount(), 1, i + 1); + } + for(unsigned int i = 0; i < OutputCubes.size(); i++) { + SetOutputBrickSize(1, OutputCubes[i]->lineCount(), 1, i + 1); + } + break; + } } - - - - } diff --git a/isis/src/base/objs/ProcessBySample/ProcessBySample.h b/isis/src/base/objs/ProcessBySample/ProcessBySample.h index 523e25189fabe027c75be6d75166bfad16dc3288..a49cc83b4e98fc902b5c020350cf7bdc03daf362 100644 --- a/isis/src/base/objs/ProcessBySample/ProcessBySample.h +++ b/isis/src/base/objs/ProcessBySample/ProcessBySample.h @@ -22,8 +22,8 @@ * http://www.usgs.gov/privacy.html. */ -#include "ProcessByBrick.h" #include "Buffer.h" +#include "ProcessByBrick.h" namespace Isis { /** @@ -36,7 +36,6 @@ namespace Isis { * the Process class which give many functions for setting up input and output * cubes. * - * * @ingroup HighLevelCubeIO * * @author 2006-03-27 Jacob Danton @@ -48,9 +47,10 @@ namespace Isis { * Added some documentation to methods. * @history 2012-02-22 Steven Lambright - Updated to have functorized and * threaded StartProcess equivalents. + * @history 2017-02-17 JP Bonn - Formatting changes, removed commented out + * code. */ class ProcessBySample : public Isis::ProcessByBrick { - public: ProcessBySample(): ProcessByBrick() { SetWrap(true); @@ -64,63 +64,54 @@ namespace Isis { int requirements = 0); void StartProcess(void funct(Isis::Buffer &inout)); - void StartProcess(void funct(Isis::Buffer &in, Isis::Buffer &out)); - void StartProcess(void funct(std::vector &in, std::vector &out)); /** * @see ProcessByBrick::ProcessCubeInPlace() - * @param funct - * @param threaded + * @param funct The processing function or functor which does your + * desired calculations. + * @param threaded True if multi-threading is supported, false otherwise. */ - - template void ProcessCubeInPlace(const Functor & funct, bool threaded = true) { - VerifyCubes(InPlace); - SetBricks(InPlace); + VerifyCubes(InPlace); + SetBricks(InPlace); //SetBrickSizesForProcessCubeInPlace(); ProcessByBrick::ProcessCubeInPlace(funct, threaded); } + /** * @see ProcessByBrick::ProcessCube() - * @param funct - * @param threaded + * @param funct The processing function or functor which does your + * desired calculations. + * @param threaded True if multi-threading is supported, false otherwise. */ - template void ProcessCube(const Functor & funct, bool threaded = true) { - VerifyCubes(InputOutput); - SetBricks(InputOutput); - //SetBrickSizesForProcessCube(); + VerifyCubes(InputOutput); + SetBricks(InputOutput); ProcessByBrick::ProcessCube(funct, threaded); } + /** * @see ProcessByBrick::ProcessCubes() - * @param funct - * @param threaded + * @param funct The processing function or functor which does your + * desired calculations. + * @param threaded True if multi-threading is supported, false otherwise. */ - template void ProcessCubes(const Functor & funct, bool threaded = true) { - VerifyCubes(InputOutputList); - SetBricks(InputOutputList); - //SetBrickSizesForProcessCubes(); + VerifyCubes(InputOutputList); + SetBricks(InputOutputList); ProcessByBrick::ProcessCubes(funct, threaded); } - private: - void SetBricks(IOCubes cn); - - //void SetBrickSizesForProcessCubeInPlace(); - //void SetBrickSizesForProcessCube(); - //void SetBrickSizesForProcessCubes(); }; }; diff --git a/isis/src/base/objs/ProcessExport/ProcessExport.cpp b/isis/src/base/objs/ProcessExport/ProcessExport.cpp index 93297d19a278b98610c87bb43597ccf69a4ba30d..9e7a8b4386ca5514ab072f498471a0debf800475 100644 --- a/isis/src/base/objs/ProcessExport/ProcessExport.cpp +++ b/isis/src/base/objs/ProcessExport/ProcessExport.cpp @@ -21,6 +21,9 @@ */ #include #include +#include +#include + #include "ProcessExport.h" #include "Preference.h" #include "IException.h" @@ -59,6 +62,9 @@ namespace Isis { p_His_Set = false; p_Hrs_Set = false; + m_cryptographicHash = new QCryptographicHash(QCryptographicHash::Md5); + m_canGenerateChecksum = false; + p_progress->SetText("Exporting"); } @@ -72,6 +78,8 @@ namespace Isis { delete p_str[i]; } p_str.clear(); + + delete m_cryptographicHash; } @@ -665,6 +673,56 @@ namespace Isis { } + /** + * @description Set m_canGenerateChecksum which determines if we can generate a MD5 checksum on + * the image data. + * + * @param flag boolean to generate the checksum or not + * + */ + void ProcessExport::setCanGenerateChecksum(bool flag) { + m_canGenerateChecksum = flag; + } + + + /** + * @description Return if we can generate a checksum + * + * @return Boolean to generate the checksum or not + * + */ + bool ProcessExport::canGenerateChecksum() { + return m_canGenerateChecksum; + } + + + /** + * @description Generates a file checksum. This must be called after StartProcess. + * + * @return QString Returns a QString of the checksum. + */ + QString ProcessExport::checksum() { + + QString checksum; + + if (!m_canGenerateChecksum) { + QString msg = "Cannot generate a checksum. Call setGenerateChecksum(true) before startProcess"; + throw IException(IException::Programmer, msg, _FILEINFO_); + } + else { + if (m_cryptographicHash == NULL) { + QString msg = "Unable to generate a checksum. Did you call startProcess?"; + throw IException(IException::Programmer, msg, _FILEINFO_); + return checksum; + } + + checksum = m_cryptographicHash->result().toHex(); + } + + return checksum; + } + + /** * @brief Set cube up for processing * @@ -984,23 +1042,48 @@ namespace Isis { throw IException(IException::Programmer, m, _FILEINFO_); } - // Loop for each line of data - for(buff->begin(); !buff->end(); buff->next()) { - // Read a line of data - InputCubes[0]->read(*buff); - // Stretch the pixels into the desired range - for(int i = 0; i < buff->size(); i++) { - (*buff)[i] = p_str[0]->Map((*buff)[i]); + //This if is the changed one + if (m_canGenerateChecksum) { + // Loop for each line of data + for(buff->begin(); !buff->end(); buff->next()) { + // Read a line of data + InputCubes[0]->read(*buff); + QByteArray byteArray; + // Stretch the pixels into the desired range + for(int i = 0; i < buff->size(); i++) { + (*buff)[i] = p_str[0]->Map((*buff)[i]); + byteArray.append((*buff)[i]); + } + if(p_pixelType == Isis::UnsignedByte) + isisOut8(*buff, fout); + else if(p_pixelType == Isis::UnsignedWord) + isisOut16u(*buff, fout); + else if(p_pixelType == Isis::SignedWord) + isisOut16s(*buff, fout); + else if(p_pixelType == Isis::Real) + isisOut32(*buff, fout); + p_progress->CheckStatus(); + m_cryptographicHash->addData(byteArray); + } + } + else { + for(buff->begin(); !buff->end(); buff->next()) { + // Read a line of data + InputCubes[0]->read(*buff); + // Stretch the pixels into the desired range + for(int i = 0; i < buff->size(); i++) { + (*buff)[i] = p_str[0]->Map((*buff)[i]); + } + if(p_pixelType == Isis::UnsignedByte) + isisOut8(*buff, fout); + else if(p_pixelType == Isis::UnsignedWord) + isisOut16u(*buff, fout); + else if(p_pixelType == Isis::SignedWord) + isisOut16s(*buff, fout); + else if(p_pixelType == Isis::Real) + isisOut32(*buff, fout); + p_progress->CheckStatus(); } - if(p_pixelType == Isis::UnsignedByte) - isisOut8(*buff, fout); - else if(p_pixelType == Isis::UnsignedWord) - isisOut16u(*buff, fout); - else if(p_pixelType == Isis::SignedWord) - isisOut16s(*buff, fout); - else if(p_pixelType == Isis::Real) - isisOut32(*buff, fout); - p_progress->CheckStatus(); } delete buff; return; diff --git a/isis/src/base/objs/ProcessExport/ProcessExport.h b/isis/src/base/objs/ProcessExport/ProcessExport.h index a7a61833b3f1f1c73f84c4f13ca66973e68f7cdd..e4169be8540bc3e11b875116a7c6ec6e50133a40 100644 --- a/isis/src/base/objs/ProcessExport/ProcessExport.h +++ b/isis/src/base/objs/ProcessExport/ProcessExport.h @@ -27,6 +27,9 @@ #include #include +#include +#include + #include "Buffer.h" #include "BufferManager.h" #include "Endian.h" @@ -101,13 +104,17 @@ namespace Isis { * InitProcess() with accessor methods for * OutputNull(), et al. Changed local variable names * in ProcessCubes for clarity. References #1380. - * @history 2015-01-15 Sasha Brownsberger - Added virtual keyword to several - * functions to ensure successful + * @history 2015-01-15 Sasha Brownsberger - Added virtual keyword to several + * functions to ensure successful * inheritance between Process and its * child classes. Added virtual keyword - * to destructor. References #2215. + * to destructor. References #2215. * @history 2016-04-21 Makayla Shepherd - Added UnsignedWord pixel type handling. - * + * @history 2017-05-17 Makayla Shepherd - Added setCanGenerateChecksum(), canGenerateChecksum(), + * and checksum(). Added m_cryptographicHash and m_canGenerateChecksum. + * This allows an MD5 checksum to be generated when exporting an image. + * This checksum is generated based on the image data. Fixes #1013. + * * @todo 2005-02-09 Stuart Sides - write documentation for CreateWorldFile * method * @todo 2005-02-09 Jeff Anderson - add coded example to class file and @@ -154,6 +161,10 @@ namespace Isis { void SetOutputEndian(enum ByteOrder endianness); void SetOutputType(Isis::PixelType pixelIn); + void setCanGenerateChecksum(bool flag); + bool canGenerateChecksum(); + QString checksum(); + double GetInputMinimum(unsigned int n=0) const; double GetInputMaximum(unsigned int n=0) const; @@ -265,6 +276,10 @@ namespace Isis { bool p_Hrs_Set; /**< Indicates whether p_Hrs has been set (i.e. if setHrs() has been called).*/ + QCryptographicHash *m_cryptographicHash; /**< A cryptographic hash that will generate an MD5 + checksum of the image data. */ + bool m_canGenerateChecksum; /**< Flag to determine if a file checksum will be generated. */ + private: //!Method for writing 8-bit unsigned pixel data to a file stream void isisOut8(Buffer &in, std::ofstream &fout); @@ -278,8 +293,8 @@ namespace Isis { /**Method for writing 32-bit signed floating point pixels data to a file stream*/ void isisOut32(Buffer &in, std::ofstream &fout); - - /**Method for writing 64-bit signed double precision floating point pixels + + /**Method for writing 64-bit signed double precision floating point pixels data to a file stream*/ void isisOut64(Buffer &in, std::ofstream &fout); diff --git a/isis/src/base/objs/ProcessExportPds/ProcessExportPds.cpp b/isis/src/base/objs/ProcessExportPds/ProcessExportPds.cpp index 943dda4975555dcedce2b707d3862715376f8b09..eed4f410feee3ad90368ef3473c4f925d356add5 100644 --- a/isis/src/base/objs/ProcessExportPds/ProcessExportPds.cpp +++ b/isis/src/base/objs/ProcessExportPds/ProcessExportPds.cpp @@ -210,9 +210,9 @@ namespace Isis { /** - * Create the standard keywords for the ROOT object in a PDS IMAGE file - * - * @param mainPvl + * Create the standard keywords for the ROOT object in a PDS IMAGE file + * + * @param mainPvl */ void ProcessExportPds::StreamImageRoot(Pvl &mainPvl) { // Create standard ROOT object keywords @@ -236,13 +236,17 @@ namespace Isis { else { mainPvl += PvlKeyword("^IMAGE", "???????", "BYTES"); } + // MD5 checksums are 128-bit -> 32 characters when stringified from hex. + if (canGenerateChecksum()) { + mainPvl += PvlKeyword("CHECKSUM", "????????????????????????????????"); + } } /** * Create the standard keywords for the ROOT object in a PDS JP2 IMAGE file - * - * @param mainPvl + * + * @param mainPvl */ void ProcessExportPds::StreamJP2ImageRoot(Pvl &mainPvl) { mainPvl.format()->add("$base/translations/pdsExportImageJP2.typ"); @@ -297,8 +301,8 @@ namespace Isis { /** * Create the fixed keywords for the ROOT object in a PDS IMAGE file - * - * @param mainPvl + * + * @param mainPvl */ void ProcessExportPds::FixedImageRoot(Pvl &mainPvl) { //Create fixed ROOT object keywords @@ -324,12 +328,15 @@ namespace Isis { else { mainPvl += PvlKeyword("^IMAGE", "???"); } + if (canGenerateChecksum()) { + mainPvl += PvlKeyword("CHECKSUM", "????????????????????????????????"); + } } /** * Create the fixed keywords for the ROOT object in a PDS JP2 IMAGE file - * + * * @param mainPvl */ void ProcessExportPds::FixedJP2ImageRoot(Pvl &mainPvl) { @@ -388,8 +395,8 @@ namespace Isis { * This should not be called until after all settings have been made. The * labels may contain the wrong data if it is. * - * @param mainPvl - * + * @param mainPvl + * * @throws Isis::IException::Message */ void ProcessExportPds::StandardImageImage(Pvl &mainPvl) { @@ -529,8 +536,8 @@ namespace Isis { * This should not be called until after all settings have been made. The * labels may contain the wrong data if it is. * - * @param mainPvl - * + * @param mainPvl + * * @throws Isis::IException::Message */ void ProcessExportPds::StandardJP2Image(Pvl &mainPvl) { @@ -672,8 +679,8 @@ namespace Isis { * Create the standard keywords for the IMAGE_MAP_PROJECTION group in a PDS * label * - * @param mainPvl - * + * @param mainPvl + * * @throws Isis::IException::Message */ void ProcessExportPds::StandardAllMapping(Pvl &outputPvl) { @@ -705,7 +712,7 @@ namespace Isis { // Add the projection name // pdsMapObj += PvlKeyword ("MAP_PROJECTION_TYPE", projName.toUpper()); - // Modify the radii to be km. + // Modify the radii to be km. PvlKeyword &aRadius = pdsMapObj["A_AXIS_RADIUS"]; QString unit = aRadius.unit(); if( (unit.toUpper() == "METERS") || (unit == "") ) { //if no units, assume in meters @@ -773,12 +780,12 @@ namespace Isis { double lineOffset = inputMapping.findKeyword("UpperLeftCornerY"); lineOffset /= (double)inputMapping.findKeyword("PixelResolution"); lineOffset *= 1.0; - lineOffset += 0.5; // Add half a line to get to the center of (1,1) + lineOffset -= 0.5; // Add half a line to get to the center of (1,1) pdsMapObj += PvlKeyword("LINE_PROJECTION_OFFSET", toString(lineOffset), "PIXEL"); double sampleOffset = inputMapping.findKeyword("UpperLeftCornerX"); sampleOffset /= (double)inputMapping.findKeyword("PixelResolution"); sampleOffset *= -1.0; - sampleOffset += 0.5; // Add half a sample to get to the center of (1,1) + sampleOffset -= 0.5; // Add half a sample to get to the center of (1,1) pdsMapObj += PvlKeyword("SAMPLE_PROJECTION_OFFSET", toString(sampleOffset), "PIXEL"); // Add units to keywords already in the IMAGE_MAP_PROJECTION object as necessary @@ -824,9 +831,9 @@ namespace Isis { /** * Return a projection name - * + * * @param inputLabel - * + * * @return String containing the name of the projection */ QString ProcessExportPds::ProjectionName(Pvl &inputLabel) { @@ -840,7 +847,7 @@ namespace Isis { /** * Return the line bytes (record size) for the input cube, at present this is * based on the number of samples and the bytes per pixel. - * + * * @return Total number of bytes per line. */ int ProcessExportPds::LineBytes() { @@ -852,9 +859,9 @@ namespace Isis { /** - * Return the size of the output PDS label. - * - * @return Number of bytes in the label. + * Return the size of the output PDS label. + * + * @return Number of bytes in the label. */ int ProcessExportPds::LabelSize() { ostringstream temp; @@ -867,11 +874,11 @@ namespace Isis { return temp.tellp(); } - /** - * Write the PDS label to the a detached file. The PDS keywords - * that have place holder "?" for their values (such as LABEL_RECORDS and - * ^IMAGE) will be updated to their correct values before they are written. - */ + /** + * Write the PDS label to the a detached file. The PDS keywords + * that have place holder "?" for their values (such as LABEL_RECORDS and + * ^IMAGE) will be updated to their correct values before they are written. + */ void ProcessExportPds::OutputDetachedLabel() { if(!m_detachedLabel) { QString msg = "Unable to output detached label. Use " @@ -887,14 +894,15 @@ namespace Isis { /** * Write the PDS label to the supplied stream. The PDS keywords that have place * holder "?" for their values (such as LABEL_RECORDS and ^IMAGE) will - * be updated to their correct values before they are written. - * + * be updated to their correct values before they are written. + * * @param Output file stream to which the pds label will be written. */ void ProcessExportPds::OutputLabel(std::ofstream &os) { int labSize = LabelSize(); // labSize will be the old label size with "?" // NOTE: WARNING: If anything changes in the next two lines, you must also changes the // corresponding lines in the StandardImageRoot member + if(m_exportType == Stream) { if(m_pdsFileType != ProcessExportPds::JP2Image) { (*m_label)["LABEL_RECORDS"].setValue(toString(labSize), "BYTES"); @@ -930,7 +938,7 @@ namespace Isis { for (unsigned int i = 0; i < m_tableRecords.size(); i++) { totalTableRecords += m_tableRecords[i]; } - int imageRecords = InputCubes[0]->lineCount() + int imageRecords = InputCubes[0]->lineCount() * InputCubes[0]->bandCount(); int fileRecords = labelRecords + imageRecords + totalTableRecords; (*m_label)["FILE_RECORDS"].setValue(toString(fileRecords)); @@ -952,37 +960,55 @@ namespace Isis { } - /** - * This method will add a table to be exported to PDS. If the output PDS - * labels are set to detached, the PDS table will be written to a detached - * file in this method. If the output PDS product is set to attached, the - * table will be added to a buffer and written to the PDS file when the - * StartProcess() method is called. Attached tables are written to the file - * after the image data. - * - * Warning: If attached tables are exported and the labels of these tables - * are modified, the start byte value of the labels will need to be - * updated. There is no existing method (UpdateAttachedTableLabels) to do - * this in ProcessExportPds. If this functionality is needed, this class - * will need to be modified accordingly. - * - * @throw IException::Unknown - "The output PDS file has been set to + + /** + * Updates the CHECKSUM value on the label and rewrites to the output file. + * + * @param std::ofstream &pdsFileStream Output file to write the label to. + */ + void ProcessExportPds::updateChecksumInLabel(std::ofstream &pdsFileStream) { + // This occurs after application has called its StartProcess and the checksum has been + // generated. We need to seek to the top of the file to rewrite the label. Since the + // CHECKSUM is MD5, we set aside 32 characters for the value of this keyword. Since + // OuputLabel() has already created the label and necessary padding, we can simply update + // the CHECKSUM value to the generated checksum and re-write the entire label. + pdsFileStream.seekp(0); + (*m_label)["CHECKSUM"].setValue(checksum()); + pdsFileStream << *m_label; + } + + + /** + * This method will add a table to be exported to PDS. If the output PDS + * labels are set to detached, the PDS table will be written to a detached + * file in this method. If the output PDS product is set to attached, the + * table will be added to a buffer and written to the PDS file when the + * StartProcess() method is called. Attached tables are written to the file + * after the image data. + * + * Warning: If attached tables are exported and the labels of these tables + * are modified, the start byte value of the labels will need to be + * updated. There is no existing method (UpdateAttachedTableLabels) to do + * this in ProcessExportPds. If this functionality is needed, this class + * will need to be modified accordingly. + * + * @throw IException::Unknown - "The output PDS file has been set to * attached and a detached PDS table file name has been * given. If detached is preferred, set the process to * detached SetDetached() and call StandardPdsLabel() before * calling ExportTable()." - * @throw IException::Unknown - "The output PDS file has been set to + * @throw IException::Unknown - "The output PDS file has been set to * detached. A file name for the detached ouput PDS table * file is required. If an attached output file is prefered, * use the method ProcessExportPds::SetAttached() before * calling ExportTable()." - + * @param isisTable The Isis3 Table object to be exported to PDS. * @param detachedPdsTableFileName The name of the exported PDS table file, * if detached. This value should not * include a path. The path from the label * file will be used. - */ + */ void ProcessExportPds::ExportTable(Table isisTable, QString detachedPdsTableFileName) { if(Attached() && detachedPdsTableFileName != "") { @@ -1007,8 +1033,8 @@ namespace Isis { // return metadata pvl containing needed information for the output label. char *tableBuffer = new char[isisTable.Records() * fileRecordBytes]; - PvlObject metadata = pdsTable.exportTable(tableBuffer, - fileRecordBytes, + PvlObject metadata = pdsTable.exportTable(tableBuffer, + fileRecordBytes, ByteOrderName(p_endianType)); QString pdsTableName = pdsTable.formatPdsTableName(); Pvl &mainPvl = *m_label; @@ -1016,7 +1042,7 @@ namespace Isis { m_tableBuffers.push_back(tableBuffer); int labSize = LabelSize(); // labSize will be the old label size with "?" int labelRecords = (int)ceil((double)labSize / (double)fileRecordBytes); - int imageRecords = InputCubes[0]->lineCount() + int imageRecords = InputCubes[0]->lineCount() * InputCubes[0]->bandCount(); int totalTableRecords = 0; for (unsigned int i = 0; i < m_tableRecords.size(); i++) { @@ -1029,7 +1055,7 @@ namespace Isis { else { mainPvl += PvlKeyword("^" + pdsTableName, detachedPdsTableFileName); FileName labelFile(m_detachedPdsLabelFile); - QString tableFileWithPath = labelFile.path() + "/" + QString tableFileWithPath = labelFile.path() + "/" + detachedPdsTableFileName; ofstream os(tableFileWithPath.toLatin1().data()); os.write(tableBuffer, isisTable.Records() * fileRecordBytes); @@ -1040,262 +1066,262 @@ namespace Isis { return; } - /** - * Mutator method to set the output PDS file to detached. In this case, + /** + * Mutator method to set the output PDS file to detached. In this case, * there will be separate output files containing the PDS label, image * data, and any PDS tables that are added. - * + * * @param detachedLabelFile A string containing the name of the detached * PDS label file - */ + */ void ProcessExportPds::SetDetached(QString detachedLabelFile) { m_detachedLabel = true; m_detachedPdsLabelFile = detachedLabelFile; return; } - /** - * Mutator method to set the output PDS file to attached. In this case, + /** + * Mutator method to set the output PDS file to attached. In this case, * there will be a single output file containing the PDS label, image * data, and any PDS tables that are added. - */ + */ void ProcessExportPds::SetAttached() { m_detachedLabel = false; m_detachedPdsLabelFile = ""; } - /** - * Accessor function returns true if the output PDS file is set to detached. - * - * @return @b bool Indicates whether the PDS file is detached. - */ + /** + * Accessor function returns true if the output PDS file is set to detached. + * + * @return @b bool Indicates whether the PDS file is detached. + */ bool ProcessExportPds::Detached() { return m_detachedLabel; } - /** - * Accessor function returns true if the output PDS file is set to attached. - * - * @return @b bool Indicates whether the PDS file is attached. - */ + /** + * Accessor function returns true if the output PDS file is set to attached. + * + * @return @b bool Indicates whether the PDS file is attached. + */ bool ProcessExportPds::Attached() { return !m_detachedLabel; } - /** + /** * Mutator method to set the output PDS image resolution to meters per pixel * or kilometers per pixel. - * + * * @param resolutionUnits Enumerated value for the units type to be set. - */ + */ void ProcessExportPds::SetPdsResolution(PdsResolution resolutionUnits) { m_exportResolution = resolutionUnits; } - /** - * Mutator method to set the output PDS image record type to stream or - * fixed. - * - * @param recordFormat Enumerated value for the record type of the exported + /** + * Mutator method to set the output PDS image record type to stream or + * fixed. + * + * @param recordFormat Enumerated value for the record type of the exported * PDS file. - */ + */ void ProcessExportPds::SetExportType(PdsExportType recordFormat) { m_exportType = recordFormat; } - /** + /** * Mutator method to set how the the BANDS keyword will be handled. If false, * the BANDS keyword will be removed from the IMAGE object of the PDS labels. * This member variable defaults to true in the ProcessExportPds constructor. - * + * * @param force Indicates whether to force the process to keep the BANDS * keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceBands(bool force) { m_forceBands = force; } - /** - * Mutator method to set how the BAND_NAME keyword will be handled. If - * false and the BAND_NAME keyword exists in the IMAGE object of the PDS - * labels, the keyword will be removed. This member variable defaults to - * true in the ProcessExportPds constructor. - * + /** + * Mutator method to set how the BAND_NAME keyword will be handled. If + * false and the BAND_NAME keyword exists in the IMAGE object of the PDS + * labels, the keyword will be removed. This member variable defaults to + * true in the ProcessExportPds constructor. + * * @param force Indicates whether to force the process to keep the BAND_NAME * keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceBandName(bool force) { m_forceBandName = force; } - /** - * Mutator method to set how the CENTER_FILTER_WAVELENGTH keyword will be - * handled. If false and the CENTER_FILTER_WAVELENGTH keyword exists in the - * IMAGE object of the PDS labels, the keyword will be removed. This + /** + * Mutator method to set how the CENTER_FILTER_WAVELENGTH keyword will be + * handled. If false and the CENTER_FILTER_WAVELENGTH keyword exists in the + * IMAGE object of the PDS labels, the keyword will be removed. This * member variable defaults to true in the ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to keep the + * + * @param force Indicates whether to force the process to keep the * CENTER_FILTER_WAVELENGTH keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceCenterFilterWavelength(bool force) { m_forceCenterFilterWavelength = force; } - /** - * Mutator method to set how the BANDWIDTH keyword will be handled. If - * false and the BANDWIDTH keyword exists in the IMAGE object of the PDS - * labels, the keyword will be removed. This member variable defaults to - * true in the ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to keep the + /** + * Mutator method to set how the BANDWIDTH keyword will be handled. If + * false and the BANDWIDTH keyword exists in the IMAGE object of the PDS + * labels, the keyword will be removed. This member variable defaults to + * true in the ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to keep the * BANDWIDTH keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceBandwidth(bool force) { m_forceBandwidth = force; } - /** - * Mutator method to set how the BAND_STORAGE_TYPE keyword will be - * handled. If true, the BAND_STORAGE_TYPE keyword will be added to the - * IMAGE object of the PDS labels. This member variable defaults to true in - * the ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the BAND_STORAGE_TYPE keyword will be + * handled. If true, the BAND_STORAGE_TYPE keyword will be added to the + * IMAGE object of the PDS labels. This member variable defaults to true in + * the ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * BAND_STORAGE_TYPE keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceBandStorageType(bool force) { m_forceBandStorageType = force; } - /** - * Mutator method to set how the OFFSET keyword will be handled. If true, - * the OFFSET keyword will be added to the IMAGE object of the PDS labels. - * This member variable defaults to true in the ProcessExportPds - * constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the OFFSET keyword will be handled. If true, + * the OFFSET keyword will be added to the IMAGE object of the PDS labels. + * This member variable defaults to true in the ProcessExportPds + * constructor. + * + * @param force Indicates whether to force the process to add the * OFFSET keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceOffset(bool force) { m_forceOffset = force; } - /** - * Mutator method to set how the SCALING_FACTOR keyword will be handled. If - * true, the SCALING_FACTOR keyword will be added to the IMAGE object of - * the PDS labels. This member variable defaults to true in the - * ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the SCALING_FACTOR keyword will be handled. If + * true, the SCALING_FACTOR keyword will be added to the IMAGE object of + * the PDS labels. This member variable defaults to true in the + * ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * SCALING_FACTOR keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceScalingFactor(bool force) { m_forceScalingFactor = force; } - /** - * Mutator method to set how the SAMPLE_BITS keyword will be handled. If - * true, the SAMPLE_BITS keyword will be added to the IMAGE object of - * the PDS labels. This member variable defaults to true in the - * ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the SAMPLE_BITS keyword will be handled. If + * true, the SAMPLE_BITS keyword will be added to the IMAGE object of + * the PDS labels. This member variable defaults to true in the + * ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * SAMPLE_BITS keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceSampleBits(bool force) { m_forceSampleBits = force; } - /** + /** * Mutator method to set how the SAMPLE_BIT_MASK keyword will be handled. If - * true, the SAMPLE_BIT_MASK keyword will be added to the IMAGE object of - * the PDS labels. This member variable defaults to true in the - * ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + * true, the SAMPLE_BIT_MASK keyword will be added to the IMAGE object of + * the PDS labels. This member variable defaults to true in the + * ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * SAMPLE_BIT_MASK keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceSampleBitMask(bool force) { m_forceSampleBitMask = force; } - /** - * Mutator method to set how the SAMPLE_TYPE keyword will be handled. If + /** + * Mutator method to set how the SAMPLE_TYPE keyword will be handled. If * true, the SAMPLE_TYPE keyword will be added to the IMAGE object of the - * PDS labels. This member variable defaults to true in the - * ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + * PDS labels. This member variable defaults to true in the + * ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * SAMPLE_TYPE keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceSampleType(bool force) { m_forceSampleType = force; } - /** - * Mutator method to set how the CORE_NULL keyword will be handled. If - * true, the CORE_NULL keyword will be added to the IMAGE object of the - * PDS labels. This member variable defaults to true in the - * ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the CORE_NULL keyword will be handled. If + * true, the CORE_NULL keyword will be added to the IMAGE object of the + * PDS labels. This member variable defaults to true in the + * ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * CORE_NULL keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceCoreNull(bool force) { m_forceCoreNull = force; } - /** - * Mutator method to set how the CORE_LOW_REPR_SATURATION keyword will be - * handled. If true, the CORE_LOW_REPR_SATURATION keyword will be added - * to the IMAGE object of the PDS labels. This member variable defaults - * to true in the ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the CORE_LOW_REPR_SATURATION keyword will be + * handled. If true, the CORE_LOW_REPR_SATURATION keyword will be added + * to the IMAGE object of the PDS labels. This member variable defaults + * to true in the ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * CORE_LOW_REPR_SATURATION keyword in the PDS image labels. - */ + */ void ProcessExportPds::ForceCoreLrs(bool force) { m_forceCoreLrs = force; } - /** - * Mutator method to set how the CORE_LOW_INSTR_SATURATION keyword will be - * handled. If true, the CORE_LOW_INSTR_SATURATION keyword will be added - * to the IMAGE object of the PDS labels. This member variable defaults - * to true in the ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the CORE_LOW_INSTR_SATURATION keyword will be + * handled. If true, the CORE_LOW_INSTR_SATURATION keyword will be added + * to the IMAGE object of the PDS labels. This member variable defaults + * to true in the ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * CORE_LOW_INSTR_SATURATION keyword in the PDS image * labels. - */ + */ void ProcessExportPds::ForceCoreLis(bool force) { m_forceCoreLis = force; } - /** - * Mutator method to set how the CORE_HIGH_REPR_SATURATION keyword will be - * handled. If true, the CORE_HIGH_REPR_SATURATION keyword will be added + /** + * Mutator method to set how the CORE_HIGH_REPR_SATURATION keyword will be + * handled. If true, the CORE_HIGH_REPR_SATURATION keyword will be added * to the IMAGE object of the PDS labels. This member variable defaults to - * true in the ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + * true in the ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * CORE_HIGH_REPR_SATURATION keyword in the PDS image * labels. - */ + */ void ProcessExportPds::ForceCoreHrs(bool force) { m_forceCoreHrs = force; } - /** - * Mutator method to set how the CORE_HIGH_INSTR_SATURATION keyword will be - * handled. If true, the CORE_HIGH_INSTR_SATURATION keyword will be added - * to the IMAGE object of the PDS labels. This member variable defaults to - * true in the ProcessExportPds constructor. - * - * @param force Indicates whether to force the process to add the + /** + * Mutator method to set how the CORE_HIGH_INSTR_SATURATION keyword will be + * handled. If true, the CORE_HIGH_INSTR_SATURATION keyword will be added + * to the IMAGE object of the PDS labels. This member variable defaults to + * true in the ProcessExportPds constructor. + * + * @param force Indicates whether to force the process to add the * CORE_HIGH_INSTR_SATURATION keyword in the PDS image * labels. - */ + */ void ProcessExportPds::ForceCoreHis(bool force) { m_forceCoreHis = force; } diff --git a/isis/src/base/objs/ProcessExportPds/ProcessExportPds.h b/isis/src/base/objs/ProcessExportPds/ProcessExportPds.h index 4df7c0302fcb2183e225cc7523bd9c29cae79506..301dca7bc025d3835dd778cdbb4868193294440b 100644 --- a/isis/src/base/objs/ProcessExportPds/ProcessExportPds.h +++ b/isis/src/base/objs/ProcessExportPds/ProcessExportPds.h @@ -32,14 +32,14 @@ namespace Isis { * @brief Process class for exporting cubes to PDS standards * * This class extends the ProcessExport class to allow the user - * to export cubes to PDS format. - * + * to export cubes to PDS format. + * * Tables from the cube may also be exported. These exported PDS tables may be - * attached or detached. This should correspond to whether the labels of the - * exported PDS file are attached or detached. NOTE: If attached, the labels - * of the table should not be altered in the export program unless - * functionality is added to deal with the new start byte values for the - * tables. + * attached or detached. This should correspond to whether the labels of the + * exported PDS file are attached or detached. NOTE: If attached, the labels + * of the table should not be altered in the export program unless + * functionality is added to deal with the new start byte values for the + * tables. * * @author 2006-09-05 Stuart Sides * @@ -58,7 +58,7 @@ namespace Isis { * @history 2009-05-31 Kris Becker - Included the number of bands in the * computation of the number of FILE_RECORDS for * fixed PDS type products. It assumed only 1 band. - * @history 2010-02-24 Janet Barrett - Added code to support JPEG2000. + * @history 2010-02-24 Janet Barrett - Added code to support JPEG2000. * @history 2010-07-21 Sharmila Prasad - Fixed error while converting * resolution from Meters to Kilometers * @history 2012-04-06 Kris Becker - Correct label padding whereby spaces @@ -72,50 +72,55 @@ namespace Isis { * functionality is added to deal with the new start * byte values. References #678. * @history 2014-06-06 Kristin Berry - Added default units to assume if there - * are no units on certain values in the input Isis cube. - * Unlabeled radii are assumed to be in meters; map scales + * are no units on certain values in the input Isis cube. + * Unlabeled radii are assumed to be in meters; map scales * to be in meters/pixel, and map resolutions to be in * pixels/degree. + * @history 2017-05-17 Makayla Shepherd & Ian Humphrey - Added updateChecksumInLabel() to + * convert the placeholder value to the actual generated checksum + * value. Modified StreamImageRoot() and FixedImageRoot() to create + * CHECKSUM placeholder in the labels if we are generating a checksum. + * Fixes #1013. */ class ProcessExportPds : public Isis::ProcessExport { public: - /** - * File type to be exported - * @see http://pds.nasa.gov/documents/sr/AppendixA.pdf + /** + * File type to be exported + * @see http://pds.nasa.gov/documents/sr/AppendixA.pdf */ enum PdsFileType { - Image, /**< Two dimensional array of line/sample values. These + Image, /**< Two dimensional array of line/sample values. These files generallly have the extension *.img or *.imq**/ Qube, /**< Multi-dimensional array (1-3 dimensional) whose axes may be interpreted as line/sample/band. These files generally have the extension *.qub**/ SpectralQube, /**< Three dimensional objects with two spatial dimensions - and one spectral dimension. These files generally + and one spectral dimension. These files generally have the extension *.qub**/ - JP2Image /**< Image coding system JPEG 2000 formatted image. These + JP2Image /**< Image coding system JPEG 2000 formatted image. These files generally have the extension *.jp2 **/ }; - + /** - * Resolution units per pixel of the exported PDS file + * Resolution units per pixel of the exported PDS file */ enum PdsResolution { Meter, //!< Meters per pixel Kilometer //!< Kilometers per pixel }; - + /** - * Record format type of exported PDS file. - * - * @see http://pds.nasa.gov/documents/sr/Chapter15.pdf + * Record format type of exported PDS file. + * + * @see http://pds.nasa.gov/documents/sr/Chapter15.pdf */ enum PdsExportType { Stream, //!< Stream Records. This type is generally used for ASCII files. - Fixed /**< Fixed length records. PDS recommends that FIXED_LENGTH + Fixed /**< Fixed length records. PDS recommends that FIXED_LENGTH records are used whenever possible.**/ }; - + ProcessExportPds(); ~ProcessExportPds(); @@ -136,11 +141,12 @@ namespace Isis { virtual Pvl &StandardPdsLabel(ProcessExportPds::PdsFileType type); void OutputLabel(std::ofstream &pdsFileStream); + void updateChecksumInLabel(std::ofstream &pdsFileStream); void OutputDetachedLabel(); void ExportTable(Isis::Table isisTable, QString detachedPdsTableFileName=""); - // include this using declaration to indicate that ProcessExportPds + // include this using declaration to indicate that ProcessExportPds // objects that call a StartProcess() method that has not been overridden // here should use the corresponding base class definitions using ProcessExport::StartProcess; @@ -178,19 +184,19 @@ namespace Isis { QString ProjectionName(Pvl &inputLabel); - PvlFormatPds *m_formatter; /**< Used to determine how to format the + PvlFormatPds *m_formatter; /**< Used to determine how to format the keyword values in the PDS file.*/ Pvl *m_label; //!< Exported PDS label. PdsExportType m_exportType; //!< Stream or Fixed private: PdsResolution m_exportResolution; //!< Meters or kilometers. - bool m_forceBands; /**< Indicates whether to keep the + bool m_forceBands; /**< Indicates whether to keep the BANDS keyword in the PDS labels.*/ - bool m_forceBandName; /**< Indicates whether to keep the + bool m_forceBandName; /**< Indicates whether to keep the BAND_NAME keyword in the PDS labels.*/ bool m_forceCenterFilterWavelength; /**< Indicates whether to keep the - CENTER_FILTER_WAVELENGTH keyword in + CENTER_FILTER_WAVELENGTH keyword in the PDS labels.*/ bool m_forceBandwidth; /**< Indicates whether to keep the BANDWIDTH keyword in the PDS labels.*/ @@ -213,7 +219,7 @@ namespace Isis { bool m_forceCoreNull; /**< Indicates whether to add the CORE_NULL keyword in the PDS labels.*/ bool m_forceCoreLrs; /**< Indicates whether to add the - CORE_LOW_REPR_SATURATION keyword in + CORE_LOW_REPR_SATURATION keyword in the PDS labels.*/ bool m_forceCoreLis; /**< Indicates whether to add the CORE_LOW_INSTR_SATURATION keyword in @@ -222,29 +228,29 @@ namespace Isis { CORE_HIGH_REPR_SATURATION keyword in the PDS labels.*/ bool m_forceCoreHis; /**< Indicates whether to add the - CORE_HIGH_INSTR_SATURATION keyword in + CORE_HIGH_INSTR_SATURATION keyword in the PDS labels.*/ bool m_detachedLabel; /**< Indicates whether the PDS file will be detached.*/ QString m_detachedPdsLabelFile;/**< The name of the detached PDS label file.*/ - PdsFileType m_pdsFileType; /**< Image, Qube, Spectral Qube, or + PdsFileType m_pdsFileType; /**< Image, Qube, Spectral Qube, or JP2 Image*/ std::vector m_tableStartRecord;/**< Record number where the added - table data begins. The order of the - tables represented in this vector - corresponds to the order of the table + table data begins. The order of the + tables represented in this vector + corresponds to the order of the table data in m_tableBuffers**/ - std::vector m_tableRecords; /**< Number of records in each added - table. The order of the tables + std::vector m_tableRecords; /**< Number of records in each added + table. The order of the tables represented in this vector corresponds to the order of the table data in m_tableBuffers. **/ - std::vector m_tableBuffers; /**< Vector containing the binary - table data for each of the added - tables. The order of the tables - represented in this vector + std::vector m_tableBuffers; /**< Vector containing the binary + table data for each of the added + tables. The order of the tables + represented in this vector corresponds to the order of the table data in m_tableRecords. **/ }; diff --git a/isis/src/base/objs/ProcessImport/ProcessImport.cpp b/isis/src/base/objs/ProcessImport/ProcessImport.cpp index 71ea2446eb0f4820a9c0e27e7cfc4dbdbc9946cf..c6ccd306bdc488d40e98b29101ba3214d9fb2a4f 100644 --- a/isis/src/base/objs/ProcessImport/ProcessImport.cpp +++ b/isis/src/base/objs/ProcessImport/ProcessImport.cpp @@ -725,7 +725,7 @@ namespace Isis { * This method returns the number of data trailer bytes */ int ProcessImport::DataTrailerBytes() const { - return p_fileTrailerBytes; + return p_dataTrailerBytes; } @@ -1373,8 +1373,7 @@ namespace Isis { fin.seekg(p_suffixData+p_fileHeaderBytes, ios_base::beg); } else { - fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg); - + fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg); } // Check the last io @@ -1490,7 +1489,6 @@ namespace Isis { } break; case Isis::Double: - //cout << "Double" << endl; (*out)[samp] = (double)swapper.Double((double *)in+samp); break; default: @@ -1636,7 +1634,7 @@ namespace Isis { fin.seekg(p_suffixData+p_fileHeaderBytes, ios_base::beg); } else { - fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg); + fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg); } // Check the last io @@ -1689,7 +1687,6 @@ namespace Isis { // Space for storing prefix and suffix data pointers vector tempPre, tempPost; - // Handle any line prefix bytes pos = fin.tellg(); if (p_saveDataPre) { @@ -1878,7 +1875,7 @@ namespace Isis { fin.seekg(p_suffixData+p_fileHeaderBytes, ios_base::beg); } else { - fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg); + fin.seekg(p_fileHeaderBytes+p_suffixData, ios_base::beg); } // Check the last io @@ -2052,6 +2049,23 @@ namespace Isis { } // End band loop + pos = fin.tellg(); + if (p_saveDataTrailer) { + p_dataTrailer.push_back(new char[p_dataTrailerBytes]); + fin.read(p_dataTrailer.back(), p_dataTrailerBytes); + } + else { + fin.seekg(p_dataTrailerBytes, ios_base::cur); + } + + // Check the last io + if (!fin.good()) { + QString msg = "Cannot read file [" + p_inFile + "]. Position [" + + toString((int)pos) + "]. Byte count [" + + toString(p_fileHeaderBytes) + "]" ; + throw IException(IException::Io, msg, _FILEINFO_); + } + p_progress->CheckStatus(); } // End line loop diff --git a/isis/src/base/objs/ProcessImport/ProcessImport.h b/isis/src/base/objs/ProcessImport/ProcessImport.h index 7abad707aac663df36e81612e72b9b68b583d7e6..c1af36fe6f0eb36d613e7403bbd0d538c8583346 100644 --- a/isis/src/base/objs/ProcessImport/ProcessImport.h +++ b/isis/src/base/objs/ProcessImport/ProcessImport.h @@ -149,7 +149,9 @@ namespace Isis { * @history 2016-04-20 Jeannie Backer - Merged Janet Barret's changes to handle SignedInteger * imports. Brought code closer to coding standards. * @history 2016-04-21 Makayla Shepherd - Added UnsignedWord pixel type handling. - * + * @history 2017-05-29 Kristin Berry - Added support for data trailers in BIP files and fixed + * a typo so that DataTrailerBytes() will return the correct value. + * References #3888. * */ class ProcessImport : public Isis::Process { diff --git a/isis/src/base/objs/ProcessImportPds/ProcessImportPds.cpp b/isis/src/base/objs/ProcessImportPds/ProcessImportPds.cpp index b52638fa761f9c6f7be8e362c74064f8ce5557b1..dd40f09e7b95344e125134c5a1bf7974a9d6d758 100644 --- a/isis/src/base/objs/ProcessImportPds/ProcessImportPds.cpp +++ b/isis/src/base/objs/ProcessImportPds/ProcessImportPds.cpp @@ -157,6 +157,12 @@ namespace Isis { trnsStrm << " InputPosition = UNCOMPRESSED_FILE" << endl; trnsStrm << " InputKey = ^IMAGE" << endl; trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = PdsCombinedSpectrum" << endl; + trnsStrm << " InputPosition = ROOT" << endl; + trnsStrm << " InputPosition = FILE" << endl; + trnsStrm << " InputPosition = UNCOMPRESSED_FILE" << endl; + trnsStrm << " InputKey = ^COMBINED_SPECTRUM" << endl; + trnsStrm << "EndGroup" << endl; trnsStrm << "Group = PdsTypeL0" << endl; trnsStrm << " InputPosition = L0_FILE" << endl; trnsStrm << " InputKey = ^L0_IMAGE" << endl; @@ -188,7 +194,7 @@ namespace Isis { trnsStrm << " InputPosition = COMPRESSED_FILE" << endl; trnsStrm << " InputKey = FILE_NAME" << endl; trnsStrm << " Translation = (*,*)" << endl; - trnsStrm << "EndGroup" << endl; + trnsStrm << "EndGroup" << endl; trnsStrm << "END"; @@ -196,29 +202,21 @@ namespace Isis { //Determine if we are processing a QUBE whose //core data type is VAX_REAL - try{ - - PvlObject obj = p_pdsLabel.findObject("QUBE"); - PvlKeyword coreKey = obj.findKeyword("CORE_ITEM_TYPE"); - PvlKeyword suffixKey = obj.findKeyword("BAND_SUFFIX_ITEM_TYPE"); + try { + PvlObject obj = p_pdsLabel.findObject("QUBE"); + PvlKeyword coreKey = obj.findKeyword("CORE_ITEM_TYPE"); + PvlKeyword suffixKey = obj.findKeyword("BAND_SUFFIX_ITEM_TYPE"); //if ( (coreKey[0] == "VAX_REAL") && (suffixKey[0] =="VAX_REAL") ) if (coreKey[0] == "VAX_REAL") { - - ProcessImport::SetVAXConvert(true); - } - + ProcessImport::SetVAXConvert(true); + } } - catch(IException &e){ - - + catch (IException &e) { } - - Isis::PvlTranslationManager pdsXlater(p_pdsLabel, trnsStrm); - // Check to see if we are dealing with a JPEG2000 file QString str; if (pdsXlater.InputHasKeyword("PdsEncodingType")) { @@ -254,8 +252,6 @@ namespace Isis { } - - // Call the correct label processing if ((allowedTypes & Image) == Image && pdsXlater.InputHasKeyword("PdsTypeImage")) { @@ -286,6 +282,11 @@ namespace Isis { ProcessPdsM3Label(pdsDataFile, Obs); } + else if ((allowedTypes & CombinedSpectrum) == CombinedSpectrum && + pdsXlater.InputHasKeyword("PdsCombinedSpectrum")) { + + ProcessPdsCombinedSpectrumLabel(pdsDataFile); + } else { QString msg = "Unknown label type in [" + p_labelFile + "]"; throw IException(IException::Io, msg, _FILEINFO_); @@ -715,13 +716,22 @@ namespace Isis { SetDataSuffixBytes(suffix); str = pdsXlater.Translate("SuffixItemSize"); - int trailer = toInt(str); - str = pdsXlater.Translate("AxisSuffixCount", 1); - trailer *= toInt(str); - str = pdsXlater.Translate("CoreSamples", samplePos); - trailer *= toInt(str); - trailer += suffix; - SetDataTrailerBytes(trailer); + + // Only set DataTrailerBytes if we haven't already set it elsewhere. (It's inialized to 0.) + if (DataTrailerBytes() == 0) { + int trailer = toInt(str); + str = pdsXlater.Translate("AxisSuffixCount", 1); + trailer *= toInt(str); + str = pdsXlater.Translate("CoreSamples", samplePos); + trailer *= toInt(str); + trailer += suffix; + SetDataTrailerBytes(trailer); + } + + // Save the Data Trailer if it exists + if (DataTrailerBytes() != 0) { + SaveDataTrailer(); + } ProcessPixelBitandType(pdsXlater); @@ -912,6 +922,96 @@ namespace Isis { } + /** + * Process the PDS label of type CombinedSpectrum. + * + * @param pdsDataFile The name of the PDS data file where the actual image/cube + * data is stored. This parameter can be an empty QString, in + * which case the label information will be searched to find + * the data file name or the data will be assumed to be + * after the label information. + * + * @throws Isis::iException::Message + */ + void ProcessImportPds::ProcessPdsCombinedSpectrumLabel(const QString &pdsDataFile) { + Isis::FileName transFile(p_transDir + "/translations/pdsCombinedSpectrum.trn"); + Isis::PvlTranslationManager pdsXlater(p_pdsLabel, transFile.expanded()); + + QString str; + + str = pdsXlater.Translate("CoreLinePrefixBytes"); + SetDataPrefixBytes(toInt(str)); + + str = pdsXlater.Translate("CoreLineSuffixBytes"); + SetDataSuffixBytes(toInt(str)); + + ProcessPixelBitandType(pdsXlater); + + str = pdsXlater.Translate("CoreByteOrder"); + SetByteOrder(Isis::ByteOrderEnumeration(str)); + + str = pdsXlater.Translate("CoreSamples"); + int ns = toInt(str); + str = pdsXlater.Translate("CoreLines"); + int nl = toInt(str); + str = pdsXlater.Translate("CoreBands"); + int nb = toInt(str); + + SetDimensions(ns, nl, nb); + + //----------------------------------------------------------------- + // Find the data filename it may be the same as the label file + // OR the label file may contain a pointer to the data + //----------------------------------------------------------------- + + // Use the name supplied by the application if it is there + if (pdsDataFile.length() > 0) { + SetInputFile(pdsDataFile); + ProcessDataFilePointer(pdsXlater, true); + } + // If the data is in JPEG 2000 format, then use the name of the file + // from the label + else if (p_jp2File.length() > 0) { + SetInputFile(p_jp2File); + ProcessDataFilePointer(pdsXlater, true); + } + // Use the "^IMAGE or ^QUBE" label to get the filename for the image data + // Get the path portion from user entered label file spec + else { + // Handle filename and offset + ProcessDataFilePointer(pdsXlater, false); + } + + //------------------------------------------------------------ + // Find the image data base and multiplier + //------------------------------------------------------------ + str = pdsXlater.Translate("CoreBase"); + SetBase(toDouble(str)); + str = pdsXlater.Translate("CoreMultiplier"); + SetMultiplier(toDouble(str)); + + // Find the organization of the image data + str = pdsXlater.Translate("CoreOrganization"); + + if (p_encodingType == JP2) { + SetOrganization(ProcessImport::JP2); + } + else if (str == "BSQ") { + SetOrganization(ProcessImport::BSQ); + } + else if (str == "BIP") { + SetOrganization(ProcessImport::BIP); + } + else if (str == "BIL") { + SetOrganization(ProcessImport::BIL); + } + else { + QString msg = "Unsupported axis order [" + str + "]"; + throw IException(IException::Programmer, msg, _FILEINFO_); + } + } + + /** * Fills the passed in label with the projection information from the PDS label * file. The application must write add the projection parameters to the output @@ -1494,11 +1594,11 @@ namespace Isis { xmult = -1.0; ymult = 1.0; - xoff = -0.5; - yoff = -0.5; + xoff = 0.5; + yoff = 0.5; // Open projectionOffsetMults file - Isis::Pvl p(p_transDir + "/" + "translations/pdsProjectionLineSampToXY.def"); + Isis::Pvl p(p_transDir + "/" + "translations/pdsProjectionLineSampToXY_V2.def"); Isis::PvlObject &projDef = p.findObject("ProjectionOffsetMults", Pvl::Traverse); diff --git a/isis/src/base/objs/ProcessImportPds/ProcessImportPds.h b/isis/src/base/objs/ProcessImportPds/ProcessImportPds.h index fd8414081d140dc7ab4f77a5293dd0b77688b1ae..499a82a1029e1086815962c58bf2973682e78e74 100644 --- a/isis/src/base/objs/ProcessImportPds/ProcessImportPds.h +++ b/isis/src/base/objs/ProcessImportPds/ProcessImportPds.h @@ -182,7 +182,7 @@ namespace Isis { * @history 2013-03-12 Steven Lambright and Tracie Sucharski - Added ProcessPdsRdnLabel() to * handle Chandrayaan M3 RDN files. Added a file type to handle * Chandrayaan Loc and Obs files on the same import as the Rdn files. - * Also added support for 64 bit input data. + * Also added support for 64 bit input data. * Note: There may be loss of precision since the output type is 32-bit. * Return reference to imported table. Needed so that M3 table data * can be flipped to match image data depending on yaw and orbit limb @@ -204,13 +204,21 @@ namespace Isis { * ProcessImportPds objects. Marked * EndProcess as deprecated. * @history 2015-01-19 Sasha Brownsberger - Made destructor virtual. References #2215. - * @history 2015-03-10 Tyler Wilson Added to unit test to test opening Galileo NIMS cube files. + * @history 2015-03-10 Tyler Wilson Added to unit test to test opening Galileo NIMS cube files. * References #2368. + * @history 2017-01-03 Jesse Mapel - Added support for importing combined spectrum + * images such as from the Hyabusa NIRS. Fixes #4573. + * @history 2017-05-29 Kristin Berry - Update to the DataTrailer handling code so that its size + * (DataTrailerBytes) is not inappropriately re-set if we have specified + * it previously. References #3888. + * * @todo 2005-02-09 Finish documentation-lots of holes with variable - * definitions in .h file and .cpp methods, and insert - * implementation example + * definitions in .h file and .cpp methods, and insert + * implementation example + * @history 2017-05-19 Christopher Combs - Modified unitTest.cpp: changed ReportError method to + * truncate paths before data directory. Allows test to pass when not + * using the default data area. Fixes #4738. * - */ class ProcessImportPds : public ProcessImport { @@ -223,7 +231,8 @@ namespace Isis { Rdn = 16, Loc = 32, Obs = 64, - All = Image | Qube | SpectralQube | L0 | Rdn | Loc | Obs + CombinedSpectrum = 128, + All = Image | Qube | SpectralQube | L0 | Rdn | Loc | Obs | CombinedSpectrum }; ProcessImportPds(); virtual ~ProcessImportPds(); @@ -272,6 +281,7 @@ namespace Isis { void ProcessPdsImageLabel(const QString &pdsDataFile); void ProcessPdsQubeLabel(const QString &pdsDataFile, const QString &transFile); void ProcessPdsM3Label(const QString &pdsDataFile, PdsFileType fileType); + void ProcessPdsCombinedSpectrumLabel(const QString &pdsDataFile); void ExtractPdsProjection(PvlTranslationManager &pdsXlater); void GetProjectionOffsetMults(double &xoff, double &yoff, @@ -340,5 +350,3 @@ namespace Isis { }; #endif - - diff --git a/isis/src/base/objs/ProcessImportPds/ProcessImportPds.truth b/isis/src/base/objs/ProcessImportPds/ProcessImportPds.truth index c5893872cc72ec800042ab3c97b05205ec24f3e7..f6e569efab3c5c5d7a9d35b915022923d32ad6b0 100644 --- a/isis/src/base/objs/ProcessImportPds/ProcessImportPds.truth +++ b/isis/src/base/objs/ProcessImportPds/ProcessImportPds.truth @@ -952,9 +952,9 @@ isisimportpds: Gathering statistics 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed 687.556 282178 -**I/O ERROR** Unable to open OriginalLabel [] in file []. -**I/O ERROR** Unable to read OriginalLabel []. -**PROGRAMMER ERROR** Unable to find OriginalLabel []. +**I/O ERROR** Unable to open OriginalLabel [IsisCube] in file [./unitTest.cub]. +**I/O ERROR** Unable to read OriginalLabel [IsisCube]. +**PROGRAMMER ERROR** Unable to find OriginalLabel [IsisCube]. Testing Isis2 file isisimportpds: Importing @@ -1301,7 +1301,7 @@ End Testing file with invalid Pds label **USER ERROR** This image does not contain a pds label. You will need an image with a PDS label or a detached PDS label for this image. -**ERROR** Unable to read PVL file [/usgs/cpkgs/isis3/data/galileo/testData/1213r.img]. +**ERROR** Unable to read PVL file [data/galileo/testData/1213r.img]. **ERROR** Error in PVL file on line [1]. **ERROR** Unable to read PVL keyword [LBLSIZE=2000 FORMAT='BYTE' TYPE='IMAGE' BUFSIZ=20480 DIM=3 EOL=0 RECSIZE=1000 ORG='BSQ' NL=800 NS=800 NB=1 N1=800 N2=800 N3=1 N4=0 NBB=200 HOST='AXP-VMS' INTFMT='LOW' REALFMT='VAX' BHOST='VAX-VMS' BINTFMT='LOW' BREALFMT='VAX' BLTYPE='' NLB=10 TASK='SSIMERGE' USER='AXC040' DAT_TIM='Tue Jan 18 16:36:41 2000' MISSION='GALILEO' SENSOR='SSI' PICNO='24I0134' RIM=5208212 MOD91=13 MOD10=0 MOD8=0 PARTITION=1 PA='24ISSTEREO01' TCA='000T07:15:09Z' TARGET='IO' SCETYEAR=1999 SCETDAY=284 SCETHOUR=9 SCETMIN=17 SCETSEC=10 SCETMSEC=480 ERTYEAR=1999 ERTDAY=316 ERTHOUR=3 ERTMIN=27 ERTSEC=8 ERTMSEC=120 FILTER=0 EXP=6.25 GAIN=2 RATE=2 TLMFMT='IM4' BOOM='N' MOFIBE='001000' ENCODING_TYPE='BARC RATE CONTROL ' TBPPXL=1.1559 TPPLNE=4.43638 INA=35.4711 EMA=30.8087 HRA=206.599 TWIST=299.208 CONE=157.429 RA=49.4416 DEC=20.7453 SMEAR=0.1 CUT_OUT_WINDOW=(1,1,800,800) PHA=24.0033 HSCL=1490.08 VSCL=1704.71 LAT=30.1268 LON=177.269 PLRANGE=569451.0 SLRANGE=145354.0 SOLRANGE=7.41096e+08 SUB_SOLAR_LATITUDE=2.99102 SUB_SOLAR_LONGITUDE=200.927 SUB_SPACECRAFT_LATITUDE=0.081587 SUB_SPACECRAFT_LONGITUDE=177.139 SUNAZ=124.394 NORAZ=256.334 SCAZ=76.1117 SMRAZ=-999.0 RAD=-999.0 SPICE_C_ID='M902' TARGET_CENTER_DISTANCE=146933.0 SUB_SPACECRAFT_LINE=1001.48 SUB_SPACECRAFT_SAMPLE=548.759 READOUTMODE='NOT APPLICABLE' INTERCEPT_POINT_LINE=400.0 INTERCEPT_POINT_LINE_SAMPLE=400.0 ENTROPY=3.39634 TASK='CATLABEL' USER='AXC040' DAT_TIM='Wed Feb 9 16:36:22 2000' TASK='BADLABEL' USER='AXC040' DAT_TIM='Wed Feb 9 16:36:39 2000' REDR_EXT='1' ]. **ERROR** Keyword has extraneous data [FORMAT='BYTE' TYPE='IMAGE' BUFSIZ=20480 DIM=3 EOL=0 RECSIZE=1000 ORG='BSQ' NL=800 NS=800 NB=1 N1=800 N2=800 N3=1 N4=0 NBB=200 HOST='AXP-VMS' INTFMT='LOW' REALFMT='VAX' BHOST='VAX-VMS' BINTFMT='LOW' BREALFMT='VAX' BLTYPE='' NLB=10 TASK='SSIMERGE' USER='AXC040' DAT_TIM='Tue Jan 18 16:36:41 2000' MISSION='GALILEO' SENSOR='SSI' PICNO='24I0134' RIM=5208212 MOD91=13 MOD10=0 MOD8=0 PARTITION=1 PA='24ISSTEREO01' TCA='000T07:15:09Z' TARGET='IO' SCETYEAR=1999 SCETDAY=284 SCETHOUR=9 SCETMIN=17 SCETSEC=10 SCETMSEC=480 ERTYEAR=1999 ERTDAY=316 ERTHOUR=3 ERTMIN=27 ERTSEC=8 ERTMSEC=120 FILTER=0 EXP=6.25 GAIN=2 RATE=2 TLMFMT='IM4' BOOM='N' MOFIBE='001000' ENCODING_TYPE='BARC RATE CONTROL ' TBPPXL=1.1559 TPPLNE=4.43638 INA=35.4711 EMA=30.8087 HRA=206.599 TWIST=299.208 CONE=157.429 RA=49.4416 DEC=20.7453 SMEAR=0.1 CUT_OUT_WINDOW=(1,1,800,800) PHA=24.0033 HSCL=1490.08 VSCL=1704.71 LAT=30.1268 LON=177.269 PLRANGE=569451.0 SLRANGE=145354.0 SOLRANGE=7.41096e+08 SUB_SOLAR_LATITUDE=2.99102 SUB_SOLAR_LONGITUDE=200.927 SUB_SPACECRAFT_LATITUDE=0.081587 SUB_SPACECRAFT_LONGITUDE=177.139 SUNAZ=124.394 NORAZ=256.334 SCAZ=76.1117 SMRAZ=-999.0 RAD=-999.0 SPICE_C_ID='M902' TARGET_CENTER_DISTANCE=146933.0 SUB_SPACECRAFT_LINE=1001.48 SUB_SPACECRAFT_SAMPLE=548.759 READOUTMODE='NOT APPLICABLE' INTERCEPT_POINT_LINE=400.0 INTERCEPT_POINT_LINE_SAMPLE=400.0 ENTROPY=3.39634 TASK='CATLABEL' USER='AXC040' DAT_TIM='Wed Feb 9 16:36:22 2000' TASK='BADLABEL' USER='AXC040' DAT_TIM='Wed Feb 9 16:36:39 2000' REDR_EXT='1'] at the end. diff --git a/isis/src/base/objs/ProcessImportPds/unitTest.cpp b/isis/src/base/objs/ProcessImportPds/unitTest.cpp index 2d82287b0f7b05bffef56b5577e2148dab8fc5c6..3615a83bfcefcde94f1e4095e90c0680ed2fd6d1 100644 --- a/isis/src/base/objs/ProcessImportPds/unitTest.cpp +++ b/isis/src/base/objs/ProcessImportPds/unitTest.cpp @@ -7,13 +7,14 @@ #include "IString.h" #include "OriginalLabel.h" #include "Statistics.h" +#include "QRegularExpression" using namespace std; using namespace Isis; /** * @internal * @history 2012-05-08 Tracie Sucharski - Moved test data to /usgs/cpks/mer/testData and - * /usgs/cpkgs/clementine1/testData. Added test for invalid label. + * /usgs/cpkgs/clementine1/testData. Added test for invalid label.z */ void IsisMain() { @@ -105,7 +106,7 @@ void IsisMain() { e.print(); } - try{// this file is saved locally since it is not needed in the data area for + try{// this file is saved locally since it is not needed in the data area for // the rest of isis cout << "Testing PDS file containing an ^IMAGE pointer and ^TABLE pointer" << endl; Isis::ProcessImportPds p; @@ -115,7 +116,7 @@ void IsisMain() { p.ImportTable("SUN_POSITION_TABLE"); p.StartProcess(); p.EndProcess(); - + cout << plab << endl; Isis::Process p2; Isis::CubeAttributeInput att; @@ -152,7 +153,7 @@ void IsisMain() { p.SetPdsFile("$galileo/testData/1213r.img", "$galileo/testData/1213r.img", plab); } catch (Isis::IException &e) { - e.print(); + ReportError(e.toString()); } } @@ -162,8 +163,11 @@ void IsisMain() { * @author Jeannie Walldren * @internal * @history 2011-08-05 Jeannie Backer - Copied from Cube class. + * + * @history 2017-05-19 Christopher Combs - Changed to remove paths that would cause the + * cause the test to fail when not using the standard data area. + * Fixes #4738. */ void ReportError(QString err) { - cout << err.replace(QRegExp("\\[[^\\]]*\\]"), "[]") << endl; + cout << err.replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data") << endl; } - diff --git a/isis/src/base/objs/ProcessMosaic/ProcessMosaic.h b/isis/src/base/objs/ProcessMosaic/ProcessMosaic.h index 6c7a38bef452c192924fda19e04d1f494872181b..03b5e7ab56a469db6b5047ba78cbcc505a94e244 100644 --- a/isis/src/base/objs/ProcessMosaic/ProcessMosaic.h +++ b/isis/src/base/objs/ProcessMosaic/ProcessMosaic.h @@ -189,6 +189,9 @@ namespace Isis { * Made destructor virtual. References #2215. * @history 2015-10-04 Jeannie Backer - Fixed SetMosaicOrigin() method to populate the input * images table properly. Fixes #1178 + * @history 2017-05-19 Christopher Combs - Modified unitTest.cpp to truncate paths before date + * directory. Allows test to pass when not using the default data area. + * Fixes #4738. */ class ProcessMosaic : public Process { diff --git a/isis/src/base/objs/ProcessMosaic/ProcessMosaic.truth b/isis/src/base/objs/ProcessMosaic/ProcessMosaic.truth index 2d84b481f4a69763e2d4d31aca2b4645643b9c26..124a1edadeebe555ae1bbac190e07d5009578c4f 100644 --- a/isis/src/base/objs/ProcessMosaic/ProcessMosaic.truth +++ b/isis/src/base/objs/ProcessMosaic/ProcessMosaic.truth @@ -1221,7 +1221,7 @@ Total Bands= "2" ********* Test imagePositions() ******** Name: "ImageLocation" -File: "/usgs/cpkgs/isis3/data/base/testData/isisTruth2.cub" +File: "isisTruth2.cub" StartSample: "1" StartLine: "3" *********************************************************************************** diff --git a/isis/src/base/objs/ProcessMosaic/unitTest.cpp b/isis/src/base/objs/ProcessMosaic/unitTest.cpp index 8c3dff8a6e545c705c4cb31e9ef0bb5ec36b3aab..9cd9fb4a855c3b08dbecd7534839a4f5fed477bd 100644 --- a/isis/src/base/objs/ProcessMosaic/unitTest.cpp +++ b/isis/src/base/objs/ProcessMosaic/unitTest.cpp @@ -325,7 +325,7 @@ void IsisMain() { qDebug() << "********* Test imagePositions() ********"; for (int i = 0; i <= m11.imagePositions().groups() - 1; i++) { qDebug() << "Name: " << m11.imagePositions().group(i).name(); - qDebug() << "File: " << m11.imagePositions().group(i).findKeyword("File")[0]; + qDebug() << "File: " << FileName(m11.imagePositions().group(i).findKeyword("File")[0]).name(); qDebug() << "StartSample: " << m11.imagePositions().group(i).findKeyword("StartSample")[0]; qDebug() << "StartLine: " << m11.imagePositions().group(i).findKeyword("StartLine")[0]; } diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher.cpp b/isis/src/base/objs/ProgramLauncher/ProgramLauncher.cpp index c7366e9f5498159b10726e6ab906a29e0e91d428..495b22998ba79b95a1698b8cc75e94446503233c 100644 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher.cpp +++ b/isis/src/base/objs/ProgramLauncher/ProgramLauncher.cpp @@ -230,4 +230,3 @@ namespace Isis { } } } //end namespace isis - diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher.h b/isis/src/base/objs/ProgramLauncher/ProgramLauncher.h index 282a380b5ad193636d1b3d84bc05b45e947a476a..84e912fb9afde45430fef8604843894b15f44ea0 100644 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher.h +++ b/isis/src/base/objs/ProgramLauncher/ProgramLauncher.h @@ -43,6 +43,9 @@ namespace Isis { * /tmp directory. * @history 2011-08-19 Kelvin Rodriguez - Added truth data for OS X 10.11 * Part of proting to 10.11. + * @history 2017-05-19 Christopher Combs - Modified unitTest.cpp: now creates unitTest.cub to + * perform tests on. Allows test to pass when not using the default data + * area. Fixes #4738. */ class ProgramLauncher { public: diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Darwin_x86_64_MacOSX10_11.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Darwin_x86_64_MacOSX10_11.truth index 785b66ee61cffa5ce1c9a04b7437dd9d93df81c1..1e649de648808ceea4e379854365ce5b2cec3323 100644 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Darwin_x86_64_MacOSX10_11.truth +++ b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Darwin_x86_64_MacOSX10_11.truth @@ -13,30 +13,31 @@ hist: Computing min/max for histogram hist: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group Testing malformed command... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. sh: -c: line 0: unexpected EOF while looking for matching `'' sh: -c: line 1: syntax error: unexpected end of file @@ -47,6 +48,8 @@ Testing non-existant Isis 3 program... **ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. Testing using Isis 3 program as a system program... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. libc++abi.dylib: terminating with uncaught exception of type Isis::IException: **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. **PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [6]. @@ -58,25 +61,24 @@ stats: Computing min/max for histogram stats: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_CentOS7.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_CentOS7.truth index cc367c7b566d4baa99a4188288f7dc4a11e13df4..2c942895d9aee177d6ba294587a3aa09fac00613 100644 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_CentOS7.truth +++ b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_CentOS7.truth @@ -13,30 +13,31 @@ hist: Computing min/max for histogram hist: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group Testing malformed command... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. sh: -c: line 0: unexpected EOF while looking for matching `'' sh: -c: line 1: syntax error: unexpected end of file @@ -47,6 +48,8 @@ Testing non-existant Isis 3 program... **ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. Testing using Isis 3 program as a system program... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. terminate called after throwing an instance of 'Isis::IException' what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. @@ -59,25 +62,24 @@ stats: Computing min/max for histogram stats: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian6_0_2.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian6_0_2.truth deleted file mode 100644 index 2e4710eaf8c287ad37122a41f3f2cc9e48e1d8a3..0000000000000000000000000000000000000000 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian6_0_2.truth +++ /dev/null @@ -1,83 +0,0 @@ -Testing ProgramLauncher Class ... - -Testing ls, grep, sed and pipes ... - -ProgramLauncher.cpp -ProgramLauncher.h -ProgramLauncher.o -ProgramLauncher.truth -Testing stats ... - -hist: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -hist: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group - -Testing malformed command... - -sh: Syntax error: Unterminated quoted string -**PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [512]. - -Testing non-existant Isis 3 program... - -**ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. - -Testing using Isis 3 program as a system program... - -terminate called after throwing an instance of 'Isis::IException' - what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. -Aborted -**PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [34304]. - -Testing using Isis 3 program as a system program without pid... - -stats: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -stats: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian7_0.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian7_0.truth deleted file mode 100644 index be43d9e21404f8b6d3e57021c0c8999540ec24af..0000000000000000000000000000000000000000 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian7_0.truth +++ /dev/null @@ -1,83 +0,0 @@ -Testing ProgramLauncher Class ... - -Testing ls, grep, sed and pipes ... - -ProgramLauncher.cpp -ProgramLauncher.h -ProgramLauncher.o -ProgramLauncher.truth -Testing stats ... - -hist: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -hist: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group - -Testing malformed command... - -sh: 1: Syntax error: Unterminated quoted string -**PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [512]. - -Testing non-existant Isis 3 program... - -**ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. - -Testing using Isis 3 program as a system program... - -terminate called after throwing an instance of 'Isis::IException' - what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. -Aborted -**PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [34304]. - -Testing using Isis 3 program as a system program without pid... - -stats: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -stats: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian8.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian8.truth index be43d9e21404f8b6d3e57021c0c8999540ec24af..1ce9d818fafa046e20b1bc1d3ee80e47ca51badb 100644 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian8.truth +++ b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Debian8.truth @@ -13,30 +13,31 @@ hist: Computing min/max for histogram hist: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group Testing malformed command... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. sh: 1: Syntax error: Unterminated quoted string **PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [512]. @@ -46,6 +47,8 @@ Testing non-existant Isis 3 program... **ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. Testing using Isis 3 program as a system program... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. terminate called after throwing an instance of 'Isis::IException' what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. @@ -59,25 +62,24 @@ stats: Computing min/max for histogram stats: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora16.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora16.truth deleted file mode 100644 index 520477492268f62516370c58c0a801cef3270e39..0000000000000000000000000000000000000000 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora16.truth +++ /dev/null @@ -1,83 +0,0 @@ -Testing ProgramLauncher Class ... - -Testing ls, grep, sed and pipes ... - -ProgramLauncher.cpp -ProgramLauncher.h -ProgramLauncher.o -ProgramLauncher.truth -Testing stats ... - -hist: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -hist: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group - -Testing malformed command... - -sh: -c: line 0: unexpected EOF while looking for matching `'' -sh: -c: line 1: syntax error: unexpected end of file -**PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [256]. - -Testing non-existant Isis 3 program... - -**ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. - -Testing using Isis 3 program as a system program... - -terminate called after throwing an instance of 'Isis::IException' - what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. -**PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [134]. - -Testing using Isis 3 program as a system program without pid... - -stats: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -stats: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora18.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora18.truth deleted file mode 100644 index 520477492268f62516370c58c0a801cef3270e39..0000000000000000000000000000000000000000 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora18.truth +++ /dev/null @@ -1,83 +0,0 @@ -Testing ProgramLauncher Class ... - -Testing ls, grep, sed and pipes ... - -ProgramLauncher.cpp -ProgramLauncher.h -ProgramLauncher.o -ProgramLauncher.truth -Testing stats ... - -hist: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -hist: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group - -Testing malformed command... - -sh: -c: line 0: unexpected EOF while looking for matching `'' -sh: -c: line 1: syntax error: unexpected end of file -**PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [256]. - -Testing non-existant Isis 3 program... - -**ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. - -Testing using Isis 3 program as a system program... - -terminate called after throwing an instance of 'Isis::IException' - what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. -**PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [134]. - -Testing using Isis 3 program as a system program without pid... - -stats: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -stats: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora21.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora21.truth index 520477492268f62516370c58c0a801cef3270e39..f68045ee0f471329de0c6cbb6c227e1a24dbbdfc 100644 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora21.truth +++ b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Fedora21.truth @@ -13,30 +13,31 @@ hist: Computing min/max for histogram hist: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group Testing malformed command... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. sh: -c: line 0: unexpected EOF while looking for matching `'' sh: -c: line 1: syntax error: unexpected end of file @@ -47,6 +48,8 @@ Testing non-existant Isis 3 program... **ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. Testing using Isis 3 program as a system program... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. terminate called after throwing an instance of 'Isis::IException' what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. @@ -59,25 +62,24 @@ stats: Computing min/max for histogram stats: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_SUSE11_3.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_SUSE11_3.truth deleted file mode 100644 index cc367c7b566d4baa99a4188288f7dc4a11e13df4..0000000000000000000000000000000000000000 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_SUSE11_3.truth +++ /dev/null @@ -1,83 +0,0 @@ -Testing ProgramLauncher Class ... - -Testing ls, grep, sed and pipes ... - -ProgramLauncher.cpp -ProgramLauncher.h -ProgramLauncher.o -ProgramLauncher.truth -Testing stats ... - -hist: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -hist: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group - -Testing malformed command... - -sh: -c: line 0: unexpected EOF while looking for matching `'' -sh: -c: line 1: syntax error: unexpected end of file -**PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [256]. - -Testing non-existant Isis 3 program... - -**ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. - -Testing using Isis 3 program as a system program... - -terminate called after throwing an instance of 'Isis::IException' - what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. -**PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [6]. - -Testing using Isis 3 program as a system program without pid... - -stats: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -stats: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu10_04.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu10_04.truth deleted file mode 100644 index 2e4710eaf8c287ad37122a41f3f2cc9e48e1d8a3..0000000000000000000000000000000000000000 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu10_04.truth +++ /dev/null @@ -1,83 +0,0 @@ -Testing ProgramLauncher Class ... - -Testing ls, grep, sed and pipes ... - -ProgramLauncher.cpp -ProgramLauncher.h -ProgramLauncher.o -ProgramLauncher.truth -Testing stats ... - -hist: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -hist: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group - -Testing malformed command... - -sh: Syntax error: Unterminated quoted string -**PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [512]. - -Testing non-existant Isis 3 program... - -**ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. - -Testing using Isis 3 program as a system program... - -terminate called after throwing an instance of 'Isis::IException' - what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. -Aborted -**PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [34304]. - -Testing using Isis 3 program as a system program without pid... - -stats: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -stats: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu12_04.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu12_04.truth deleted file mode 100644 index 9cfb86d6cda860d887d893cef6ece082fd46715d..0000000000000000000000000000000000000000 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu12_04.truth +++ /dev/null @@ -1,83 +0,0 @@ -Testing ProgramLauncher Class ... - -Testing ls, grep, sed and pipes ... - -ProgramLauncher.cpp -ProgramLauncher.h -ProgramLauncher.o -ProgramLauncher.truth -Testing stats ... - -hist: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -hist: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group - -Testing malformed command... - -sh: 1: Syntax error: Unterminated quoted string -**PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [512]. - -Testing non-existant Isis 3 program... - -**ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. - -Testing using Isis 3 program as a system program... - -terminate called after throwing an instance of 'Isis::IException' - what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. -Aborted (core dumped) -**PROGRAMMER ERROR** Executing command [$ISISROOT/bin/stats from=\$base/testData/ab102401_ideal.cub -pid=999 -preference=\$ISISROOT/src/base/objs/Preference/TestPreferences] failed with return status [34304]. - -Testing using Isis 3 program as a system program without pid... - -stats: Computing min/max for histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -stats: Gathering histogram -0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed -Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub - Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 - OverValidMaximumPixels = 0 - UnderValidMinimumPixels = 0 - NullPixels = 353897 - LisPixels = 0 - LrsPixels = 0 - HisPixels = 0 - HrsPixels = 20398 -End_Group diff --git a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu14_04.truth b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu14_04.truth index 9cfb86d6cda860d887d893cef6ece082fd46715d..cb41cef4aedeaae94eea496d3aaa62f566069999 100644 --- a/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu14_04.truth +++ b/isis/src/base/objs/ProgramLauncher/ProgramLauncher_Linux_x86_64_Ubuntu14_04.truth @@ -13,30 +13,31 @@ hist: Computing min/max for histogram hist: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group Testing malformed command... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. sh: 1: Syntax error: Unterminated quoted string **PROGRAMMER ERROR** Executing command [ls -l * | grep Program | sed 's/\(.*\)\(ProgramLauncher.*\)/\2/] failed with return status [512]. @@ -46,6 +47,8 @@ Testing non-existant Isis 3 program... **ERROR** Program [chocolatelab] does not appear to be a valid Isis 3 program. Testing using Isis 3 program as a system program... +NOTE: The exit code for this test differs on each OS. +That is the reason for the OS specific truth files. Please ignore the exit codes. terminate called after throwing an instance of 'Isis::IException' what(): **ERROR** This process (program) was executed by an existing Isis 3 process. However, we failed to establish a communication channel with the parent (launcher) process. The parent process has a PID of [999]. @@ -59,25 +62,24 @@ stats: Computing min/max for histogram stats: Gathering histogram 0% Processed 10% Processed 20% Processed 30% Processed 40% Processed 50% Processed 60% Processed 70% Processed 80% Processed 90% Processed 100% Processed Group = Results - From = /usgs/cpkgs/isis3/data/base/testData/ab102401_ide- - al.cub + From = unitTest.cub Band = 1 - Average = 0.040536894512714 - StandardDeviation = 0.01519314883071 - Variance = 2.30831771392117e-04 - Median = 0.037797920878468 - Mode = 0.034160507255072 - Skew = 0.54083067271281 - Minimum = 0.010204331949353 - Maximum = 0.095491595566273 - Sum = 31525.745547011 - TotalPixels = 1152000 - ValidPixels = 777705 + Average = 24.999999961853 + StandardDeviation = 14.728323083889 + Variance = 216.92350086341 + Median = 24.489967193103 + Mode = 0.0 + Skew = 0.10388815464838 + Minimum = 0.0 + Maximum = 50.0 + Sum = 62499.999904633 + TotalPixels = 2500 + ValidPixels = 2500 OverValidMaximumPixels = 0 UnderValidMinimumPixels = 0 - NullPixels = 353897 + NullPixels = 0 LisPixels = 0 LrsPixels = 0 HisPixels = 0 - HrsPixels = 20398 + HrsPixels = 0 End_Group diff --git a/isis/src/base/objs/ProgramLauncher/unitTest.cpp b/isis/src/base/objs/ProgramLauncher/unitTest.cpp index a8425ce7602a51a86cab67a1343f8f95a53031de..a51e77ab12d9d0b889e48682a4e5aa419d5ac61b 100644 --- a/isis/src/base/objs/ProgramLauncher/unitTest.cpp +++ b/isis/src/base/objs/ProgramLauncher/unitTest.cpp @@ -6,6 +6,7 @@ #include "IString.h" #include "Preference.h" #include "ProgramLauncher.h" +#include "QRegularExpression" using namespace Isis; using namespace std; @@ -23,12 +24,16 @@ void IsisMain() { cerr << "Testing stats ... " << endl; cerr << endl; + ProgramLauncher::RunSystemCommand("greyscale to=unitTest.cub enddn=50.0 samples=50 lines=50"); + ProgramLauncher::RunIsisProgram("stats", - "from=$base/testData/ab102401_ideal.cub " + "from=unitTest.cub " "-preference=$ISISROOT/src/base/objs/Preference/TestPreferences"); cerr << endl; cerr << "Testing malformed command... " << endl; + cerr << "NOTE: The exit code for this test differs on each OS." << endl; + cerr << "That is the reason for the OS specific truth files. Please ignore the exit codes." << endl; cerr << endl; try { ProgramLauncher::RunSystemCommand("ls -l * | grep Program | " @@ -53,6 +58,8 @@ void IsisMain() { cerr << endl; cerr << "Testing using Isis 3 program as a system program... " << endl; + cerr << "NOTE: The exit code for this test differs on each OS." << endl; + cerr << "That is the reason for the OS specific truth files. Please ignore the exit codes." << endl; cerr << endl; try { ProgramLauncher::RunSystemCommand("$ISISROOT/bin/stats " @@ -70,7 +77,7 @@ void IsisMain() { cerr << endl; try { ProgramLauncher::RunSystemCommand("$ISISROOT/bin/stats " - "from=\\$base/testData/ab102401_ideal.cub " + "from=unitTest.cub " "-preference=\\$ISISROOT/src/base/objs/Preference/TestPreferences"); } catch(IException &e) { diff --git a/isis/src/base/objs/ProgramLauncher/unitTest.exclude b/isis/src/base/objs/ProgramLauncher/unitTest.exclude index d612b37cd24078671ef8b73da44ab8081d2ef07e..5edd4a0de1f08da34c73b26bba5361548db64259 100644 --- a/isis/src/base/objs/ProgramLauncher/unitTest.exclude +++ b/isis/src/base/objs/ProgramLauncher/unitTest.exclude @@ -1,3 +1,4 @@ StandardDeviation Variance Skew +Sum diff --git a/isis/src/base/objs/PvlContainer/PvlContainer.cpp b/isis/src/base/objs/PvlContainer/PvlContainer.cpp index 63f2770eb9caccf305783d877da5b77adbe3c370..c58f484bd9588969c0af3213215a7c3a40255dd1 100644 --- a/isis/src/base/objs/PvlContainer/PvlContainer.cpp +++ b/isis/src/base/objs/PvlContainer/PvlContainer.cpp @@ -157,7 +157,7 @@ namespace Isis { for(PvlKeywordIterator key = begin() + index + 1; key < end(); key ++) { if(current == *key) { - m_keywords.erase(key); + key = m_keywords.erase(key); keywordDeleted = true; } } diff --git a/isis/src/base/objs/PvlContainer/PvlContainer.h b/isis/src/base/objs/PvlContainer/PvlContainer.h index a7af546e5f6b199b15e25ed559330cda970bd8d8..46c136ce2c4b582fce991ddf65573c5f6c1b0b9e 100644 --- a/isis/src/base/objs/PvlContainer/PvlContainer.h +++ b/isis/src/base/objs/PvlContainer/PvlContainer.h @@ -2,8 +2,6 @@ #define PvlContainer_h /** * @file - * $Revision: 1.12 $ - * $Date: 2010/04/14 00:21:53 $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for @@ -60,6 +58,7 @@ namespace Isis { * @history 2010-10-18 Sharmila Prasad - Added more options for the keyword validation * @history 2013-03-11 Steven Lambright and Mathew Eis - Brought method names and member variable * names up to the current Isis 3 coding standards. Fixes #1533. + * @history 2015-05-15 J Bonn - fixed usage of iterator that had been deleted. */ class PvlContainer { public: diff --git a/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.cpp b/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.cpp index e48388e505f90a8238bbcf1fb9eeb6f0229b0413..d22924b802cf1968e9b6f8065d19ad70d491309c 100644 --- a/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.cpp +++ b/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.cpp @@ -19,19 +19,48 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. */ +#include "LabelTranslationManager.h" +#include "IException.h" #include "IString.h" #include "Message.h" -#include "IException.h" +#include "Pvl.h" +#include "PvlContainer.h" +#include "PvlGroup.h" +#include "PvlKeyword.h" +#include "PvlObject.h" #include "PvlTranslationManager.h" using namespace std; namespace Isis { - PvlTranslationManager::PvlTranslationManager(const QString &transFile) { - AddTable(transFile); + /** + * Constructs and initializes a TranslationManager object from given the + * Pvl translation file. If this constructor is used, the user will need to + * set the input label before translating. This may be done by using + * SetLabel(Pvl inputLabel) or Auto(Pvl inputLabel, Pvl outputLabel). + * + * @param transFile The translation file to be used to tranlate keywords in + * the input label. + */ + PvlTranslationManager::PvlTranslationManager(const QString &transFile) + : LabelTranslationManager(transFile) { + } + + /** + * Constructs and initializes a TranslationManager object from the given + * input stream. If this constructor is used, the user will need to set the + * input label before translating. This may be done by using SetLabel(Pvl + * inputLabel) or Auto(Pvl inputLabel, Pvl outputLabel). + * + * @param transStrm A stream containing the tranlation table to be used to + * tranlate keywords in the input label. + */ + PvlTranslationManager::PvlTranslationManager(std::istream &transStrm) + : LabelTranslationManager(transStrm) { } + /** * Constructs and initializes a TranslationManager object * @@ -40,14 +69,13 @@ namespace Isis { * @param transFile The translation file to be used to tranlate keywords in * the input label. */ - PvlTranslationManager::PvlTranslationManager(Isis::Pvl &inputLabel, - const QString &transFile) { + PvlTranslationManager::PvlTranslationManager(Pvl &inputLabel, + const QString &transFile) + : LabelTranslationManager(transFile) { p_fLabel = inputLabel; - - // Internalize the translation table - AddTable(transFile); } + /** * Constructs and initializes a TranslationManager object * @@ -56,14 +84,23 @@ namespace Isis { * @param transStrm A stream containing the tranlation table to be used to * tranlate keywords in the input label. */ - PvlTranslationManager::PvlTranslationManager(Isis::Pvl &inputLabel, - std::istream &transStrm) { + PvlTranslationManager::PvlTranslationManager(Pvl &inputLabel, + std::istream &transStrm) + : LabelTranslationManager(transStrm) { p_fLabel = inputLabel; + } + - // Internalize the translation table - AddTable(transStrm); + //! Destroys the TranslationManager object. + PvlTranslationManager::~PvlTranslationManager() { } + + void PvlTranslationManager::SetLabel(Pvl &inputLabel) { + p_fLabel = inputLabel; + } + + /** * Returns a translated value. The output name is used to find the input * group, keyword, default and tranlations in the translation table. If the @@ -80,7 +117,7 @@ namespace Isis { * @return string */ QString PvlTranslationManager::Translate(QString nName, int findex) { - const Isis::PvlContainer *con; + const PvlContainer *con; int inst = 0; PvlKeyword grp; @@ -93,9 +130,10 @@ namespace Isis { } } - return Isis::PvlTranslationTable::Translate(nName); + return PvlTranslationTable::Translate(nName); } + /** * Translate the requested output name to output values using the input name * and values or default value @@ -103,12 +141,11 @@ namespace Isis { * @param nName The output name used to identify the input keyword to be * translated. * - * @return Isis::PvlKeyword + * @return PvlKeyword */ - Isis::PvlKeyword PvlTranslationManager::DoTranslation( - const QString nName) { - const Isis::PvlContainer *con = NULL; - Isis::PvlKeyword key; + PvlKeyword PvlTranslationManager::DoTranslation(const QString nName) { + const PvlContainer *con = NULL; + PvlKeyword key; int inst = 0; PvlKeyword grp; @@ -119,7 +156,7 @@ namespace Isis { key.setName(OutputName(nName)); for(int v = 0; v < (*con)[(InputKeywordName(nName))].size(); v++) { - key.addValue(Isis::PvlTranslationTable::Translate(nName, + key.addValue(PvlTranslationTable::Translate(nName, (*con)[InputKeywordName(nName)][v]), (*con)[InputKeywordName(nName)].unit(v)); } @@ -129,24 +166,37 @@ namespace Isis { } } - return Isis::PvlKeyword(OutputName(nName), + return PvlKeyword(OutputName(nName), PvlTranslationTable::Translate(nName, "")); } + /** + * Automatically translate all the output names found in the translation table + * If a output name does not translate an error will be thrown by one + * of the support members + * Store the translated key, value pairs in the argument pvl + */ + void PvlTranslationManager::Auto(Pvl &inputLabel, Pvl &outputLabel) { + p_fLabel = inputLabel; + Auto(outputLabel); + } + - // Automatically translate all the output names found in the translation table - // If a output name does not translate an error will be thrown by one - // of the support members - // Store the translated key, value pairs in the argument pvl - void PvlTranslationManager::Auto(Isis::Pvl &outputLabel) { + /** + * Automatically translate all the output names found in the translation table + * If a output name does not translate an error will be thrown by one + * of the support members + * Store the translated key, value pairs in the argument pvl + */ + void PvlTranslationManager::Auto(Pvl &outputLabel) { // Attempt to translate every group in the translation table for(int i = 0; i < TranslationTable().groups(); i++) { - Isis::PvlGroup &g = TranslationTable().group(i); + PvlGroup &g = TranslationTable().group(i); if(IsAuto(g.name())) { try { - Isis::PvlContainer *con = CreateContainer(g.name(), outputLabel); - (*con) += PvlTranslationManager::DoTranslation(g.name()); + PvlContainer *con = CreateContainer(g.name(), outputLabel); + (*con) += DoTranslation(g.name()); } catch(IException &e) { if(!IsOptional(g.name())) { @@ -157,6 +207,7 @@ namespace Isis { } } + /** * Returns the ith input value assiciated with the output name argument. * @@ -164,10 +215,9 @@ namespace Isis { * * @param findex The index into the input keyword array. Defaults to 0 * - * @throws Isis::IException::Programmer + * @throws IException::Programmer */ - const PvlKeyword &PvlTranslationManager::InputKeyword( - const QString nName) const { + const PvlKeyword &PvlTranslationManager::InputKeyword(const QString nName) const { int instanceNumber = 0; PvlKeyword inputGroupKeyword = InputGroup(nName, instanceNumber); @@ -218,7 +268,7 @@ namespace Isis { // Set the current position in the input label pvl // by finding the input group corresponding to the output group - const Isis::PvlContainer *con; + const PvlContainer *con; int inst = 0; //while ((con = GetContainer(InputGroup(nName, inst++))) != NULL) { //if ((con = GetContainer (InputGroup(nName))) != NULL) { @@ -233,25 +283,9 @@ namespace Isis { return false; } - /* - * Indicates if the input group corresponding to the output name exists in - * the label - * - * @param nName The output name used to identify the input keyword. - - bool PvlTranslationManager::InputHasGroup (const QString nName) { - - if (GetContainer (InputGroup(nName)) != NULL) { - return true; - } - - return false; - } - */ - // Return a container from the input label according tund - const Isis::PvlContainer *PvlTranslationManager::GetContainer( - const PvlKeyword &inputGroup) const { + //! Return a container from the input label according tund + const PvlContainer *PvlTranslationManager::GetContainer(const PvlKeyword &inputGroup) const { // Return the root container if "ROOT" is the ONLY thing in the list @@ -260,7 +294,7 @@ namespace Isis { return &p_fLabel; } - const Isis::PvlObject *currentObject = &p_fLabel; + const PvlObject *currentObject = &p_fLabel; // Search for object containing our solution int objectIndex; @@ -288,38 +322,12 @@ namespace Isis { } - // Create the requsted container and any containers above it and - // return a reference to the container - // list is an Isis::PvlKeyword with an array of container types an their names - Isis::PvlContainer *PvlTranslationManager::CreateContainer(const QString nName, - Isis::Pvl &pvl) { - - // Get the array of Objects/Groups from the OutputName keyword - Isis::PvlKeyword np = OutputPosition(nName); - - Isis::PvlObject *obj = &pvl; - - // Look at every pair in the output position - for(int c = 0; c < np.size(); c += 2) { - // If this pair is an object - if(np[c].toUpper() == "OBJECT") { - // If the object doesn't exist create it - if(!obj->hasObject(np[c+1])) { - obj->addObject(np[c+1]); - } - obj = &(obj->findObject(np[c+1])); - } - // If this pair is a group - else if(np[c].toUpper() == "GROUP") { - // If the group doesn't exist create it - if(!obj->hasGroup(np[c+1])) { - obj->addGroup(np[c+1]); - } - return (Isis::PvlContainer *) & (obj->findGroup(np[c+1])); - - } - } - - return (Isis::PvlContainer *) obj; + /** + * Create the requsted container and any containers above it and + * return a reference to the container + * list is an PvlKeyword with an array of container types an their names + */ + PvlContainer *PvlTranslationManager::CreateContainer(const QString nName, Pvl &pvl) { + return LabelTranslationManager::CreateContainer(nName, pvl); } } // end namespace isis diff --git a/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.h b/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.h index 30a42f1a2a1d19d6f1d68b2551c5e87abfa9dcd5..c4d8e1912da28b4f11d1ef974461d62f82e010ee 100644 --- a/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.h +++ b/isis/src/base/objs/PvlTranslationManager/PvlTranslationManager.h @@ -21,15 +21,18 @@ * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on * http://www.usgs.gov/privacy.html. */ +#include "LabelTranslationManager.h" -#include #include +#include #include "FileName.h" #include "PvlTokenizer.h" -#include "PvlTranslationTable.h" namespace Isis { + class Pvl; + class PvlContainer; + class PvlKeyword; /** * @brief Allows applications to translate simple text files * @@ -68,46 +71,48 @@ namespace Isis { * DoTranslation to remove ambiguity * with a parent method, instead of * using a dummy parameter. + * @history 2017-01-11 Jeannie Backer - Moved several methods to a generic + * parent class, LabelTranslationManager. Fixes #4584. * @todo 2005-02-15 Stuart Sides - add coded example and implementation example * to class documentation, and finish * documentation */ - class PvlTranslationManager : public PvlTranslationTable { + class PvlTranslationManager : public LabelTranslationManager { public: PvlTranslationManager(const QString &transFile); - PvlTranslationManager(Isis::Pvl &inputLabel, + PvlTranslationManager(std::istream &transStrm); + + PvlTranslationManager(Pvl &inputLabel, const QString &transFile); - PvlTranslationManager(Isis::Pvl &inputLabel, + PvlTranslationManager(Pvl &inputLabel, std::istream &transStrm); - //! Destroys the TranslationManager object. - ~PvlTranslationManager() {}; + virtual ~PvlTranslationManager(); // Attempt to translate the requested output name to output value // using the input name and value/default value - QString Translate(QString nName, int findex = 0); + virtual QString Translate(QString nName, int findex = 0); // Translate all translation table groups which contain "Auto" - void Auto(Isis::Pvl &outputLabel); + void Auto(Pvl &outputLabel); + void Auto(Pvl &inputLabel, Pvl &outputLabel); // Return the ith input value associated with a output name - const PvlKeyword &InputKeyword(const QString nName) const; + virtual const PvlKeyword &InputKeyword(const QString nName) const; // Return true if the input lable contains the translated group and key names - bool InputHasKeyword(const QString nName); + virtual bool InputHasKeyword(const QString nName); - void SetLabel(Isis::Pvl &lab) { - p_fLabel = lab; - } - private: - - Isis::Pvl p_fLabel; //!> p_trnsTbl; } + //! Construct an empty PvlTranslationTable PvlTranslationTable::PvlTranslationTable() { } + + //! Destroys the PvlTranslationTable object. + PvlTranslationTable::~PvlTranslationTable() { + } + + + //! Protected accessor for pvl translation table passed into class. + Pvl &PvlTranslationTable::TranslationTable() { + return p_trnsTbl; + } + + + //! Protected accessor for const pvl translation table passed into class. + const Pvl &PvlTranslationTable::TranslationTable() const { + return p_trnsTbl; + } + + /** * Adds the contents of a translation table to the searchable groups/keys * @@ -67,6 +87,7 @@ namespace Isis { p_trnsTbl.read(FileName(transFile).expanded()); } + /** * Adds the contents of a translation table to the searchable groups/keys * Also performs a verification, to ensure that the translation table @@ -76,6 +97,10 @@ namespace Isis { */ void PvlTranslationTable::AddTable(std::istream &transStm) { transStm >> p_trnsTbl; + + // pair< name, size > of acceptable keywords. + // A size of -1 means non-zero size. + vector< pair > validKeywordSizes = validKeywords(); for(int i = 0; i < p_trnsTbl.groups(); i++) { PvlGroup currGrp = p_trnsTbl.group(i); @@ -87,20 +112,6 @@ namespace Isis { throw IException(IException::User, message, _FILEINFO_); } - // pair< name, size > of acceptable keywords. - // A size of -1 means non-zero size. - vector< pair > validKeywords; - - validKeywords.push_back(pair("Translation", 2)); - validKeywords.push_back(pair("OutputName", 1)); - validKeywords.push_back(pair("InputGroup", -1)); - validKeywords.push_back(pair("InputPosition", -1)); - validKeywords.push_back(pair("OutputPosition", -1)); - validKeywords.push_back(pair("Auto", 0)); - validKeywords.push_back(pair("Optional", 0)); - validKeywords.push_back(pair("InputKey", 1)); - validKeywords.push_back(pair("InputDefault", -1)); - for(int j = 0; j < currGrp.keywords(); j++) { bool validKeyword = false; bool keywordSizeMismatch = false; @@ -109,20 +120,20 @@ namespace Isis { // Test this keyword for validity for(int key = 0; - !validKeyword && key < (int)validKeywords.size(); + !validKeyword && key < (int)validKeywordSizes.size(); key++) { // If this is the right keyword (names match) then test sizes - if(currKey.name() == validKeywords[key].first) { + if(currKey.name() == validKeywordSizes[key].first) { // if -1 then test that size() > 0 - if(validKeywords[key].second == -1) { + if(validKeywordSizes[key].second == -1) { if(currKey.size() > 0) { validKeyword = true; } } // otherwise should exact match - else if(currKey.size() == validKeywords[key].second) { + else if(currKey.size() == validKeywordSizes[key].second) { validKeyword = true; } else { @@ -153,6 +164,30 @@ namespace Isis { } } } + + + /** + * Returns a vector of valid keyword names and their sizes. A size of -1 + * indicates that the keyword can be any size. + * + * @return @b vector> A vector of valid keyword names and their sizes. + */ + vector< pair > PvlTranslationTable::validKeywords() const { + + vector< pair > validKeywords; + validKeywords.push_back(pair("Translation", 2)); + validKeywords.push_back(pair("OutputName", 1)); + validKeywords.push_back(pair("InputGroup", -1)); + validKeywords.push_back(pair("InputPosition", -1)); + validKeywords.push_back(pair("OutputPosition", -1)); + validKeywords.push_back(pair("Auto", 0)); + validKeywords.push_back(pair("Optional", 0)); + validKeywords.push_back(pair("InputKey", 1)); + validKeywords.push_back(pair("InputDefault", -1)); + + return validKeywords; + } + /** * Translates the output name and input value. @@ -220,6 +255,7 @@ namespace Isis { throw IException(IException::Programmer, msg, _FILEINFO_); } + /** * Returns the input group name from the translation table corresponding to * the output name argument. @@ -251,7 +287,7 @@ namespace Isis { int currentInstance = 0; - // If no InputGroup keywords exist, the answer is root + // If no InputPosition keyword exists, the answer is root if(inst == 0 && it == transGrp.end()) { PvlKeyword root("InputPosition"); root += "ROOT"; @@ -298,6 +334,7 @@ namespace Isis { return empty; } + /** * Returns the input keyword name from the translation table corresponding to * the output name argument. @@ -316,12 +353,13 @@ namespace Isis { throw IException(IException::Programmer, msg, _FILEINFO_); } - Isis::PvlGroup tgrp = p_trnsTbl.findGroup(nName); + PvlGroup tgrp = p_trnsTbl.findGroup(nName); if(tgrp.hasKeyword("InputKey")) return tgrp["InputKey"]; return ""; } + /** * Returns the input default value from the translation table corresponding * to the output name argument. @@ -340,12 +378,25 @@ namespace Isis { throw IException(IException::Programmer, msg, _FILEINFO_); } - Isis::PvlGroup tgrp = p_trnsTbl.findGroup(nName); + PvlGroup tgrp = p_trnsTbl.findGroup(nName); if(tgrp.hasKeyword("InputDefault")) return tgrp["InputDefault"]; return ""; } + bool PvlTranslationTable::hasInputDefault(const QString nName) { + if(!p_trnsTbl.hasGroup(nName)) { + QString msg = "Unable to find translation group [" + nName + + "] in file [" + p_trnsTbl.fileName() + "]"; + throw IException(IException::Programmer, msg, _FILEINFO_); + } + + PvlGroup &tgrp = p_trnsTbl.findGroup(nName); + if(tgrp.hasKeyword("InputDefault")) return true; + + return false; + } + bool PvlTranslationTable::IsAuto(const QString nName) { if(!p_trnsTbl.hasGroup(nName)) { QString msg = "Unable to find translation group [" + nName + @@ -353,7 +404,7 @@ namespace Isis { throw IException(IException::Programmer, msg, _FILEINFO_); } - Isis::PvlGroup &tgrp = p_trnsTbl.findGroup(nName); + PvlGroup &tgrp = p_trnsTbl.findGroup(nName); if(tgrp.hasKeyword("Auto")) return true; return false; @@ -366,21 +417,20 @@ namespace Isis { throw IException(IException::Programmer, msg, _FILEINFO_); } - Isis::PvlGroup &tgrp = p_trnsTbl.findGroup(nName); + PvlGroup &tgrp = p_trnsTbl.findGroup(nName); if(tgrp.hasKeyword("Optional")) return true; return false; } - Isis::PvlKeyword &PvlTranslationTable::OutputPosition( - const QString nName) { + PvlKeyword &PvlTranslationTable::OutputPosition(const QString nName) { if(!p_trnsTbl.hasGroup(nName)) { QString msg = "Unable to find translation group [" + nName + "] in file [" + p_trnsTbl.fileName() + "]"; throw IException(IException::Programmer, msg, _FILEINFO_); } - Isis::PvlGroup &tgrp = p_trnsTbl.findGroup(nName); + PvlGroup &tgrp = p_trnsTbl.findGroup(nName); if(!tgrp.hasKeyword("OutputPosition")) { QString msg = "Unable to find translation keyword [OutputPostion] in [" + nName + "] in file [" + p_trnsTbl.fileName() + "]"; @@ -399,7 +449,7 @@ namespace Isis { throw IException(IException::Programmer, msg, _FILEINFO_); } - Isis::PvlGroup tgrp = p_trnsTbl.findGroup(nName); + PvlGroup tgrp = p_trnsTbl.findGroup(nName); if(tgrp.hasKeyword("OutputName")) { return tgrp["OutputName"]; } diff --git a/isis/src/base/objs/PvlTranslationTable/PvlTranslationTable.h b/isis/src/base/objs/PvlTranslationTable/PvlTranslationTable.h index 792100e727861dee9345f813d1ddc43b2f680c8b..1ddaf352b2c083a43f992e3bbc69a139359773f4 100644 --- a/isis/src/base/objs/PvlTranslationTable/PvlTranslationTable.h +++ b/isis/src/base/objs/PvlTranslationTable/PvlTranslationTable.h @@ -126,18 +126,17 @@ namespace Isis { public: // Constructors - PvlTranslationTable(Isis::FileName transFile); + PvlTranslationTable(FileName transFile); PvlTranslationTable(std::istream &istr); PvlTranslationTable(); - //! Destroys the PvlTranslationTable object. - ~PvlTranslationTable() { }; + virtual ~PvlTranslationTable(); // Return the associated input group from the trans table - PvlKeyword InputGroup(const QString nName, const int inst = 0) const; + virtual PvlKeyword InputGroup(const QString nName, const int inst = 0) const; // Return the associated input keyword name from the trans table - QString InputKeywordName(const QString nName) const; + virtual QString InputKeywordName(const QString nName) const; // Return the associated input default value from the trans table QString InputDefault(const QString nName) const; @@ -150,13 +149,11 @@ namespace Isis { void AddTable(const QString &transFile); protected: - Pvl &TranslationTable() { - return p_trnsTbl; - } - const Pvl &TranslationTable() const { - return p_trnsTbl; - } + Pvl &TranslationTable(); + const Pvl &TranslationTable() const; + virtual std::vector< std::pair > validKeywords() const; + bool hasInputDefault(const QString nName); bool IsAuto(const QString nName); bool IsOptional(const QString nName); PvlKeyword &OutputPosition(const QString nName); diff --git a/isis/src/base/objs/Sensor/Sensor.truth b/isis/src/base/objs/Sensor/Sensor.truth index e326cc928d86e9a1f25fc2ace1c0a20ee324ae81..49c3b7661c2d4e025827f4056a184c545bb1b5e0 100644 --- a/isis/src/base/objs/Sensor/Sensor.truth +++ b/isis/src/base/objs/Sensor/Sensor.truth @@ -7,8 +7,8 @@ Longitude = 226.1634 Point = -1938.87 -2019.2509 1911.8602 Local Radius = 3389955.8 Phase = 86.285045 -Emission = 0.25072288 -Incidence = 86.142522 +Emission = 0.14421565 +Incidence = 86.225373 Look Direction = -2.220446e-16 -1.6653345e-16 1 Spacecraft Surface Vector = 0.56921896 0.5950668 -0.56734934 Slant Distance = 170.66603 @@ -22,8 +22,8 @@ Longitude = 225.81107 Point = -2010.048 -2067.7771 1783.8147 Local Radius = 3390868.6 Phase = 85.492574 -Emission = 0.24295659 -Incidence = 85.352414 +Emission = 0.14002742 +Incidence = 85.431674 Look Direction = -1.110223e-16 0 1 Spacecraft Surface Vector = 0.59021578 0.60939776 -0.52941449 Slant Distance = 171.72738 @@ -37,8 +37,8 @@ Longitude = 225.47082 Point = -2077.2235 -2111.6458 1652.2701 Local Radius = 3391740.3 Phase = 84.708581 -Emission = 0.23393131 -Incidence = 84.572519 +Emission = 0.13352229 +Incidence = 84.647314 Look Direction = -1.110223e-16 -2.220446e-16 1 Spacecraft Surface Vector = 0.61004873 0.62233527 -0.49044813 Slant Distance = 176.2139 @@ -52,8 +52,8 @@ Longitude = 225.14107 Point = -2140.1559 -2150.7204 1517.7659 Local Radius = 3392562.3 Phase = 83.939733 -Emission = 0.22780812 -Incidence = 83.805516 +Emission = 0.12485404 +Incidence = 83.875079 Look Direction = 2.220446e-16 -1.110223e-16 1 Spacecraft Surface Vector = 0.62858924 0.63386318 -0.45065844 Slant Distance = 184.11191 @@ -67,8 +67,8 @@ Longitude = 224.82075 Point = -2198.6247 -2184.9109 1380.8989 Local Radius = 3393327 Phase = 83.184275 -Emission = 0.21456725 -Incidence = 83.054372 +Emission = 0.11978455 +Incidence = 83.118064 Look Direction = 2.7755576e-16 -2.220446e-16 1 Spacecraft Surface Vector = 0.64585959 0.64398006 -0.41006716 Slant Distance = 195.39355 @@ -82,8 +82,8 @@ Longitude = 224.50888 Point = -2252.4794 -2214.1913 1242.2234 Local Radius = 3394028 Phase = 82.446678 -Emission = 0.20351038 -Incidence = 82.321543 +Emission = 0.11094563 +Incidence = 82.378862 Look Direction = 2.7755576e-16 1.6653345e-16 1 Spacecraft Surface Vector = 0.66176458 0.65261669 -0.36899741 Slant Distance = 210.01719 @@ -97,8 +97,8 @@ Longitude = 224.2044 Point = -2301.6035 -2238.5554 1102.3637 Local Radius = 3394659.7 Phase = 81.728891 -Emission = 0.18483679 -Incidence = 81.609391 +Emission = 0.10804949 +Incidence = 81.659984 Look Direction = 1.110223e-16 0 1 Spacecraft Surface Vector = 0.67629688 0.65985385 -0.32743768 Slant Distance = 227.92865 @@ -112,8 +112,8 @@ Longitude = 223.90671 Point = -2345.9387 -2258.0764 961.85791 Local Radius = 3395218.4 Phase = 81.033212 -Emission = 0.16878349 -Incidence = 80.919995 +Emission = 0.10119439 +Incidence = 80.963652 Look Direction = 1.110223e-16 1.6653345e-16 1 Spacecraft Surface Vector = 0.68941526 0.66562283 -0.28574963 Slant Distance = 249.06263 @@ -127,8 +127,8 @@ Longitude = 223.61515 Point = -2385.4609 -2272.8465 821.29857 Local Radius = 3395701.2 Phase = 80.359554 -Emission = 0.14790274 -Incidence = 80.25532 +Emission = 0.095131558 +Incidence = 80.291979 Look Direction = -1.110223e-16 -1.6653345e-16 1 Spacecraft Surface Vector = 0.70114803 0.66997788 -0.24396942 Slant Distance = 273.34447 @@ -142,8 +142,8 @@ Longitude = 223.32865 Point = -2420.2184 -2282.9842 681.22342 Local Radius = 3396106.5 Phase = 79.71488 -Emission = 0.12669945 -Incidence = 79.616456 +Emission = 0.09414848 +Incidence = 79.646192 Look Direction = -5.5511151e-17 -1.110223e-16 1 Spacecraft Surface Vector = 0.71143216 0.67301795 -0.20226496 Slant Distance = 300.69043 @@ -161,8 +161,8 @@ Longitude = 223.32865 Point = -2420.2184 -2282.9842 681.22342 Local Radius = 3396106.5 Phase = 79.71488 -Emission = 0.12669945 -Incidence = 79.616456 +Emission = 0.094148483 +Incidence = 79.646192 Look Direction = 1.0772112e-09 1.738141e-08 300.69043 Spacecraft Surface Vector = 213.92084 202.37006 -60.819137 Slant Distance = 300.69043 @@ -178,8 +178,8 @@ Radius = 3400 Point = -2.4229931 -2.2856015 0.68200442 Local Radius = 3400 Phase = 79.62357 -Emission = 0.010314973 -Incidence = 79.615558 +Emission = 0.13936281 +Incidence = 79.645294 Look Direction = -6.0874283 -4.3850492 3693.3886 Spacecraft Surface Vector = 2631.7163 2483.0686 -741.36055 Slant Distance = 3693.3962 @@ -199,8 +199,8 @@ Longitude = 226.16335 Point = -1938.0269 -2018.3696 1911.02 Local Radius = 3388474.8 Phase = 86.285045 -Emission = 0.25083247 -Incidence = 86.14246 +Emission = 0.14415892 +Incidence = 86.22531 Look Direction = -2.220446e-16 -1.6653345e-16 1 Spacecraft Surface Vector = 0.56921896 0.5950668 -0.56734934 Slant Distance = 172.14707 @@ -214,8 +214,8 @@ Longitude = 225.81103 Point = -2009.2393 -2066.9421 1783.0892 Local Radius = 3389498.4 Phase = 85.492573 -Emission = 0.24305481 -Incidence = 85.352357 +Emission = 0.13997938 +Incidence = 85.431617 Look Direction = -1.110223e-16 0 1 Spacecraft Surface Vector = 0.59021578 0.60939776 -0.52941449 Slant Distance = 173.09763 @@ -229,8 +229,8 @@ Longitude = 225.47081 Point = -2077.0054 -2111.4234 1652.0948 Local Radius = 3391382.8 Phase = 84.708581 -Emission = 0.23395596 -Incidence = 84.572505 +Emission = 0.13351092 +Incidence = 84.647299 Look Direction = -1.110223e-16 -2.220446e-16 1 Spacecraft Surface Vector = 0.61004873 0.62233527 -0.49044813 Slant Distance = 176.57132 @@ -244,8 +244,8 @@ Longitude = 225.14104 Point = -2139.6639 -2150.2242 1517.4132 Local Radius = 3391779.6 Phase = 83.939733 -Emission = 0.22786069 -Incidence = 83.805485 +Emission = 0.12483346 +Incidence = 83.875047 Look Direction = 2.220446e-16 -1.110223e-16 1 Spacecraft Surface Vector = 0.62858924 0.63386318 -0.45065844 Slant Distance = 184.8946 @@ -259,8 +259,8 @@ Longitude = 224.82071 Point = -2197.6988 -2183.9877 1380.311 Local Radius = 3391893.4 Phase = 83.184275 -Emission = 0.21465793 -Incidence = 83.054317 +Emission = 0.11975426 +Incidence = 83.118009 Look Direction = 2.7755576e-16 -2.220446e-16 1 Spacecraft Surface Vector = 0.64585959 0.64398006 -0.41006716 Slant Distance = 196.8271 @@ -274,8 +274,8 @@ Longitude = 224.50911 Point = -2258.1772 -2219.8103 1245.4005 Local Radius = 3402637.9 Phase = 82.44668 -Emission = 0.20299542 -Incidence = 82.321862 +Emission = 0.11107759 +Incidence = 82.379182 Look Direction = 2.7755576e-16 1.6653345e-16 1 Spacecraft Surface Vector = 0.66176458 0.65261669 -0.36899741 Slant Distance = 201.4072 @@ -289,8 +289,8 @@ Longitude = 224.20475 Point = -2310.6415 -2247.3737 1106.7396 Local Radius = 3408023.6 Phase = 81.728894 -Emission = 0.18411199 -Incidence = 81.609863 +Emission = 0.10818315 +Incidence = 81.660457 Look Direction = 1.110223e-16 0 1 Spacecraft Surface Vector = 0.67629688 0.65985385 -0.32743768 Slant Distance = 214.56472 @@ -304,8 +304,8 @@ Longitude = 223.907 Point = -2353.6501 -2265.5217 965.05413 Local Radius = 3406403.8 Phase = 81.033215 -Emission = 0.16822926 -Incidence = 80.92037 +Emission = 0.10124195 +Incidence = 80.964028 Look Direction = 1.110223e-16 1.6653345e-16 1 Spacecraft Surface Vector = 0.68941526 0.66562283 -0.28574963 Slant Distance = 237.87722 @@ -319,8 +319,8 @@ Longitude = 223.61517 Point = -2386.1476 -2273.5027 821.53751 Local Radius = 3396680.5 Phase = 80.359554 -Emission = 0.1478601 -Incidence = 80.255351 +Emission = 0.095131742 +Incidence = 80.292009 Look Direction = -1.110223e-16 -1.6653345e-16 1 Spacecraft Surface Vector = 0.70114803 0.66997788 -0.24396942 Slant Distance = 272.36511 @@ -334,8 +334,8 @@ Longitude = 223.32861 Point = -2419.1314 -2281.9558 680.91437 Local Radius = 3394578.5 Phase = 79.714879 -Emission = 0.12675648 -Incidence = 79.616411 +Emission = 0.094155978 +Incidence = 79.646147 Look Direction = -5.5511151e-17 -1.110223e-16 1 Spacecraft Surface Vector = 0.71143216 0.67301795 -0.20226496 Slant Distance = 302.21838 @@ -353,8 +353,8 @@ Longitude = 223.32865 Point = -2419.1295 -2281.957 680.91693 Local Radius = 3394578.5 Phase = 79.714382 -Emission = 0.12605889 -Incidence = 79.616456 +Emission = 0.094063307 +Incidence = 79.646192 Look Direction = -0.002741531 -0.0019748318 302.21836 Spacecraft Surface Vector = 215.00972 203.39719 -61.125625 Slant Distance = 302.21837 @@ -370,8 +370,8 @@ Radius = 3400 Point = -2.4229931 -2.2856015 0.68200442 Local Radius = 3400 Phase = 79.62357 -Emission = 0.010314973 -Incidence = 79.615558 +Emission = 0.13936281 +Incidence = 79.645294 Look Direction = -6.0874283 -4.3850492 3693.3886 Spacecraft Surface Vector = 2631.7163 2483.0686 -741.36055 Slant Distance = 3693.3962 diff --git a/isis/src/base/objs/SerialNumberList/SerialNumberList.cpp b/isis/src/base/objs/SerialNumberList/SerialNumberList.cpp index a3d0480e4823eec6656ae641e6b8a0c5a1c60bd2..b8951e1720c3c24f71459ec6da850a34c5758166 100644 --- a/isis/src/base/objs/SerialNumberList/SerialNumberList.cpp +++ b/isis/src/base/objs/SerialNumberList/SerialNumberList.cpp @@ -201,7 +201,7 @@ namespace Isis { /** * @brief Overloaded add method that takes char * parameters * - * @description Adds a new filename / serial number pair to the SerialNumberList + * Adds a new filename / serial number pair to the SerialNumberList * * @param serialNumber The serial number to be added * @param filename The filename to be added diff --git a/isis/src/base/objs/ShapeModel/ShapeModel.cpp b/isis/src/base/objs/ShapeModel/ShapeModel.cpp index 37d7142d64e677e0d2e0bde0ca45d0745410948b..942591c8266aae3d4f4a2b1f2d658d26c1ffa1e8 100644 --- a/isis/src/base/objs/ShapeModel/ShapeModel.cpp +++ b/isis/src/base/objs/ShapeModel/ShapeModel.cpp @@ -1,7 +1,8 @@ #include "ShapeModel.h" #include - +#include +#include #include #include #include @@ -75,35 +76,6 @@ namespace Isis { } - /** - * Calculates the ellipsoidal surface normal. - */ - void ShapeModel::calculateEllipsoidalSurfaceNormal() { - // The below code is not truly normal unless the ellipsoid is a sphere. TODO Should this be - // fixed? Send an email asking Jeff and Stuart. See Naif routine surfnm.c to get the true - // for an ellipsoid. For testing purposes to match old results do as Isis3 currently does until - // Jeff and Stuart respond. - - if (!m_hasIntersection || !surfaceIntersection()->Valid()) { - QString msg = "A valid intersection must be defined before computing the surface normal"; - throw IException(IException::Programmer, msg, _FILEINFO_); - } - - // Get the coordinates of the current surface point - SpiceDouble pB[3]; - pB[0] = surfaceIntersection()->GetX().kilometers(); - pB[1] = surfaceIntersection()->GetY().kilometers(); - pB[2] = surfaceIntersection()->GetZ().kilometers(); - - // Unitize the vector - SpiceDouble upB[3]; - SpiceDouble dist; - unorm_c(pB, upB, &dist); - memcpy(&m_normal[0], upB, sizeof(double) * 3); - - m_hasNormal = true; - } - /** * Computes and returns emission angle, in degrees, given the observer diff --git a/isis/src/base/objs/ShapeModel/ShapeModel.h b/isis/src/base/objs/ShapeModel/ShapeModel.h index 7cd9bb7444185de20efe2e0b737c30a701cdb869..d751e16ed59d238a3268c7cc2cab8e97525178d6 100644 --- a/isis/src/base/objs/ShapeModel/ShapeModel.h +++ b/isis/src/base/objs/ShapeModel/ShapeModel.h @@ -64,6 +64,9 @@ namespace Isis { * closer to ISIS coding standards. References #1438 * @history 2016-06-13 Kelvin Rodriguez - Removed redundant contructor ShapeModel(Target, Pvl). * Fixes #2214 + * @history 2017-05-19 Tyler Wilson - Removed the calculateEllipsoidalSurfaceNormal() function, + * as this is now being handled in the EllipsoidShape class. + * References #1028. */ class ShapeModel { public: @@ -146,7 +149,7 @@ namespace Isis { // Set shape name void setName(QString name); - void calculateEllipsoidalSurfaceNormal(); + //void calculateEllipsoidalSurfaceNormal(); bool hasEllipsoidIntersection(); // Intersect ellipse diff --git a/isis/src/base/objs/ShapeModel/ShapeModel.truth b/isis/src/base/objs/ShapeModel/ShapeModel.truth index 60b7eaa2ec0aaf9dc45fd0b6735c7dc1211f31a3..fa208088ae81002b8e8381a72bf7ddde0802f072 100644 --- a/isis/src/base/objs/ShapeModel/ShapeModel.truth +++ b/isis/src/base/objs/ShapeModel/ShapeModel.truth @@ -80,7 +80,7 @@ Begin testing Shape Model base class.... surface point = (-2105.83, -2380.77, 1189.41) Testing method calculateEllipsoidalSurfaceNormal with invalid intersection... -**PROGRAMMER ERROR** A valid intersection must be defined before computing the surface normal. +**PROGRAMMER ERROR** Cannot convert an invalid surface point to a naif array. Testing method setHasIntersection false... Do we have an intersection? 0 @@ -88,7 +88,7 @@ Begin testing Shape Model base class.... **PROGRAMMER ERROR** No valid intersection point for computing resolution. Testing method calculateEllipsoidalSurfaceNormal with no intersection... -**PROGRAMMER ERROR** A valid intersection must be defined before computing the surface normal. +**PROGRAMMER ERROR** Cannot convert an invalid surface point to a naif array. Testing method calculateEllipsoidalSurfaceNormal with valid intersection... intersectSurface called with observer position = -2399.54, -2374.03, 1277.68 @@ -96,7 +96,7 @@ Begin testing Shape Model base class.... Intersection set Do we have a normal? 0 Do we have a normal? 1 - local normal = (-0.620509, -0.701524, 0.350474) + local normal = (-0.6196, -0.700497, 0.354117) Testing method targetRadii... true normal = (-0.6196, -0.700497, 0.354117) diff --git a/isis/src/base/objs/ShapeModel/unitTest.cpp b/isis/src/base/objs/ShapeModel/unitTest.cpp index 5ffa22e2989faa01c72679bd41edb7d09f726c95..d11183babf516c316746aff85920e88525349084 100644 --- a/isis/src/base/objs/ShapeModel/unitTest.cpp +++ b/isis/src/base/objs/ShapeModel/unitTest.cpp @@ -171,7 +171,15 @@ class MyEllipse : public ShapeModel { } virtual void calculateLocalNormal(QVector cornerNeighborPoints) { - calculateEllipsoidalSurfaceNormal(); + + std::vector radii = targetRadii(); + std::vector normal(3, 0.); + SpiceDouble point[3]; + surfaceIntersection()->ToNaifArray(point); + surfnm_c(radii[0].kilometers(), radii[1].kilometers(), radii[2].kilometers(), point, (SpiceDouble *) &normal[0]); + setNormal(normal); + setHasNormal(true); + } virtual void calculateSurfaceNormal() { diff --git a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.cpp b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.cpp index 2699a6a49140cd526e722cdd103b608ba733e976..708e3eeb39f67b52b6a7af16e906705d63be8acb 100644 --- a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.cpp +++ b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.cpp @@ -163,7 +163,7 @@ namespace Isis { //-------------- Is the shape model an ISIS DEM? ------------------------------// // TODO Deal with stacks -- this could be a list of DEMs - Isis::Cube* shapeModelCube = new Isis::Cube(); + Isis::Cube* shapeModelCube = new Isis::Cube; try { // first, try to open the shape model file as an Isis3 cube shapeModelCube->open(FileName(shapeModelFilenames).expanded(), "r" ); @@ -192,6 +192,9 @@ namespace Isis { } if (projection->IsEquatorialCylindrical()) { + + delete shapeModelCube; + // If the EquatorialCylindricalShape constructor throws an error or returns null, the // following exception will be appended to the fileError. (Later added to the finalError) QString msg = "Unable to construct a DEM shape model from the given " diff --git a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.h b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.h index 5bb9d6e42a938a75136d9575d67e8b3a375dda74..1e2f3a972cbe6fef14a92fa3a1b0473bc3ab9b97 100644 --- a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.h +++ b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.h @@ -30,7 +30,7 @@ namespace Isis { /** * This class is used to create ShapeModel objects. It determines the type - * of shape model in the input Pvl object and creates the appropriate type of + * of shape model in the input Pvl object and creates the appropriate type of * shape model. * * @author 2010-07-29 Debbie A. Cook @@ -40,6 +40,9 @@ namespace Isis { * @history 2014-01-14 - Jeannie Backer - Improved error message. Fixes #1957. * @history 2015-03-08 - Jeannie Backer - Added implementation for NAIF DSK * models. References #2035. + * @history 2017-05-19 Christopher Combs - Modified unitTest.cpp: added ReportError method to + * truncate paths before data directory. Allows test to pass when not + * using the default data area. Fixes #4738. */ class ShapeModelFactory { public: diff --git a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth index 4dc794825952c6ea002b1dd85a753861cb162997..a96d78fe396fa86334cec058fab9335bd870574b 100644 --- a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth +++ b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth @@ -39,12 +39,12 @@ Unit test for Isis::ShapeModel Testing Isis cube file for dem that is not map projected **PROGRAMMER ERROR** Unable to create a shape model from given target and pvl. -**I/O ERROR** Invalid shape model file [/usgs/cpkgs/isis3/data/mgs/testData/ab102401.cub] in Kernels group. +**I/O ERROR** Invalid shape model file [data/mgs/testData/ab102401.cub] in Kernels group. **ERROR** The given shape model file is not a valid ISIS DEM cube. It is not map-projected. -**ERROR** Unable to initialize cube projection from file [/usgs/cpkgs/isis3/data/mgs/testData/ab102401.cub]. -**ERROR** Unable to find PVL group [Mapping] in file [/usgs/cpkgs/isis3/data/mgs/testData/ab102401.cub]. +**ERROR** Unable to initialize cube projection from file [data/mgs/testData/ab102401.cub]. +**ERROR** Unable to find PVL group [Mapping] in file [data/mgs/testData/ab102401.cub]. **ERROR** The given shape model file is not a valid NAIF DSK file. Unable to construct a NAIF DSK shape model. -**ERROR** An unknown NAIF error has been encountered. The short explanation provided by NAIF is [SPICE(UNKNOWNFILARC)]. The Naif error is [The file, /usgs/cpkgs/isis3/data/mgs/testData/ab102401.cub, has a unidentified file architecture. Check that this file is a properly created binary SPICE kernel.]. +**ERROR** An unknown NAIF error has been encountered. The short explanation provided by NAIF is [SPICE(UNKNOWNFILARC)]. The Naif error is [The file, data/mgs/testData/ab102401.cub, has a unidentified file architecture. Check that this file is a properly created binary SPICE kernel.]. Testing Isis cube file for dem that is missing shape model statistics **PROGRAMMER ERROR** Unable to create a shape model from given target and pvl. diff --git a/isis/src/base/objs/ShapeModelFactory/unitTest.cpp b/isis/src/base/objs/ShapeModelFactory/unitTest.cpp index 7cc438f45f2c04ad511a5fef7f1c78852170af1b..36bb21288ce896ea34df407433e35ea905ab536e 100644 --- a/isis/src/base/objs/ShapeModelFactory/unitTest.cpp +++ b/isis/src/base/objs/ShapeModelFactory/unitTest.cpp @@ -7,6 +7,7 @@ #include "Preference.h" #include "CameraFactory.h" #include "Target.h" +#include "QRegularExpression" /** * This application tests the ShapeModelFactory class. @@ -21,11 +22,11 @@ using namespace std; using namespace Isis; /** - * - * @internal + * + * @internal * @history 2015-02-25 Jeannie Backer - Added test for Null ElevationModel. Added test for DSK Shape Model. * Code coverage: 81.818% scope, 84.058% line and 100% function. - * + * * @todo code coverage - need RingPlane shape that passes * @todo code coverage - need RingPlane shape that throws error on construction * @todo code coverage - need Null shape that throws error on EllipsoidShape construction @@ -34,6 +35,11 @@ using namespace Isis; * @todo code coverage - need constructor (EllipsoidShape, PlaneShape, EquatorialCylindricalShape, * or DemShape to return null shape. */ + + void ReportError(QString err) { + cout << err.replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data") << endl; + } + int main() { try { Isis::Preference::Preferences(true); @@ -124,7 +130,7 @@ int main() { cout << " Successfully created shape " << smElNull->name() << endl; delete smElNull; - // Test ShapeModel dem that's not Equatorial Cylindrical + // Test ShapeModel dem that's not Equatorial Cylindrical cout << endl << " Testing DEM not equatorial cylindrical" << endl; PvlGroup kern6 = kern1; kern6 += PvlKeyword("ShapeModel", dir3 + "ab102402.lev2.cub"); @@ -136,7 +142,7 @@ int main() { cout << " Successfully created shape " << smDem->name() << endl; delete smDem; - // Test ShapeModel keyword with DSK + // Test ShapeModel keyword with DSK cout << endl << " Testing DSK file..." << endl; PvlGroup kern7 = kern1; FileName f7("$hayabusa/kernels/dsk"); @@ -231,7 +237,7 @@ int main() { delete smBadFile; } catch(Isis::IException &e) { - e.print(); + ReportError(e.toString()); } try { @@ -250,7 +256,7 @@ int main() { catch (Isis::IException &e) { e.print(); } - } + } catch (IException &e) { IException(e, IException::Programmer, "\n\n\n------------Unit Test Failed.------------", diff --git a/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.cpp b/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.cpp index ad775ee41b7e5d55c09ebada0d654e0e370d0a32..6dad4aa3735b8e165e11163ceb87bc878a773d58 100644 --- a/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.cpp +++ b/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.cpp @@ -23,6 +23,14 @@ using namespace boost::numeric::ublas; namespace Isis { + /** + * Default constructor. + */ + SparseBlockColumnMatrix::SparseBlockColumnMatrix() { + m_startColumn = 0; + } + + /** * Destructor. See description of wipe method below. */ @@ -71,6 +79,8 @@ namespace Isis { // insert matrix into map this->insert(it.key(),m); } + + m_startColumn = src.startColumn(); } @@ -116,13 +126,33 @@ namespace Isis { // zero matrix elements m->clear(); - // insert matrix into map + // insert matrix into map this->insert(nColumnBlock,m); return true; } + /** + * Sets starting column for block in full matrix. + * + * @param nStartColumn value for starting column in full matrix for this block columns + */ + void SparseBlockColumnMatrix::setStartColumn(int nStartColumn) { + m_startColumn = nStartColumn; + } + + + /** + * Sets starting column for block in full matrix. + * + * @return int returns the starting column in the full matrix + */ + int SparseBlockColumnMatrix::startColumn() const { + return m_startColumn; + } + + /** * Returns total number of matrix elements in map (NOTE: NOT the number of matrix blocks). The sum * of all the elements in all of the matrix blocks. diff --git a/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.h b/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.h index 125fd4dd98f58bb2c47ca05ecc4ee0d2d8ab1a31..1fd4c328e6f9f60b30187ddbcea4f4184c34fbea 100644 --- a/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.h +++ b/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.h @@ -62,12 +62,15 @@ namespace Isis { * ISIS coding standards. * @history 2016-08-10 Jeannie Backer - Replaced boost matrix with Isis::LinearAlgebra::Matrix. * References #4163. + * @history 2017-05-09 Ken Edmundson - Added m_startColumn member and mutator/accessor methods + * to SparseBlockColumnMatrix. Done to eliminate lengthy computation of + * leading colums and rows. References #4664. */ class SparseBlockColumnMatrix : public QMap< int, LinearAlgebra::Matrix * > { public: - SparseBlockColumnMatrix(){} // default constructor + SparseBlockColumnMatrix(); // default constructor ~SparseBlockColumnMatrix(); // destructor // copy constructor @@ -80,11 +83,19 @@ namespace Isis { void zeroBlocks(); bool insertMatrixBlock(int nColumnBlock, int nRows, int nCols); + + void setStartColumn(int nStartColumn); + int startColumn() const; int numberOfElements(); int numberOfRows(); int numberOfColumns(); void print(std::ostream& outstream); void printClean(std::ostream& outstream); + + protected: + int m_startColumn; /**< starting column for this Block Column in full matrix + e.g. for Block Column 4, if the preceding Block Columns each have 6 + columns, then the starting column for Block Column 4 is 24 */ }; // operators to read/write SparseBlockColumnMatrix to/from binary disk file diff --git a/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.truth b/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.truth index 10e8baae6a6184f027dc376461c2c7f1831381e1..686ac95c46865c6a907166e38fe1784bb174769c 100644 --- a/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.truth +++ b/isis/src/base/objs/SparseBlockMatrix/SparseBlockMatrix.truth @@ -149,6 +149,28 @@ Printing SparseBlockColumnMatrix... Empty SparseBlockColumnMatrix... +----- Insert boost block matrix of zeros in each column, set values, and startColumn + # block columns: 3 + # matrix blocks: 3 + # diagonal matrix blocks: 1 +# off-diagonal matrix blocks: 2 + block 0 startColumn: 0 + block 1 startColumn: 3 + block 2 startColumn: 6 +Printing SparseBlockMatrix... +Printing SparseBlockColumnMatrix... +0 +[3,3]((0,1,2),(3,4,5),(6,7,8)) + +Printing SparseBlockColumnMatrix... +2 +[3,3]((0,1,2),(3,4,5),(6,7,8)) + +Printing SparseBlockColumnMatrix... +3 +[3,3]((0,1,2),(3,4,5),(6,7,8)) + + ----- copy method # matrix blocks: 1 # diagonal matrix blocks: 1 diff --git a/isis/src/base/objs/SparseBlockMatrix/unitTest.cpp b/isis/src/base/objs/SparseBlockMatrix/unitTest.cpp index f091f77a0a4d882b8c387c4bffe33172514275af..31abc5af27dc20bc5c0e2671d4dce241217459f9 100644 --- a/isis/src/base/objs/SparseBlockMatrix/unitTest.cpp +++ b/isis/src/base/objs/SparseBlockMatrix/unitTest.cpp @@ -345,6 +345,47 @@ int main(int argc, char *argv[]) { catch(IException &e) { e.print(); } + +try { + cerr << endl << "----- Insert boost block matrix of zeros in each column, set values, and startColumn" << endl; + SparseBlockMatrix sbm; + sbm.setNumberOfColumns(3); + sbm.insertMatrixBlock(0, 0, 3, 3); + sbm.insertMatrixBlock(1, 2, 3, 3); + sbm.insertMatrixBlock(2, 3, 3, 3); + + for ( int i = 0; i < 3; i++ ) { + for ( int j = 0; j < 3; j++ ) { + (*(*sbm[0])[0])(i,j) = 3*i+j; + } + } + for ( int i = 0; i < 3; i++ ) { + for ( int j = 0; j < 3; j++ ) { + (*(*sbm[1])[2])(i,j) = 3*i+j; + } + } + for ( int i = 0; i < 3; i++ ) { + for ( int j = 0; j < 3; j++ ) { + (*(*sbm[2])[3])(i,j) = 3*i+j; + } + } + + sbm.at(0)->setStartColumn(0); + sbm.at(1)->setStartColumn(3); + sbm.at(2)->setStartColumn(6); + + cerr << " # block columns: " << sbm.size() << endl; + cerr << " # matrix blocks: " << sbm.numberOfBlocks() << endl; + cerr << " # diagonal matrix blocks: " << sbm.numberOfDiagonalBlocks() << endl; + cerr << "# off-diagonal matrix blocks: " << sbm.numberOfOffDiagonalBlocks() << endl; + cerr << " block 0 startColumn: " << sbm.at(0)->startColumn() << endl; + cerr << " block 1 startColumn: " << sbm.at(1)->startColumn() << endl; + cerr << " block 2 startColumn: " << sbm.at(2)->startColumn() << endl; + sbm.print(std::cerr); + } + catch(IException &e) { + e.print(); + } try { cerr << endl << "----- copy method" << endl; diff --git a/isis/src/base/objs/Spice/LightTimeCorrectionState.cpp b/isis/src/base/objs/Spice/LightTimeCorrectionState.cpp index 83ed703f9e06389267f947c53532785744f861ee..2d6decefe4b152a132af2a864cac84b137f1a418 100644 --- a/isis/src/base/objs/Spice/LightTimeCorrectionState.cpp +++ b/isis/src/base/objs/Spice/LightTimeCorrectionState.cpp @@ -1,7 +1,7 @@ /** * @file - * $Revision$ - * $Date$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/base/objs/Spice/LightTimeCorrectionState.h b/isis/src/base/objs/Spice/LightTimeCorrectionState.h index 2f9616d2d20150d3dc471d0e07328ed671aeef38..bb485da6049f8f837ff40e6ab6d372f459048ff2 100644 --- a/isis/src/base/objs/Spice/LightTimeCorrectionState.h +++ b/isis/src/base/objs/Spice/LightTimeCorrectionState.h @@ -2,8 +2,8 @@ #define LightTimeCorrectionState_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6314 $ + * $Date: 2015-08-12 15:30:27 -0700 (Wed, 12 Aug 2015) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * intellectual property information,user agreements, and related information. diff --git a/isis/src/base/objs/Spice/SpacecraftPosition.cpp b/isis/src/base/objs/Spice/SpacecraftPosition.cpp index 5aab1f0554bf6c2650d92771fdc3432a8a039015..dcd48795ac78e42dbf83670572cfd219139b1660 100644 --- a/isis/src/base/objs/Spice/SpacecraftPosition.cpp +++ b/isis/src/base/objs/Spice/SpacecraftPosition.cpp @@ -1,7 +1,7 @@ /** * @file - * $Revision$ - * $Date$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/base/objs/Spice/SpacecraftPosition.h b/isis/src/base/objs/Spice/SpacecraftPosition.h index 2fbb919fbd793252e3c1a7365ebba7ba50bed060..fa5ae386d9cabbce782f849579d6aebdcf151e46 100644 --- a/isis/src/base/objs/Spice/SpacecraftPosition.h +++ b/isis/src/base/objs/Spice/SpacecraftPosition.h @@ -2,8 +2,8 @@ #define SpacecraftPosition_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * intellectual property information,user agreements, and related information. diff --git a/isis/src/base/objs/Spice/Spice.cpp b/isis/src/base/objs/Spice/Spice.cpp index fa3d3cf58cafa0c709c0e143b3175fdad8145849..8b4ae4887e2cec558f4ca0449496c286ac8fec50 100644 --- a/isis/src/base/objs/Spice/Spice.cpp +++ b/isis/src/base/objs/Spice/Spice.cpp @@ -1,7 +1,7 @@ /** * @file - * $Revision$ - * $Date$ + * $Revision: 7229 $ + * $Date: 2016-11-10 21:04:46 -0700 (Thu, 10 Nov 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/base/objs/Spice/Spice.h b/isis/src/base/objs/Spice/Spice.h index faf32b5868e39534c63afeaa63a9cc0687910bc9..ab0631b7e271dc63cda537667f3a714ccf7256cf 100644 --- a/isis/src/base/objs/Spice/Spice.h +++ b/isis/src/base/objs/Spice/Spice.h @@ -2,8 +2,8 @@ #define Spice_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 7229 $ + * $Date: 2016-11-10 21:04:46 -0700 (Thu, 10 Nov 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * intellectual property information,user agreements, and related information. diff --git a/isis/src/base/objs/SpiceRotation/qmini.cpp b/isis/src/base/objs/SpiceRotation/qmini.cpp index cb11ed6947cca11c72bf243849c6b437e767c76d..8311aa9dc5f2809145380d6634918aa923323213 100644 --- a/isis/src/base/objs/SpiceRotation/qmini.cpp +++ b/isis/src/base/objs/SpiceRotation/qmini.cpp @@ -8,7 +8,7 @@ using namespace std; using namespace Isis; /* qmini.f -- translated by f2c (version 19980913). You must link the resulting object file with the libraries: - -lf2c -lm (in that order) + -lf2c -lm (in that order) */ //#include "f2c.h" diff --git a/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.cpp b/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.cpp index ca885a8ab62026de4b9f434e08e348d5fd326576..729d8ce7518c262e86c417ce4379eaab9b533632 100644 --- a/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.cpp +++ b/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.cpp @@ -65,8 +65,7 @@ namespace Isis { StatCumProbDistDynCalc::StatCumProbDistDynCalc(const StatCumProbDistDynCalc &other) - : m_id(new QUuid(other.m_id->toString())), - m_numberCells(other.m_numberCells), + : m_numberCells(other.m_numberCells), m_numberQuantiles(other.m_numberQuantiles), m_numberObservations(other.m_numberObservations), m_quantiles(other.m_quantiles), @@ -81,8 +80,6 @@ namespace Isis { * Destroys StatCumProbDistDynCalc object. */ StatCumProbDistDynCalc::~StatCumProbDistDynCalc() { - delete m_id; - m_id = NULL; } @@ -90,10 +87,6 @@ namespace Isis { StatCumProbDistDynCalc &StatCumProbDistDynCalc::operator=(const StatCumProbDistDynCalc &other) { if (&other != this) { - delete m_id; - m_id = NULL; - m_id = new QUuid(other.m_id->toString()); - m_numberCells = other.m_numberCells; m_numberQuantiles = other.m_numberQuantiles; m_numberObservations = other.m_numberObservations; @@ -115,7 +108,6 @@ namespace Isis { * will be dynamically tracked */ void StatCumProbDistDynCalc::initialize() { - m_id = NULL; m_numberCells = m_numberQuantiles = m_numberObservations = 0; m_quantiles.clear(); m_observationValues.clear(); @@ -127,8 +119,6 @@ namespace Isis { void StatCumProbDistDynCalc::setQuantiles(unsigned int nodes) { initialize(); - m_id = new QUuid(QUuid::createUuid()); - if (nodes < 3) { m_numberQuantiles = 3; } @@ -514,7 +504,6 @@ namespace Isis { void StatCumProbDistDynCalc::save(QXmlStreamWriter &stream, const Project *project) const { // TODO: does xml stuff need project??? stream.writeStartElement("statCumProbDistDynCalc"); - stream.writeTextElement("id", m_id->toString()); stream.writeTextElement("numberCells", toString(m_numberCells)); stream.writeTextElement("numberQuantiles", toString(m_numberQuantiles)); stream.writeTextElement("numberObservations", toString(m_numberObservations)); @@ -595,11 +584,7 @@ namespace Isis { const QString &localName, const QString &qName) { if (!m_xmlHandlerCharacters.isEmpty()) { - if (qName == "id") { - m_xmlHandlerCumProbCalc->m_id = NULL; - m_xmlHandlerCumProbCalc->m_id = new QUuid(m_xmlHandlerCharacters); - } - else if (qName == "numberCells") { + if (qName == "numberCells") { m_xmlHandlerCumProbCalc->m_numberCells = toInt(m_xmlHandlerCharacters); } else if (qName == "numberQuantiles") { @@ -617,9 +602,8 @@ namespace Isis { QDataStream &StatCumProbDistDynCalc::write(QDataStream &stream) const { - stream << m_id->toString() - << (qint32)m_numberCells - << (qint32)m_numberQuantiles + stream << (qint32)m_numberCells + << (qint32)m_numberQuantiles << (qint32)m_numberObservations << m_quantiles << m_observationValues @@ -633,8 +617,7 @@ namespace Isis { QDataStream &StatCumProbDistDynCalc::read(QDataStream &stream) { QString id; qint32 numCells, numQuantiles, numObservations; - stream >> id - >> numCells + stream >> numCells >> numQuantiles >> numObservations >> m_quantiles @@ -642,10 +625,6 @@ namespace Isis { >> m_idealNumObsBelowQuantile >> m_numObsBelowQuantile; - delete m_id; - m_id = NULL; - m_id = new QUuid(id); - m_numberCells = (unsigned int)numCells; m_numberQuantiles = (unsigned int)numQuantiles; m_numberObservations = (unsigned int)numObservations; diff --git a/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.h b/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.h index 980c2ec3f2443d3bc068edf63ecad92fd51506b1..088529dd7ca68efa4552f88fa60e3c487dc7f39c 100644 --- a/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.h +++ b/isis/src/base/objs/StatCumProbDistDynCalc/StatCumProbDistDynCalc.h @@ -132,9 +132,6 @@ namespace Isis { QString m_xmlHandlerCharacters; }; - QUuid *m_id; /**< A unique ID for this object (useful for others to reference this object when - saving to disk).*/ - unsigned int m_numberCells; /**< The number of cells or histogram bins that are being used to model the probility density function.*/ diff --git a/isis/src/base/objs/Statistics/Statistics.cpp b/isis/src/base/objs/Statistics/Statistics.cpp index 1f67f314333d4a4096a0726a184ef401cb04d995..3cbfc12bfdf7f20d5d72ec5dcfc349e45dc42e41 100644 --- a/isis/src/base/objs/Statistics/Statistics.cpp +++ b/isis/src/base/objs/Statistics/Statistics.cpp @@ -27,10 +27,6 @@ #include -#include -#include -#include - #include "IException.h" #include "IString.h" #include "Project.h" @@ -939,86 +935,4 @@ namespace Isis { return statistics.read(stream); } -//??? not working for prog14/15??? -// dyld: Symbol not found: __ZN2H58PredType12NATIVE_INT64E -// Referenced from: /usgs/pkgs/isis3beta2015-12-24/isis/bin/../lib/libisis3.4.12.dylib -// Expected in: flat namespace -// in /usgs/pkgs/isis3beta2015-12-24/isis/bin/../lib/libisis3.4.12.dylib - - /** - * H5 compound data type uses the offesets from the QDataStream returned by - * the write(QDataStream &stream) method. - */ - H5::CompType Statistics::compoundH5DataType() { - - H5::CompType compoundDataType((size_t)124); - - size_t offset = 0; - compoundDataType.insertMember("Sum", offset, H5::PredType::NATIVE_DOUBLE); - - // offset += sizeof(m_sum); - offset += sizeof(double); - compoundDataType.insertMember("SumSquared", offset, H5::PredType::NATIVE_DOUBLE); - - // offset += sizeof(m_sumsum); - offset += sizeof(double); - compoundDataType.insertMember("Minimum", offset, H5::PredType::NATIVE_DOUBLE); - - // offset += sizeof(m_minimum); - offset += sizeof(double); - compoundDataType.insertMember("Maximum", offset, H5::PredType::NATIVE_DOUBLE); - - // offset += sizeof(m_maximum); - offset += sizeof(double); - compoundDataType.insertMember("ValidMinimum", offset, H5::PredType::NATIVE_DOUBLE); - - // offset += sizeof(m_validMinimum); - offset += sizeof(double); - compoundDataType.insertMember("ValidMaximum", offset, H5::PredType::NATIVE_DOUBLE); - - // offset += sizeof(m_validMaximum); - offset += sizeof(double); - compoundDataType.insertMember("TotalPixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_totalPixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("ValidPixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_validPixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("NullPixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_nullPixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("LRSPixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_lrsPixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("LISPixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_lisPixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("HRSPixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_hrsPixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("HISPixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_hisPixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("UnderRangePixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_underRangePixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("OverRangePixels", offset, H5::PredType::NATIVE_INT64); - - // offset += sizeof(m_overRangePixels); - offset += sizeof(BigInt); - compoundDataType.insertMember("RemovedData", offset, H5::PredType::NATIVE_HBOOL); - // mac osx has problem with "sizeof" commented lines and the native data - // types too... will consider this later when ready to add serialization. - - return compoundDataType; - } - } // end namespace isis diff --git a/isis/src/base/objs/Statistics/Statistics.h b/isis/src/base/objs/Statistics/Statistics.h index f9cb67517a28e48c5bf8735c37a50ec3cdb3de73..e8f8ad57f8471abfb124c032da56f55df79ac3ef 100644 --- a/isis/src/base/objs/Statistics/Statistics.h +++ b/isis/src/base/objs/Statistics/Statistics.h @@ -23,10 +23,6 @@ #include #include -#include -#include -#include - #include "Constants.h" #include "PvlGroup.h" #include "SpecialPixel.h" @@ -100,6 +96,8 @@ namespace Isis { * @history 2016-07-15 Ian Humphrey - Added constructor that initializes a Statistics object * from a PvlGroup. Added toPvl() and fromPvl() methods to allow * Statistics serialization/unserialization. References #2282. + * @history 2017-04-20 Makayla Shepherd - Removed the hdf5 code because we are using XML for + * serialization. Fixes #4795. * * @todo 2005-02-07 Deborah Lee Soltesz - add example using cube data to the class documentation * @todo 2015-08-13 Jeannie Backer - Clean up header and implementation files once @@ -169,8 +167,6 @@ namespace Isis { QDataStream &write(QDataStream &stream) const; QDataStream &read(QDataStream &stream); - static H5::CompType compoundH5DataType(); - private: void fromPvl(const PvlGroup &inStats); diff --git a/isis/src/base/objs/TProjection/TProjection.cpp b/isis/src/base/objs/TProjection/TProjection.cpp index b0f080ff9648b6ffa2dedc10a9eb8aace8051cd6..fc667b77437ee46d2427e5398d4646328e60b3aa 100644 --- a/isis/src/base/objs/TProjection/TProjection.cpp +++ b/isis/src/base/objs/TProjection/TProjection.cpp @@ -71,36 +71,36 @@ namespace Isis { * End * @endcode * - * @throw IException::Unknown - "Projection failed. No target radii + * @throw IException::Unknown - "Projection failed. No target radii * available through keywords [EquatorialRadius and * PolarRadius] or [TargetName]." - * @throw IException::Unknown - "Projection failed. Invalid value + * @throw IException::Unknown - "Projection failed. Invalid value * for keyword [EquatorialRadius]. It must be greater than * zero." - * @throw IException::Unknown - "Projection failed. Invalid value + * @throw IException::Unknown - "Projection failed. Invalid value * for keyword [PolarRadius]. It must be greater than zero." - * @throw IException::Unknown - "Projection failed. Invalid value + * @throw IException::Unknown - "Projection failed. Invalid value * for keyword [LatitudeType] must be [Planetographic or * Planetocentric]" - * @throw IException::Unknown - "Projection failed. Invalid value + * @throw IException::Unknown - "Projection failed. Invalid value * for keyword [LongitudeDirection] must be [PositiveWest or * PositiveEast]" - * @throw IException::Unknown - "Projection failed. Invalid value + * @throw IException::Unknown - "Projection failed. Invalid value * for keyword [LongitudeDomain] must be [180 or 360]" - * @throw IException::Unknown - "Projection failed. + * @throw IException::Unknown - "Projection failed. * [MinimumLatitude] is outside the range of [-90:90]" - * @throw IException::Unknown - "Projection failed. + * @throw IException::Unknown - "Projection failed. * [MaximumLatitude] is outside the range of [-90:90]" - * @throw IException::Unknown - "Projection failed. + * @throw IException::Unknown - "Projection failed. * [MinimumLatitude,MaximumLatitude] are not properly ordered" - * @throw IException::Unknown - "Projection failed. + * @throw IException::Unknown - "Projection failed. * [MinimumLongitude,MaximumLongitude] are not properly ordered" - * @throw IException::Unknown - "Projection failed. Invalid keyword + * @throw IException::Unknown - "Projection failed. Invalid keyword * value(s). [EquatorialRadius] must be greater than or equal to * [PolarRadius]" - * @throw IException::Unknown - "Projection failed. Invalid label + * @throw IException::Unknown - "Projection failed. Invalid label * group [Mapping]" - * + * */ TProjection::TProjection(Pvl &label) : Projection::Projection(label) { try { @@ -214,7 +214,7 @@ namespace Isis { if (m_minimumLongitude >= m_maximumLongitude) { QString msg = "Projection failed. " "[MinimumLongitude,MaximumLongitude] of [" - + toString(m_minimumLongitude) + "," + + toString(m_minimumLongitude) + "," + toString(m_maximumLongitude) + "] are not " + "properly ordered"; throw IException(IException::Unknown, msg, _FILEINFO_); @@ -263,11 +263,11 @@ namespace Isis { } /** - * This method determines whether two map projection objects are equal by - * comparing the equatorial radius, polar radius, latitude type, longitude - * direction, resolution, and projection name. - * - * @param proj A reference to a TProjection object to which this TProjection + * This method determines whether two map projection objects are equal by + * comparing the equatorial radius, polar radius, latitude type, longitude + * direction, resolution, and projection name. + * + * @param proj A reference to a TProjection object to which this TProjection * will be compared. * * @return bool Indicates whether the TProjection objects are equivalent. @@ -304,15 +304,15 @@ namespace Isis { } /** - * This returns the eccentricity of the target, - * - * @f[ - * e = \sqrt{1 - \frac{PR^2}{ER^2}} - * @f] - * where PR is the polar radius and ER is the equatorial radius. Since - * polar and equatorial radii are required to be greater than zero, it - * follows that @f$ 0 \le e < 1 @f$ . Note that if the body is - * spherical, then PR = ER and so @a e = 0. + * This returns the eccentricity of the target, + * + * @f[ + * e = \sqrt{1 - \frac{PR^2}{ER^2}} + * @f] + * where PR is the polar radius and ER is the equatorial radius. Since + * polar and equatorial radii are required to be greater than zero, it + * follows that @f$ 0 \le e < 1 @f$ . Note that if the body is + * spherical, then PR = ER and so @a e = 0. * * @return double */ @@ -322,27 +322,27 @@ namespace Isis { /** * This method returns the local radius in meters at the specified latitude - * position. For this method, the local radius is defined as the distance - * from the center of the planet to the surface of the planet at the given - * latitude. - * - * @f[ + * position. For this method, the local radius is defined as the distance + * from the center of the planet to the surface of the planet at the given + * latitude. + * + * @f[ * LR = \frac{ER*PR}{\sqrt{PR^2 \cos^2(LAT)+ER^2 \sin^2(LAT)}} - * @f] - * + * @f] + * * @param latitude A latitude in degrees (assumed to be of the correct * LatitudeType). - * - * @throw IException::Unknown - "The given latitude is invalid." - * - * @return double The value for the local radius, in meters, at the given + * + * @throw IException::Unknown - "The given latitude is invalid." + * + * @return double The value for the local radius, in meters, at the given * latitude. */ double TProjection::LocalRadius(double latitude) const { if (latitude == Null) { - throw IException(IException::Unknown, - "Unable to calculate local radius. The given latitude value [" - + toString(latitude) + "] is invalid.", + throw IException(IException::Unknown, + "Unable to calculate local radius. The given latitude value [" + + toString(latitude) + "] is invalid.", _FILEINFO_); } double a = m_equatorialRadius; @@ -362,7 +362,7 @@ namespace Isis { * position. This is only usable if the use of SetGround or SetCoordinate was * successful. * - * @return double The value for the local radius, in meters, at the current + * @return double The value for the local radius, in meters, at the current * latitude. */ double TProjection::LocalRadius() const { @@ -371,12 +371,12 @@ namespace Isis { /** - * This method returns the latitude of true scale. It is a virtual function - * and if it is not overriden the default latitude of true scale is 0 (at - * the equator). Otherwise it is projection specific. For example, the - * center latitude for Mercator, Equidistant, or a parallel for conic - * projections. This method is used by the Scale routine to ensure the - * local radius is used in the computation. + * This method returns the latitude of true scale. It is a virtual function + * and if it is not overriden the default latitude of true scale is 0 (at + * the equator). Otherwise it is projection specific. For example, the + * center latitude for Mercator, Equidistant, or a parallel for conic + * projections. This method is used by the Scale routine to ensure the + * local radius is used in the computation. * * @return double The latitude where the projection is not distorted. */ @@ -420,14 +420,14 @@ namespace Isis { } /** - * This method converts a planetographic latitude to a planetocentric - * latitude. It utilizes the equatorial and polar radii found in the - * labels to perform the computation. + * This method converts a planetographic latitude to a planetocentric + * latitude. It utilizes the equatorial and polar radii found in the + * labels to perform the computation. * * @param lat Planetographic latitude to convert. - * - * @see ToPlanetocentric(lat, eRadius, pRadius) - * + * + * @see ToPlanetocentric(lat, eRadius, pRadius) + * * @return double The latitude, converted to planetocentric. */ double TProjection::ToPlanetocentric(const double lat) const { @@ -435,23 +435,23 @@ namespace Isis { } /** - * This method converts a planetographic latitude to a planetocentric + * This method converts a planetographic latitude to a planetocentric * latitude. * * @param lat Planetographic latitude to convert. * @param eRadius Equatorial radius. * @param pRadius Polar radius * - * @throw IException::Unknown - "The given latitude is invalid." - * + * @throw IException::Unknown - "The given latitude is invalid." + * * @return double The latitude, converted to planetocentric. */ double TProjection::ToPlanetocentric(const double lat, double eRadius, double pRadius) { if (lat == Null || abs(lat) > 90.0) { - throw IException(IException::Unknown, - "Unable to convert to Planetocentric. The given latitude value [" - + toString(lat) + "] is invalid.", + throw IException(IException::Unknown, + "Unable to convert to Planetocentric. The given latitude value [" + + toString(lat) + "] is invalid.", _FILEINFO_); } double mylat = lat; @@ -466,13 +466,13 @@ namespace Isis { /** * This method converts a planetocentric latitude to a planetographic - * latitude. It utilizes the equatorial and polar radii found in the - * labels to perform the computation. + * latitude. It utilizes the equatorial and polar radii found in the + * labels to perform the computation. * * @param lat Planetocentric latitude to convert. * * @see ToPlanetographic(lat, eRadius, pRadius) - * + * * @return double The latitude, converted to planetographic. */ double TProjection::ToPlanetographic(const double lat) const { @@ -488,8 +488,8 @@ namespace Isis { * @param eRadius Equatorial radius. * @param pRadius Polar radius * - * @throw IException::Unknown - "The given latitude is invalid." - * + * @throw IException::Unknown - "The given latitude is invalid." + * * @return double The latitude, converted to planetographic. */ double TProjection::ToPlanetographic(double lat, @@ -499,9 +499,9 @@ namespace Isis { lat = qRound(lat); } if (lat == Null || fabs(lat) > 90.0) { - throw IException(IException::Unknown, - "Unable to convert to Planetographic. The given latitude value [" - + toString(lat) + "] is invalid.", + throw IException(IException::Unknown, + "Unable to convert to Planetographic. The given latitude value [" + + toString(lat) + "] is invalid.", _FILEINFO_); } double mylat = lat; @@ -527,7 +527,7 @@ namespace Isis { /** * This indicates if the longitude direction type is positive west (as - * opposed to postive east). The longitude type was obtained from the + * opposed to postive east). The longitude type was obtained from the * label during object construction. * * @return bool @@ -538,7 +538,7 @@ namespace Isis { /** * This indicates if the longitude direction type is positive east (as - * opposed to postive west). The longitude type was obtained from the + * opposed to postive west). The longitude type was obtained from the * label during object construction. * * @return bool @@ -551,20 +551,20 @@ namespace Isis { * This method converts a longitude into the positive east direction. * * @param lon Longitude to convert into the positive east direction. - * @param domain Must be an integer value of 180 (for -180 to 180) or 360 (for + * @param domain Must be an integer value of 180 (for -180 to 180) or 360 (for * 0 to 360). - * - * @throw IException::Unknown - "The given longitude is invalid." + * + * @throw IException::Unknown - "The given longitude is invalid." * @throw IException::Unknown - "Unable to convert longitude. Domain is * not 180 or 360." - * + * * @return double Longitude value, in positive east direction. */ double TProjection::ToPositiveEast(const double lon, const int domain) { if (lon == Null) { - throw IException(IException::Unknown, - "Unable to convert to PositiveEast. The given longitude value [" - + toString(lon) + "] is invalid.", + throw IException(IException::Unknown, + "Unable to convert to PositiveEast. The given longitude value [" + + toString(lon) + "] is invalid.", _FILEINFO_); } double mylon = lon; @@ -578,7 +578,7 @@ namespace Isis { mylon = To180Domain(mylon); } else { - QString msg = "Unable to convert longitude. Domain [" + toString(domain) + QString msg = "Unable to convert longitude. Domain [" + toString(domain) + "] is not 180 or 360."; throw IException(IException::Unknown, msg, _FILEINFO_); } @@ -590,20 +590,20 @@ namespace Isis { * This method converts a longitude into the positive west direction. * * @param lon Longitude to convert into the positive west direction. - * @param domain Must be an integer value of 180 (for -180 to 180) or 360 (for + * @param domain Must be an integer value of 180 (for -180 to 180) or 360 (for * 0 to 360). * - * @throw IException::Unknown - "The given longitude is invalid." + * @throw IException::Unknown - "The given longitude is invalid." * @throw IException::Unknown - "Unable to convert longitude. Domain is * not 180 or 360." - * + * * @return double Longitude value, in positive west direction. */ double TProjection::ToPositiveWest(const double lon, const int domain) { if (lon == Null) { - throw IException(IException::Unknown, - "Unable to convert to PositiveWest. The given longitude value [" - + toString(lon) + "] is invalid.", + throw IException(IException::Unknown, + "Unable to convert to PositiveWest. The given longitude value [" + + toString(lon) + "] is invalid.", _FILEINFO_); } double mylon = lon; @@ -629,7 +629,7 @@ namespace Isis { * This method returns the longitude direction as a string. It will return * either PositiveEast or PositiveWest. * - * @return string The longitude direction, "PositiveEast" or + * @return string The longitude direction, "PositiveEast" or * "PositiveWest". */ QString TProjection::LongitudeDirectionString() const { @@ -665,22 +665,22 @@ namespace Isis { * * @param lon Longitude to convert into the -180 to 180 domain. * - * @throw IException::Unknown - "The given longitude is invalid." - * + * @throw IException::Unknown - "The given longitude is invalid." + * * @return double The longitude, converted to 180 domain. */ double TProjection::To180Domain(const double lon) { if (lon == Null) { - throw IException(IException::Unknown, - "Unable to convert to 180 degree domain. The given longitude value [" - + toString(lon) + "] is invalid.", + throw IException(IException::Unknown, + "Unable to convert to 180 degree domain. The given longitude value [" + + toString(lon) + "] is invalid.", _FILEINFO_); } return Isis::Longitude(lon, Angle::Degrees).force180Domain().degrees(); } /** - * This method converts a longitude into the 0 to 360 domain. It will leave + * This method converts a longitude into the 0 to 360 domain. It will leave * the longitude unchanged if it is already in the domain. * * @param lon Longitude to convert into the 0 to 360 domain. @@ -689,9 +689,9 @@ namespace Isis { */ double TProjection::To360Domain(const double lon) { if (lon == Null) { - throw IException(IException::Unknown, - "Unable to convert to 360 degree domain. The given longitude value [" - + toString(lon) + "] is invalid.", + throw IException(IException::Unknown, + "Unable to convert to 360 degree domain. The given longitude value [" + + toString(lon) + "] is invalid.", _FILEINFO_); } double result = lon; @@ -716,8 +716,8 @@ namespace Isis { } /** - * This returns the minimum latitude of the area of interest. The value - * was obtained from the labels during object construction. This method + * This returns the minimum latitude of the area of interest. The value + * was obtained from the labels during object construction. This method * can only be used if HasGroundRange returns a true. * * @return double @@ -727,8 +727,8 @@ namespace Isis { } /** - * This returns the maximum latitude of the area of interest. The value - * was obtained from the labels during object construction. This method + * This returns the maximum latitude of the area of interest. The value + * was obtained from the labels during object construction. This method * can only be used if HasGroundRange returns a true. * * @return double @@ -739,7 +739,7 @@ namespace Isis { /** * This returns the minimum longitude of the area of interest. The value - * was obtained from the labels during object construction. This method + * was obtained from the labels during object construction. This method * can only be used if HasGroundRange returns a true. * * @return double @@ -750,7 +750,7 @@ namespace Isis { /** * This returns the maximum longitude of the area of interest. The value - * was obtained from the labels during object construction. This method + * was obtained from the labels during object construction. This method * can only be used if HasGroundRange returns a true. * * @return double @@ -789,10 +789,10 @@ namespace Isis { /** * This method is used to set the projection x/y. The Set forces an attempted * calculation of the corresponding latitude/longitude position. This may or - * may not be successful and a status is returned as such. Usually this - * method is overridden in a dervied class, for example, Sinusoidal. If not - * the default method simply copies x/y to lat/lon to x/y which is no - * projection. + * may not be successful and a status is returned as such. Usually this + * method is overridden in a dervied class, for example, Sinusoidal. If not + * the default method simply copies x/y to lat/lon to x/y which is no + * projection. * * @param x X coordinate of the projection in units that are the same as the * radii in the label @@ -829,9 +829,9 @@ namespace Isis { /** * This returns a longitude with correct longitude direction and domain as - * specified in the label object. The method can only be used if - * SetGround, SetCoordinate, SetUniversalGround, or SetWorld return with - * success. Success can also be checked using the IsGood method. + * specified in the label object. The method can only be used if + * SetGround, SetCoordinate, SetUniversalGround, or SetWorld return with + * success. Success can also be checked using the IsGood method. * * @return double */ @@ -945,33 +945,33 @@ namespace Isis { * class (e.g., Sinusoidal). The method may fail as indicated by its return * value. * - * - * @param &minX Reference to the address where the minimum x + * + * @param &minX Reference to the address where the minimum x * coordinate value will be written. The Minimum x projection * coordinate calculated by this method covers the * latitude/longitude range specified in the labels. * - * @param &maxX Reference to the address where the maximum x + * @param &maxX Reference to the address where the maximum x * coordinate value will be written. The Maximum x projection * coordinate calculated by this method covers the * latitude/longitude range specified in the labels. * - * @param &minY Reference to the address where the minimum y + * @param &minY Reference to the address where the minimum y * coordinate value will be written. The Minimum y projection * coordinate calculated by this method covers the * latitude/longitude range specified in the labels. * - * @param &maxY Reference to the address where the maximum y + * @param &maxY Reference to the address where the maximum y * coordinate value will be written. The Maximum y projection * coordinate calculated by this method covers the * latitude/longitude range specified in the labels. - * - * @return bool Indicates whether the method was able to determine the X/Y + * + * @return bool Indicates whether the method was able to determine the X/Y * Range of the projection. If yes, minX, maxX, minY, maxY will * be set with these values. * */ - bool TProjection::XYRange(double &minX, double &maxX, + bool TProjection::XYRange(double &minX, double &maxX, double &minY, double &maxY) { if (minX == Null || maxX == Null || minY == Null || maxY == Null) { return false; @@ -990,22 +990,32 @@ namespace Isis { * This convience function is established to assist in the development of the * XYRange virtual method. It allows the developer to test ground points * (lat/lon) to see if they produce a minimum/maximum projection coordinate. - * For example in Sinusoidal, + * + * This method will first verify that the given latitude and longitude values + * are not Null. If so, the method will change the status of the object to + * good=false before returning (i.e IsGood() returns false). + * + * If both of those test pass, it attempts to set the ground to the given + * latitude and longitude and, if successful, compares the new x and y with + * the saved min/max x and y values. + * + * For example in Sinusoidal this method is called in the following way: * @code * bool Sinusoidal::XYRange(double &minX, double &maxX, - * double &minY, double &maxY) { - * // Check the corners of the lat/lon range + * double &minY, double &maxY) { + * + * // Check the corners of the lat/lon range * XYRangeCheck (m_minimumLatitude,m_minimumLongitude); * XYRangeCheck (m_maximumLatitude,m_minimumLongitude); * XYRangeCheck (m_minimumLatitude,m_maximumLongitude); * XYRangeCheck (m_maximumLatitude,m_maximumLongitude); * - * // If the latitude crosses the equator check there - * if ((m_minimumLatitude < 0.0) && (m_maximumLatitude > 0.0)) { + * // In case the latitude crosses the equator, check there + * if (inLatitudeRange(0.0)) { * XYRangeCheck (0.0,m_minimumLongitude); * XYRangeCheck (0.0,m_maximumLongitude); * } - * + * * // Make sure everything is ordered * if (m_minimumX >= m_maximumX) return false; * if (m_minimumY >= m_maximumY) return false; @@ -1018,16 +1028,25 @@ namespace Isis { * return true; * } * @endcode - * - * + * + * Note: It is a good habit to call the inLatitudeRange and inLongitudeRange + * functions to verify that the values are in range before passing it to + * XYRangeCheck. + * + * @see inLongitudeRange(minLon, maxLon, longitude) + * @see inLongitudeRange(longitude) + * @see inLatitudeRange(latitude) + * * @param latitude Test for min/max projection coordinates at this latitude * @param longitude Test for min/max projection coordinates at this longitude */ void TProjection::XYRangeCheck(const double latitude, const double longitude) { + if (latitude == Null || longitude == Null) { m_good = false; return; } + SetGround(latitude, longitude); if (!IsGood()) return; @@ -1038,10 +1057,104 @@ namespace Isis { return; } + /** - * This method is used to find the XY range for oblique aspect projections - * (non-polar projections) by "walking" around each of the min/max lat/lon. - * + * Determine whether the given longitude is within the range of the given min + * and max longitudes. + * + * Note: It is a good habit to call this function to verify that a value is + * in range before passing it to XYRangeCheck. + * + * @see inLongitudeRange(longitude) + * @see inLatitudeRange(latitude) + * @see XYRangeCheck(latitude, longitude) + * + * @param minLon The lower end of longitude range. + * @param maxLon The upper end of longitude range. + * @param longitude The longitude to check. + * + * @return @b bool Indicates whether minLon <= longitude <= maxLon. + */ + bool TProjection::inLongitudeRange(double minLon, + double maxLon, + double longitude) { + // get the min/max range closest to 0.0 lon + double adjustedLon = To360Domain(longitude); + double adjustedMinLon = To360Domain(minLon); + double adjustedMaxLon = To360Domain(maxLon); + + if (adjustedMinLon > adjustedMaxLon) { + if (adjustedLon > adjustedMinLon) { + adjustedLon -= 360; + } + adjustedMinLon -= 360; + } + + // if this range covers all longitudes, then the given longitude is clearly in range + if (qFuzzyCompare(maxLon - minLon, 360.0)) { + return true; + } + else if (adjustedMinLon <= adjustedLon && adjustedLon <= adjustedMaxLon) { + return true; + } + else { + return false; + } + } + + + /** + * Determine whether the given longitude is within the range of the + * MinimumLongitude and MaximumLongitude range of this projection. + * + * Note: It is a good habit to call this function to verify that a value is + * in range before passing it to XYRangeCheck. + * + * @see inLongitudeRange(minLon, maxLon, longitude) + * @see inLatitudeRange(latitude) + * @see XYRangeCheck(latitude, longitude) + * + * @param longitude The longitude to check. + * + * @return @b bool Indicates whether MinimumLongitude <= longitude <= MaximumLongitude. + */ + bool TProjection::inLongitudeRange(double longitude) { + return inLongitudeRange(MinimumLongitude(), MaximumLongitude(), longitude); + } + + + /** + * Determine whether the given latitude is within the range of the + * MinimumLatitude and MaximumLatitude range of this projection. + * + * Note: It is a good habit to call this function to verify that a value is + * in range before passing it to XYRangeCheck. + * + * @see inLongitudeRange(minLon, maxLon, longitude) + * @see inLongitudeRange(longitude) + * @see XYRangeCheck(latitude, longitude) + * + * @param latitude The latitude to check. + * + * @return @b bool Indicates whether MinimumLatitude <= latitude <= MaximumLatitude. + */ + bool TProjection::inLatitudeRange(double latitude) { + if (MaximumLatitude() - MinimumLatitude() == 180) { + return true; + } + else if (MinimumLatitude() <= latitude && latitude <= MaximumLatitude()) { + return true; + } + else { + return false; + } + } + + + /** + * This method is used to find the XY range for oblique aspect projections + * (non-polar projections) by "walking" around each of the min/max lat/lon. + * * @param minX Minimum x projection coordinate which covers the latitude * longitude range specified in the labels. * @param maxX Maximum x projection coordinate which covers the latitude @@ -1050,23 +1163,23 @@ namespace Isis { * longitude range specified in the labels. * @param maxY Maximum y projection coordinate which covers the latitude * longitude range specified in the labels. - * + * * @return @b bool Indicates whether the method was successful. * @see XYRange() - * @author Stephen Lambright + * @author Stephen Lambright * @internal * @history 2011-07-02 Jeannie Backer - Moved this code from * ObliqueCylindrical class to its own method here. * @history 2012-11-30 Debbie A. Cook - Changed to use TProjection instead of Projection. * References #775. */ - bool TProjection::xyRangeOblique(double &minX, double &maxX, + bool TProjection::xyRangeOblique(double &minX, double &maxX, double &minY, double &maxY) { if (minX == Null || maxX == Null || minY == Null || maxY == Null) { return false; } //For oblique, we'll have to walk all 4 sides to find out min/max x/y values - if (!HasGroundRange()) return false; // Don't have min/max lat/lon, + if (!HasGroundRange()) return false; // Don't have min/max lat/lon, //can't continue m_specialLatCases.clear(); @@ -1077,16 +1190,16 @@ namespace Isis { double minFoundY1, minFoundY2; // Search for minX between minlat and maxlat along minlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), minFoundX1, MinimumLongitude(), true, true, true); // Search for minX between minlat and maxlat along maxlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), minFoundX2, MaximumLongitude(), true, true, true); // Search for minY between minlat and maxlat along minlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), minFoundY1, MinimumLongitude(), false, true, true); // Search for minY between minlat and maxlat along maxlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), minFoundY2, MaximumLongitude(), false, true, true); // Second, search latitude for min X/Y @@ -1094,16 +1207,16 @@ namespace Isis { double minFoundY3, minFoundY4; // Search for minX between minlon and maxlon along minlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), minFoundX3, MinimumLatitude(), true, false, true); // Search for minX between minlon and maxlon along maxlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), minFoundX4, MaximumLatitude(), true, false, true); // Search for minY between minlon and maxlon along minlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), minFoundY3, MinimumLatitude(), false, false, true); // Search for minY between minlon and maxlon along maxlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), minFoundY4, MaximumLatitude(), false, false, true); // We've searched all possible minimums, go ahead and store the lowest @@ -1120,16 +1233,16 @@ namespace Isis { double maxFoundY1, maxFoundY2; // Search for maxX between minlat and maxlat along minlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), maxFoundX1, MinimumLongitude(), true, true, false); // Search for maxX between minlat and maxlat along maxlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), maxFoundX2, MaximumLongitude(), true, true, false); // Search for maxY between minlat and maxlat along minlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), maxFoundY1, MinimumLongitude(), false, true, false); // Search for maxY between minlat and maxlat along maxlon - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), maxFoundY2, MaximumLongitude(), false, true, false); // Search latitude for max X/Y @@ -1137,16 +1250,16 @@ namespace Isis { double maxFoundY3, maxFoundY4; // Search for maxX between minlon and maxlon along minlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), maxFoundX3, MinimumLatitude(), true, false, false); // Search for maxX between minlon and maxlon along maxlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), maxFoundX4, MaximumLatitude(), true, false, false); // Search for maxY between minlon and maxlon along minlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), maxFoundY3, MinimumLatitude(), false, false, false); // Search for maxY between minlon and maxlon along maxlat - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), maxFoundY4, MaximumLatitude(), false, false, false); // We've searched all possible maximums, go ahead and store the highest @@ -1160,22 +1273,22 @@ namespace Isis { // Look along discontinuities for more extremes vector specialLatCases = m_specialLatCases; - for (unsigned int specialLatCase = 0; - specialLatCase < specialLatCases.size(); + for (unsigned int specialLatCase = 0; + specialLatCase < specialLatCases.size(); specialLatCase ++) { double minX, maxX, minY, maxY; // Search for minX between minlon and maxlon along latitude discontinuities - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), minX, specialLatCases[specialLatCase], true, false, true); // Search for minY between minlon and maxlon along latitude discontinuities - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), minY, specialLatCases[specialLatCase], false, false, true); // Search for maxX between minlon and maxlon along latitude discontinuities - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), maxX, specialLatCases[specialLatCase], true, false, false); // Search for maxX between minlon and maxlon along latitude discontinuities - doSearch(MinimumLongitude(), MaximumLongitude(), + doSearch(MinimumLongitude(), MaximumLongitude(), maxY, specialLatCases[specialLatCase], false, false, false); m_minimumX = min(minX, m_minimumX); @@ -1185,22 +1298,22 @@ namespace Isis { } vector specialLonCases = m_specialLonCases; - for (unsigned int specialLonCase = 0; - specialLonCase < specialLonCases.size(); + for (unsigned int specialLonCase = 0; + specialLonCase < specialLonCases.size(); specialLonCase ++) { double minX, maxX, minY, maxY; // Search for minX between minlat and maxlat along longitude discontinuities - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), minX, specialLonCases[specialLonCase], true, true, true); // Search for minY between minlat and maxlat along longitude discontinuities - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), minY, specialLonCases[specialLonCase], false, true, true); // Search for maxX between minlat and maxlat along longitude discontinuities - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), maxX, specialLonCases[specialLonCase], true, true, false); // Search for maxY between minlat and maxlat along longitude discontinuities - doSearch(MinimumLatitude(), MaximumLatitude(), + doSearch(MinimumLatitude(), MaximumLatitude(), maxY, specialLonCases[specialLonCase], false, true, false); m_minimumX = min(minX, m_minimumX); @@ -1227,33 +1340,33 @@ namespace Isis { /** * This method searches for extreme (min/max/discontinuity) coordinate values - * along the constBorder line between minBorder and maxBorder (that is, + * along the constBorder line between minBorder and maxBorder (that is, * across latitudes/longitudes). This method locates the extrema by utilizing - * the findExtreme() method until the coordinate values converge. Then, - * extremeVal parameter is updated with this value before returning. - * - * Discontinuities are stored in m_specialLatCases and m_specialLonCases so - * they may be checked again later, which creates significantly more accuracy - * in some cases. - * + * the findExtreme() method until the coordinate values converge. Then, + * extremeVal parameter is updated with this value before returning. + * + * Discontinuities are stored in m_specialLatCases and m_specialLonCases so + * they may be checked again later, which creates significantly more accuracy + * in some cases. + * * @param minBorder Minimum latitude or longitude to search between. * @param maxBorder Maximum latitude or longitude to search between. - * @param extremeVal The resulting global coordinate value (min or max + * @param extremeVal The resulting global coordinate value (min or max * value for x or y, depending on findMin and searchX) on the * constBorder. - * @param constBorder The latitude or longitude that remains constant. The + * @param constBorder The latitude or longitude that remains constant. The * method will step along this border. - * @param searchX Indicates whether the method is searching for a min or max + * @param searchX Indicates whether the method is searching for a min or max * x-coordinate. If false the method searches for min or max * y-coordinate. - * @param searchLongitude Indicates whether the method will search + * @param searchLongitude Indicates whether the method will search * along a longitude. If true, constBorder is longitude and all * other borders are latitudes. If false, the method searches a * latitude (constBorder is a lat, other borders lons). - * @param findMin Indicates whether the method is looking for a minimum + * @param findMin Indicates whether the method is looking for a minimum * coordinate value. If false, the method is looking for a maximum * value. - * @author Steven Lambright + * @author Steven Lambright * @internal * @history 2011-07-02 Jeannie Backer - Moved this code from * ObliqueCylindrical class to its own method @@ -1262,39 +1375,39 @@ namespace Isis { * TOLERANCE with 1/2 pixel resolution. * (Defaults to 0.5) */ - void TProjection::doSearch(double minBorder, double maxBorder, - double &extremeVal, const double constBorder, + void TProjection::doSearch(double minBorder, double maxBorder, + double &extremeVal, const double constBorder, bool searchX, bool searchLongitude, bool findMin) { if (minBorder == Null || maxBorder == Null || constBorder == Null) { return; } const double TOLERANCE = PixelResolution()/2; - const int NUM_ATTEMPTS = (unsigned int)DBL_DIG; // It's unsafe to go past + const int NUM_ATTEMPTS = (unsigned int)DBL_DIG; // It's unsafe to go past // this precision double minBorderX, minBorderY, maxBorderX, maxBorderY; int attempts = 0; do { - findExtreme(minBorder, maxBorder, minBorderX, minBorderY, maxBorderX, + findExtreme(minBorder, maxBorder, minBorderX, minBorderY, maxBorderX, maxBorderY, constBorder, searchX, searchLongitude, findMin); - if (minBorderX == Null && maxBorderX == Null + if (minBorderX == Null && maxBorderX == Null && minBorderY == Null && maxBorderY == Null ) { attempts = NUM_ATTEMPTS; continue; } attempts ++; } - while ((fabs(minBorderX - maxBorderX) > TOLERANCE + while ((fabs(minBorderX - maxBorderX) > TOLERANCE || fabs(minBorderY - maxBorderY) > TOLERANCE) - && (attempts < NUM_ATTEMPTS)); + && (attempts < NUM_ATTEMPTS)); // check both x and y distance in case symmetry of map // For example, if minBorderX = maxBorderX but minBorderY = -maxBorderY, // these points may not be close enough. if (attempts >= NUM_ATTEMPTS) { // We zoomed in on a discontinuity because our range never shrank, this - // will need to be rechecked later. + // will need to be rechecked later. // *min and max border should be nearly identical, so it doesn't matter // which is used here if (searchLongitude) { @@ -1318,57 +1431,57 @@ namespace Isis { } /** - * Searches for extreme (min/max/discontinuity) coordinate values across - * latitudes/longitudes. - * - * This method looks for these extrema along the constBorder between minBorder - * and maxBorder by stepping along constBorder (10 times) from the minBorder - * and maxBorder. Then, the range of this extreme value is recorded in - * minBorder and maxBorder and the coordinate values corresponding to these - * new borders are stored in minBorderX, minBorderY, maxBorderX and - * maxBorderY. - * - * This function should be used by calling it repeatedly until minBorderX and - * minBorderY do not equal maxBorderX and maxBorderY, respectively. - * Discontinuities will cause the minBorderX, minBorderY, maxBorderX and - * maxBorderY to never converge. If minBorderX never comes close to maxBorderX - * or minBorderY never comes close to maxBorderY, then between minBorder and - * maxBorder is the value of the most extreme value. In this case, either the - * smaller or larger of the x or y values found will be correct, depending on - * the values of findMin and searchX. - * - * - * - * - * @param minBorder Minimum latitude or longitude to search between. This + * Searches for extreme (min/max/discontinuity) coordinate values across + * latitudes/longitudes. + * + * This method looks for these extrema along the constBorder between minBorder + * and maxBorder by stepping along constBorder (10 times) from the minBorder + * and maxBorder. Then, the range of this extreme value is recorded in + * minBorder and maxBorder and the coordinate values corresponding to these + * new borders are stored in minBorderX, minBorderY, maxBorderX and + * maxBorderY. + * + * This function should be used by calling it repeatedly until minBorderX and + * minBorderY do not equal maxBorderX and maxBorderY, respectively. + * Discontinuities will cause the minBorderX, minBorderY, maxBorderX and + * maxBorderY to never converge. If minBorderX never comes close to maxBorderX + * or minBorderY never comes close to maxBorderY, then between minBorder and + * maxBorder is the value of the most extreme value. In this case, either the + * smaller or larger of the x or y values found will be correct, depending on + * the values of findMin and searchX. + * + * + * + * + * @param minBorder Minimum latitude or longitude to search between. This * value gets updated to a more precise range. - * @param maxBorder Maximum latitude or longitude to search between. This + * @param maxBorder Maximum latitude or longitude to search between. This * value gets updated to a more precise range. - * @param minBorderX The x-value corresponding to the lower resultant + * @param minBorderX The x-value corresponding to the lower resultant * minBorder and the constBorder, which is more accurate when * nearly equal to maxBorderX. - * @param minBorderY The y-value corresponding to the lower resultant + * @param minBorderY The y-value corresponding to the lower resultant * minBorder and the constBorder, which is more accurate when * nearly equal to maxBorderY. - * @param maxBorderX The x-value corresponding to the higher resultant + * @param maxBorderX The x-value corresponding to the higher resultant * maxBorder and the constBorder, which is more accurate when * nearly equal to minBorderX. - * @param maxBorderY The y-value corresponding to the higher resultant + * @param maxBorderY The y-value corresponding to the higher resultant * maxBorder and the constBorder, which is more accurate when * nearly equal to minBorderY. - * @param constBorder The latitude or longitude that remains constant. The + * @param constBorder The latitude or longitude that remains constant. The * method will step along this border. - * @param searchX Indicates whether the method is searching for a min or max + * @param searchX Indicates whether the method is searching for a min or max * x-coordinate. If false the method searches for min or max * y-coordinate. - * @param searchLongitude Indicates whether the method will search + * @param searchLongitude Indicates whether the method will search * along a longitude. If true, constBorder is longitude and all * other borders are latitudes. If false, the method searches a * latitude (constBorder is a lat, other borders lons). - * @param findMin Indicates whether the method is looking for a minimum + * @param findMin Indicates whether the method is looking for a minimum * coordinate value. If false, the method is looking for a maximum * value. - * @author Stephen Lambright + * @author Stephen Lambright * @internal * @history 2011-07-02 Jeannie Backer - Moved this code from * ObliqueCylindrical class to its own method here. @@ -1378,8 +1491,8 @@ namespace Isis { */ void TProjection::findExtreme(double &minBorder, double &maxBorder, double &minBorderX, double &minBorderY, - double &maxBorderX, double &maxBorderY, - const double constBorder, bool searchX, + double &maxBorderX, double &maxBorderY, + const double constBorder, bool searchX, bool searchLongitude, bool findMin) { if (minBorder == Null || maxBorder == Null || constBorder == Null) { minBorderX = Null; @@ -1392,13 +1505,12 @@ namespace Isis { setSearchGround(minBorder, constBorder, searchLongitude); minBorderX = XCoord(); minBorderY = YCoord(); - maxBorderX = minBorderX; maxBorderY = minBorderY; return; } // Always do 10 steps const double STEP_SIZE = (maxBorder - minBorder) / 10.0; - const double LOOP_END = maxBorder + (STEP_SIZE / 2.0); // This ensures we do + const double LOOP_END = maxBorder + (STEP_SIZE / 2.0); // This ensures we do // all of the steps // properly double currBorderVal = minBorder; @@ -1419,6 +1531,7 @@ namespace Isis { if (!m_good) { minBorderX = Null; minBorderY = minBorderX; + minBorderX = minBorderX; minBorderY = minBorderX; return; } @@ -1437,7 +1550,7 @@ namespace Isis { double value1 = (searchX) ? XCoord() : YCoord(); double value2 = value1; - // initialize the extreme coordinate value + // initialize the extreme coordinate value // -- this is the largest coordinate value found so far double extremeVal2 = value2; @@ -1460,20 +1573,20 @@ namespace Isis { // update the current border value along constBorder currBorderVal += STEP_SIZE; setSearchGround(currBorderVal, constBorder, searchLongitude); - if (!m_good){ + if (!m_good){ continue; - } - - // update the border and coordinate values + } + + // update the border and coordinate values border3 = border2; border2 = border1; - border1 = currBorderVal; + border1 = currBorderVal; value2 = value1; value1 = (searchX) ? XCoord() : YCoord(); - if ((findMin && value2 < extremeVal2) + if ((findMin && value2 < extremeVal2) || (!findMin && value2 > extremeVal2)) { - // Compare the coordinate value associated with the center border with + // Compare the coordinate value associated with the center border with // the current extreme. If the updated coordinate value is more extreme // (smaller or larger, depending on findMin), then we update the // extremeVal and it's borders. @@ -1484,12 +1597,12 @@ namespace Isis { } } - // update min/max border values to the values on either side of the most + // update min/max border values to the values on either side of the most // extreme coordinate found in this call to this method - + minBorder = extremeBorder3; // Border 3 is lagging and thus smaller - // since the loop steps past the original maxBorder, we want to retain + // since the loop steps past the original maxBorder, we want to retain // the original maxBorder value so we don't go outside of the original // min/max range given if (extremeBorder1 <= maxBorder ) { @@ -1499,7 +1612,7 @@ namespace Isis { // update minBorder coordinate values setSearchGround(minBorder, constBorder, searchLongitude); // if (!m_good){ - // this should not happen since minBorder has already been verified in + // this should not happen since minBorder has already been verified in // the while loop above // } @@ -1519,29 +1632,29 @@ namespace Isis { } /** - * This function sets the ground for the given border values. It calls the - * SetGround(lat, lon) method with the appropriate lat/lon values, depending - * on whether variableIsLat is true. - * - * This method is used by doSearch and findExtreme in order to set the ground - * correctly each time. - * - * @param variableBorder The latitude or longitude that is variable in the + * This function sets the ground for the given border values. It calls the + * SetGround(lat, lon) method with the appropriate lat/lon values, depending + * on whether variableIsLat is true. + * + * This method is used by doSearch and findExtreme in order to set the ground + * correctly each time. + * + * @param variableBorder The latitude or longitude that is variable in the * search methods. - * @param constBorder The latitude or longitude that is constant in the search + * @param constBorder The latitude or longitude that is constant in the search * methods. - * @param variableIsLat Indicates whether variableBorder is the latittude + * @param variableIsLat Indicates whether variableBorder is the latittude * value and constBorder is the longitude value. If false, * variableBorder is the longitude value and constBorder is the * latitude value. - * @author Stephen Lambright + * @author Stephen Lambright * @internal * @history 2011-07-02 Jeannie Backer - Moved this code from * ObliqueCylindrical class to its own method here. * Added error. */ - void TProjection::setSearchGround(const double variableBorder, - const double constBorder, + void TProjection::setSearchGround(const double variableBorder, + const double constBorder, bool variableIsLat) { if (variableBorder == Null || constBorder == Null) { return; @@ -1618,24 +1731,24 @@ namespace Isis { } /** - * A convience method to compute Snyder's @a q equation (3-12) for a given - * latitude, @f$\phi@f$ - * - * @f[ - * q = (1 - e^2) \left[ \frac{\sin(\phi)}{1 - e^2 - * \sin^2(\phi)} - * - - * \frac{1}{2e} \ln\left(\frac{1 - e \sin(\phi)}{1 + e + * A convience method to compute Snyder's @a q equation (3-12) for a given + * latitude, @f$\phi@f$ + * + * @f[ + * q = (1 - e^2) \left[ \frac{\sin(\phi)}{1 - e^2 + * \sin^2(\phi)} + * - + * \frac{1}{2e} \ln\left(\frac{1 - e \sin(\phi)}{1 + e * \sin(\phi)}\right) \right] - * @f] - * where @f$e@f$ is the eccentricity for the body. - * - * @param sinPhi The sine value for a latitude, phi. - * - * @throw IException::Unknown - "Snyder's q variable should only be + * @f] + * where @f$e@f$ is the eccentricity for the body. + * + * @param sinPhi The sine value for a latitude, phi. + * + * @throw IException::Unknown - "Snyder's q variable should only be * computed for ellipsoidal projections." - * - * @return @b double Value for Snyder's q variable. + * + * @return @b double Value for Snyder's q variable. */ double TProjection::qCompute(const double sinPhi) const { if (m_eccentricity < DBL_EPSILON) { @@ -1645,28 +1758,28 @@ namespace Isis { } double eSinPhi = m_eccentricity * sinPhi; return (1 - m_eccentricity * m_eccentricity) - * (sinPhi / (1 - eSinPhi * eSinPhi) + * (sinPhi / (1 - eSinPhi * eSinPhi) - 1 / (2 * m_eccentricity) * log( (1 - eSinPhi) / (1 + eSinPhi) )); - // Note: We know that q is well defined since - // 0 < e < 1 and -1 <= sin(phi) <= 1 + // Note: We know that q is well defined since + // 0 < e < 1 and -1 <= sin(phi) <= 1 // implies that -1 < e*sin(phi) < 1 - // Thus, there are no 0 denominators and the log domain is + // Thus, there are no 0 denominators and the log domain is // satisfied, (1-e*sin(phi))/(1+e*sin(phi)) > 0 } /** - * A convience method to compute latitude angle phi2 given small t, from + * A convience method to compute latitude angle phi2 given small t, from * Syder's recursive equation (7-9) - * - * @f[ - * \phi_{i+1} = \frac{\pi}{2} - 2\arctan\left(t + * + * @f[ + * \phi_{i+1} = \frac{\pi}{2} - 2\arctan\left(t * \left[\frac{1-e\sin(\phi_i)}{1+e\sin(\phi_i)}\right]^{e/2}\right) * @f] - * where @f$e@f$ is the eccentricity for the body and @f$ \phi_0 = - * \frac{\pi}{2} - 2\arctan(t) @f$ . - * + * where @f$e@f$ is the eccentricity for the body and @f$ \phi_0 = + * \frac{\pi}{2} - 2\arctan(t) @f$ . + * * @param t small t - * + * * @throw IException::Unknown - "Failed to converge in Projection::phi2Compute()" * @return double The value for the latitude. */ @@ -1701,14 +1814,14 @@ namespace Isis { } /** - * A convience method to compute Snyder's @a m equation (14-15) for a given - * latitude, @f$\phi@f$ - * - * @f[ - * m = \frac{\cos(\phi)}{\sqrt{1-e^2 \sin^2(\phi)}} - * @f] - * where @f$e@f$ is the eccentricity for the body. - * + * A convience method to compute Snyder's @a m equation (14-15) for a given + * latitude, @f$\phi@f$ + * + * @f[ + * m = \frac{\cos(\phi)}{\sqrt{1-e^2 \sin^2(\phi)}} + * @f] + * where @f$e@f$ is the eccentricity for the body. + * * @param sinphi sine of phi * @param cosphi cosine of phi * @@ -1721,16 +1834,16 @@ namespace Isis { } /** - * A convience method to compute Snyder's @a t equation (15-9) for a given - * latitude, @f$\phi@f$ - * - * @f[ - * t = + * A convience method to compute Snyder's @a t equation (15-9) for a given + * latitude, @f$\phi@f$ + * + * @f[ + * t = * \frac{\tan\left(\frac{\pi}{4} - \frac{\phi}{2}\right)} * {\left[\frac{1-e\sin(\phi)} * {1+e\sin(\phi)}\right]^{e/2}} - * @f] - * where @f$e@f$ is the eccentricity for the body. + * @f] + * where @f$e@f$ is the eccentricity for the body. * * @param phi phi * @param sinphi sin of phi @@ -1748,14 +1861,14 @@ namespace Isis { } /** - * A convience method to compute - * - * @f[ - * e4 = + * A convience method to compute + * + * @f[ + * e4 = * \sqrt{(1+e )^{1+e}(1-e)^{1-e}} - * @f] + * @f] * where @a e is the eccentricity of the body. - * + * * @return double The value for the e4 formula. */ double TProjection::e4Compute() const { @@ -1767,3 +1880,5 @@ namespace Isis { } } //end namespace isis + + diff --git a/isis/src/base/objs/TProjection/TProjection.h b/isis/src/base/objs/TProjection/TProjection.h index 5c94584bc60a780ff3c999d87f60b7c8a896c232..ab634264c3c880be649ab3ad60bb4d146071ae48 100644 --- a/isis/src/base/objs/TProjection/TProjection.h +++ b/isis/src/base/objs/TProjection/TProjection.h @@ -25,8 +25,8 @@ #include #include -#include "Projection.h" -#include "PvlGroup.h" // protected data member object (m_mappingGrp) +#include "Projection.h" +#include "PvlGroup.h" // protected data member object (m_mappingGrp) namespace Isis { class Displacement; @@ -38,10 +38,10 @@ namespace Isis { * @brief Base class for Map TProjections * * This is a second level virtual base class for map projections of triaxial bodies. It - * must be used to create specific map projection classes such as Sinusoidal, - * Mercator, etc. The foundation of this class is the ability to convert ground + * must be used to create specific map projection classes such as Sinusoidal, + * Mercator, etc. The foundation of this class is the ability to convert ground * coordinates (latitude and longitude) into projection coordinates (x and y) and - * vice versa. Options exist to allow conversion to and from programmer specified + * vice versa. Options exist to allow conversion to and from programmer specified * world coordinates. The world coordinates can be cube pixels, paper units in * millimeters, or any other unit the program may need. Generally, you should * never directly instantiate this class. @@ -128,7 +128,7 @@ namespace Isis { * iterations for vesta (an asteroid). Fixes #279 * @history 2012-03-01 Jeff Anderson - Fixed bug in SetUpperLeftCorner by * adding Pvl::Replace when updating the mapping - * labels + * labels * @history 2012-03-30 Steven Lambright and Stuart Sides - To360Domain() and * To180Domain() are now constant time operations. * Fixes #656. @@ -164,9 +164,11 @@ namespace Isis { * TargetRadii() methods to find radii values using the given * NAIF target code. Fixes #3892 * @history 2016-05-10 Jeannie Backer - Moved TargetRadii() methods to Target class. + * @history 2016-05-25 Jeannie Backer - Updated documentation. References #3877 * @history 2016-08-28 Kelvin Rodriguez - Removed redundant var=var lines - * causing warnings in clang. Part of porting to OS X 10.11. - * + * causing warnings in clang. Part of porting to OS X 10.11. + * @history 2016-12-28 Jeannie Backer - Added inLatitudeRange, and inLongitudeRange methods. + * References #3877 * @todo Continue to modify Projection class to comply with coding * standards. Some of these include, but may not be limited to remove * "Get" from methods GetX and GetY, change methods to lower camel @@ -180,7 +182,6 @@ namespace Isis { virtual ~TProjection(); virtual bool operator== (const Projection &proj); - // These return properties of the target double EquatorialRadius() const; double PolarRadius() const; double Eccentricity() const; @@ -189,14 +190,16 @@ namespace Isis { // These return or change properties of the projection, independent of calculations /** - * This method returns the name of the map projection. It is a pure - * virtual method (requires all subclasses to override). + * This method returns the name of the map projection. It is a pure + * virtual method (requires all subclasses to override). * * @return string The name of the map projection. */ virtual QString Name() const = 0; + + /** - * This method returns the Version of the map projection. It is a pure + * This method returns the Version of the map projection. It is a pure * virtual method (requires all subclasses to override). * * @return string The Version number of the map projection. @@ -204,21 +207,20 @@ namespace Isis { virtual QString Version() const = 0; virtual double TrueScaleLatitude() const; virtual bool IsEquatorialCylindrical(); + + /** * This enum defines the types of Latitude supported in this class */ - enum LatitudeType { Planetocentric, /**< Latitudes are measured as the - angle from the equatorial - plane to the plane through the - center of the planet and a given - point on the surface of the - planet.*/ - Planetographic /**< Latitudes are measured as the - angle from the equatorial plane - to the normal to the surface of - the planet at a given point.*/ - - }; + enum LatitudeType { + Planetocentric, /**< Latitudes are measured as the angle from the equatorial plane + to the plane through the center of the planet and a given point + on the surface of the planet.*/ + Planetographic /**< Latitudes are measured as the angle from the equatorial plane + to the normal to the surface of the planet at a given point.*/ + }; + + // Check latitude type or get latitude type as a string bool IsPlanetocentric() const; bool IsPlanetographic() const; @@ -228,12 +230,11 @@ namespace Isis { double ToPlanetographic(const double lat) const; /** - * This enum defines the types of Longitude directions supported in this - * class. + * This enum defines the types of Longitude directions supported in this class. */ - enum LongitudeDirection { PositiveEast, /**< Longitude values increase in + enum LongitudeDirection { PositiveEast, /**< Longitude values increase in the easterly direction.*/ - PositiveWest /**< Longitude values increase in + PositiveWest /**< Longitude values increase in the westerly direction.*/ }; @@ -274,7 +275,7 @@ namespace Isis { double Scale() const; // Return the x/y range which covers the lat/lon range in the labels - virtual bool XYRange(double &minX, double &maxX, + virtual bool XYRange(double &minX, double &maxX, double &minY, double &maxY); // get mapping information @@ -291,13 +292,16 @@ namespace Isis { static double ToPositiveEast(const double lon, const int domain); static double ToPositiveWest(const double lon, const int domain); - // change longitude domain + // change longitude domain static double To180Domain(const double lon); static double To360Domain(const double lon); protected: void XYRangeCheck(const double latitude, const double longitude); - bool xyRangeOblique(double &minX, double &maxX, + bool inLongitudeRange(double longitude); + bool inLongitudeRange(double minLon, double maxLon, double longitude); + bool inLatitudeRange(double latitude); + bool xyRangeOblique(double &minX, double &maxX, double &minY, double &maxY); // Convience methods for typical projection computations from Snyder @@ -308,76 +312,72 @@ namespace Isis { double e4Compute() const; // page 161 private: - void doSearch(double minBorder, double maxBorder, + void doSearch(double minBorder, double maxBorder, double &extremeVal, const double constBorder, bool searchX, bool searchLongitude, bool findMin); - void findExtreme(double &minBorder, double &maxBorder, - double &minBorderX, double &minBorderY, - double &maxBorderX, double &maxBorderY, - const double constBorder, bool searchX, + void findExtreme(double &minBorder, double &maxBorder, + double &minBorderX, double &minBorderY, + double &maxBorderX, double &maxBorderY, + const double constBorder, bool searchX, bool searchLongitude, bool findMin); - void setSearchGround(const double variableBorder, + void setSearchGround(const double variableBorder, const double constBorder, bool variableIsLat); protected: - double m_latitude; /**< This contain a latitude value. The value is - only usable if m_good is true.*/ - double m_longitude; /**< This contain a longitude value. The value is - only usable if m_good is true.*/ - - LatitudeType m_latitudeType; /**< An enumerated type indicating the - LatitudeType read from the labels. It - can be either Planetographic or - Planetocentric.**/ - - LongitudeDirection m_longitudeDirection; /**< An enumerated type indicating the - LongitudeDirection read from the - labels. It can be either PositiveEast - or PositiveWest. Indicating which - direction the positive axis for - longitude is.**/ + double m_latitude; /**< This contains the currently set latitude value. + The value is only usable if m_good is true.*/ + double m_longitude; /**< This contains the currently set longitude value. + The value is only usable if m_good is true.*/ + + LatitudeType m_latitudeType; /**< An enumerated type indicating the LatitudeType read from the + labels. It can be either Planetographic or Planetocentric.*/ + + LongitudeDirection m_longitudeDirection; /**< An enumerated type indicating the + LongitudeDirection read from the labels. + It can be either PositiveEast or PositiveWest. + Indicating which direction the positive axis for + longitude is.*/ // TODO** Can this be generalized for both longitude and azimuth??? - int m_longitudeDomain; /**< This integer is either 180 or 360 and is read - from the labels. It represents the longitude - domain when returning values through Longitude - method. The domain is either -180 to 180 or - 0 to 360.**/ - - double m_equatorialRadius; /**< Polar radius of the target. This is a - unitless value so that if the radius are - in inches then the m_x and m_y will be in - inches. The value is read from the - labels.**/ - double m_polarRadius; /**< Polar radius of the target. This is a - unitless value so that if the radius are - in inches then the m_x and m_y will be in - inches. Of course the units must be the - same as the equatorial radius. The value - is read from the labels.*/ - - double m_eccentricity; //!< Planet Eccentricity - - double m_minimumLatitude; /**< Contains the minimum latitude for the - entire ground range. Only usable if - m_groundRangeGood is true.*/ - double m_maximumLatitude; /**< Contains the maximum latitude for the - entire ground range. Only usable if - m_groundRangeGood is true.*/ - double m_minimumLongitude; /**< Contains the minimum longitude for the - entire ground range. Only usable if - m_groundRangeGood is true.*/ - double m_maximumLongitude; /**< Contains the maximum longitude for the - entire ground range. Only usable if - m_groundRangeGood is true.*/ + int m_longitudeDomain; /**< This integer is either 180 or 360 and is read from the labels. + It represents the longitude domain when returning values through + Longitude method. The domain is either -180 to 180 or 0 to 360.*/ + double m_equatorialRadius; /**< Polar radius of the target. This is a unitless value so that + if the radii are in inches then the m_x and m_y will be in + inches. This value is set on construction. It is either read + directly from the mapping group of the given PVL label or it + is found in NAIF kernels by using the Target value + in the given label. When pulled from NAIF kernels, the + equatorial radius is the first value of NAIF's radii array.*/ + double m_polarRadius; /**< Polar radius of the target. This is a unitless value so that + if the radii are in inches then the m_x and m_y will be in + inches. Of course the units must be the same as the + equatorial radius. This value is set on construction. + It is either read directly from the mapping group of the + given PVL label or it is found in NAIF kernels by using the + Target value in the given label.When pulled from NAIF + kernels, the equatorial radius is the third value of NAIF's + radii array.*/ + + double m_eccentricity; //!< The eccentricity of the target body. + + double m_minimumLatitude; /**< Contains the minimum latitude for the entire ground range. + Only usable if m_groundRangeGood is true.*/ + double m_maximumLatitude; /**< Contains the maximum latitude for the entire ground range. + Only usable if m_groundRangeGood is true.*/ + double m_minimumLongitude; /**< Contains the minimum longitude for the entire ground range. + Only usable if m_groundRangeGood is true.*/ + double m_maximumLongitude; /**< Contains the maximum longitude for the entire ground range. + Only usable if m_groundRangeGood is true.*/ private: - // These are necessary for calculating oblique X/Y range with + // These are necessary for calculating oblique X/Y range with // discontinuity - std::vector m_specialLatCases; /**< Constant Latitudes that - intersect a discontinuity.**/ - std::vector m_specialLonCases; /**< Constant Longitudes that - intersect a discontinuity.**/ + std::vector m_specialLatCases; /**< Constant Latitudes that + intersect a discontinuity.*/ + std::vector m_specialLonCases; /**< Constant Longitudes that + intersect a discontinuity.*/ }; }; #endif + diff --git a/isis/src/base/objs/TProjection/TProjection.truth b/isis/src/base/objs/TProjection/TProjection.truth index 3feca3ac2876db3c300be6a4c9d8af29d4752f09..004803a920a1981860c50b5342cf1a2069aed900 100644 --- a/isis/src/base/objs/TProjection/TProjection.truth +++ b/isis/src/base/objs/TProjection/TProjection.truth @@ -127,6 +127,16 @@ Minimum latitude: 45 Maximum latitude: 80 Minimum longitude: 15 Maximum longitude: 190 + +Testing inLatitudeRange, inLongitudeRange methods... + +InLongitudeRange (15,190,0): 0 +InLongitudeRange (15,190,100): 1 +InLongitudeRange (100): 1 +InLongitudeRange (-12): 0 +InLatitudeRange (-70): 0 +InLatitudeRange (70): 1 + Find coordinate range ... Minimum X: 150 Maximum X: 1900 diff --git a/isis/src/base/objs/TProjection/unitTest.cpp b/isis/src/base/objs/TProjection/unitTest.cpp index 235a06d883fdab5df1c7e151335a5235c488a9b4..82f1428de0ad7bb56d75d014b13f1d9f51e156f0 100644 --- a/isis/src/base/objs/TProjection/unitTest.cpp +++ b/isis/src/base/objs/TProjection/unitTest.cpp @@ -21,6 +21,8 @@ * @history 2016-08-26 Kelvin Rodriguez - Changed invalidValue varible to have * both an int and double version to avoid undefined behavior in * trying to convert double to int. Part of porting to OSX 10.11 + * @history 2016-12-28 Kristin Berry - Updated to test inLatitude range and two new + * inLongitudeRange functions. */ using namespace std; @@ -86,6 +88,20 @@ class MyProjection : public Isis::TProjection { return xyRangeOblique(minX, maxX, minY, maxY); } + // create wrappers to test protected methods + bool testinLongitudeRange(double longitude) { + return inLongitudeRange(longitude); + } + + bool testinLongitudeRange(double minLon, double maxLon, double longitude) { + return inLongitudeRange(minLon, maxLon, longitude); + } + + bool testinLatitudeRange(double latitude) { + return inLatitudeRange(latitude); + } + + // create output method to print results of private methods void Output() const { cout << "tCompute(0,sin(0)): " << tCompute(0.0, 0.0) << endl; @@ -100,6 +116,7 @@ class MyProjection : public Isis::TProjection { cout << "phi2Compute(1000): " << phi2Compute(1000.0) << endl; cout << "qCompute(sin(0)): " << qCompute(0.0) << endl; } + double testqCompute(const double sinPhi) const { return qCompute(sinPhi); } @@ -310,6 +327,16 @@ int main(int argc, char *argv[]) { cout << "Maximum latitude: " << p2.MaximumLatitude() << endl; cout << "Minimum longitude: " << p2.MinimumLongitude() << endl; cout << "Maximum longitude: " << p2.MaximumLongitude() << endl; + cout << endl; + + cout << "Testing inLatitudeRange, inLongitudeRange methods...\n" << endl; + cout << "InLongitudeRange (15,190,0): " << p2.testinLongitudeRange(15.0, 190.0, 0.0) << endl; + cout << "InLongitudeRange (15,190,100): " << p2.testinLongitudeRange(15.0,190.0, 100.0) << endl; + cout << "InLongitudeRange (100): " << p2.testinLongitudeRange(100.0) << endl; + cout << "InLongitudeRange (-12): " << p2.testinLongitudeRange(-12.0) << endl; + cout << "InLatitudeRange (-70): " << p2.testinLatitudeRange(-70.0) << endl; + cout << "InLatitudeRange (70): " << p2.testinLatitudeRange(70.0) << endl; + cout << endl; double minX, maxX, minY, maxY; p2.XYRange(minX, maxX, minY, maxY); diff --git a/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/Makefile b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..f122bc88227c5c7ebd108dea5d339d1d2e074d82 --- /dev/null +++ b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/Makefile @@ -0,0 +1,7 @@ +ifeq ($(ISISROOT), $(BLANK)) +.SILENT: +error: + echo "Please set ISISROOT"; +else + include $(ISISROOT)/make/isismake.objs +endif \ No newline at end of file diff --git a/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/Projection.plugin b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/Projection.plugin new file mode 100644 index 0000000000000000000000000000000000000000..7549be0a9638e8d620a43c46e50023dca3d3e143 --- /dev/null +++ b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/Projection.plugin @@ -0,0 +1,6 @@ +Group = UpturnedEllipsoidTransverseAzimuthal + Library = UpturnedEllipsoidTransverseAzimuthal + Routine = UpturnedEllipsoidTransverseAzimuthalPlugin + Keyword = CenterLongitude +EndGroup + diff --git a/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.cpp b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d95fa282868165d5fa7495c1348c49a51955d93b --- /dev/null +++ b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.cpp @@ -0,0 +1,767 @@ +/** + * @file + * $Revision: 1.8 $ + * $Date: 2009/03/20 22:30:23 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "UpturnedEllipsoidTransverseAzimuthal.h" + +#include +#include +#include +#include + +#include + +#include "Constants.h" +#include "IException.h" +#include "IString.h" +#include "TProjection.h" +#include "Pvl.h" +#include "PvlGroup.h" +#include "PvlKeyword.h" +#include "SpecialPixel.h" + +using namespace std; +namespace Isis { + /** + * Constructs an upturned ellipsoid transverse azimuthal map projection object + * + * @param label This argument must be a label containing the proper mapping + * information, as indicated in the Projection class. + * Additionally, the UpturnedEllipsoidTransverseAzimuthal projection + * requires the center longitude and center latitude to be + * defined in the keywords CenterLongitude and CenterLatitude, + * respectively. + * + * @param allowDefaults If set to false, the constructor expects that + * keywords of CenterLongitude and CenterLatitude will be + * in the label. Otherwise, it will attempt to compute + * the center longitude and center latitude using + * the midpoints of the longitude and latitude ranges + * specified in the labels, respectively. Defaults to + * false. + * + * @author 2016-03-18 Jeannie Backer + */ + UpturnedEllipsoidTransverseAzimuthal::UpturnedEllipsoidTransverseAzimuthal(Pvl &label, + bool allowDefaults) : + TProjection::TProjection(label) { + try { + // This algorithm can be found in the professional paper + // Cartographic Projections for Small Bodies of the Solar System + // by Maria E Fleis, Kira B Shingareva, + // Michael M Borisov, Michael V Alexandrovich, and Philip Stooke + + // Try to read the mapping group + PvlGroup &mapGroup = label.findGroup("Mapping", Pvl::Traverse); + + // Compute and write the default center longitude if allowed and + // necessary + double centerLongitude = 0.0; + if (!mapGroup.hasKeyword("CenterLongitude")) { + if (allowDefaults) { + // centerLongitude still 0.0 here + mapGroup += PvlKeyword("CenterLongitude", toString(centerLongitude), "Degrees"); + } + else { + QString message = "Cannot project using upturned ellipsoid Transverse Azimuthal"; + message += " without [CenterLongitude] value. Keyword does not exist"; + message += " in labels and defaults are not allowed."; + throw IException(IException::Unknown, message, _FILEINFO_); + } + } + else { + centerLongitude = mapGroup["CenterLongitude"]; + } + + if (MinimumLongitude() < centerLongitude - 90.0) { + QString message = "MinimumLongitude [" + + toString(MinimumLongitude()) + + "] is invalid. Must be within -90 degrees of the CenterLongitude [" + + toString(centerLongitude) + "]."; + throw IException(IException::Unknown, message, _FILEINFO_); + } + if (MaximumLongitude() > centerLongitude + 90.0) { + QString message = "MaximumLongitude [" + + toString(MaximumLongitude()) + + "] is invalid. Must be within +90 degrees of the CenterLongitude [" + + toString(centerLongitude) + "]."; + throw IException(IException::Unknown, message, _FILEINFO_); + } + + // Get the center longitude & latitude + // initialize member variables + init(centerLongitude); + } + catch(IException &e) { + QString message = "Invalid label group [Mapping]"; + throw IException(e, IException::Unknown, message, _FILEINFO_); + } + } + + + /** + * Destroys the UpturnedEllipsoidTransverseAzimuthal object + * + * @author 2016-03-18 Jeannie Backer + */ + UpturnedEllipsoidTransverseAzimuthal::~UpturnedEllipsoidTransverseAzimuthal() { + } + + + /** + * Compares two Projection objects to see if they are equal + * + * @param proj Projection object to do comparison on + * + * @return @b bool Returns true if the Projection objects are equal, and false if + * they are not + * + * @author 2016-03-18 Jeannie Backer + */ + bool UpturnedEllipsoidTransverseAzimuthal::operator== (const Projection &proj) { + // don't do the below it is a recursive plunge + // if (Projection::operator!=(proj)) return false; + + // all other data members calculated using m_lambda0, m_a and m_b. + UpturnedEllipsoidTransverseAzimuthal *tcyl = (UpturnedEllipsoidTransverseAzimuthal *) &proj; + if ((tcyl->m_lambda0 != m_lambda0) || + (tcyl->m_a != m_a) || + (tcyl->m_b != m_b)) return false; + + return true; + } + + + /** + * Returns the name of the map projection. + * + * @return @b QString Name of projection + * + * @author 2016-03-18 Jeannie Backer + */ + QString UpturnedEllipsoidTransverseAzimuthal::Name() const { + return "UpturnedEllipsoidUpturnedEllipsoidTransverseAzimuthal"; + } + + + /** + * Returns the version of the map projection. + * + * @return @b QString Version number + */ + QString UpturnedEllipsoidTransverseAzimuthal::Version() const { + return "1.0"; + } + + + /** + * Initialize member variables. + * + * @param centerLatitude The center latitude value found in the labels of the + * mapping group. + * @param centerLongitude The center longitude value found in the labels of + * the mapping group. + * + * + * @author 2016-03-18 Jeannie Backer + */ + void UpturnedEllipsoidTransverseAzimuthal::init(double centerLongitude) { + + // adjust for positive east longitude direction and convert to radians + if (IsPositiveEast()) { + m_lambda0 = centerLongitude * DEG2RAD; + } + else { + m_lambda0 = ToPositiveEast(centerLongitude, 360) * DEG2RAD; + } + if (Has180Domain()) { + m_lambda0 = To180Domain(m_lambda0); + } + else { + m_lambda0 = To360Domain(m_lambda0); + } + + // Initialize miscellaneous protected data elements + m_good = false; + + m_minimumX = DBL_MAX; + m_maximumX = -DBL_MAX; + m_minimumY = DBL_MAX; + m_maximumY = -DBL_MAX; + + // Descriptions of the variables a, e + double axis1 = EquatorialRadius(); + double axis2 = PolarRadius(); + m_a = qMax(axis1, axis2); // major axis. generally, this is the larger of the equatorial axes + m_b = qMin(axis1, axis2); // minor axis. generally, this is the polar axis + m_e = Eccentricity(); // e = sqrt(1 - (b/a)^2) + // must be 0 <= e < 1 + if (qFuzzyCompare(0.0, m_e)) { + m_e = 0.0; + } + + // to reduce calculations, calculate some scalar constants: + double t0 = m_b / m_a; // equals sqrt( 1 - m_e * m_e ); + m_t = t0 * t0; // equals 1 - m_e * m_e ; + m_t1 = m_e * t0; // equals e/sqrt( 1 - m_e * m_e ); + double k1 = 2 * m_a * exp(m_t1 * atan(m_t1)); + // k = radius of the Equator of transverse graticule on Azimuthal projection + // under condition of no distortion in the center of projection + m_k = k1 * m_t; + } + + + /** + * This method is used to set the ground latitude/longitude values and + * compute the corresponding x/y values of the projection. The method + * assumes the latitude and longitude given to be non-Null and of the + * correct LatitudeType, LongitudeDirection, and LongitudeDomain. If the + * computation of the x/y coordinate values is unsuccessful, this method + * returns false. + * + * @param lat Latitude value to project, in degrees. Must be between -90 + * and 90. + * @param lon Longitude value to project, in degrees + * + * @return @b bool Indicates whether the x/y coordinate calculation was + * successful. + * + * @author 2016-03-18 Jeannie Backer + */ + bool UpturnedEllipsoidTransverseAzimuthal::SetGround(const double lat, + const double lon) { + // when lat/lon is Null we can't set ground + if (lat == Null || lon == Null) { + m_good = false; + return m_good; + } + + // convert given lat to radians, planetocentric + // phiNorm = The planetocentric latitude, in normal aspect. + double phiNorm; + // when lat just barely beyond pole, set equal to pole + if (qFuzzyCompare(90.0, qAbs(lat)) && qAbs(lat) > 90.0) { + phiNorm = copysign(HALFPI, lat); // returns sign(lat) * PI/2 + } + // if well beyond pole, it's bad + else if (qAbs(lat) > 90.0) { + m_good = false; + return m_good; + } + else if (IsPlanetocentric()) { + phiNorm = lat * DEG2RAD; + } + else { + // equations expect ocentric latitudes. + phiNorm = ToPlanetocentric(lat) * DEG2RAD; + } + + // convert given lon to positive east, then subtract center lon to get + // lambdaNorm = longitude east of the center of projection + double lambdaNorm; + if (IsPositiveEast()) { + lambdaNorm = lon * DEG2RAD - m_lambda0; + } + else { + lambdaNorm = ToPositiveEast(lon, 360) * DEG2RAD - m_lambda0; + } + + // Compute the rectangular x,y coordinate using the appropriate set of equations below + double x,y; + + // NOTE: z = the angular distance from the center of projection. + double cosz = cos(phiNorm) * cos(lambdaNorm); + + // First, we take care of the edge cases where + // 1. a rounding error causes cosz to be outside of the range of cosine + // 2. z == 0 (this could be handled by the next set of equations, + // but taking care of it here reduces calculations.) + if (cosz >= 1) { + // This is the origin, + // at lat = equator, lon = centerlon + x = 0.0; + y = 0.0; + } + + // This condition is used for the set of equations that are + // written to exclude the singularities where z == 0 or z == PI + // (i.e. the given longitude is equal to the center longitude + // or 180 degrees from it). + // Use these equations for 0.5 < cosz < 1.0, i.e. 0 < z < PI/3 + else if (cosz > 0.5) { // && cosz < 1 is implied by bounds on cosine + // use pythagorean identity to get sine + double sinz = sqrt( 1 - cosz*cosz ); // due to restrictions above sinz != 0 + // phi = the latitude at "upturned" ellipsoid of revolution + // NOTE: Since cos(z) > 0.5 or cos(z) < -0.5, + // there is no risk of zero denominator when dividing by cosz + double phi = HALFPI - atan2( sinz, m_t * cosz ); + double sinPhi = sin(phi); + // rhoOverTanZ = rho/tanz + // where rho = the radius of latitude circle (transverse graticule) + // NOTE: We know sin(phi) = -1 only if + // phi = PI/2 - arctan(angle) = -PI/2 or 3PI/2 + // but the range of arctangent is (-PI/2, PI/2), + // so there is no risk of zero denominator dividing by (1+sin(phi)) + double rhoOverTanZ = m_k * sinPhi / ( ( 1 + sinPhi ) + * m_t + * exp( m_t1 * atan( m_t1 * sinPhi ) ) ); + x = rhoOverTanZ * tan(lambdaNorm); + y = rhoOverTanZ * (sin(phiNorm) / cosz ); // Note: cos(z) > 0.5, so no dividing by zero + } + + // This condition is used for the set of equations that are + // written to exclude the singularity where z == PI/2. + // Use these equations for -1 <= cosz <= 0.5, i.e. PI/3 <= z < PI. + else { + // For this case, we will restrict z near multiples of PI using a + // tolerance value in order to avoid singularities at 0 and PI. We + // define zmin and zmax by: + // + // zmin = minimal value of angular distance from the center of projection + // = 0 + angular tolerance + // zmax = maximal value of angular distance from the center of projection + // in the neighborhood of point opposite to the center of projection + // = PI - angular tolerance + double tolerance = 0.0016;//??? + double coszmax = cos(PI - tolerance); + double lambdaModulus = fmod(lambdaNorm, TWOPI); + if (cosz < coszmax) { + cosz = coszmax; // prevents cosz from equalling -1 + // The following prevent lambdaNorm from being too close to +/-PI + + // if the given longitude is within tolerance of -PI and less than -PI, + // set it to -PI - tolerance) + //if (qFuzzyCompare(lambdaNorm, -PI) && lambdaNorm <= -PI) { + if (-PI - tolerance < lambdaModulus && lambdaModulus <= -PI) { + lambdaNorm = -PI - tolerance; + } + // if the given longitude is within tolerance of -PI and greater than -PI, + // set it to -zmax (i.e. -PI + tolerance) + // + //if (qFuzzyCompare(lambdaNorm, -PI) && lambdaNorm > -PI) { + else if (-PI < lambdaModulus && lambdaModulus <= -PI + tolerance) { + lambdaNorm = -PI + tolerance; + } + // if the given longitude is within tolerance of PI and less than PI, + // set it to zmax (i.e. PI - tolerance) + // + //if (qFuzzyCompare(lambdaNorm, PI) && lambdaNorm <= PI) { + else if (PI - tolerance < lambdaModulus && lambdaModulus <= PI) { + lambdaNorm = PI - tolerance; + } + // if the given longitude is within tolerance of PI and greater than PI, + // set it to PI + tolerance + // + //if (qFuzzyCompare(lambdaNorm, PI) && lambdaNorm > PI) { + else if (PI < lambdaModulus && lambdaModulus < PI + tolerance) { + lambdaNorm = PI + tolerance; + } + } + // use pythagorean identity to get sine + double sinz = sqrt( 1 - cosz*cosz ); // due to restrictions above, we know sinz != 0 + + // phi = latitude at "upturned" ellipsoid of revolution + // NOTE: On the interval, PI/3 <= z < PI, + // we know 0 < sin(z) <= 1, + // so there is no risk of zero denom when dividing by sinz + double phi = atan2( m_t * cosz, sinz ); + double sinPhi = sin(phi); + // Note: We know sin(phi) = -1 only if + // phi = arctan(angle) = -PI/2 + // but the range of arctangent is the open interval (-PI/2, PI/2), + // so there is no risk of zero denominator dividing by (1+sin(phi)) + double rhoOverSinZ = m_k * cos(phi) / ( ( 1 + sinPhi ) + * sinz + * exp( m_t1 * atan(m_t1 * sinPhi ) ) ); + x = rhoOverSinZ * cos(phiNorm) * sin(lambdaNorm); + y = rhoOverSinZ * sin(phiNorm); + } + + // set member data and return status + m_good = true; + m_latitude = lat; + m_longitude = lon; + SetComputedXY(x, y); // sets m_x = x and m_y = y and handles rotation + // Note: if x or y are Null, sets m_good back to false + return m_good; + } + + + /** + * This method is used to set the projection x/y and compute the + * corresponding latitude/longitude position. The method assumes the x/y are + * not Null. If the computation of the latitude/longitude position values is + * unsuccessful, this method returns false. + * + * @param x X coordinate of the projection in units that are the same as the + * radii in the label + * + * @param y Y coordinate of the projection in units that are the same as the + * radii in the label + * + * @return bool Indicates whether the latitude/longitude position + * calculation was successful. + * + * @author 2016-03-18 Jeannie Backer + */ + bool UpturnedEllipsoidTransverseAzimuthal::SetCoordinate(const double x, + const double y) { + if (x == Null || y == Null) { + m_good = false; + return m_good; + } + // Save the coordinate + SetXY(x, y); + + if (qFuzzyCompare(x + 1.0, 1.0) && qFuzzyCompare(y + 1.0, 1.0)) { + // origin + m_latitude = 0.0; + m_longitude = m_lambda0 * RAD2DEG; + } + else { + + // We are given the following forward equations: + // + // x = (rho/sin(z)) * cos(phiNorm) * sin(lambdaNorm) + // y = (rho/sin(z)) * sin(phiNorm) + // rho/sin(z) = ( k*cos(phi) / [(1+sin(phi))*sin(z)*e^{t1*arctan(t1*sin(phi)}] ) + // phi = arctan( (1-e^2)*cos(z) / sin(z) ) + // + // So, after simplifying, we can verify x^2 + y^2 = rho^2 + // Thus, we have two solutions for rho: + // + // rho = +/- sqrt(x^2 + y^2) + // rho = ( k*cos(phi) / [(1+sin(phi))*e^{t1*arctan(t1*sin(phi)}] ) + // + // Now, we can use Newton's root finding method for the function + // f(phi) = g(phi) - h(phi) on [-pi/2, pi/2] + // where + // g(phi) = k*cos(phi) / [(1+sin(phi))*e^{t1*arctan(t1*sin(phi)}] + // and + // h(phi) = sqrt(x^2 + y^2). + // + // After simplifying, the derivative with respect to phi is + // f'(phi) = -k * (1 + t1^2) / + // [(1 + sin(phi)) * e^{t1 * arctan(t1 * sin(phi)} * (1 + t1^2 * sin^2(phi))] + + double phi0, fphi0, fprimephi0, phi1; + bool converged = false; + int iterations = 0; + double tolerance = 10e-10; + phi0 = 0.0; // start at the equator??? + while (!converged && iterations < 1000) { + fphi0 = m_k * cos(phi0) / ((1 + sin(phi0)) * exp(m_t1 * atan( m_t1 * sin(phi0) ))) + - sqrt(x*x + y*y); + + fprimephi0 = -m_k * (1 + m_t1 * m_t1) + / ((1 + sin(phi0)) + * exp(m_t1 * atan( m_t1 * sin(phi0) )) + * (1 + m_t1 * m_t1 * sin(phi0) * sin(phi0))); + phi1 = phi0 - fphi0 / fprimephi0; + // if phi wrapped at the poles, make sure phi is on [-pi/2, pi/2] + if (qAbs(phi1) > HALFPI) { + double phiDegrees = To180Domain(phi1*RAD2DEG); + if (phiDegrees > 90.0) { + phiDegrees -= 90.0; + } + if (phiDegrees < -180.0) { + phiDegrees += 90.0; + } + phi1 = phiDegrees * DEG2RAD; + } + if (qAbs(phi0 - phi1) < tolerance) { + converged = true; + } + else { + phi0 = phi1; + iterations++; + } + } + + if (!converged) { + m_good = false; + return m_good; + } + + // Now we have phi, the latitude at "upturned" ellipsoid of revolution. + double phi = phi1; + + // Now use the forward equation for phi to solve for z, the angular distance from the center + // of projection: + // + // phi = arctan( (1-e^2) * cos(z) / sin(z)) + // + double z = atan2((1 - m_e * m_e), tan(phi)); // see handling of cylind??? + + // Get phiNorm,the planetocentric latitude, in normal aspect. The range of arcsine is + // [-pi/2, pi/2] so we are guaranteed to get an angle between the poles. Use the forward + // equation: + // + // y = (rho / sinz ) * sin(phiNorm) + //double rho = ( m_k * cos(phi) / ((1+sin(phi))*exp(m_e, m_t1*arctan(m_t1*sin(phi))) ); + double rho = sqrt(x*x + y*y); + double phiNorm = asin( y * sin(z) / rho ); + + // Get lambdaNorm, the longitude east of lambda0, using the forward equation + // cos(z) = cos(phiNorm) * cos(lambdaNorm) + double lambdaNorm; + + // make sure we are in the correct quadrant... + double cosLambdaNorm = cos(z) / cos(phiNorm); + if (cosLambdaNorm > 1.0) { + lambdaNorm = 0.0; + } + else if (cosLambdaNorm < -1.0) { + lambdaNorm = PI; // +/- PI doesn't matter here... same answer either way + } + else if (x >= 0 && y >= 0) { + lambdaNorm = acos(cosLambdaNorm); + } + else if (x < 0 && y >= 0) {// fix conditional??? + lambdaNorm = -acos(cosLambdaNorm); + } + else if (y < 0 && x >= 0) {// fix conditional??? + lambdaNorm = acos(cosLambdaNorm); + } + else { // y < 0 && x < 0 + lambdaNorm = -acos(cosLambdaNorm); + } + + // calculations give positive east longitude + m_longitude = (lambdaNorm + m_lambda0) * RAD2DEG; + m_latitude = phiNorm * RAD2DEG; + } + + // Cleanup the latitude + if (IsPlanetocentric()) { + m_latitude = ToPlanetocentric(m_latitude); + } + + // Cleanup the longitude + if (IsPositiveWest()) { + m_longitude = ToPositiveWest(m_longitude, m_longitudeDomain); + } + + if (Has180Domain()) { + m_longitude = To180Domain(m_longitude); + } + else { + // Do this because longitudeDirection could cause (-360,0) + m_longitude = To360Domain(m_longitude); + } + + m_good = true; + return m_good; + } + + + /** + * This method is used to determine the x/y range which completely covers the + * area of interest specified by the lat/lon range. The latitude/longitude + * range may be obtained from the labels. The purpose of this method is to + * return the x/y range so it can be used to compute how large a map may need + * to be. For example, how big a piece of paper is needed or how large of an + * image needs to be created. The method may fail as indicated by its return + * value. + * + * @param &minX Reference to the address where the minimum x + * coordinate value will be written. The Minimum x projection + * coordinate calculated by this method covers the + * latitude/longitude range specified in the labels. + * + * @param &maxX Reference to the address where the maximum x + * coordinate value will be written. The Maximum x projection + * coordinate calculated by this method covers the + * latitude/longitude range specified in the labels. + * + * @param &minY Reference to the address where the minimum y + * coordinate value will be written. The Minimum y projection + * coordinate calculated by this method covers the + * latitude/longitude range specified in the labels. + * + * @param &maxY Reference to the address where the maximum y + * coordinate value will be written. The Maximum y projection + * coordinate calculated by this method covers the + * latitude/longitude range specified in the labels. + * + * @return @b bool Indicates whether the method was able to determine the X/Y + * Range of the projection. If yes, minX, maxX, minY, maxY will + * be set with these values. + * + * + * @author 2016-03-18 Jeannie Backer + */ + bool UpturnedEllipsoidTransverseAzimuthal::XYRange(double &minX, double &maxX, + double &minY, double &maxY) { + + // First check combinations of the lat/lon range boundaries + XYRangeCheck(m_minimumLatitude, m_minimumLongitude); + XYRangeCheck(m_maximumLatitude, m_minimumLongitude); + XYRangeCheck(m_minimumLatitude, m_maximumLongitude); + XYRangeCheck(m_maximumLatitude, m_maximumLongitude); + + double centerLongitude = m_lambda0 * RAD2DEG; + + bool centerLongitudeInRange = TProjection::inLongitudeRange(centerLongitude); + bool centerLongitude90InRange = TProjection::inLongitudeRange(centerLongitude + 90.0); + bool centerLongitude180InRange = TProjection::inLongitudeRange(centerLongitude + 180.0); + bool centerLongitude270InRange = TProjection::inLongitudeRange(centerLongitude + 270.0); + + if (centerLongitudeInRange) { + XYRangeCheck(m_minimumLatitude, centerLongitude); + XYRangeCheck(m_maximumLatitude, centerLongitude); + } + if (centerLongitude90InRange) { + XYRangeCheck(m_minimumLatitude, centerLongitude + 90.0); + XYRangeCheck(m_maximumLatitude, centerLongitude + 90.0); + } + if (centerLongitude180InRange) { + XYRangeCheck(m_minimumLatitude, centerLongitude + 180.0); + XYRangeCheck(m_maximumLatitude, centerLongitude + 180.0); + } + if (centerLongitude270InRange) { + XYRangeCheck(m_minimumLatitude, centerLongitude + 270.0); + XYRangeCheck(m_maximumLatitude, centerLongitude + 270.0); + } + + if (TProjection::inLatitudeRange(0.0)) { + XYRangeCheck(0.0, m_minimumLongitude); + XYRangeCheck(0.0, m_maximumLongitude); + if (centerLongitudeInRange) { + XYRangeCheck(0.0, centerLongitude); + } + if (centerLongitude90InRange) { + XYRangeCheck(0.0, centerLongitude + 90.0); + } + if (centerLongitude180InRange) { + XYRangeCheck(0.0, centerLongitude + 180.0); + } + if (centerLongitude270InRange) { + XYRangeCheck(0.0, centerLongitude + 270.0); + } + } + + // Make sure everything is ordered + if (m_minimumX >= m_maximumX) return false; + if (m_minimumY >= m_maximumY) return false; + + // Return X/Y min/maxs + minX = m_minimumX; + maxX = m_maximumX; + minY = m_minimumY; + maxY = m_maximumY; + return true; + } + + + /** + * This function returns a PvlGroup containing the keywords that this + * projection uses. For example, + * @code + * Group = Mapping + * ProjectionName = UpturnedEllipsoidTransverseAzimuthal + * EquatorialRadius = 1.0 + * PolarRadius = 1.0 + * LatitudeType = Planetographic + * LongitudeDirection = PositiveEast + * LongitudeDomain = 180 + * PixelResolution = 0.001 + * MinimumLatitude = 20.0 + * MaximumLatitude = 80.0 + * MinimumLongitude = -180.0 + * MaximumLongitude = 180.0 + * CenterLongitude = 0 + * End_Group + * End + * + * @return @b PvlGroup The keywords that this projection uses. + * + * @author 2016-03-18 Jeannie Backer + */ + PvlGroup UpturnedEllipsoidTransverseAzimuthal::Mapping() { + PvlGroup mapping = TProjection::Mapping(); + mapping += PvlKeyword("CenterLongitude", toString(m_lambda0 * RAD2DEG)); + return mapping; + } + + + /** + * This function returns a PvlGroup containing the latitude keywords that this + * projection uses. For example, + * @code + * Group = Mapping + * MinimumLatitude = 20.0 + * MaximumLatitude = 80.0 + * End_Group + * End + * + * @return @b PvlGroup The latitude keywords that this projection uses. + * + * @author 2016-03-18 Jeannie Backer + */ + PvlGroup UpturnedEllipsoidTransverseAzimuthal::MappingLatitudes() { + return TProjection::MappingLatitudes(); + } + + + /** + * This function returns a PvlGroup containing the keyword CenterLongitude, + * the only longitude keywords that this projection uses. For example, + * @code + * Group = Mapping + * MinimumLongitude = -180.0 + * MaximumLongitude = 180.0 + * CenterLongitude = 0 + * End_Group + * End + * + * @return @b PvlGroup The longitude keywords that this projection uses. + * + * @author 2016-03-18 Jeannie Backer + */ + PvlGroup UpturnedEllipsoidTransverseAzimuthal::MappingLongitudes() { + PvlGroup mapping = TProjection::MappingLongitudes(); + mapping += PvlKeyword("CenterLongitude", toString(m_lambda0 * RAD2DEG)); + return mapping; + } + +} // end namespace isis + +/** + * This is the function that is called in order to instantiate a + * UpturnedEllipsoidTransverseAzimuthal object. + * + * @param lab Cube labels with appropriate Mapping information. + * + * @param allowDefaults Indicates whether CenterLatitude and CenterLongitude + * are allowed to be calculated by the midpoints of the + * latitude and longitude ranges. + * + * @return @b Isis::Projection* Pointer to a UpturnedEllipsoidTransverseAzimuthal + * projection object. + * + * @author 2016-03-18 Jeannie Backer + */ +extern "C" Isis::Projection *UpturnedEllipsoidTransverseAzimuthalPlugin(Isis::Pvl &lab, + bool allowDefaults) { + return new Isis::UpturnedEllipsoidTransverseAzimuthal(lab, allowDefaults); +} + diff --git a/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.h b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.h new file mode 100644 index 0000000000000000000000000000000000000000..8c0a94af1e6f1c104f56cb32ff623fd793440042 --- /dev/null +++ b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.h @@ -0,0 +1,101 @@ +#ifndef UpturnedEllipsoidTransverseAzimuthal_h +#define UpturnedEllipsoidTransverseAzimuthal_h +/** + * @file + * $Revision: 1.5 $ + * $Date: 2009/03/20 22:30:23 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "TProjection.h" + +namespace Isis { + class Pvl; + class PvlGroup; + /** + * @brief Upturned Ellipsoid Transverse Azimuthal Map Projection + * + * This class provides methods for the forward and inverse formulas of a + * Upturned Ellipsoid Transverse Azimuthal map projection + * + * + * This class inherits Projection and implements the virtual methods + *
    + *
  • SetGround - forward projection takes an lat/lon value from the given + * planet and calculates the corresponding x/y value on the projected plane + *
  • SetCoordinate - inverse projection takes an x/y coordinate from the + * plane and calculates the lat/lon value on the planet + *
  • XYRange - obtains projection coordinate coverage for a + * latitude/longitude window + *
+ * + * Please see the Projection class for a full accounting of all the methods + * available. + * + * @see Carographic Projections For Small Bodies of the Solar System + * by Maria E. Fleis, Michael M. Borisov, Michael V. Alexandrovich, + * Philip Stooke, and Kira B Shingareva + * + * @ingroup MapProjection + * + * @author 2016-03-18 Jeannie Backer + * + * @internal + * @history 2016-03-18 Jeannie Backer - Original version. Fixes #3877. + * @history 2016-12-28 Kristin Berry - Minor coding standards and documentation updates for + * checkin. + */ + class UpturnedEllipsoidTransverseAzimuthal : public TProjection { + public: + UpturnedEllipsoidTransverseAzimuthal(Pvl &label, bool allowDefaults = false); + ~UpturnedEllipsoidTransverseAzimuthal(); + bool operator== (const Projection &proj); + + virtual QString Name() const; + virtual QString Version() const; + + virtual bool SetGround(const double lat, const double lon); + virtual bool SetCoordinate(const double x, const double y); + virtual bool XYRange(double &minX, double &maxX, double &minY, double &maxY); + + virtual PvlGroup Mapping(); + virtual PvlGroup MappingLatitudes(); + virtual PvlGroup MappingLongitudes(); + + private: + void init(double centerLongitude); + void checkLongitude(double longitude); + + + double m_a; /**< Semi-major axis of the ellipse. For prolate bodies, + this will be the polar radius.*/ + double m_b; /**< Semi-minor axis of the ellipse. For prolate bodies, + this will be the equatorial radius.*/ + double m_e; /**< Eccentricity of the ellipse.*/ + double m_lambda0; /**< The longitude of the center of the projection. + This is value is 0 or 180 degrees.*/ + double m_t; /**< Auxiliary value used to reduce calculations. t = 1 - eccentricity^2. */ + double m_t1; /**< Auxiliary value used to reduce calculations. + t1 = e / sqrt( 1 - eccentricity^2 ) */ + double m_k; /**< The radius of the Equator of the transverse graticule on the + Azimuthal projection under the condition of no distortion in the + center of the projection.*/ + }; +}; + +#endif diff --git a/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.truth b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.truth new file mode 100644 index 0000000000000000000000000000000000000000..376bf960cef10aba6dc6a3efba9fbd0ae4564086 --- /dev/null +++ b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/UpturnedEllipsoidTransverseAzimuthal.truth @@ -0,0 +1,534 @@ +UNIT TEST FOR UpturnedEllipsoidTransverseAzimuthal projection + +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + PLANETOGRAPHIC-POSITIVEWEST-180 +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + +CenterLongitude = 0.0 +EquatorialRadius = 1.0 +PolarRadius = 1.0 +Eccentricity = 0 +TrueScaleLatitude = 0 + + + /-----------------------------------------/ + + Testing SetGround... +[Lat/Lon (90.0, -360.0)] ----> [x/y (-0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, -288.0)] ----> [x/y (-0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, -216.0)] ----> [x/y (-0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, -144.0)] ----> [x/y (0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, -72.0)] ----> [x/y (0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, 0.0)] ----> [x/y (0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, 72.0)] ----> [x/y (-0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, 144.0)] ----> [x/y (-0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, 216.0)] ----> [x/y (0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, 288.0)] ----> [x/y (0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (90.0, 360.0)] ----> [x/y (0.00000, 2.00000)] ----> [Lat/Lon (90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (72.0, -360.0)] ----> [x/y (-0.00000, 1.45309)] ----> [Lat/Lon (72.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, -288.0)] ----> [x/y (-0.53655, 1.73631)] ----> [Lat/Lon (72.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, -216.0)] ----> [x/y (-0.48436, 2.53615)] ----> [Lat/Lon (72.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, -144.0)] ----> [x/y (0.48436, 2.53615)] ----> [Lat/Lon (72.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, -72.0)] ----> [x/y (0.53655, 1.73631)] ----> [Lat/Lon (72.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, 0.0)] ----> [x/y (0.00000, 1.45309)] ----> [Lat/Lon (72.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, 72.0)] ----> [x/y (-0.53655, 1.73631)] ----> [Lat/Lon (72.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, 144.0)] ----> [x/y (-0.48436, 2.53615)] ----> [Lat/Lon (72.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, 216.0)] ----> [x/y (0.48436, 2.53615)] ----> [Lat/Lon (72.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, 288.0)] ----> [x/y (0.53655, 1.73631)] ----> [Lat/Lon (72.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (72.0, 360.0)] ----> [x/y (0.00000, 1.45309)] ----> [Lat/Lon (72.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (54.0, -360.0)] ----> [x/y (-0.00000, 1.01905)] ----> [Lat/Lon (54.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, -288.0)] ----> [x/y (-0.94617, 1.36932)] ----> [Lat/Lon (54.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, -216.0)] ----> [x/y (-1.31748, 3.08507)] ----> [Lat/Lon (54.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, -144.0)] ----> [x/y (1.31748, 3.08507)] ----> [Lat/Lon (54.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, -72.0)] ----> [x/y (0.94617, 1.36932)] ----> [Lat/Lon (54.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, 0.0)] ----> [x/y (0.00000, 1.01905)] ----> [Lat/Lon (54.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, 72.0)] ----> [x/y (-0.94617, 1.36932)] ----> [Lat/Lon (54.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, 144.0)] ----> [x/y (-1.31748, 3.08507)] ----> [Lat/Lon (54.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, 216.0)] ----> [x/y (1.31748, 3.08507)] ----> [Lat/Lon (54.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, 288.0)] ----> [x/y (0.94617, 1.36932)] ----> [Lat/Lon (54.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (54.0, 360.0)] ----> [x/y (0.00000, 1.01905)] ----> [Lat/Lon (54.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (36.0, -360.0)] ----> [x/y (-0.00000, 0.64984)] ----> [Lat/Lon (36.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, -288.0)] ----> [x/y (-1.23107, 0.94046)] ----> [Lat/Lon (36.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, -216.0)] ----> [x/y (-2.75276, 3.40260)] ----> [Lat/Lon (36.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, -144.0)] ----> [x/y (2.75276, 3.40260)] ----> [Lat/Lon (36.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, -72.0)] ----> [x/y (1.23107, 0.94046)] ----> [Lat/Lon (36.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, 0.0)] ----> [x/y (0.00000, 0.64984)] ----> [Lat/Lon (36.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, 72.0)] ----> [x/y (-1.23107, 0.94046)] ----> [Lat/Lon (36.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, 144.0)] ----> [x/y (-2.75276, 3.40260)] ----> [Lat/Lon (36.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, 216.0)] ----> [x/y (2.75276, 3.40260)] ----> [Lat/Lon (36.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, 288.0)] ----> [x/y (1.23107, 0.94046)] ----> [Lat/Lon (36.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (36.0, 360.0)] ----> [x/y (0.00000, 0.64984)] ----> [Lat/Lon (36.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (18.0, -360.0)] ----> [x/y (-0.00000, 0.31677)] ----> [Lat/Lon (18.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (18.0, -288.0)] ----> [x/y (-1.39812, 0.47765)] ----> [Lat/Lon (18.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (18.0, -216.0)] ----> [x/y (-4.84881, 2.68036)] ----> Reverse Projection Fails +[Lat/Lon (18.0, -144.0)] ----> [x/y (4.84881, 2.68036)] ----> Reverse Projection Fails +[Lat/Lon (18.0, -72.0)] ----> [x/y (1.39812, 0.47765)] ----> [Lat/Lon (18.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (18.0, 0.0)] ----> [x/y (0.00000, 0.31677)] ----> [Lat/Lon (18.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (18.0, 72.0)] ----> [x/y (-1.39812, 0.47765)] ----> [Lat/Lon (18.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (18.0, 144.0)] ----> [x/y (-4.84881, 2.68036)] ----> Reverse Projection Fails +[Lat/Lon (18.0, 216.0)] ----> [x/y (4.84881, 2.68036)] ----> Reverse Projection Fails +[Lat/Lon (18.0, 288.0)] ----> [x/y (1.39812, 0.47765)] ----> [Lat/Lon (18.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (18.0, 360.0)] ----> [x/y (0.00000, 0.31677)] ----> [Lat/Lon (18.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (0.0, -360.0)] ----> [x/y (0.00000, 0.00000)] ----> [Lat/Lon (0.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, -288.0)] ----> [x/y (-1.45309, 0.00000)] ----> [Lat/Lon (0.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, -216.0)] ----> [x/y (-6.15537, 0.00000)] ----> [Lat/Lon (0.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, -144.0)] ----> [x/y (6.15537, 0.00000)] ----> [Lat/Lon (0.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, -72.0)] ----> [x/y (1.45309, 0.00000)] ----> [Lat/Lon (0.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, 0.0)] ----> [x/y (0.00000, 0.00000)] ----> [Lat/Lon (0.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, 72.0)] ----> [x/y (-1.45309, 0.00000)] ----> [Lat/Lon (0.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, 144.0)] ----> [x/y (-6.15537, 0.00000)] ----> [Lat/Lon (0.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, 216.0)] ----> [x/y (6.15537, 0.00000)] ----> [Lat/Lon (0.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, 288.0)] ----> [x/y (1.45309, 0.00000)] ----> [Lat/Lon (0.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (0.0, 360.0)] ----> [x/y (0.00000, 0.00000)] ----> [Lat/Lon (0.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (-18.0, -360.0)] ----> [x/y (-0.00000, -0.31677)] ----> [Lat/Lon (-18.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-18.0, -288.0)] ----> [x/y (-1.39812, -0.47765)] ----> [Lat/Lon (-18.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-18.0, -216.0)] ----> [x/y (-4.84881, -2.68036)] ----> Reverse Projection Fails +[Lat/Lon (-18.0, -144.0)] ----> [x/y (4.84881, -2.68036)] ----> Reverse Projection Fails +[Lat/Lon (-18.0, -72.0)] ----> [x/y (1.39812, -0.47765)] ----> [Lat/Lon (-18.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-18.0, 0.0)] ----> [x/y (0.00000, -0.31677)] ----> [Lat/Lon (-18.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-18.0, 72.0)] ----> [x/y (-1.39812, -0.47765)] ----> [Lat/Lon (-18.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-18.0, 144.0)] ----> [x/y (-4.84881, -2.68036)] ----> Reverse Projection Fails +[Lat/Lon (-18.0, 216.0)] ----> [x/y (4.84881, -2.68036)] ----> Reverse Projection Fails +[Lat/Lon (-18.0, 288.0)] ----> [x/y (1.39812, -0.47765)] ----> [Lat/Lon (-18.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-18.0, 360.0)] ----> [x/y (0.00000, -0.31677)] ----> [Lat/Lon (-18.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (-36.0, -360.0)] ----> [x/y (-0.00000, -0.64984)] ----> [Lat/Lon (-36.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, -288.0)] ----> [x/y (-1.23107, -0.94046)] ----> [Lat/Lon (-36.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, -216.0)] ----> [x/y (-2.75276, -3.40260)] ----> [Lat/Lon (-36.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, -144.0)] ----> [x/y (2.75276, -3.40260)] ----> [Lat/Lon (-36.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, -72.0)] ----> [x/y (1.23107, -0.94046)] ----> [Lat/Lon (-36.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, 0.0)] ----> [x/y (0.00000, -0.64984)] ----> [Lat/Lon (-36.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, 72.0)] ----> [x/y (-1.23107, -0.94046)] ----> [Lat/Lon (-36.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, 144.0)] ----> [x/y (-2.75276, -3.40260)] ----> [Lat/Lon (-36.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, 216.0)] ----> [x/y (2.75276, -3.40260)] ----> [Lat/Lon (-36.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, 288.0)] ----> [x/y (1.23107, -0.94046)] ----> [Lat/Lon (-36.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-36.0, 360.0)] ----> [x/y (0.00000, -0.64984)] ----> [Lat/Lon (-36.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (-54.0, -360.0)] ----> [x/y (-0.00000, -1.01905)] ----> [Lat/Lon (-54.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, -288.0)] ----> [x/y (-0.94617, -1.36932)] ----> [Lat/Lon (-54.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, -216.0)] ----> [x/y (-1.31748, -3.08507)] ----> [Lat/Lon (-54.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, -144.0)] ----> [x/y (1.31748, -3.08507)] ----> [Lat/Lon (-54.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, -72.0)] ----> [x/y (0.94617, -1.36932)] ----> [Lat/Lon (-54.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, 0.0)] ----> [x/y (0.00000, -1.01905)] ----> [Lat/Lon (-54.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, 72.0)] ----> [x/y (-0.94617, -1.36932)] ----> [Lat/Lon (-54.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, 144.0)] ----> [x/y (-1.31748, -3.08507)] ----> [Lat/Lon (-54.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, 216.0)] ----> [x/y (1.31748, -3.08507)] ----> [Lat/Lon (-54.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, 288.0)] ----> [x/y (0.94617, -1.36932)] ----> [Lat/Lon (-54.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-54.0, 360.0)] ----> [x/y (0.00000, -1.01905)] ----> [Lat/Lon (-54.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (-72.0, -360.0)] ----> [x/y (-0.00000, -1.45309)] ----> [Lat/Lon (-72.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, -288.0)] ----> [x/y (-0.53655, -1.73631)] ----> [Lat/Lon (-72.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, -216.0)] ----> [x/y (-0.48436, -2.53615)] ----> [Lat/Lon (-72.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, -144.0)] ----> [x/y (0.48436, -2.53615)] ----> [Lat/Lon (-72.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, -72.0)] ----> [x/y (0.53655, -1.73631)] ----> [Lat/Lon (-72.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, 0.0)] ----> [x/y (0.00000, -1.45309)] ----> [Lat/Lon (-72.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, 72.0)] ----> [x/y (-0.53655, -1.73631)] ----> [Lat/Lon (-72.0, 72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, 144.0)] ----> [x/y (-0.48436, -2.53615)] ----> [Lat/Lon (-72.0, 144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, 216.0)] ----> [x/y (0.48436, -2.53615)] ----> [Lat/Lon (-72.0, -144.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, 288.0)] ----> [x/y (0.53655, -1.73631)] ----> [Lat/Lon (-72.0, -72.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-72.0, 360.0)] ----> [x/y (0.00000, -1.45309)] ----> [Lat/Lon (-72.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + +[Lat/Lon (-90.0, -360.0)] ----> [x/y (-0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, -288.0)] ----> [x/y (-0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, -216.0)] ----> [x/y (-0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, -144.0)] ----> [x/y (0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, -72.0)] ----> [x/y (0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, 0.0)] ----> [x/y (0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, 72.0)] ----> [x/y (-0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, 144.0)] ----> [x/y (-0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, 216.0)] ----> [x/y (0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, 288.0)] ----> [x/y (0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** +[Lat/Lon (-90.0, 360.0)] ----> [x/y (0.00000, -2.00000)] ----> [Lat/Lon (-90.0, 0.0)] ****[Lat Ok] [Lon Ok]**** + + + /-----------------------------------------/ + + Testing SetGround... +Latitude: -20.00000 +Longitude: 100.00000 +XCoord: -2.21174 +YCoord: -0.81742 + Reverse (SetCoordinate)... +Latitude: -20.00000 +Longitude: 100.00000 +XCoord: -2.21174 +YCoord: -0.81742 + /-----------------------------------------/ + + Testing projection to origin and back + SetGround(0, center longitude) +Latitude: 0.00000 +Longitude: 0.00000 +XCoord: 0.00000 +YCoord: 0.00000 + SetCoordinate(0, 0) +Latitude: 0.00000 +Longitude: 0.00000 +XCoord: 0.00000 +YCoord: 0.00000 + + /-----------------------------------------/ + + Testing projection to north pole and back + SetGround(90, 0) +Latitude: 90.00000 +Longitude: 0.00000 +XCoord: 0.00000 +YCoord: 2.00000 + SetCoordinate(0, PI*sphRad) +Latitude: 64.96327 +Longitude: -180.00000 +XCoord: 0.00000 +YCoord: 3.14159 + + /-----------------------------------------/ + + Testing XYRange method +Given: + Minimum Latitude: 20.0000000 + Maximum Latitude: 80.0000000 + Minimum Longitude: -90.0000000 + Maximum Longitude: 90.0000000 + Mapping Group: +Group = Mapping + ProjectionName = UpturnedEllipsoidTransverseAzimuthal + EquatorialRadius = 1.0 + PolarRadius = 1.0 + LatitudeType = Planetographic + LongitudeDirection = PositiveWest + LongitudeDomain = 180 + PixelResolution = .001 + MinimumLatitude = 20.0 + MaximumLatitude = 80.0 + MinimumLongitude = -90.0 + MaximumLongitude = 90.0 + CenterLongitude = 0.0 +End_Group +End + +XYRange method returns + Minimum X: -1.8793852 + Maximum X: 1.8793852 + Minimum Y: 0.3526540 + Maximum Y: 1.9696155 + + SetCoordinate(maxX, 0) returns lat/lon = 0.0000000 / -86.4383578 + SetCoordinate(0, maxY) returns lat/lon = 89.1229028 / -0.0000324 + SetCoordinate(minX, 0) returns lat/lon = 0.0000000 / 86.4383578 + SetCoordinate(0, minY) returns lat/lon = 20.0000000 / -0.0000000 + + SetGround(20, -90) returns x max? (x,y) = (1.8793852, 0.6840403) + SetGround(20, 0) returns y min? (x,y) = (0.0000000, 0.3526540) + SetGround(20, 90) returns x min? (x,y) = (-1.8793852, 0.6840403) + SetGround(80, 90) returns y max? (x,y) = (-0.3472964, 1.9696155) + + +Given: + Minimum Latitude: -90.0000000 + Maximum Latitude: 90.0000000 + Minimum Longitude: -80.0000000 + Maximum Longitude: -30.0000000 + + Mapping Group: +Group = Mapping + ProjectionName = UpturnedEllipsoidTransverseAzimuthal + EquatorialRadius = 1.0 + PolarRadius = 1.0 + LatitudeType = Planetographic + LongitudeDirection = PositiveWest + LongitudeDomain = 180 + PixelResolution = .001 + MinimumLatitude = -90.0 + MaximumLatitude = 90.0 + MinimumLongitude = -80.0 + MaximumLongitude = -30.0 + CenterLongitude = 0.0 +End_Group +End + +XYRange method returns + Minimum X: 0.0000000 + Maximum X: 1.6781993 + Minimum Y: -2.0000000 + Maximum Y: 2.0000000 + + SetCoordinate(maxX, 0) returns lat/lon = 0.0000000 / -80.0000000 + SetCoordinate(minX, minY) returns lat/lon = -90.0000000 / -0.0000000 + SetCoordinate(minX, maxY) returns lat/lon = 90.0000000 / -0.0000000 + + SetGround(90, 0) returns x min and y max? (x,y) = (0.0000000, 2.0000000) + SetGround(-90, 0) returns x min and y min? (x,y) = (0.0000000, -2.0000000) + SetGround(equator, minLon) returns x max? (x,y) = (1.6781993, 0.0000000) + + +Given: + Minimum Latitude: -90.0000000 + Maximum Latitude: 90.0000000 + Minimum Longitude: -90.0000000 + Maximum Longitude: 90.0000000 + +Group = Mapping + ProjectionName = UpturnedEllipsoidTransverseAzimuthal + EquatorialRadius = 1.0 + PolarRadius = 1.0 + LatitudeType = Planetographic + LongitudeDirection = PositiveWest + LongitudeDomain = 180 + PixelResolution = .001 + MinimumLatitude = -90.0 + MaximumLatitude = 90.0 + MinimumLongitude = -90.0 + MaximumLongitude = 90.0 + CenterLongitude = 0.0 +End_Group +End + +XYRange method returns + Minimum X: -2.0000000 + Maximum X: 2.0000000 + Minimum Y: -2.0000000 + Maximum Y: 2.0000000 + + SetCoordinate(maxX,0) returns lat/lon = 0.0000000 / -90.0000000 + SetCoordinate(0,maxY) returns lat/lon = 90.0000000 / -0.0000000 + SetCoordinate(minX,0) returns lat/lon = 0.0000000 / 90.0000000 + SetCoordinate(0,minY) returns lat/lon = -90.0000000 / -0.0000000 + + SetGround(0, -90) returns x max? (x,y) = (2.0000000, 0.0000000) + SetGround(90, 0) returns near y max? (x,y) = (0.0000000, 2.0000000) + SetGround(0, 90) returns x min? (x,y) = (-2.0000000, 0.0000000) + SetGround(-90, 0) returns y min? (x,y) = (0.0000000, -2.0000000) + + + + +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + PLANETOCENTRIC-POSITIVEEAST-360 +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + +CenterLongitude = 180.0 +EquatorialRadius = 3.0000000 +PolarRadius = 1.0000000 +Eccentricity = 0.9428090 +TrueScaleLatitude = 0.0000000 + + /-----------------------------------------/ + + Testing SetGround... +Latitude: -20.0000000 +Longitude: 100.0000000 +XCoord: -0.6743679 +YCoord: -0.2492363 + + /-----------------------------------------/ + + Testing SetCoordinate... +Latitude: 0.1368093 +Longitude: 1.2950601 +XCoord: -4.2339303 +YCoord: 4.0257775 + + /-----------------------------------------/ + + Testing projection to origin and back + SetGround(0, 180) +Latitude: 0.0000000 +Longitude: 180.0000000 +XCoord: 0.0000000 +YCoord: 0.0000000 + SetCoordinate(0, 0) +Latitude: 0.0000000 +Longitude: 180.0000000 +XCoord: 0.0000000 +YCoord: 0.0000000 + + /-----------------------------------------/ + + Testing projection to north pole and back + SetGround(90, 0) +Latitude: 90.0000000 +Longitude: 0.0000000 +XCoord: -0.0000000 +YCoord: 0.7336148 + SetCoordinate(0, 0.7336148) +Latitude: 89.9998835 +Longitude: 180.0000000 +XCoord: 0.0000000 +YCoord: 0.7336148 + + /-----------------------------------------/ + Testing XYRange method + +Given: + Minimum Latitude: -90.0000000 + Maximum Latitude: 90.0000000 + Minimum Longitude: 90.0000000 + Maximum Longitude: 270.0000000 + + Mapping Group: +Group = Mapping + ProjectionName = UpturnedEllipsoidTransverseAzimuthal + EquatorialRadius = 3.0 + PolarRadius = 1.0 + LatitudeType = Planetocentric + LongitudeDirection = PositiveEast + LongitudeDomain = 360 + PixelResolution = .001 + MinimumLatitude = -90.0 + MaximumLatitude = 90.0 + MinimumLongitude = 90 + MaximumLongitude = 270 + CenterLongitude = 180.0 +End_Group +End + +XYRange method returns + Minimum X: -0.7336148 + Maximum X: 0.7336148 + Minimum Y: -0.7336148 + Maximum Y: 0.7336148 + + SetCoordinate(maxX,0) returns lat/lon = 0.000 / 270.000 + SetCoordinate(0,maxY) returns lat/lon = 90.000 / 180.000 + SetCoordinate(minX,0) returns lat/lon = 0.000 / 90.000 + SetCoordinate(0,minY) returns lat/lon = -90.000 / 180.000 + + SetGround(0, 270) returns x max? (x,y) = (0.734, 0.000) + SetGround(90, 180) returns y max? (x,y) = (0.000, 0.734) + SetGround(0, 90) returns x min? (x,y) = (-0.734, 0.000) + SetGround(-90, 180) returns y min? (x,y) = (0.000, -0.734) + + +Given: + Minimum Latitude: -90.0000000 + Maximum Latitude: 90.0000000 + Minimum Longitude: 100.0000000 + Maximum Longitude: 110.0000000 + + Mapping Group: +Group = Mapping + ProjectionName = UpturnedEllipsoidTransverseAzimuthal + EquatorialRadius = 3.0 + PolarRadius = 1.0 + LatitudeType = Planetocentric + LongitudeDirection = PositiveEast + LongitudeDomain = 360 + PixelResolution = .001 + MinimumLatitude = -90.0 + MaximumLatitude = 90.0 + MinimumLongitude = 100.0 + MaximumLongitude = 110.0 + CenterLongitude = 180.0 +End_Group +End + +XYRange method returns + Minimum X: -0.7179923 + Maximum X: -0.0000000 + Minimum Y: -0.7336148 + Maximum Y: 0.7336148 + + + SetCoordinate(maxX, 0) returns lat/lon = 0.0000000 / 180.0000000 + SetCoordinate(0, maxY) returns lat/lon = 90.0000000 / 180.0000000 + SetCoordinate(minX, 0) returns lat/lon = 0.0000000 / 100.0000000 + SetCoordinate(maxX, minY) returns lat/lon = -90.0000000 / 180.0000000 + + SetGround(0, 180) returns x max? (x,y) = (0.0000000, 0.0000000) + SetGround(90, 180) returns y max? (x,y) = (0.0000000, 0.7336148) + SetGround(0, 100) returns x min? (x,y) = (-0.7179923, 0.0000000) + SetGround(-90, 180) returns y min? (x,y) = (0.0000000, -0.7336148) + + + + +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + TESTING OTHER METHODS +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + +Name: UpturnedEllipsoidUpturnedEllipsoidTransverseAzimuthal +Version: 1.0 +Rotation: 0.0000000 +TrueScaleLatitude: 0.0000000 +Testing operator== (True): 1 +Testing operator== (True): 1 +Testing operator== (True): 1 +Testing operator== (False-different CenterLongitude): 0 +Testing operator== (False-different EquatorialRadius): 0 +Testing operator== (False-different Eccentricity): 0 + + /-----------------------------------------/ + +Testing Mapping() methods +Mapping() = +Group = Mapping + ProjectionName = UpturnedEllipsoidTransverseAzimuthal + EquatorialRadius = 1.0 + PolarRadius = 1.0 + LatitudeType = Planetographic + LongitudeDirection = PositiveWest + LongitudeDomain = 180 + PixelResolution = .001 + MinimumLatitude = 20.0 + MaximumLatitude = 80.0 + MinimumLongitude = -90.0 + MaximumLongitude = 90.0 + CenterLongitude = 0.0 +End_Group +End +MappingLatitudes() = +Group = Mapping + MinimumLatitude = 20.0 + MaximumLatitude = 80.0 +End_Group +End +MappingLongitudes() = +Group = Mapping + MinimumLongitude = -90.0 + MaximumLongitude = 90.0 + CenterLongitude = 0.0 +End_Group +End + + + + +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + TESTING GOOD = FALSE +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + +Set Ground using invalid Latitude/Longitude value +SetGround(Null, 0): 0 +SetGround(0, Null): 0 +SetGround(-91, 0): 0 +Set Coordinate using invalid x/y value +SetCoordinate(Null, 0): 0 +SetCoordinate(0, Null): 0 +Set Coordinate using x/y value off the planet +SetCoordinate(100000, 0): 0 + + /-----------------------------------------/ + +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + TESTING ERRORS +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + +Error check: Missing center longitude keyword when default is not allowed +**ERROR** Invalid label group [Mapping]. +**ERROR** Cannot project using upturned ellipsoid Transverse Azimuthal without [CenterLongitude] value. Keyword does not exist in labels and defaults are not allowed. + + /-----------------------------------------/ + +Error check: Min/Max Longitude not within 90 degrees of Center Longitude +**ERROR** Invalid label group [Mapping]. +**ERROR** MinimumLongitude [0.0] is invalid. Must be within -90 degrees of the CenterLongitude [180.0]. +**ERROR** Invalid label group [Mapping]. +**ERROR** MaximumLongitude [360.0] is invalid. Must be within +90 degrees of the CenterLongitude [180.0]. + + /-----------------------------------------/ diff --git a/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/unitTest.cpp b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/unitTest.cpp new file mode 100644 index 0000000000000000000000000000000000000000..4883c3df08289d90c569efeec6a71c14d9cd98c6 --- /dev/null +++ b/isis/src/base/objs/UpturnedEllipsoidTransverseAzimuthal/unitTest.cpp @@ -0,0 +1,736 @@ +#include +#include +#include + +#include "Camera.h" +#include "CameraFactory.h" +#include "IException.h" +#include "Projection.h" +#include "ProjectionFactory.h" +#include "Preference.h" +#include "Pvl.h" +#include "PvlGroup.h" +#include "PvlKeyword.h" +#include "TProjection.h" +#include "UpturnedEllipsoidTransverseAzimuthal.h" + +using namespace std; +using namespace Isis; + +void testSetGround(TProjection *p); +void printErrors(double origLat, double projectedLat, double origLon, double projectedLon); + +/** + * Unit test for UpturnedEllipsoidTransverseAzimuthal map projection class + * + * @author 2016-05-25 Jeannie Backer + * @internal + * @history 2016-05-25 Jeannie Backer - Original version. + * @history 2016-12-28 Kristin Berry - Updated for longitude restriction to center longitue +/- + * 90 degrees and fixes for some output values. + * + * @todo Test coverage: + * CONSTRUCTOR: + * if (mapGroup.hasKeyword("CenterLongitude")) + * if (!mapGroup.hasKeyword("CenterLongitude") && allowDefaults) + * if (!mapGroup.hasKeyword("CenterLongitude") && !allowDefaults) THROWS ERROR + * if (MaximumLongitude() - MinimumLongitude() > 360.0) THROWS ERROR + * INIT + * if (IsPositiveEast()) + * if (IsPositiveWest()) + * if (Has180Domain() + * if (Has360Domain() + * if (qFuzzyCompare(0.0, m_e)) (EQUATORIAL RAD = POLAR RAD) + * OPERATOR== + * if (!Projection::operator==(proj)) return false; + * ELSE + * SETGROUND + * if (lat == Null) + * if (lon == Null) + * if (qFuzzyCompare(90.0, qAbs(lat)) && lat > 90.0) + * if (qFuzzyCompare(90.0, qAbs(lat)) && lat < -90.0) + * if lat no where near poles + * if (IsPlanetographic()) + * if (IsPlanetocentric()) + * if (IsPositiveEast()) + * if (IsPositiveWest()) + * if the given longitude is within tolerance of -PI and less than -PI, + * set it to -PI - tolerance) + * if the given longitude is within tolerance of -PI and greater than -PI, + * set it to -zmax (i.e. -PI + tolerance) + * if the given longitude is non-negative and within tolerance of zero, + * set it to zmin (i.e 0 + tolerance) + * if the given longitude is within tolerance of PI and less than PI, + * set it to zmax (i.e. PI - tolerance) + * if the given longitude is within tolerance of PI and greater than PI, + * set it to PI + tolerance + * if the given longitude is within tolerance of 2PI and less than 2PI, + * set it to 2PI - tolerance + * if (cosaz <= -1) { + * else if (cosaz >= 1) { + * else if (phiNorm >= 0) { // northern hemisphere, i.e. cos(phiNorm)sin(phiNorm) >= 0 + * else { // phiNorm is in southern hemisphere i.e. cos(phiNorm)sin(phiNorm) < 0 + * // if azimuth is acute or negative, increase by 2pi + * if (az <= HALFPI) + * SETCOORDINATE + * if (x == Null) + * if (y == Null + * if (IsPlanetographic()) + * if (IsPlanetocentric()) + * if (y >= 0) { + * if (y < 0) { + * if (IsPositiveEast()) + * if (IsPositiveWest()) + * if (Has180Domain() + * if (Has360Domain() + * XYRANGE + * CHECKLONGITUDE + * + */ +int main(int argc, char *argv[]) { + Preference::Preferences(true); + + cout << "UNIT TEST FOR UpturnedEllipsoidTransverseAzimuthal projection" << endl << endl; + + Pvl lab; + lab.addGroup(PvlGroup("Mapping")); + PvlGroup &mapGroup = lab.findGroup("Mapping"); + mapGroup += PvlKeyword("EquatorialRadius", "1.0"); + mapGroup += PvlKeyword("PolarRadius", "1.0"); + mapGroup += PvlKeyword("LatitudeType", "Planetographic"); + mapGroup += PvlKeyword("LongitudeDirection", "PositiveWest"); + mapGroup += PvlKeyword("LongitudeDomain", "180"); + mapGroup += PvlKeyword("MinimumLatitude", "20.0"); + mapGroup += PvlKeyword("MaximumLatitude", "80.0"); + mapGroup += PvlKeyword("MinimumLongitude", "-90.0"); + mapGroup += PvlKeyword("MaximumLongitude", "90.0"); + mapGroup += PvlKeyword("ProjectionName", "UpturnedEllipsoidTransverseAzimuthal"); + mapGroup += PvlKeyword("PixelResolution", ".001"); + + try { + string border = "||||||||||||||||||||||||||||||||||||||||" + "||||||||||||||||||||||||||||||||||||||||"; + + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + cout << border << endl; + cout << "\t\t\t PLANETOGRAPHIC-POSITIVEWEST-180" << endl; + cout << border << endl << endl; + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + Projection &proj = *ProjectionFactory::Create(lab, true); + TProjection *p1 = (TProjection *) &proj; + cout << mapGroup["CenterLongitude"] << endl; + cout << mapGroup["EquatorialRadius"] << endl; + cout << mapGroup["PolarRadius"] << endl; + cout << "Eccentricity = " << p1->Eccentricity() << endl; + cout << "TrueScaleLatitude = " << p1->TrueScaleLatitude() << endl << endl; + + cout << std::fixed; + cout << std::setprecision(5); + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + cout << " Testing SetGround..." << endl; + testSetGround(p1); + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + cout << " Testing SetGround..." << endl; + if (p1->SetGround(-20, 100)) { + cout << "Latitude: " << p1->Latitude() << endl; + cout << "Longitude: " << p1->Longitude() << endl; + cout << "XCoord: " << p1->XCoord() << endl; + cout << "YCoord: " << p1->YCoord() << endl; + cout << " Reverse (SetCoordinate)..." << endl; + if (p1->SetCoordinate(p1->XCoord(), p1->YCoord())) { + cout << "Latitude: " << p1->Latitude() << endl; + cout << "Longitude: " << p1->Longitude() << endl; + cout << "XCoord: " << p1->XCoord() << endl; + cout << "YCoord: " << p1->YCoord() << endl; + } + else { + cout << "SetCoordinate failed for x/y (" + << toString(p1->XCoord()) << ", " << toString(p1->XCoord()) << ")" << endl; + } + } + else { + cout << "SetGround failed for lat/lon (-20, 100)" << endl; + } + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + cout << " Testing projection to origin and back\n" + " SetGround(0, center longitude)" << endl; + p1->SetGround(0.0, 0.0); + cout << "Latitude: " << p1->Latitude() << endl; + cout << "Longitude: " << p1->Longitude() << endl; + cout << "XCoord: " << p1->XCoord() << endl; + cout << "YCoord: " << p1->YCoord() << endl; + cout << " SetCoordinate(0, 0)" << endl; + p1->SetCoordinate(0.0, 0.0); + cout << "Latitude: " << p1->Latitude() << endl; + cout << "Longitude: " << p1->Longitude() << endl; + cout << "XCoord: " << p1->XCoord() << endl; + cout << "YCoord: " << p1->YCoord() << endl; + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + cout << " Testing projection to north pole and back\n" + " SetGround(90, 0)" << endl; + p1->SetGround(90.0, 0.0); + cout << "Latitude: " << p1->Latitude() << endl; + cout << "Longitude: " << p1->Longitude() << endl; + cout << "XCoord: " << p1->XCoord() << endl; + cout << "YCoord: " << p1->YCoord() << endl; + cout << " SetCoordinate(0, PI*sphRad)" << endl; + p1->SetCoordinate(0.0, PI); + cout << "Latitude: " << p1->Latitude() << endl; + cout << "Longitude: " << p1->Longitude() << endl; + cout << "XCoord: " << p1->XCoord() << endl; + cout << "YCoord: " << p1->YCoord() << endl; + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + + cout << std::setprecision(7); + cout << " Testing XYRange method" << endl; + cout << "Given: " << endl; + cout << " Minimum Latitude: " << p1->MinimumLatitude() << endl; + cout << " Maximum Latitude: " << p1->MaximumLatitude() << endl; + cout << " Minimum Longitude: " << p1->MinimumLongitude() << endl; + cout << " Maximum Longitude: " << p1->MaximumLongitude() << endl; + cout << " Mapping Group: " << endl; + Pvl pvl1; + pvl1.addGroup(p1->Mapping()); + cout << pvl1 << endl << endl; + + double minX, maxX, minY, maxY; + p1->XYRange(minX, maxX, minY, maxY); + cout << "XYRange method returns" << endl; + cout << " Minimum X: " << minX << endl; + cout << " Maximum X: " << maxX << endl; + cout << " Minimum Y: " << minY << endl; + cout << " Maximum Y: " << maxY << endl; + cout << endl; + if (p1->SetCoordinate(maxX, 0.0)) { + cout << " SetCoordinate(maxX, 0) returns lat/lon = " + << p1->Latitude() << " / " << p1->Longitude() << endl; + } + if (p1->SetCoordinate(0.0, maxY)) { + cout << " SetCoordinate(0, maxY) returns lat/lon = " + << p1->Latitude() << " / " << p1->Longitude() << endl; + } + if (p1->SetCoordinate(minX, 0.0)) { + cout << " SetCoordinate(minX, 0) returns lat/lon = " + << p1->Latitude() << " / " << p1->Longitude() << endl; + } + if (p1->SetCoordinate(0, minY)) { + cout << " SetCoordinate(0, minY) returns lat/lon = " + << p1->Latitude() << " / " << p1->Longitude() << endl; + } + cout << endl; + if (p1->SetGround(20.0, -90.0)) { + cout << " SetGround(20, -90) returns x max? "; + cout << "(x,y) = (" << p1->XCoord() << ", " << p1->YCoord() << ")"<< endl; + } + if (p1->SetGround(20.0, 0.0)) { + cout << " SetGround(20, 0) returns y min? "; + cout << "(x,y) = (" << p1->XCoord() << ", " << p1->YCoord() << ")"<< endl; + } + if (p1->SetGround(20.0, 90.0)) { + cout << " SetGround(20, 90) returns x min? "; + cout << "(x,y) = (" << p1->XCoord() << ", " << p1->YCoord() << ")"<< endl; + } + if (p1->SetGround(80.0, 90.0)) { + cout << " SetGround(80, 90) returns y max? "; + cout << "(x,y) = (" << p1->XCoord() << ", " << p1->YCoord() << ")"<< endl; + } + cout << endl; + cout << endl; + mapGroup.findKeyword("MinimumLatitude").setValue("-90.0"); + mapGroup.findKeyword("MaximumLatitude").setValue("90.0"); + mapGroup.findKeyword("MinimumLongitude").setValue("-80.0"); + mapGroup.findKeyword("MaximumLongitude").setValue("-30.0"); + /* + * + * + * : : + * ::: ::: + * :::::::: :::::::: + * :::::::::::::::::::::::::: + * :::::::::::::::::::::::::::: + * :::::::::::::::::::::::::: + * :::::::::::::::::::: + * ::::::::::::: + * ::::::: + * + */ + TProjection *p1a = (TProjection *) ProjectionFactory::Create(lab); + cout << "Given: " << endl; + cout << " Minimum Latitude: " << p1a->MinimumLatitude() << endl; + cout << " Maximum Latitude: " << p1a->MaximumLatitude() << endl; + cout << " Minimum Longitude: " << p1a->MinimumLongitude() << endl; + cout << " Maximum Longitude: " << p1a->MaximumLongitude() << endl << endl; + cout << " Mapping Group: " << endl; + Pvl pvl1a; + pvl1a.addGroup(p1a->Mapping()); + cout << pvl1a << endl << endl; + + p1a->XYRange(minX, maxX, minY, maxY); + cout << "XYRange method returns" << endl; + cout << " Minimum X: " << minX << endl; + cout << " Maximum X: " << maxX << endl; + cout << " Minimum Y: " << minY << endl; + cout << " Maximum Y: " << maxY << endl; + cout << endl; + if (p1a->SetCoordinate(maxX, 0.0)) { + cout << " SetCoordinate(maxX, 0) returns lat/lon = " + << p1a->Latitude() << " / " << p1a->Longitude() << endl; + } + if (p1a->SetCoordinate(minX, minY)) { + cout << " SetCoordinate(minX, minY) returns lat/lon = " + << p1a->Latitude() << " / " << p1a->Longitude() << endl; + } + if (p1a->SetCoordinate(minX, maxY)) { + cout << " SetCoordinate(minX, maxY) returns lat/lon = " + << p1a->Latitude() << " / " << p1a->Longitude() << endl; + } + cout << endl; + if (p1a->SetGround(90.0, 0.0)) { + cout << " SetGround(90, 0) returns x min and y max? "; + cout << "(x,y) = (" << p1a->XCoord() << ", " << p1a->YCoord() << ")"<< endl; + } + if (p1a->SetGround(-90.0, 0.0)) { + cout << " SetGround(-90, 0) returns x min and y min? "; + cout << "(x,y) = (" << p1a->XCoord() << ", " << p1a->YCoord() << ")"<< endl; + } + if (p1a->SetGround(0.0, -80.0)) { + cout << " SetGround(equator, minLon) returns x max? "; + cout << "(x,y) = (" << p1a->XCoord() << ", " << p1a->YCoord() << ")"<< endl; + } + cout << endl; + cout << endl; + mapGroup.findKeyword("MinimumLongitude").setValue("-90.0"); + mapGroup.findKeyword("MaximumLongitude").setValue("90.0"); + cout << "Given: " << endl; + TProjection *p1b = (TProjection *) ProjectionFactory::Create(lab); + cout << " Minimum Latitude: " << p1b->MinimumLatitude() << endl; + cout << " Maximum Latitude: " << p1b->MaximumLatitude() << endl; + cout << " Minimum Longitude: " << p1b->MinimumLongitude() << endl; + cout << " Maximum Longitude: " << p1b->MaximumLongitude() << endl << endl; + Pvl pvl1b; + pvl1b.addGroup(p1b->Mapping()); + cout << pvl1b << endl << endl; + + p1b->XYRange(minX, maxX, minY, maxY); + p1b->XYRange(minX, maxX, minY, maxY); + cout << "XYRange method returns" << endl; + cout << " Minimum X: " << minX << endl; + cout << " Maximum X: " << maxX << endl; + cout << " Minimum Y: " << minY << endl; + cout << " Maximum Y: " << maxY << endl; + cout << endl; + if (p1b->SetCoordinate(maxX,0)) { + cout << " SetCoordinate(maxX,0) returns lat/lon = " + << p1b->Latitude() << " / " << p1b->Longitude() << endl; + } + if (p1b->SetCoordinate(0, maxY)) { + cout << " SetCoordinate(0,maxY) returns lat/lon = " + << p1b->Latitude() << " / " << p1b->Longitude() << endl; + } + if (p1b->SetCoordinate(minX,0)) { + cout << " SetCoordinate(minX,0) returns lat/lon = " + << p1b->Latitude() << " / " << p1b->Longitude() << endl; + } + if (p1b->SetCoordinate(0, minY)) { + cout << " SetCoordinate(0,minY) returns lat/lon = " + << p1b->Latitude() << " / " << p1b->Longitude() << endl; + } + cout << endl; + if (p1b->SetGround(0.0, -90.0)) { + cout << " SetGround(0, -90) returns x max? "; + cout << "(x,y) = (" << p1b->XCoord() << ", " << p1b->YCoord() << ")"<< endl; + } + if (p1b->SetGround(90.0, 0.0)) { + cout << " SetGround(90, 0) returns near y max? "; + cout << "(x,y) = (" << p1b->XCoord() << ", " << p1b->YCoord() << ")"<< endl; + } + if (p1b->SetGround(0.0, 90.0)) { + cout << " SetGround(0, 90) returns x min? "; + cout << "(x,y) = (" << p1b->XCoord() << ", " << p1b->YCoord() << ")"<< endl; + } + if (p1b->SetGround(-90.0, 0.0)) { + cout << " SetGround(-90, 0) returns y min? "; + cout << "(x,y) = (" << p1b->XCoord() << ", " << p1b->YCoord() << ")"<< endl; + } + cout << endl; + cout << endl; + cout << endl; + cout << endl; + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + cout << border << endl; + cout << "\t\t\t PLANETOCENTRIC-POSITIVEEAST-360" << endl; + cout << border << endl << endl; + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + mapGroup.findKeyword("LatitudeType").setValue("Planetocentric"); + mapGroup.findKeyword("LongitudeDirection").setValue("PositiveEast"); + mapGroup.findKeyword("EquatorialRadius").setValue("3.0"); + mapGroup.findKeyword("PolarRadius").setValue("1.0"); + + mapGroup.findKeyword("CenterLongitude").setValue("180.0"); + mapGroup.findKeyword("MinimumLatitude").setValue("-90.0"); + mapGroup.findKeyword("MaximumLatitude").setValue("90.0"); + mapGroup.findKeyword("MinimumLongitude").setValue("90"); + mapGroup.findKeyword("MaximumLongitude").setValue("270"); + mapGroup.findKeyword("LongitudeDomain").setValue("360"); + + TProjection *p2 = (TProjection *) ProjectionFactory::Create(lab); + cout << mapGroup["CenterLongitude"] << endl; + cout << "EquatorialRadius = " << p2->EquatorialRadius() << endl; + cout << "PolarRadius = " << p2->PolarRadius() << endl; + cout << "Eccentricity = " << p2->Eccentricity() << endl; + cout << "TrueScaleLatitude = " << p2->TrueScaleLatitude() << endl << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + + cout << " Testing SetGround..." << endl; + p2->SetGround(-20, 100); + cout << "Latitude: " << p2->Latitude() << endl; + cout << "Longitude: " << p2->Longitude() << endl; + cout << "XCoord: " << p2->XCoord() << endl; + cout << "YCoord: " << p2->YCoord() << endl; + // we do not have relative scale factor methods in Projection as of 06/2012 + // so these need to be tested with a UpturnedEllipsoidTransverseAzimuthal object + // specifically. The following values were calculated by hand to verify. + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + + cout << " Testing SetCoordinate..." << endl; + p2->SetCoordinate(-4.2339303, 4.0257775); + cout << "Latitude: " << p2->Latitude() << endl; + cout << "Longitude: " << p2->Longitude() << endl; + cout << "XCoord: " << p2->XCoord() << endl; + cout << "YCoord: " << p2->YCoord() << endl; + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + + cout << " Testing projection to origin and back\n" + " SetGround(0, 180)" << endl; + p2->SetGround(0.0, 180.0); + cout << "Latitude: " << p2->Latitude() << endl; + cout << "Longitude: " << p2->Longitude() << endl; + cout << "XCoord: " << p2->XCoord() << endl; + cout << "YCoord: " << p2->YCoord() << endl; + cout << " SetCoordinate(0, 0)" << endl; + + p2->SetCoordinate(0.0, 0.0); + cout << "Latitude: " << p2->Latitude() << endl; + cout << "Longitude: " << p2->Longitude() << endl; + cout << "XCoord: " << p2->XCoord() << endl; + cout << "YCoord: " << p2->YCoord() << endl; + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + + cout << " Testing projection to north pole and back\n" + " SetGround(90, 0)" << endl; + p2->SetGround(90.0, 0.0); + cout << "Latitude: " << p2->Latitude() << endl; + cout << "Longitude: " << p2->Longitude() << endl; + cout << "XCoord: " << p2->XCoord() << endl; + cout << "YCoord: " << p2->YCoord() << endl; + + cout << " SetCoordinate(0, 0.7336148)" << endl; + p2->SetCoordinate(0.0, 0.7336148); + cout << "Latitude: " << p2->Latitude() << endl; + cout << "Longitude: " << p2->Longitude() << endl; + cout << "XCoord: " << p2->XCoord() << endl; + cout << "YCoord: " << p2->YCoord() << endl; + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + + cout << " Testing XYRange method" << endl; + cout << endl; + cout << "Given: " << endl; + cout << std::setprecision(7); + cout << " Minimum Latitude: " << p2->MinimumLatitude() << endl; + cout << " Maximum Latitude: " << p2->MaximumLatitude() << endl; + cout << " Minimum Longitude: " << p2->MinimumLongitude() << endl; + cout << " Maximum Longitude: " << p2->MaximumLongitude() << endl << endl; + cout << " Mapping Group: " << endl; + + Pvl pvl2; + pvl2.addGroup(p2->Mapping()); + cout << pvl2 << endl << endl; + + minX=0; maxX=0; minY=0; maxY=0; + p2->XYRange(minX, maxX, minY, maxY); + cout << "XYRange method returns" << endl; + cout << " Minimum X: " << minX << endl; + cout << " Maximum X: " << maxX << endl; + cout << " Minimum Y: " << minY << endl; + cout << " Maximum Y: " << maxY << endl; + cout << endl; + + p2->SetCoordinate(maxX,0); + cout << std::setprecision(3); + if (p2->SetCoordinate(maxX,0)) { + cout << " SetCoordinate(maxX,0) returns lat/lon = " + << p2->Latitude() << " / " << p2->Longitude() << endl; + } + if (p2->SetCoordinate(0, maxY)) { + cout << " SetCoordinate(0,maxY) returns lat/lon = " << + p2->Latitude() << " / " << p2->Longitude() << endl; + } + if (p2->SetCoordinate(minX,0)) { + cout << " SetCoordinate(minX,0) returns lat/lon = " + << p2->Latitude() << " / " << p2->Longitude() << endl; + } + if (p2->SetCoordinate(0, minY)) { + cout << " SetCoordinate(0,minY) returns lat/lon = " + << p2->Latitude() << " / " << p2->Longitude() << endl; + } + cout << endl; + if (p2->SetGround(0.0, 270.0)) { + cout << " SetGround(0, 270) returns x max? "; + cout << "(x,y) = (" << p2->XCoord() << ", " << p2->YCoord() << ")"<< endl; + } + if (p2->SetGround(90.0, 180.0)) { + cout << " SetGround(90, 180) returns y max? "; + cout << "(x,y) = (" << p2->XCoord() << ", " << p2->YCoord() << ")"<< endl; + } + if (p2->SetGround(0.0, 90.0)) { + cout << " SetGround(0, 90) returns x min? "; + cout << "(x,y) = (" << p2->XCoord() << ", " << p2->YCoord() << ")"<< endl; + } + if (p2->SetGround(-90.0, 180.0)) { + cout << " SetGround(-90, 180) returns y min? "; + cout << "(x,y) = (" << p2->XCoord() << ", " << p2->YCoord() << ")"<< endl; + } + cout << endl; + cout << endl; + + mapGroup.findKeyword("MaximumLatitude").setValue("90.0"); + mapGroup.findKeyword("MinimumLongitude").setValue("100.0"); + mapGroup.findKeyword("MaximumLongitude").setValue("110.0"); + + TProjection *p2a = (TProjection *) ProjectionFactory::Create(lab); + cout << std::setprecision(7); + cout << "Given: " << endl; + cout << " Minimum Latitude: " << p2a->MinimumLatitude() << endl; + cout << " Maximum Latitude: " << p2a->MaximumLatitude() << endl; + cout << " Minimum Longitude: " << p2a->MinimumLongitude() << endl; + cout << " Maximum Longitude: " << p2a->MaximumLongitude() << endl << endl; + cout << " Mapping Group: " << endl; + Pvl pvl2a; + pvl2a.addGroup(p2a->Mapping()); + cout << pvl2a << endl << endl; + + minX=0; maxX=0; minY=0; maxY=0; + p2a->XYRange(minX, maxX, minY, maxY); + cout << "XYRange method returns" << endl; + cout << " Minimum X: " << minX << endl; + cout << " Maximum X: " << maxX << endl; + cout << " Minimum Y: " << minY << endl; + cout << " Maximum Y: " << maxY << endl; + cout << endl; + cout << endl; + + if(p2a->SetCoordinate(maxX, 0.0)) { + cout << " SetCoordinate(maxX, 0) returns lat/lon = " + << p2a->Latitude() << " / " << p2a->Longitude() << endl; + } + if(p2a->SetCoordinate(0.0, maxY)) { + cout << " SetCoordinate(0, maxY) returns lat/lon = " << + p2a->Latitude() << " / " << p2a->Longitude() << endl; + } + if(p2a->SetCoordinate(minX, 0.0)) { + cout << " SetCoordinate(minX, 0) returns lat/lon = " + << p2a->Latitude() << " / " << p2a->Longitude() << endl; + } + if(p2a->SetCoordinate(maxX, minY)) { + cout << " SetCoordinate(maxX, minY) returns lat/lon = " + << p2a->Latitude() << " / " << p2a->Longitude() << endl; + } + cout << endl; + if (p2a->SetGround(0.0, 180.0)) { + cout << " SetGround(0, 180) returns x max? "; + cout << "(x,y) = (" << p2a->XCoord() << ", " << p2a->YCoord() << ")"<< endl; + } + if (p2a->SetGround(90.0, 180.0)) { + cout << " SetGround(90, 180) returns y max? "; + cout << "(x,y) = (" << p2a->XCoord() << ", " << p2a->YCoord() << ")"<< endl; + } + if (p2a->SetGround(0.0, 100.0)) { + cout << " SetGround(0, 100) returns x min? "; + cout << "(x,y) = (" << p2a->XCoord() << ", " << p2a->YCoord() << ")"<< endl; + } + if (p2a->SetGround(-90.0, 180.0)) { + cout << " SetGround(-90, 180) returns y min? "; + cout << "(x,y) = (" << p2a->XCoord() << ", " << p2a->YCoord() << ")"<< endl; + } + cout << endl; + cout << endl; + cout << endl; + cout << endl; + + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + cout << border << endl; + cout << "\t\t\t TESTING OTHER METHODS" << endl; + cout << border << endl << endl; + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + mapGroup.findKeyword("PolarRadius").setValue(toString(p2a->EquatorialRadius())); + TProjection *p9 = (TProjection *) ProjectionFactory::Create(lab); + TProjection *s = p1; + cout << "Name: " << s->Name() << endl; + cout << "Version: " << p1->Version() << endl; + cout << "Rotation: " << p1->Rotation() << endl; + cout << "TrueScaleLatitude: " << p1->TrueScaleLatitude() << endl; + cout << "Testing operator== (True): " << (*s == *s) << endl; + cout << "Testing operator== (True): " << (*s == proj) << endl; + // different lat/lon range, all other properties the same + cout << "Testing operator== (True): " << (*p1 == *p1a) << endl; + // same CenterLatitude, different CenterLongitude + cout << "Testing operator== (False-different CenterLongitude): " << (p2a == p1) << endl; + // same CenterLatitude/CenterLongitude, different EquatorialRadius + cout << "Testing operator== (False-different EquatorialRadius): " << (p2 == p1) << endl; + // same CenterLatitude/CenterLongitude/EquatorialRadius, different eccentricity + cout << "Testing operator== (False-different Eccentricity): " << (p2a == p9) << endl; + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + cout << "Testing Mapping() methods" << endl; + Pvl tmp1; + tmp1.addGroup(p1->Mapping()); + cout << "Mapping() = " << endl; + cout << tmp1 << endl; + Pvl tmp2; + tmp2.addGroup(p1->MappingLatitudes()); + cout << "MappingLatitudes() = " << endl; + cout << tmp2 << endl; + Pvl tmp3; + tmp3.addGroup(p1->MappingLongitudes()); + cout << "MappingLongitudes() = " << endl; + cout << tmp3 << endl; + cout << endl; + cout << endl; + cout << endl; + cout << endl; + + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + cout << border << endl; + cout << "\t\t\t TESTING GOOD = FALSE" << endl; + cout << border << endl << endl; + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + cout << "Set Ground using invalid Latitude/Longitude value" << endl; + cout << "SetGround(Null, 0): " << p1->SetGround( Null, 0.0) << endl; + cout << "SetGround(0, Null): " << p1->SetGround( 0.0, Null) << endl; + cout << "SetGround(-91, 0): " << p1->SetGround(-91.0, 0.0) << endl; + cout << "Set Coordinate using invalid x/y value" << endl; + cout << "SetCoordinate(Null, 0): " << p1->SetCoordinate(Null, 0.0) << endl; + cout << "SetCoordinate(0, Null): " << p1->SetCoordinate(0.0, Null) << endl; + cout << "Set Coordinate using x/y value off the planet" << endl; + cout << "SetCoordinate(100000, 0): " << p1->SetCoordinate(100000, 0) << endl; + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + cout << border << endl; + cout << "\t\t\t TESTING ERRORS" << endl; + cout << border << endl << endl; + //|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| + mapGroup.deleteKeyword("CenterLongitude"); + cout << "Error check: Missing center longitude keyword when default is not allowed" << endl; + try { + UpturnedEllipsoidTransverseAzimuthal p(lab); + } + catch(IException &e) { + e.print(); + } + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + cout << endl; + cout << "Error check: Min/Max Longitude not within 90 degrees of Center Longitude" << endl; + + // Minimum Longitude too small case + try { + mapGroup += PvlKeyword("CenterLongitude", "180.0"); + mapGroup.findKeyword("MinimumLongitude").setValue("0.0"); + mapGroup.findKeyword("MaximumLongitude").setValue("270.0"); + UpturnedEllipsoidTransverseAzimuthal p(lab); + } + catch(IException &e) { + e.print(); + } + + // Maximum Longitude too large case + try { + mapGroup += PvlKeyword("CenterLongitude", "180.0"); + mapGroup.findKeyword("MinimumLongitude").setValue("90.0"); + mapGroup.findKeyword("MaximumLongitude").setValue("360.0"); + UpturnedEllipsoidTransverseAzimuthal p(lab); + } + catch(IException &e) { + e.print(); + } + cout << endl; + cout << "\t\t\t\t/-----------------------------------------/" << endl; + } + catch(IException &e) { + e.print(); + } +} + +// The Latitude step of 18 is 180/10 (Test values at 10 equally-spaced latitudes.) +// The Longitude step of 72 is 360/10 (Test values at 10 equally-space longitudes for each lat.) +void testSetGround(TProjection *p) { + for (double lat = 90.0; lat >= -90.0; lat-=18.0) { + for (double lon = -360.0; lon <= 360.0; lon+=72.0) { + cout << "[Lat/Lon (" + << toString(lat) << ", " << toString(lon) << ")]"; + bool success = p->SetGround(lat, lon); + if (success) { + cout << " ----> [x/y (" + << p->XCoord() << ", " << p->YCoord() << ")]"; + success = p->SetCoordinate(p->XCoord(), p->YCoord()); + if (success) { + cout << " ----> [Lat/Lon (" + << toString(p->Latitude()) << ", " << toString(p->Longitude()) << ")]"; + printErrors(lat, p->Latitude(), lon, p->Longitude()); + } + else { + cout << " ----> Reverse Projection Fails"; + } + cout << endl; + } + else { + cout << " ----> Forward Projection Fails"; + } + } + cout << endl; + } +} + + +void printErrors(double origLat, double projectedLat, double origLon, double projectedLon) { + double latErr = qAbs(origLat - projectedLat); + double lonErr = qAbs(TProjection::To360Domain(origLon) - TProjection::To360Domain(projectedLon)); + + if (latErr < 1.0e-13) { + cout << " ****[Lat Ok] "; + } + else { + cout << "[Lat Error: " << toString(latErr) << "] "; + } + + if (lonErr > 180) { + lonErr = 360.0 - lonErr; + } + if (lonErr < 1.0e-10 || qFuzzyCompare(90.0, qAbs(origLat))) { + cout << "[Lon Ok]****"; + } + else { + cout << "[Lon Error: " << toString(lonErr) << "]****"; + } +} diff --git a/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.cpp b/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.cpp index 129e03bc17e70e83e75dad214a257e108c1a55e1..fe82d38251d54701b2da59922f751ba48ff828d3 100644 --- a/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.cpp +++ b/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.cpp @@ -25,6 +25,10 @@ namespace Isis { } + /** + * @brief Switch to a new content handler and continue processing using the new handler. + * + */ void XmlStackedHandler::switchToNewHandler(XmlStackedHandler *nextHandler) { nextHandler->startElement(m_lastStartNamespaceURI, m_lastStartLocalName, m_lastStartQName, m_lastStartAtts); diff --git a/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.h b/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.h index b4ea381da8efde697c231cd297f545ce49b37cd4..cfdf0f46370f93401e818f70bbd3ecd42ac1d125 100644 --- a/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.h +++ b/isis/src/base/objs/XmlStackedHandler/XmlStackedHandler.h @@ -12,34 +12,99 @@ namespace Isis { /** * @brief XML Handler that parses XMLs in a stack-oriented way * + * IPCE does not have a single XML file for the whole project + * but breaks the project into multiple XML files with the Project.xml file + * being the top level. @see Project + * + * **Serialization Basics** + * + * IPCE mostly follows the standard convention of each object being responsible for + * serializing itself. Each Object to be serialized must have a "save" method to + * write the object out as XML. The first thing the save method does is write an XML element + * indicating what type of object is being serialized. This allows the deserialization to know + * how to parse the data (in our case what type of XmlHandler to push). If the object being + * serialized contains another object the save method of the contained object is called. This + * results in a XML file hierarchy as shown below. + * + * For deserialization each serialized object implements an XmlHandler class. The + * XmlHandler::startElement method handles reading of the XML file and initializing the + * member variables for the object. The class must also define a constructor that takes a + * XmlStackedHandlerReader as a parameter (Note the IPCE signatures vary on this method). + * The constructor pushes it's own content handler (the XmlHandler class) on the reader + * to allow parsing to continue with this object. Note the push of the content handler + * does not return until the XML is parsed, specifically the push of the content handler + * calls XmlHandler::startElement() for the handler just pushed. (Actually the behavior + * of XmlStackedHandlerReader::pushContentHandler() varies - if there are no contentHandlers + * on the content handler stack when it is called it returns immediately and parse() + * must be called to start parsing. If there is a content handler already on the stack + * the push results in a call to startElement() and it does not return until the + * corresponding end element.) + * + * If a contained object + * is found while parsing the XML, the constructor for the contained object that takes a + * XmlStackedHandlerReader as a parameter is called. This will result in the contained + * object pushing it's content handler and parsing the relevant XML. When the constructor + * returns, XML parsing can continue for this object. + * + * *Potential issue* + * There appears to be no support for cycles or joins in the object graph when serializing + * or deserializing. This means that if multiple pointers point to the same object ensure + * the object is only serialized once and that all pointers are properly restored on + * deserialization. Currently many of the ISIS objects have unique IDs and IPCE encapsulates + * the underlying ISIS object. One option would be to use the ISIS ids to uniquely identify + * the objects during serialization. + * + * *Versioning* + * To ensure backwards compatibility versioning is done per object. This keeps version + * information for a class within a single source file with no need to know Project file + * structure and where Project level file information is saved. The version number + * for a class should be incremented by 1 each time the XML for that object changes. + * When reading old version XML, files the class should choose a sensible default for the + * missing XML elements and write out the XML in the newest format. + * * This XML handler is designed to work with the XmlStackedHandlerReader. This XML handler class * handles passing off parsing to another handler. For example, if your XML is: * * 
    *     
-   *       
-   *         
-   *       
+   *        
+   *        
+   *             
+   *             
+   *                
+   *             
+   *             
+   *        
+   *        
    *     
    *
* + * To start the processing of the XML, an initial XML content handler is pushed onto the + * stack of content handlers. In the example above this initial content handler only + * processes elements associated with xmlTag1. In IPCE the xmlTag1 elements will be the + * member variables associated with a class. The xmlTag2 contains XML for an object + * contained within the first class. When the xmlTag2 element is encountered the + * XML content handler (the xmlTag2::XmlHandler class) will be pushed and take over + * parsing. + * * If this handler is pushed onto the reader (which is the parser stack) when the startElement * of xmlTag2 is seen, then this XML handler will see all of the xml data up to and including * the xmlTag2 close tag. This handler would never see xmlTag1. Here is an example of how * this works: * * 
-   *   --> Push initial XML handler (Handler1)
+   *   --> Push initial XML content handler for xmlTag1 (Handler1)
    *    -- Handler1::startElement
-   *      -- Handler1::startElement: calls reader()->pushContentHandler(Handler2)
-   *               -- Handler2::startElement
-   *        -- Handler2::startElement
-   *                   -- Handler2::endElement
-   *      -- Handler2::endElement
-   *                -- Handler1::endElement
+   *      -- Handler1::startElement: calls reader()->pushContentHandler(HandlerForXmlTag2)
+   *               -- HandlerForXmlTag2::startElement
+   *        -- HandlerForXmlTag3::startElement
+   *                   -- HandlerForXmlTag3::endElement
+   *      -- HandlerForXmlTag2::endElement
    *    -- Handler1::endElement
    *
* + * + * * @author 2012-??-?? Steven Lambright * * @internal diff --git a/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.cpp b/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.cpp index 3b3aaf161832c9b1550b4ee46230814cb268059d..b0904619bfe1ffc2b572692c92f03eb4635e6b60 100644 --- a/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.cpp +++ b/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.cpp @@ -31,6 +31,21 @@ namespace Isis { } + /** + * @brief Push a contentHandler and maybe continue parsing... + * + * Push a contentHadler on the content handler stack. If there are currently + * no other handlers on the stack that is all that happens. + * + * If there are other content handlers on the stack it is assumed that + * a XML file is being processed and processing continues by calling + * startElement() of the newly pushed handler. In this case + * pushContentHandler() will not return until the element has been + * fully processed. + * + * @see XmlStackedHandler + * + */ void XmlStackedHandlerReader::pushContentHandler(XmlStackedHandler *newHandler) { XmlStackedHandler *old = topContentHandler(); @@ -40,6 +55,8 @@ namespace Isis { setContentHandler(m_contentHandlers->top()); if (old) { + // Switch to newHandler and continue parsing + // This will call newHandler->startElement(...) old->switchToNewHandler(topContentHandler()); } } diff --git a/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.h b/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.h index 0dbfdd7e903cc24fede155a7cff42680f0f948c3..25c2cdccbd9e5bfc0935283f45b1d0461e71f866 100644 --- a/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.h +++ b/isis/src/base/objs/XmlStackedHandlerReader/XmlStackedHandlerReader.h @@ -9,13 +9,12 @@ namespace Isis { class XmlStackedHandler; /** - * his enables stack-based XML parsing of XML files. This class is designed to work with the - * XmlStackedHandler class. Use this in-place of a QXmlSimpleReader if you want to use - * stack-based Xml parsing. The XmlStackedHandler class has an explanation as to how this - * is designed to work. * - * The naming of this class is: - * XmlStackedHandler + Reader (parent class). + * @brief Manage a stack of content handlers for reading XML files. + * + * This class is designed to work with the XmlStackedHandler class. Use this + * in-place of a QXmlSimpleReader if you want to use stack-based Xml parsing. The + * XmlStackedHandler class has an explanation as to how this is designed to work. * * @see XmlStackedHandler * diff --git a/isis/src/base/objs/XmlToPvlTranslationManager/Makefile b/isis/src/base/objs/XmlToPvlTranslationManager/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..f122bc88227c5c7ebd108dea5d339d1d2e074d82 --- /dev/null +++ b/isis/src/base/objs/XmlToPvlTranslationManager/Makefile @@ -0,0 +1,7 @@ +ifeq ($(ISISROOT), $(BLANK)) +.SILENT: +error: + echo "Please set ISISROOT"; +else + include $(ISISROOT)/make/isismake.objs +endif \ No newline at end of file diff --git a/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.cpp b/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.cpp new file mode 100644 index 0000000000000000000000000000000000000000..3854ce82a0fa8fbace95c4e1af8c876a3c0a6b7b --- /dev/null +++ b/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.cpp @@ -0,0 +1,524 @@ +/** + * @file + * $Revision: 1.10 $ + * $Date: 2010/01/04 18:01:31 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include "LabelTranslationManager.h" + +#include + +#include +#include +#include + +#include "IException.h" +#include "IString.h" +#include "Message.h" +#include "Pvl.h" +#include "PvlContainer.h" +#include "PvlGroup.h" +#include "PvlKeyword.h" +#include "PvlObject.h" +#include "XmlToPvlTranslationManager.h" + +using namespace std; +namespace Isis { + + /** + * Constructs and initializes an XmlToPvlTranslationManager object from the given + * Pvl translation file. If this constructor is used, the user will need to + * set the input label before translating. This may be done by using + * SetLabel(FileName inputLabel) or Auto(FileName inputLabel, Pvl + * outputLabel). + * + * @param transFile The translation file to be used to tranlate keywords in + * the input label. + */ + XmlToPvlTranslationManager::XmlToPvlTranslationManager(const QString &transFile) + : LabelTranslationManager() { + AddTable(transFile); + } + + /** + * Constructs and initializes an XmlToPvlTranslationManager object from the given + * input stream. If this constructor is used, the user will need to set the + * input label before translating. This may be done by using SetLabel(FileName + * inputLabel) or Auto(FileName inputLabel, Pvl outputLabel). + * + * + * @param transStrm A stream containing the tranlation table to be used to + * tranlate keywords in the input label. + */ + XmlToPvlTranslationManager::XmlToPvlTranslationManager(std::istream &transStrm) + : LabelTranslationManager() { + AddTable(transStrm); + } + + + /** + * Constructs and initializes an XmlToPvlTranslationManager object from the given + * Pvl translation file and input label. + * + * @param inputLabel The Xml holding the input label. + * + * @param transFile The translation file to be used to tranlate keywords in + * the input label. + */ + XmlToPvlTranslationManager::XmlToPvlTranslationManager(FileName &inputLabel, + const QString &transFile) + : LabelTranslationManager() { + AddTable(transFile); + parseFile(inputLabel); + } + + + /** + * Constructs and initializes an XmlToPvlTranslationManager object from the given + * input stream and input label. + * + * @param inputLabel The Xml holding the input label. + * + * @param transStrm A stream containing the tranlation table to be used to + * tranlate keywords in the input label. + */ + XmlToPvlTranslationManager::XmlToPvlTranslationManager(FileName &inputLabel, + std::istream &transStrm) + : LabelTranslationManager() { + AddTable(transStrm); + parseFile(inputLabel); + } + + + /** + * Destroys the XmlToPvlTranslationManager object. + */ + XmlToPvlTranslationManager::~XmlToPvlTranslationManager() { + } + + + /** + * Reads an Xml label file and internalizes it for translation. + * + * @param inputLabel The input label file + */ + void XmlToPvlTranslationManager::SetLabel(FileName &inputLabel) { + parseFile(inputLabel); + } + + + /** + * Returns a vector of valid keyword names and their sizes. A size of -1 + * indicates that the keyword can be any size. + * + * @return @b vector> A vector of valid keyword names and their sizes. + */ + vector< pair > XmlToPvlTranslationManager::validKeywords() const { + + vector< pair > validKeywords = PvlTranslationTable::validKeywords(); + validKeywords.push_back(pair("InputKeyAttribute", -1)); + validKeywords.push_back(pair("InputKeyDependencies", -1)); + validKeywords.push_back(pair("Debug", 0)); + + return validKeywords; + } + + /** + * Returns a translated value. The output name is used to find the input + * group, keyword, default and tranlations in the translation table. If the + * keyword does not exist in the input label, the input default if + * available will be used as the input value. This input value + * is then used to search all of the translations. If a match is + * found the translated value is returned. + * + * @param outputName The output name used to identify the input keyword to + * be translated. + * + * @param index The index into the input keyword array. Defaults to 0 + * + * @return string The ISIS cube label value for the outputName. + * + * @throws IException::Unknown "Failed to translate output value." + * @throws IException::Unknown "Cannot translate value. Xml files can only + * store a single value in each element." + * @throws IException::Unknown "Unable to retrieve translation group from + * translation table." + * @throws IException::Unknown "Unable to retrieve [InputPosition] keyword + * from translation group." + * @throws IException::Unknown "Unable to retrieve [InputKey] keyword from + * translation group." + * @throws IException::Unknown "Failed traversing input position. Element + * does not have the named child element." + * @throws IException::Unknown "Could not find an input value or default value." + * @throws IException::Unknown "Input element does not have the named attribute." + */ + QString XmlToPvlTranslationManager::Translate(QString outputName, int index) { + try { + if (index != 0) { + QString msg = "Cannot translate value at index [" + toString(index) + + "]. Xml files can only store a single value in each element."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + + const Pvl &transTable = TranslationTable(); + PvlGroup transGroup; + try { + transGroup = transTable.findGroup(outputName); + } + catch (IException &e){ + QString msg = "Unable to retrieve translation group from translation table."; + throw IException(e, IException::Unknown, msg, _FILEINFO_); + } + + // get input position values + PvlKeyword inputPosition; + try { + inputPosition = transGroup["InputPosition"]; + } + catch (IException &e){ + QString msg = "Unable to retrieve [InputPosition] keyword from " + "translation group."; + throw IException(e, IException::Unknown, msg, _FILEINFO_); + } + QString inputParentName = inputPosition[inputPosition.size() - 1]; + + // get input key (tag or att) + QString inputKey; + try { + inputKey = transGroup["InputKey"][0]; + } + catch (IException &e){ + QString msg = "Unable to retrieve [InputKey] keyword from " + "translation group."; + throw IException(e, IException::Unknown, msg, _FILEINFO_); + } + QString attributeName; + if (transGroup.hasKeyword("InputKeyAttribute")) { + attributeName = transGroup["InputKeyAttribute"][0]; + } + + // get dependencies + PvlKeyword keyDependencies; + if (transGroup.hasKeyword("InputKeyDependencies")) { + keyDependencies = transGroup["InputKeyDependencies"]; + } + + // Check for debug + bool isDebug = transGroup.hasKeyword("Debug"); + + // Notify what we are translating and what the translating group is. + if (isDebug) { + cout << endl << " ==================== " << endl; + cout << endl << "Translating output keyword: " << outputName << endl; + cout << endl << "Translation group:" << endl; + cout << transGroup << endl << endl; + } + + // read input value + QDomElement inputParentElement = m_xmlLabel.documentElement(); + QString indent = ""; + if (isDebug) { + cout << endl << "Finding input element:" << endl << endl; + cout << inputParentElement.tagName() << endl; + } + for (int i = 0; i < inputPosition.size(); i++) { + QString childName = inputPosition[i]; + inputParentElement = inputParentElement.firstChildElement(childName); + if(inputParentElement.isNull()) { + if ( hasInputDefault(outputName) ) { + if (isDebug) { + cout << endl << "Could not traverse input position, " << + "using default value: " << + InputDefault(outputName) << endl; + } + return PvlTranslationTable::Translate( outputName ); + } + else { + QString msg = "Failed traversing input position. [" + + inputParentElement.parentNode().toElement().tagName() + + "] element does not have a child element named [" + + childName + "]."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + } + if (isDebug) { + indent += " "; + cout << indent << inputParentElement.tagName() << endl; + } + } + QDomElement inputKeyElement = inputParentElement.firstChildElement(inputKey); + if (isDebug) { + indent += " "; + cout << indent << inputKeyElement.tagName() << endl; + } + + // Check dependencies + while ( !inputParentElement.isNull() && + !checkDependencies(inputKeyElement, keyDependencies, isDebug) ) { + if (isDebug) { + cout << endl << "Dependencies failed, checking next candidate." << endl; + } + // Check if a sibling satisfies the dependencies + inputKeyElement = inputKeyElement.nextSiblingElement(inputKey); + // If there are no siblings to check, try cousins. + while ( inputKeyElement.isNull() ) { + inputParentElement = inputParentElement.nextSiblingElement(inputParentName); + // If there are no more siblings of the parent we've run out of things to check. + if ( inputParentElement.isNull() ) { + break; + } + inputKeyElement = inputParentElement.firstChildElement(inputKey); + } + } + + // If the parent element is NULL at this point then we traversed every + // potential input element and none of them satisfied the dependencies. + if ( inputParentElement.isNull() ) { + if ( hasInputDefault(outputName) ) { + if (isDebug) { + cout << endl << "No input value found, using default value: " << + InputDefault(outputName) << endl; + } + return PvlTranslationTable::Translate( outputName ); + } + else { + QString msg = "Could not find an input value or default value."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + } + + // translate value to output value + QString inputValue = inputKeyElement.text(); + // for attributes, overwrite inputValue + if (attributeName.size() > 0) { + if ( inputKeyElement.hasAttribute(attributeName) ) { + inputValue = inputKeyElement.attribute(attributeName); + } + else if (hasInputDefault(outputName) ) { + if (isDebug) { + cout << endl << "No input value found, using default value: " << + InputDefault(outputName) << endl; + } + return PvlTranslationTable::Translate( outputName ); + } + else { + QString msg = "Input element [" + inputKeyElement.tagName() + + "] does not have an attribute named [" + + attributeName + "]."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + } + if (isDebug) { + cout << endl << "Translating input value: " << inputValue << endl; + } + return PvlTranslationTable::Translate( outputName, inputValue.trimmed() ); + } + catch (IException &e){ + QString msg = "Failed to translate output value for [" + outputName + "]."; + throw IException(e, IException::Unknown, msg, _FILEINFO_); + } + } + + + /** + * @brief Checks if a element in the xml label satisfies a list of + * dependencies. + * + * Checks if a element in the xml label satisfies a list of dependencies. The + * dependencies are requirements on the values of attributes of the element + * and/or the values of sibling elements. The dependencies are specified by + * strings that are formatted as follows + * [tag/att]\@[tagName/attName]:[value] + * + * @param element The element to check dependencies on. + * @param dependencies A multi-valued keyword were every entry specifies a + * requirement upon either an attribute of the element or + * a sibling of the element. + * + * @return @b bool If the element passed the dependencies check + * + * @throws IException::Unknown "Parsing error, dependency type is not [att] or [tag]." + */ + bool XmlToPvlTranslationManager::checkDependencies(QDomElement element, + PvlKeyword dependencies, + bool isDebug) const{ + + if (isDebug) { + cout << endl << "Testing dependencies:" << endl; + } + for (int i = 0; i < dependencies.size(); i++) { + QStringList specification = parseDependency(dependencies[i]); + if (isDebug) { + cout << endl << "Testing dependency number " << toString(i+1) << endl; + cout << " Specification: " << dependencies[i] << endl; + cout << endl; + cout << " Dependency type: " << specification[0] << endl; + cout << " Dependency name: " << specification[1] << endl; + cout << " Dependency value: " << specification[2] << endl; + } + if (specification[0] == "att") { + if ( element.hasAttributes() ) { + QDomNamedNodeMap atts = element.attributes(); + QString attributeValue = atts.namedItem(specification[1]).nodeValue(); + if (isDebug) { + cout << endl; + cout << " Attribute name: " << atts.namedItem(specification[1]).nodeName(); + cout << " Attribute value: " << attributeValue << endl; + } + if ( attributeValue != specification[2] ) { + // attribute value does not match specification or + // element does not have the named attribute + return false; + } + } + else { + // element does not have any attributes + return false; + } + } + + else if (specification[0] == "tag") { + QDomElement candidateSibling = element.parentNode().firstChildElement(specification[1]); + QString siblingValue = candidateSibling.text(); + if (isDebug) { + cout << endl; + cout << " Tag name: " << candidateSibling.tagName() << endl; + cout << " Tag value: " << siblingValue << endl; + } + if (siblingValue != specification[2] ) { + // sibling tag value does not match specification or + // named sibling tag does not exist + return false; + } + } + + else { + QString msg = "Parsing error, dependency type [" + specification[0] + + "] is not [att] or [tag]."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + } + + // No dependencies failed! + return true; + } + + + /** + * Parses and validates a dependency specification. + * + * @param specification The dependency specification string. + * + * @return @b QStringList The dependency split into 3 components + *
    + *
  1. the type (att or tag)
    2. + *
  2. the name of what to check
    3. + *
  3. the value to check for
    4. + *
+ * + * @throws IException::Unknown "Malformed dependency specification." + * @throws IException::Unknown "Specification does not have two components + * separated by [@], the type of dependency and + * the name-value pair. + * @throws IException::Unknown "Dependency type specification is invalid. + * Valid types are [att] and [tag]" + * @throws IException::Unknown "Name-value specification does not have two + * components separated by [:]." + * + * @see XmlToPvlTranslationManager::checkDependencies + */ + QStringList XmlToPvlTranslationManager::parseDependency(QString specification) const { + + QStringList parsedSpecification; + + try { + QStringList typeSplit = specification.split("@", QString::SkipEmptyParts); + if (typeSplit.size() != 2) { + QString msg = "Specification does not have two components separated " + "by [@], the type of dependency and the name-value pair."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + if (typeSplit[0].toLower() != "att" && + typeSplit[0].toLower() != "tag") { + QString msg = "Dependency type specification [" + typeSplit[0] + + "] is invalid. Valid types are [att] and [tag]"; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + parsedSpecification.append(typeSplit[0].toLower()); + + QStringList nameValueSplit = typeSplit[1].split(":", QString::SkipEmptyParts); + if (nameValueSplit.size() != 2) { + QString msg = "Name-value specification [" + typeSplit[1] + "] does " + "not have two components separated by [:]."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + parsedSpecification.append(nameValueSplit); + } + catch (IException &e) { + QString msg = "Malformed dependency specification [" + specification + "]."; + throw IException(e, IException::Unknown, msg, _FILEINFO_); + } + + return parsedSpecification; + } + + + /** + * Automatically translate all the output names flagged with the Auto keyword + * in the translation table and store the translated key, value pairs in the + * argument pvl. + * + * @param inputLabel The input label file to be translated. + * @param outputLabel The output translated Pvl. + */ + void XmlToPvlTranslationManager::Auto(FileName &inputLabel, Pvl &outputLabel) { + parseFile(inputLabel); + Auto(outputLabel); + } + + + /** + * Opens, parses, and internalizes an Xml label file. + * + * @param xmlFileName The Xml label file. + * + * @throws IException::Unknown "Could not open label file." + * @throws IException::Unknown "XML read/parse error in file." + */ + void XmlToPvlTranslationManager::parseFile(const FileName &xmlFileName) { + QFile xmlFile(xmlFileName.expanded()); + if ( !xmlFile.open(QIODevice::ReadOnly) ) { + QString msg = "Could not open label file [" + xmlFileName.expanded() + + "]."; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + + QString errmsg; + int errline, errcol; + if ( !m_xmlLabel.setContent(&xmlFile, false, &errmsg, &errline, &errcol) ) { + xmlFile.close(); + QString msg = "XML read/parse error in file [" + xmlFileName.expanded() + + "] at line [" + toString(errline) + "], column [" + toString(errcol) + + "], message: " + errmsg; + throw IException(IException::Unknown, msg, _FILEINFO_); + } + + xmlFile.close(); + return; + } +} // end namespace isis diff --git a/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.h b/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.h new file mode 100644 index 0000000000000000000000000000000000000000..2b86f13645781707aa48f7f6fd87fc3655629b1b --- /dev/null +++ b/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.h @@ -0,0 +1,166 @@ +#ifndef XmlToPvlTranslationManager_h +#define XmlToPvlTranslationManager_h +/** + * @file + * $Revision: 1.6 $ + * $Date: 2010/01/04 18:01:31 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include "LabelTranslationManager.h" + +#include +#include + +#include + +#include "FileName.h" +#include "PvlTokenizer.h" + +namespace Isis { + class Pvl; + class PvlContainer; + class PvlKeyword; + /** + * @brief Allows applications to translate Xml label files + * + *

+ * This class allows for translating Xml label files into Pvl objects. + * The translation process is driven by the output keyword names. Given an + * output keyword name, the Translate method uses the translation table to + * find the input value and then translates it into the output value. + *

+ *

+ * The translation table is a Pvl object containing a Pvl group for each + * output keyword. The translation group for an output keyword is named the + * output keyword's name. The required PvlKeywords in a translation group + * are: + *

+ *
    + *
  • InputPosition: The series of element tag names leading from + * the second highest level element to the parent + * element of the input element.
    • + *
  • InputKey: The tag name of the input element. The text value + * of this element is the input value for the + * translation.
    • + *
  • OutputName: The output keyword's name.
    • + *
  • OutputPosition: The location of the output keyword + * in the output label.
    • + *
  • Translation: a pair defining how to convert the input + * value into the output value. The pair + * is consists of an output value and then + * the specific input value that will be + * converted into that output value. A star + * [*] for the output value indicates that + * the input value will not be changes and a + * star [*] for the input value matches any + * input value.
    • + *
+ *

+ * There are also optional keywords to modify the translation: + *

+ *
    + *
  • InputDefault: A default value that will be used for the input + * value if no input value can be found in the + * label.
    • + *
  • Auto: The Auto keyword is not associated with a value. It + * indicates that the output keyword should be translated + * when the Auto() method is called.
    • + *
  • Optional: The Optional keyword is not associated with a + * value. It indicates that the output keyword is not + * necessary. If an input value or default value is + * not found for an optional keyword, it will be + * skipped and translation will continue.
    • + *
  • Debug: The Debug keyword is not associated with a value. It + * indicates that debug information is to be output when + * the translation is performed.
    • + *
  • InputKeyAttribute: The name of the attribute of the input + * element that the input value will be read + * from. This will override reading the input + * value from the input element's text.
    • + *
  • InputKeyDependencies: A list of dependencies that uniquely + * identify the input element. Each entry + * consists of a string specifying either + * the text value of a sibling element of + * the input element or the value of one + * of the input element's attributes. The + * specification string is formatted as + * TYPE\@NAME:VALUE. The + * type is either tag or + * att indicating to check + * the value of an element of attribute + * respectively.
    • + *
+ *

+ * An example Xml translation table can be found at + * $base/translations/XmlLabel.trn. + *

+ * + * @ingroup Parsing + * + * @author 2017-01-12 Jeannie Backer + * + * @internal + * @history 2017-01-12 Jeannie Backer - Original version. Adapted from + * PvlTranslationManager class. Fixes #4584. + * @history 2017-01-13 Jeannie Backer and Jesse Mapel - Initial Translate + * and Auto design. Added dependencies for uniquely + * identifying input elements. Fixes #4584. + * @history 2017-01-18 Jesse Mapel - Updated documentation and error messages. Fixes #4584. + * @history 2017-01-25 Jesse Mapel - Created unit test. Fixes #4584. + * @history 2017-05-30 Makayla Shepherd - Renamed from XmlTranslationManager to + * XmlToPvlTranslationManager. Fixes #4889. + */ + class XmlToPvlTranslationManager : public LabelTranslationManager { + public: + XmlToPvlTranslationManager(const QString &transFile); + + XmlToPvlTranslationManager(std::istream &transStrm); + + XmlToPvlTranslationManager(FileName &inputLabel, + const QString &transFile); + + XmlToPvlTranslationManager(FileName &inputLabel, + std::istream &transStrm); + + virtual ~XmlToPvlTranslationManager(); + + // Attempt to translate the requested output name to output value + // using the input name and value/default value + virtual QString Translate(QString nName, int findex = 0); + + // Translate all translation table groups which contain "Auto" + using LabelTranslationManager::Auto; + void Auto(FileName &inputLabel, Pvl &outputLabel); + + void SetLabel(FileName &inputLabel); + + protected: + virtual std::vector< std::pair > validKeywords() const; + bool checkDependencies(QDomElement element, PvlKeyword dependencies, bool isDebug) const; + QStringList parseDependency(QString specification) const; + void parseFile(const FileName &xmlFileName); + + private: + QDomDocument m_xmlLabel; //!< The contents of the xml label. + + }; +}; + +#endif + + diff --git a/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.truth b/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.truth new file mode 100644 index 0000000000000000000000000000000000000000..83e610fe2e45fb2b89d5e444032f7b50b49f77d4 --- /dev/null +++ b/isis/src/base/objs/XmlToPvlTranslationManager/XmlToPvlTranslationManager.truth @@ -0,0 +1,415 @@ +Testing string stream translation specification + +Testing Translate method + +Translation of InstrumentIfovWithUnits: 1.140e-005 + +Testing Auto method + + + ==================== + +Translating output keyword: Version + +Translation group: +Group = Version + Auto = Null + Debug = Null + InputPosition = Identification_Area + InputKey = version_id + OutputPosition = (group, instrument) + OutputName = Version + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + Identification_Area + version_id + +Testing dependencies: + +Translating input value: UNK + + ==================== + +Translating output keyword: Host + +Translation group: +Group = Host + Auto = Null + Debug = Null + InputPosition = (Observation_Area, Investigation_Area) + InputKey = Instrument_Host_Id + OutputPosition = (group, instrument) + OutputName = Host + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + Observation_Area + Investigation_Area + Instrument_Host_Id + +Testing dependencies: + +Translating input value: TGO + + ==================== + +Translating output keyword: BandWidth + +Translation group: +Group = BandWidth + Auto = Null + Debug = Null + InputPosition = Observation_Area + InputKey = Science_Facets + InputKeyAttribute = bandwidth + OutputPosition = (group, instrument) + OutputName = BandWidth + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + Observation_Area + Science_Facets + +Testing dependencies: + +Translating input value: Broad + + ==================== + +Translating output keyword: SpacecraftName + +Translation group: +Group = SpacecraftName + Auto = Null + Debug = Null + InputPosition = (Observation_Area, Observing_System, + Observing_System_Component) + InputKey = name + InputKeyDependencies = tag@type:Spacecraft + OutputPosition = (group, instrument) + OutputName = SpacecraftName + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + Observation_Area + Observing_System + Observing_System_Component + name + +Testing dependencies: + +Testing dependency number 1 + Specification: tag@type:Spacecraft + + Dependency type: tag + Dependency name: type + Dependency value: Spacecraft + + Tag name: type + Tag value: Spacecraft + +Translating input value: TGO + + ==================== + +Translating output keyword: InstrumentId + +Translation group: +Group = InstrumentId + Auto = Null + Debug = Null + InputPosition = (Observation_Area, Observing_System, + Observing_System_Component) + InputKey = name + InputKeyDependencies = tag@type:Instrument + OutputPosition = (group, instrument) + OutputName = InstrumentId + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + Observation_Area + Observing_System + Observing_System_Component + name + +Testing dependencies: + +Testing dependency number 1 + Specification: tag@type:Instrument + + Dependency type: tag + Dependency name: type + Dependency value: Instrument + + Tag name: type + Tag value: Spacecraft + +Dependencies failed, checking next candidate. + +Testing dependencies: + +Testing dependency number 1 + Specification: tag@type:Instrument + + Dependency type: tag + Dependency name: type + Dependency value: Instrument + + Tag name: type + Tag value: JunkComponent + +Dependencies failed, checking next candidate. + +Testing dependencies: + +Testing dependency number 1 + Specification: tag@type:Instrument + + Dependency type: tag + Dependency name: type + Dependency value: Instrument + + Tag name: type + Tag value: Instrument + +Translating input value: CaSSIS + + ==================== + +Translating output keyword: OnboardImageAcquisitionTimeUTC + +Translation group: +Group = OnboardImageAcquisitionTimeUTC + Auto = Null + Debug = Null + InputPosition = (CaSSIS_Header, DERIVED_HEADER_DATA) + InputKey = OnboardImageAcquisitionTime + InputKeyDependencies = att@Time_Base:UTC + OutputPosition = (group, instrument) + OutputName = OnboardImageAcquisitionTimeUTC + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + CaSSIS_Header + DERIVED_HEADER_DATA + OnboardImageAcquisitionTime + +Testing dependencies: + +Testing dependency number 1 + Specification: att@Time_Base:UTC + + Dependency type: att + Dependency name: Time_Base + Dependency value: UTC + + Attribute name: Time_Base Attribute value: UTC + +Translating input value: 2016-11-26T23:24:52.080 + + ==================== + +Translating output keyword: OnboardImageAcquisitionTimeET + +Translation group: +Group = OnboardImageAcquisitionTimeET + Auto = Null + Debug = Null + InputPosition = (CaSSIS_Header, DERIVED_HEADER_DATA) + InputKey = OnboardImageAcquisitionTime + InputKeyDependencies = att@Time_Base:ET + OutputPosition = (group, instrument) + OutputName = OnboardImageAcquisitionTimeET + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + CaSSIS_Header + DERIVED_HEADER_DATA + OnboardImageAcquisitionTime + +Testing dependencies: + +Testing dependency number 1 + Specification: att@Time_Base:ET + + Dependency type: att + Dependency name: Time_Base + Dependency value: ET + + Attribute name: Time_Base Attribute value: UTC + +Dependencies failed, checking next candidate. + +Testing dependencies: + +Testing dependency number 1 + Specification: att@Time_Base:ET + + Dependency type: att + Dependency name: Time_Base + Dependency value: ET + + Attribute name: Time_Base Attribute value: ET + +Translating input value: 20161126.232452080 + + ==================== + +Translating output keyword: CoreBands + +Translation group: +Group = CoreBands + Auto = Null + Debug = Null + InputPosition = (Product_Observational, File_Area_Observational, + Array_2D_Image, Axis_Array) + InputKeyDependencies = tag@axis_name:Band + InputKey = elements + InputDefault = 1 + OutputPosition = (group, CoreCube) + OutputName = CoreBands + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + +Could not traverse input position, using default value: 1 + + ==================== + +Translating output keyword: CoreSamples + +Translation group: +Group = CoreSamples + Auto = Null + Debug = Null + InputPosition = (Product_Observational, File_Area_Observational, + Array_2D_Image, Axis_Array) + InputKeyDependencies = tag@axis_name:Sample + InputKey = elements + InputKeyAttribute = Units + InputDefault = 2 + OutputPosition = (group, CoreCube) + OutputName = CoreSamples + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + +Could not traverse input position, using default value: 2 + + ==================== + +Translating output keyword: CoreLines + +Translation group: +Group = CoreLines + Auto = Null + Debug = Null + InputPosition = (Product_Observational, Bad_Parent) + InputKey = elements + InputDefault = 10 + OutputPosition = (group, CoreCube) + OutputName = CoreLines + Translation = (*, *) +End_Group + + +Finding input element: + +Product_Observational + +Could not traverse input position, using default value: 10 + +Group = instrument + Version = UNK + Host = TGO + BandWidth = Broad + SpacecraftName = TGO + InstrumentId = CaSSIS + OnboardImageAcquisitionTimeUTC = 2016-11-26T23:24:52.080 + OnboardImageAcquisitionTimeET = 20161126.232452080 +End_Group + +Group = CoreCube + CoreBands = 1 + CoreSamples = 2 + CoreLines = 10 +End_Group +End + +Testing error throws + +**ERROR** Failed to translate output value for [InstrumentIfovWithUnits]. +**ERROR** Cannot translate value at index [2]. Xml files can only store a single value in each element. + +**ERROR** Failed to translate output value for [NoInputPosition]. +**ERROR** Unable to retrieve [InputPosition] keyword from translation group. +**ERROR** PVL Keyword [InputPosition] does not exist in [Group = NoInputPosition]. + +**ERROR** Failed to translate output value for [BadInputPosition]. +**ERROR** Failed traversing input position. [] element does not have a child element named [Bad_Parent]. + +**ERROR** Failed to translate output value for [InputKeyDoesNotExist]. +**PROGRAMMER ERROR** No value or default value to translate for translation group [InputKeyDoesNotExist] in file []. + +**ERROR** Failed to translate output value for [InputKeyAttributeDoesNotExist]. +**ERROR** Input element [INSTRUMENT_IFOV] does not have an attribute named [Bad_Input_Element_Attribute]. + +**ERROR** Failed to translate output value for [NoDependencyType]. +**ERROR** Malformed dependency specification [type:Spacecraft]. +**ERROR** Specification does not have two components separated by [@], the type of dependency and the name-value pair. + +**ERROR** Failed to translate output value for [BadDependencyType]. +**ERROR** Malformed dependency specification [bad@type:Spacecraft]. +**ERROR** Dependency type specification [bad] is invalid. Valid types are [att] and [tag]. + +**ERROR** Failed to translate output value for [NoDependencyValue]. +**ERROR** Malformed dependency specification [bad@type]. +**ERROR** Dependency type specification [bad] is invalid. Valid types are [att] and [tag]. + +**ERROR** Failed to translate output value for [NotInTranslationTable]. +**ERROR** Unable to retrieve translation group from translation table. +**ERROR** Unable to find PVL group [NotInTranslationTable]. + +**USER ERROR** Keyword [Debug] does not have the correct number of elements. Error in file []. + +**ERROR** Could not open label file [DoesNotExist.xml]. + +**ERROR** XML read/parse error in file [data/base/translations/pdsImage.trn] at line [1], column [1], message: error occurred while parsing element. + diff --git a/isis/src/base/objs/XmlToPvlTranslationManager/unitTest.cpp b/isis/src/base/objs/XmlToPvlTranslationManager/unitTest.cpp new file mode 100644 index 0000000000000000000000000000000000000000..50f7a0b60d15574b49aa652114a92ab96156814c --- /dev/null +++ b/isis/src/base/objs/XmlToPvlTranslationManager/unitTest.cpp @@ -0,0 +1,366 @@ +#include +#include "XmlToPvlTranslationManager.h" +#include "FileName.h" +#include "Preference.h" +#include "IException.h" +#include "IString.h" +#include "Preference.h" +#include "QRegularExpression" + +using namespace Isis; +using namespace std; + +void ReportError(QString err) { + cout << err.replace(QRegularExpression("(\\/[\\w\\-\\. ]*)+\\/data"), "data") << endl; +} + +int main(void) { + Preference::Preferences(true); + + try { + + FileName fLabel("$base/testData/xmlTestLabel.xml"); + + stringstream trnsStrm; + + trnsStrm << "Group = Version" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Identification_Area)" << endl; + trnsStrm << " InputKey = version_id" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = Version" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = Host" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Observation_Area, Investigation_Area)" << endl; + trnsStrm << " InputKey = Instrument_Host_Id" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = Host" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = BandWidth" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Observation_Area)" << endl; + trnsStrm << " InputKey = Science_Facets" << endl; + trnsStrm << " InputKeyAttribute = bandwidth" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = BandWidth" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = SpacecraftName" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Observation_Area, Observing_System, Observing_System_Component)" << endl; + trnsStrm << " InputKey = name" << endl; + trnsStrm << " InputKeyDependencies = tag@type:Spacecraft" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = SpacecraftName" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = InstrumentId" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Observation_Area, Observing_System, Observing_System_Component)" << endl; + trnsStrm << " InputKey = name" << endl; + trnsStrm << " InputKeyDependencies = tag@type:Instrument" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = InstrumentId" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = InstrumentIfovWithUnits" << endl; + trnsStrm << " InputPosition = (CaSSIS_Header, CaSSIS_General)" << endl; + trnsStrm << " InputKey = INSTRUMENT_IFOV" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = InstrumentIfovWithUnits" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = OnboardImageAcquisitionTimeUTC" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (CaSSIS_Header, DERIVED_HEADER_DATA)" << endl; + trnsStrm << " InputKey = OnboardImageAcquisitionTime" << endl; + trnsStrm << " InputKeyDependencies = att@Time_Base:UTC" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = OnboardImageAcquisitionTimeUTC" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = OnboardImageAcquisitionTimeET" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (CaSSIS_Header, DERIVED_HEADER_DATA)" << endl; + trnsStrm << " InputKey = OnboardImageAcquisitionTime" << endl; + trnsStrm << " InputKeyDependencies = att@Time_Base:ET" << endl; + trnsStrm << " OutputPosition = (group, instrument)" << endl; + trnsStrm << " OutputName = OnboardImageAcquisitionTimeET" << endl; + trnsStrm << " Translation = (*,*)" << endl; + trnsStrm << "EndGroup" << endl; + trnsStrm << "Group = CoreBands" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Product_Observational, File_Area_Observational," << endl; + trnsStrm << " Array_2D_Image, Axis_Array)" << endl; + trnsStrm << " InputKeyDependencies = \"tag@axis_name:Band\"" << endl; + trnsStrm << " InputKey = elements" << endl; + trnsStrm << " InputDefault = 1" << endl; + trnsStrm << " OutputPosition = (group, CoreCube)" << endl; + trnsStrm << " OutputName = CoreBands" << endl; + trnsStrm << " Translation = (*, *)" << endl; + trnsStrm << "End_Group" << endl; + trnsStrm << "Group = CoreSamples" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Product_Observational, File_Area_Observational," << endl; + trnsStrm << " Array_2D_Image, Axis_Array)" << endl; + trnsStrm << " InputKeyDependencies = \"tag@axis_name:Sample\"" << endl; + trnsStrm << " InputKey = elements" << endl; + trnsStrm << " InputKeyAttribute = Units" << endl; + trnsStrm << " InputDefault = 2" << endl; + trnsStrm << " OutputPosition = (group, CoreCube)" << endl; + trnsStrm << " OutputName = CoreSamples" << endl; + trnsStrm << " Translation = (*, *)" << endl; + trnsStrm << "End_Group" << endl; + trnsStrm << "Group = CoreLines" << endl; + trnsStrm << " Auto" << endl; + trnsStrm << " Debug" << endl; + trnsStrm << " InputPosition = (Product_Observational, Bad_Parent)" << endl; + trnsStrm << " InputKey = elements" << endl; + trnsStrm << " InputDefault = 10" << endl; + trnsStrm << " OutputPosition = (group, CoreCube)" << endl; + trnsStrm << " OutputName = CoreLines" << endl; + trnsStrm << " Translation = (*, *)" << endl; + trnsStrm << "End_Group" << endl; + + trnsStrm << "End" << endl; + + stringstream badTrnsStrm; + + badTrnsStrm << "Group = NoInputPosition" << endl; + badTrnsStrm << " InputKey = INSTRUMENT_IFOV" << endl; + badTrnsStrm << " OutputPosition = (group, instrument)" << endl; + badTrnsStrm << " OutputName = NoInputPosition" << endl; + badTrnsStrm << " Translation = (*,*)" << endl; + badTrnsStrm << "EndGroup" << endl; + badTrnsStrm << "Group = BadInputPosition" << endl; + badTrnsStrm << " InputPosition = (CaSSIS_Header, CaSSIS_General, Bad_Parent)" << endl; + badTrnsStrm << " InputKey = INSTRUMENT_IFOV" << endl; + badTrnsStrm << " OutputPosition = (group, instrument)" << endl; + badTrnsStrm << " OutputName = BadInputPosition" << endl; + badTrnsStrm << " Translation = (*,*)" << endl; + badTrnsStrm << "EndGroup" << endl; + badTrnsStrm << "Group = InputKeyDoesNotExist" << endl; + badTrnsStrm << " InputPosition = (CaSSIS_Header, CaSSIS_General)" << endl; + badTrnsStrm << " InputKey = Bad_Input_Element" << endl; + badTrnsStrm << " OutputPosition = (group, instrument)" << endl; + badTrnsStrm << " OutputName = InputKeyDoesNotExist" << endl; + badTrnsStrm << " Translation = (*,*)" << endl; + badTrnsStrm << "EndGroup" << endl; + badTrnsStrm << "Group = InputKeyAttributeDoesNotExist" << endl; + badTrnsStrm << " InputPosition = (CaSSIS_Header, CaSSIS_General)" << endl; + badTrnsStrm << " InputKey = INSTRUMENT_IFOV" << endl; + badTrnsStrm << " InputKeyAttribute = Bad_Input_Element_Attribute" << endl; + badTrnsStrm << " OutputPosition = (group, instrument)" << endl; + badTrnsStrm << " OutputName = InputKeyAttributeDoesNotExist" << endl; + badTrnsStrm << " Translation = (*,*)" << endl; + badTrnsStrm << "EndGroup" << endl; + badTrnsStrm << "Group = NoDependencyType" << endl; + badTrnsStrm << " InputPosition = (Observation_Area, Observing_System, Observing_System_Component)" << endl; + badTrnsStrm << " InputKey = name" << endl; + badTrnsStrm << " InputKeyDependencies = type:Spacecraft" << endl; + badTrnsStrm << " OutputPosition = (group, instrument)" << endl; + badTrnsStrm << " OutputName = NoDependencyType" << endl; + badTrnsStrm << " Translation = (*,*)" << endl; + badTrnsStrm << "EndGroup" << endl; + badTrnsStrm << "Group = BadDependencyType" << endl; + badTrnsStrm << " InputPosition = (Observation_Area, Observing_System, Observing_System_Component)" << endl; + badTrnsStrm << " InputKey = name" << endl; + badTrnsStrm << " InputKeyDependencies = bad@type:Spacecraft" << endl; + badTrnsStrm << " OutputPosition = (group, instrument)" << endl; + badTrnsStrm << " OutputName = BadDependencyType" << endl; + badTrnsStrm << " Translation = (*,*)" << endl; + badTrnsStrm << "EndGroup" << endl; + badTrnsStrm << "Group = NoDependencyValue" << endl; + badTrnsStrm << " InputPosition = (Observation_Area, Observing_System, Observing_System_Component)" << endl; + badTrnsStrm << " InputKey = name" << endl; + badTrnsStrm << " InputKeyDependencies = bad@type" << endl; + badTrnsStrm << " OutputPosition = (group, instrument)" << endl; + badTrnsStrm << " OutputName = NoDependencyValue" << endl; + badTrnsStrm << " Translation = (*,*)" << endl; + badTrnsStrm << "EndGroup" << endl; + + badTrnsStrm << "End"; + + stringstream invalidTrnsStrm; + + invalidTrnsStrm << "Group = InstrumentIfovWithUnits" << endl; + invalidTrnsStrm << " InputPosition = (CaSSIS_Header, CaSSIS_General)" << endl; + invalidTrnsStrm << " InputKey = INSTRUMENT_IFOV" << endl; + invalidTrnsStrm << " InputKeyAttribute = (Units, Attribute_2)" << endl; + invalidTrnsStrm << " OutputPosition = (group, instrument)" << endl; + invalidTrnsStrm << " OutputName = InstrumentIfovWithUnits" << endl; + invalidTrnsStrm << " Translation = (*,*)" << endl; + invalidTrnsStrm << "EndGroup" << endl; + invalidTrnsStrm << "Group = InstrumentIfovWithUnits" << endl; + invalidTrnsStrm << " InputPosition = (CaSSIS_Header, CaSSIS_General)" << endl; + invalidTrnsStrm << " InputKey = INSTRUMENT_IFOV" << endl; + invalidTrnsStrm << " InputKeyDependencies = \"tag@name:value\"" << endl; + invalidTrnsStrm << " OutputPosition = (group, instrument)" << endl; + invalidTrnsStrm << " OutputName = InstrumentIfovWithUnits" << endl; + invalidTrnsStrm << " Translation = (*,*)" << endl; + invalidTrnsStrm << "EndGroup" << endl; + invalidTrnsStrm << "Group = InstrumentIfovWithUnits" << endl; + invalidTrnsStrm << " Debug = Bad_Value" << endl; + invalidTrnsStrm << " InputPosition = (CaSSIS_Header, CaSSIS_General)" << endl; + invalidTrnsStrm << " InputKey = INSTRUMENT_IFOV" << endl; + invalidTrnsStrm << " OutputPosition = (group, instrument)" << endl; + invalidTrnsStrm << " OutputName = InstrumentIfovWithUnits" << endl; + invalidTrnsStrm << " Translation = (*,*)" << endl; + invalidTrnsStrm << "EndGroup" << endl; + + invalidTrnsStrm << "End"; + + cout << "Testing string stream translation specification" << endl << endl; + + XmlToPvlTranslationManager transMgr(fLabel, trnsStrm); + + cout << "Testing Translate method" << endl << endl; + cout << "Translation of InstrumentIfovWithUnits: " << + transMgr.Translate("InstrumentIfovWithUnits") << endl << endl; + + cout << "Testing Auto method" << endl << endl; + Pvl outputLabel; + transMgr.Auto(outputLabel); + cout << endl << outputLabel << endl << endl; + + cout << "Testing error throws" << endl << endl; + XmlToPvlTranslationManager badTransMgr(fLabel, badTrnsStrm); + + try { + transMgr.Translate("InstrumentIfovWithUnits", 2); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("NoInputPosition"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("BadInputPosition"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("InputKeyDoesNotExist"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("InputKeyAttributeDoesNotExist"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("NoDependencyType"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("BadDependencyType"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("NoDependencyValue"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + badTransMgr.Translate("NotInTranslationTable"); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + XmlToPvlTranslationManager invalidTransMgr(fLabel, invalidTrnsStrm); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + FileName nonExistantFile("DoesNotExist.xml"); + stringstream simpleTrans; + simpleTrans << "Group = Version" << endl; + simpleTrans << " Auto" << endl; + simpleTrans << " Debug" << endl; + simpleTrans << " InputPosition = (Identification_Area)" << endl; + simpleTrans << " InputKey = version_id" << endl; + simpleTrans << " OutputPosition = (group, instrument)" << endl; + simpleTrans << " OutputName = Version" << endl; + simpleTrans << " Translation = (*,*)" << endl; + simpleTrans << "EndGroup" << endl; + XmlToPvlTranslationManager nonExistantFileManager(nonExistantFile, simpleTrans); + } + catch(IException &e) { + e.print(); + cout << endl; + } + + try { + FileName pvlFile("$base/translations/pdsImage.trn"); + stringstream simpleTrans; + simpleTrans << "Group = Version" << endl; + simpleTrans << " Auto" << endl; + simpleTrans << " Debug" << endl; + simpleTrans << " InputPosition = (Identification_Area)" << endl; + simpleTrans << " InputKey = version_id" << endl; + simpleTrans << " OutputPosition = (group, instrument)" << endl; + simpleTrans << " OutputName = Version" << endl; + simpleTrans << " Translation = (*,*)" << endl; + simpleTrans << "EndGroup" << endl; + XmlToPvlTranslationManager pvlTransFileManager(pvlFile, simpleTrans); + } + catch(IException &e) { + ReportError(e.toString()); + cout << endl; + } + + + } + catch(IException &e) { + e.print(); + } + + return 0; +} diff --git a/isis/src/cassini/apps/cisscal/assets/Cal_paper_submitted_5_24_2010.pdf b/isis/src/cassini/apps/cisscal/assets/Cal_paper_submitted_5_24_2010.pdf new file mode 100644 index 0000000000000000000000000000000000000000..5c43d3007640e2f857e22765fa576b4db586b0d5 Binary files /dev/null and b/isis/src/cassini/apps/cisscal/assets/Cal_paper_submitted_5_24_2010.pdf differ diff --git a/isis/src/cassini/apps/cisscal/assets/cisscal_manual.pdf b/isis/src/cassini/apps/cisscal/assets/cisscal_manual.pdf new file mode 100644 index 0000000000000000000000000000000000000000..73d0ab14e797a40e0aee528ab0ad0eebcd595385 Binary files /dev/null and b/isis/src/cassini/apps/cisscal/assets/cisscal_manual.pdf differ diff --git a/isis/src/cassini/apps/cisscal/assets/edrsis.pdf b/isis/src/cassini/apps/cisscal/assets/edrsis.pdf new file mode 100644 index 0000000000000000000000000000000000000000..b7a1b47cca167e3d1fd0173cac2489ab486ccaf2 Binary files /dev/null and b/isis/src/cassini/apps/cisscal/assets/edrsis.pdf differ diff --git a/isis/src/cassini/apps/cisscal/assets/theoretical_basis.pdf b/isis/src/cassini/apps/cisscal/assets/theoretical_basis.pdf new file mode 100644 index 0000000000000000000000000000000000000000..bd9ebd0e98d0897102feae3ef7778ab94c77310d Binary files /dev/null and b/isis/src/cassini/apps/cisscal/assets/theoretical_basis.pdf differ diff --git a/isis/src/cassini/apps/cisscal/cisscal.xml b/isis/src/cassini/apps/cisscal/cisscal.xml index afcc1fabd8d9a83b5daa9a1a76b18f96c1f7da46..cc668cdebd3b0f1686b74d3420cf631b2e114ec3 100644 --- a/isis/src/cassini/apps/cisscal/cisscal.xml +++ b/isis/src/cassini/apps/cisscal/cisscal.xml @@ -3,50 +3,50 @@ - Radiometric correction of Cassini ISS camera images. + Radiometric correction of Cassini ISS camera images.

- This program performs radiometric corrections on images acquired by the - Cassisi Imaging Science Subsystem (ISS) camera. It performs bitweight - correction, bias subtraction, dark subtraction, non-linearity correction, - flat field correction, DN to flux conversion, and correction factor - division. The user may choose between intensity units and I/F for the DN - to flux conversion. This application is derived from the IDL CISSCAL - application developed by the Cassini Imaging Central Laboratory for + This program performs radiometric corrections on images acquired by the + Cassisi Imaging Science Subsystem (ISS) camera. It performs bitweight + correction, bias subtraction, dark subtraction, non-linearity correction, + flat field correction, DN to flux conversion, and correction factor + division. The user may choose between intensity units and I/F for the DN + to flux conversion. This application is derived from the IDL CISSCAL + application developed by the Cassini Imaging Central Laboratory for Operations (CICLPOS) using the following set of steps:

Step 1: Correct Bitweight - This step is performed on images that do not have a data conversion - type of "Table" or compression type of "Lossy" due to loss of + This step is performed on images that do not have a data conversion + type of "Table" or compression type of "Lossy" due to loss of information in these processses. This step is also skipped if the image - has a zero gain state due to the lack of data for this case. Bitweight - correction requires no user defined parameters. It uses a bitweight file + has a zero gain state due to the lack of data for this case. Bitweight + correction requires no user defined parameters. It uses a bitweight file found in the Cassini calibration bitweight directory.

- Step 2: Subtract Bias - - This step defaults to a method that uses a line dependent bias. That + Step 2: Subtract Bias + + This step defaults to a method that uses a line dependent bias. That method derives the bias by performing a linear fit to an array of - overclocked pixels taken out of the binary prefix data and saved off by - the ciss2isis application. This method cannot be - performed if the image has a compression type of "Lossy". In that case, - the BiasStripMean value found in the Instrument Group of the cube's labels - is subtracted from every pixel. This alternative method cannot be - implemented if the instrument used was CAS-ISS3 or earlier since, - according to the SIS, the BiasStripMean keyword contains invalid data for + overclocked pixels taken out of the binary prefix data and saved off by + the ciss2isis application. This method cannot be + performed if the image has a compression type of "Lossy". In that case, + the BiasStripMean value found in the Instrument Group of the cube's labels + is subtracted from every pixel. This alternative method cannot be + implemented if the instrument used was CAS-ISS3 or earlier since, + according to the SIS, the BiasStripMean keyword contains invalid data for these images. Bias subtraction requires no user defined parameters.

Step 3: Subtract Dark - + This step uses a spline interpolation to construct a dark image by calculating, for each pixel, a duration to be used with the coefficients found in the dark parmeter file. Dark current removal requires no user @@ -57,76 +57,76 @@

Step 4: Linearize - + This step corrects for non-linearity. It requires no user defined parameters and should be performed on all images. It uses a linearity correction table found in the Cassini calibration linearize directory.

- Step 5: Correct Flat field - + Step 5: Correct Flat field + This step consists of two parts: dust ring removal and division by flat field. Dust ring removal only applies to images from narrow angle cameras. This process masks a dust ring found on images and, if the image has SummingMode equal to 1 (i.e. it is a full, 1024x1024 image) and is recent (after 286th day of 2003), divides out a mottle map. Flat field correction is applied to all images. During - this process, each pixel is divided by the average of the center of the - image. For SummingMode 2 or 4, the results from this method diverge from - the IDL results due to differences in the bilinear method used to expand - the flat file image. Flat field correction requires no user defined - parameters. If narrow angle, it uses a dust ring file found in the Cassini - calibration dustring directory. If narrow and full, it also uses a mottle - file and an effective wavelength file found in dustring and efficiency - directories. And, for any image a slope database and a flat file are used, - found in slope and slope/slope2flat directories. + this process, each pixel is divided by the average of the center of the + image. For SummingMode 2 or 4, the results from this method diverge from + the IDL results due to differences in the bilinear method used to expand + the flat file image. Flat field correction requires no user defined + parameters. If narrow angle, it uses a dust ring file found in the Cassini + calibration dustring directory. If narrow and full, it also uses a mottle + file and an effective wavelength file found in dustring and efficiency + directories. And, for any image a slope database and a flat file are used, + found in slope and slope/slope2flat directories.

Step 6: Convert DN to Flux - - This step consists of 4 processes and the user must enter a value of + + This step consists of 4 processes and the user must enter a value of "intensity" or "I/F" for the parameter "units". In the first process, DNs are converted to electrons by multiplying by the true - gain. Second, the image is divided by the exposure time, - correcting for shutter offset effect. Third, the image is - divided by the optics area and, if intensity units are - chosen, divided by the solid angle. In the last process, - each pixel is divided by an efficiency factor. This value - is dependent on the flux units chosen by the user: intensity units - (photons/cm2/s/nm/ster) or I/F (irradiance over solar flux). - If "I/F" is chosen, the input cube must have been run through the Isis3 - application spiceinit to be able to calculate Solar - Distance. The results from this method diverge from the IDL results due - to differences in the way they calculate solar distance. However, the DN - results are still within 0.2% after we divide by the efficiency factor. DN - to Flux conversion should be performed on all images. Converting DN to - flux units requires a shutter offset file, a spectral file (if I/F is - chosen), a transmission file, and a quantum efficiency correction file - found in the Cassini calibration offset, efficiency, efficiency/systrans + gain. Second, the image is divided by the exposure time, + correcting for shutter offset effect. Third, the image is + divided by the optics area and, if intensity units are + chosen, divided by the solid angle. In the last process, + each pixel is divided by an efficiency factor. This value + is dependent on the flux units chosen by the user: intensity units + (photons/cm2/s/nm/ster) or I/F (irradiance over solar flux). + If "I/F" is chosen, the input cube must have been run through the Isis3 + application spiceinit to be able to calculate Solar + Distance. The results from this method diverge from the IDL results due + to differences in the way they calculate solar distance. However, the DN + results are still within 0.2% after we divide by the efficiency factor. DN + to Flux conversion should be performed on all images. Converting DN to + flux units requires a shutter offset file, a spectral file (if I/F is + chosen), a transmission file, and a quantum efficiency correction file + found in the Cassini calibration offset, efficiency, efficiency/systrans and correction directories.

Step 7: Divide by Correction Factor - + This step is implemented in order to force theory and observation to match. - It consists of 2 processes. First, if polarized, (i.e. a filter value of + It consists of 2 processes. First, if polarized, (i.e. a filter value of IRP0, IRP90, P0, P60, or P120) the image is divided by a polarization - factor. Next, the image is divided by its correction factor. This step - requires no user defined parameters. It uses a polarization factor file - and a correction factor file found in the Cassini calibration correction + factor. Next, the image is divided by its correction factor. This step + requires no user defined parameters. It uses a polarization factor file + and a correction factor file found in the Cassini calibration correction directory. -

+

- Omitted IDL Steps: - - In the original IDL program, there were 2 steps that were omitted in this + Omitted IDL Steps: + + In the original IDL program, there were 2 steps that were omitted in this application since they act as noise removal that can be filtered using - other applications after calibration is complete. - + other applications after calibration is complete. + The first omitted step is 2-Hz noise removal. This is meant to remove horizontal banding patterns introduced during image readout of Cassini ISS images and has two peaks in the power spectrum near 2Hz. There @@ -135,14 +135,14 @@ frequency random noise, slow-varying, and DC-offset components. The second method requires large regions of dark sky pixels present for all lines and uses an image mean to construct a 2-Hz signal. - - The second omited step is A-B pixel pairs correction - (also referred to as anti-blooming correction or bright/dark pixel pair - removal). In the IDL program, this correction is only performed if the - labels of the image indicate that the AntiBloomingStateFlag is "On" and - the InstrumentModeId is "Full" (i.e., SummingMode is 1). In this - correction, bright/dark pixel pairs are identified and replaced with a - boxcar average of their horizontal neighbors. + + The second omited step is A-B pixel pairs correction + (also referred to as anti-blooming correction or bright/dark pixel pair + removal). In the IDL program, this correction is only performed if the + labels of the image indicate that the AntiBloomingStateFlag is "On" and + the InstrumentModeId is "Full" (i.e., SummingMode is 1). In this + correction, bright/dark pixel pairs are identified and replaced with a + boxcar average of their horizontal neighbors.

@@ -158,7 +158,7 @@ Fixed bug in bitweight correction. Updated documentation. - Updated user documentation "Related Objects and Documents" section + Updated user documentation "Related Objects and Documents" section document web links. @@ -168,22 +168,22 @@ Fixed bug that caused errors on other compilers. - Modified the "I/F" option to make 2 attempts to locate the the target - before throwing an exception. First, the Isis::Camera class is used to - look for the target at the center point of the cube. If this fails, the - subspacecraft point is used to find the target. Only if both fail will + Modified the "I/F" option to make 2 attempts to locate the the target + before throwing an exception. First, the Isis::Camera class is used to + look for the target at the center point of the cube. If this fails, the + subspacecraft point is used to find the target. Only if both fail will the application throw an error. - Modified cisscal and its DarkCurrent class to reflect updates to the new - idl cisscal program version, 3.6. Updated documentation and app test to + Modified cisscal and its DarkCurrent class to reflect updates to the new + idl cisscal program version, 3.6. Updated documentation and app test to reflect these changes. Added new in-flight calibration document to "See Also". - Updated documentation in cpp file and moved call to set output cube to + Updated documentation in cpp file and moved call to set output cube to top of main method to check user preferences before computations. @@ -201,6 +201,15 @@ Added new appTest to make sure that the dust ring file location is tested. References #775. + + Updated the pdf links to Cassini ISS Software Interface Specification, CISSCAL User Guide, + Cassini ISS Image Calibration: Theoretical Basis, and In-flight Calibration of the Cassini Imaging Science Subsystem Cameras + to local assests in case the pdf sites are taken down. Fixes #2358. + + + Changed pvl.DIFF of input for all app tests to ignore file names. Allows test to pass when not + using default data area. Fixes #4738. + @@ -223,7 +232,7 @@ edrsis.pdf - http://pds-imaging.jpl.nasa.gov/data/cassini/cassini_orbiter/coiss_0011_v2/document/ + assets/ Charles Avis and Carolyn Porco Cassini Electronic Library @@ -234,7 +243,7 @@ cisscal_manual.pdf - http://pds-imaging.jpl.nasa.gov/data/cassini/cassini_orbiter/coiss_0011_v2/document/ + assets/ Planetary Data System Rings Node @@ -244,7 +253,7 @@ theoretical_basis.pdf - http://pds-imaging.jpl.nasa.gov/data/cassini/cassini_orbiter/coiss_0011_v2/document/ + assets/ R. West Planetary Data System Rings Node @@ -262,7 +271,7 @@ - Cassini ISS Calibration Report: 7.0 Radiometric Calibration Steps + Cassini ISS Calibration Report: 7.0 Radiometric Calibration Steps @@ -294,9 +303,9 @@ Input Isis cube - Use this parameter to choose an Isis cube to be calibrated. To ensure - that it contains all needed keywords in its label, input cube should - have been imported using ciss2isis and, if "I/F" is chosen, input cube + Use this parameter to choose an Isis cube to be calibrated. To ensure + that it contains all needed keywords in its label, input cube should + have been imported using ciss2isis and, if "I/F" is chosen, input cube must have been run through spiceinit application. @@ -312,7 +321,7 @@ Output Isis cube - Use this parameter to select the output filename of the calibrated + Use this parameter to select the output filename of the calibrated Isis cube. @@ -326,22 +335,22 @@ Options for converted flux units A list of the types of units to which user may choose to convert from - DNs. + DNs. I/F @@ -353,14 +362,14 @@ Cube calibrated using intensity units. - This example shows how to calibrate a Cassini ISS cube, converting to + This example shows how to calibrate a Cassini ISS cube, converting to intensity units. - + from=../IN/inputCube.cub to=../OUT/outputCube.cub units=INTENSITY - + Run the cisscal application to calibrate the cube. @@ -383,8 +392,8 @@ Stats on output cube - This pvl file contains the results of the stats application run on - the example 1 output cube. This may be compared with the pvl file + This pvl file contains the results of the stats application run on + the example 1 output cube. This may be compared with the pvl file of the same application run on the example 2 output cube. @@ -398,7 +407,7 @@ Input image - This is a Titan narrow-angle image that was imported into Isis cube + This is a Titan narrow-angle image that was imported into Isis cube format using ciss2isis. @@ -413,7 +422,7 @@ Output image - This is the Titan narrow-angle image calibrated and converted to + This is the Titan narrow-angle image calibrated and converted to intensity units. @@ -426,14 +435,14 @@ Cube calibrated using I/F. - This example shows how to calibrate a Cassini ISS cube, converting to + This example shows how to calibrate a Cassini ISS cube, converting to I/F. - + from=../IN/inputCube.cub to=../OUT/outputCube.cub - + Run the cisscal application to calibrate the cube. @@ -456,8 +465,8 @@ Stats on output cube - This pvl file contains the results of the stats application run on - the example 2 output cube. This may be compared with the pvl file + This pvl file contains the results of the stats application run on + the example 2 output cube. This may be compared with the pvl file of the same application run on the example 1 output cube. @@ -471,7 +480,7 @@ Input image - This is a Titan narrow-angle image that was imported into Isis cube + This is a Titan narrow-angle image that was imported into Isis cube format using ciss2isis and run through spiceinit. @@ -486,7 +495,7 @@ Output image - This is the Titan narrow-angle image calibrated and converted to + This is the Titan narrow-angle image calibrated and converted to I/F. diff --git a/isis/src/cassini/apps/vimscal/README.txt b/isis/src/cassini/apps/vimscal/README.txt new file mode 100644 index 0000000000000000000000000000000000000000..e56d903be1609d9c2e711310449bf51eb1800cc5 --- /dev/null +++ b/isis/src/cassini/apps/vimscal/README.txt @@ -0,0 +1,105 @@ + +****INTRODUCTION**** + +The VIMS IR wavelengths have been gradually shifting throughout the Cassini mission. +A model of this shifting over time (in years) exists, but it changes how the calibration +is done for the mission. In this application, the calibration files are stored as cube +files. In RC17, four calibration cubes are read from by the application. In +RC19 (which takes into account the wavelength shift), a calibration cube for each year +of the mission is generated from a text file. In the event that there will be future +calibration files that need to be generated, this README provides instructions for +generating those files. + + + +****HOW TO MAKE THE CALIBRATION CUBES**** + +After the calibration files are extracted, there should be four separate folders in +the calibration folder (cal_files), each containing 14 files calibration files: + +cal_files + | + |----------band-wavelengths + | | + | |---------------wavelengths.2004.txt + | |---------------wavelengths.2005.txt + | | : + | | : + | |---------------wavelengths.2017.txt + | + |----------RC19-mults + | | + | |---------------RC19-2004.txt + | |---------------RC19-2005.txt + | | : + | | : + | |---------------RC19-2017.txt + | |---------------AAA.readme.txt + | + |----------wave-cal + | | + | |---------------wave-cal.2004.txt + | |---------------wave-cal.2005.txt + | | : + | | : + | |---------------wave-cal.2017.txt + | |---------------AAA.readme.txt + | + |----------solar-spectrum + | | + | |---------------solar.2004.txt + | |---------------solar.2005.txt + | | : + | | : + | |---------------solar.2017.txt + | |---------------AAA.readme.txt + + +To generate the cubes, first call setisis to set an ISIS version. Then run the makecubes.py +Python script. The syntax for this script is as follows: + +python makecubes.py + +: The path to the the subfolder in cal_files. + : A prefix that uniquely identifies the calibration txt files + from other files. If we are in the RC19-mults folder, + the prefix would be RC19. + : A four digit number identifying the current calibration version. Currently, + the version is 0001. If this is the next version, it would be 0002. + +Example: If the cal_files and the makecubes.py script are both located in /scratch and we want to +generate the solar-spectrum cubes for version 0002, the command for doing that looks like: + +$python makecubes.py /scratch/cal_files/solar-spectrum solar 0002 + + +After the cubes are generated, then copy them to the appropriate folder in: + +$ISIS3DATA/cassini/calibration/vims/RC19 + +RC19 has the same subfolders as those enumerated above. Obviously you will need to be logged +in as isis3mgr to do this. + + +****THE PVL MULTIPLIER FILE**** + +In $ISIS3DATA/cassini/calibration/vims, there is a file called: vimsCalibration????.trn which +looks like this: + +Group=CalibrationMultipliers + version = RC19 + RC = 29554 + solar = 1000.0 + wave-cal=1000.0 +EndGroup + +End + +The AAA.readme.txt files contain the multiplier values which are in this file. The calibration +version also needs to be updated. Note: the calibration version here is not the same as the +file version which is used as an argument to the makecubes script. + + + + + diff --git a/isis/src/cassini/apps/vimscal/makecubes.py b/isis/src/cassini/apps/vimscal/makecubes.py new file mode 100644 index 0000000000000000000000000000000000000000..007089e8987ba6ff35febcaa4b0c48fcfd730dea --- /dev/null +++ b/isis/src/cassini/apps/vimscal/makecubes.py @@ -0,0 +1,164 @@ +import os +import re +import subprocess +import sys +import numpy as np + +""" +Author: 2016-09-09 Tyler Wilson +History: + +Description: This script creates calibration cubes for use +by the VIMS calibration program vimscal. + +Input: Calibration text files. +Output: Calibration cubes. + +Usage: python makecubes.py + +Example: python makecubes.py /home/tjwilson/cal_files/RC19-mults RC19 0001 + +The calibration files in RC19-mults are named RC19-2004.txt, RC19-2005.txt,.... +so the file prefix is: RC19 + +The version number must be a 4-digit number. + +""" + + +stderrors = [] +stdoutput = [] + +usage = "\nUsage: python makecubes.py \n" +example_usage = "Example: python makecubes.py /home/tjwilson/cal_files/RC19-mults RC19\n" + + +def cleanup(filepath): + """Cleaner function which attempts to remove temporary cubes and cube lists. + + Args: + filepath: The path to the directory containing the filewe wish to remove. + + Raises: A general exception if anything goes wrong. The script exits at that point. + """ + + try: + os.system("rm "+filepath+"/temp_*.cub") + except: + sys.exit("Something went wrong when attempting to delete the temp cubes in: "+ filepath) + try: + os.system("rm "+filepath+"/*.lis") + except: + sys.exit("Something went wrong when attempting to delete the cube lists in: "+filepath) + + +try: + datapath = sys.argv[1] +except IndexError: + print("Please enter a valid path to the calibration files.") + print(usage) + sys.exit(example_usage) + +try: + files = os.listdir(sys.argv[1]) +except OSError: + print("There is no directory named: "+datapath) + print(usage) + sys.exit(example_usage) + +if (len(files) == 0): + sys.exit("There are no calibration files in directory: "+datapath) + +try: + prefix = sys.argv[2] +except IndexError: + print("Please enter a valid prefix for the calibration files.") + print(usage) + sys.exit(example_usage) + +version = sys.argv[3] +match = re.search(r'[0-9]{4}',version) +if (match == None): + sys.exit("Please enter a 4 digit version number such as: 0001") + +''' +try: + precision=sys.argv[4] +except IndexError: + print("Please enter an integer value for the number of decimal places in the calibration files.") + sys.exit(example_usage) +''' + +precision=10 + +filtered = [] +#This is to ensure that we are only grabbing the txt calibration files and not +#anything else which might be in the directory. +for f in files: + if (f.startswith(prefix) and f.endswith('.txt') ): + filtered.append(f) + +if ( len(filtered) == 0): + print("Please enter a valid prefix for the calibration files.\n") + sys.exit("Example: If the calibration file has the name solar.2006.txt, then a prefix of solar would work.\n") + + + +for datafile in filtered: + try: + #datafile without it's extension + datafilename=os.path.splitext(datafile)[0] + if (datafilename.find("-") > 0 ): + datafilename.replace("-",".") + #import the datafile into a matrix + data = np.genfromtxt(datapath+"/"+datafile) + bandvals = data[:,1] + args3="samples=64" + args4 ="lines=64" + args5="bands=1" + i=1 + # This cubelist stores the list of temporary cubes which will be stacked together + # to form the calibration cube. + cubelistname = datafilename+".lis" + cubelist=open(datapath+"/"+cubelistname,"w") + #makecube creates a temporary cube of dimension (64,64,1) where each DN = bandval + for band in bandvals: + cmd="makecube" + tempcubepath=datapath+"/temp_"+datafilename+"_"+str(i)+".cub" + args1="to="+tempcubepath + format_string = '{0:.'+str(precision)+'f}' + fstring = format_string.format(float(band)) + args2="value="+fstring + #print(fstring) + try: + p=subprocess.Popen([cmd,args1,args2,args3,args4,args5],stdout=subprocess.PIPE,stderr=subprocess.PIPE) + except OSError: + sys.exit("Please set a valid ISIS3 version before executing this script.") + except: + sys.exit("Something went wrong. Please set a valid ISIS3 version before executing this script.") + out,err = p.communicate() + if (str (err) ): + print(err) + + cubelist.write(tempcubepath+"\n") + print(tempcubepath) + i = i+1 + + cubelist.close() + #Stack the temp cubes (there are 352 of them) into the calibration cube using cubeit + cmd = "cubeit" + args1="fromlist="+datapath+"/"+cubelistname + args2="to="+datapath+"/"+datafilename+"_v"+version+".cub" + p=subprocess.Popen([cmd,args1,args2],stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out,err=p.communicate() + if (str (err)): + print(err) + print("Finished: "+datafilename+"_v"+version+".cub") + except KeyboardInterrupt: + cleanup(datapath) + sys.exit("Program exiting.") + + + cleanup(datapath) + + diff --git a/isis/src/cassini/apps/vimscal/tsts/flatfield/Makefile b/isis/src/cassini/apps/vimscal/tsts/flatfield/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..7d700d0827ab89be80b00d0a9993c52e03c6d2e9 --- /dev/null +++ b/isis/src/cassini/apps/vimscal/tsts/flatfield/Makefile @@ -0,0 +1,23 @@ +APPNAME = vimscal +#vimscal from=/work/projects/isis/latest/m04370a/isis/src/cassini/apps/vimscal/rawcubes/ir/V1824733761_1.ir.cub to=/work/projects/isis/latest/m04370a/isis/src/cassini/apps/vimscal/rawcubes/ir/C1824733761_1.ir.2013Flat.cub flatfield=2013flat + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(APPNAME) FROM=$(INPUT)/V1824733761_1.ir.cub \ + TO=$(OUTPUT)/C1824733761_1.ir.2006Flat.cub \ + flatfield=2006FLAT > /dev/null; + catlab from=$(OUTPUT)/C1824733761_1.ir.2006Flat.cub \ + TO=$(OUTPUT)/C1824733761_1.ir.2006Flat.pvl > /dev/null; + $(APPNAME) FROM=$(INPUT)/V1824733761_1.ir.cub \ + TO=$(OUTPUT)/C1824733761_1.ir.2006SSFlat.cub \ + flatfield=2006SSFLAT > /dev/null; + catlab from=$(OUTPUT)/C1824733761_1.ir.2006SSFlat.cub \ + TO=$(OUTPUT)/C1824733761_1.ir.2006SSFlat.pvl > /dev/null; + $(APPNAME) FROM=$(INPUT)/V1824733761_1.ir.cub \ + TO=$(OUTPUT)/C1824733761_1.ir.2013Flat.cub \ + flatfield=2013FLAT > /dev/null; + catlab from=$(OUTPUT)/C1824733761_1.ir.2013Flat.cub \ + TO=$(OUTPUT)/C1824733761_1.ir.2013Flat.pvl > /dev/null; + + $(RM) $(OUTPUT)/*.cub diff --git a/isis/src/cassini/apps/vimscal/vimscal.cpp b/isis/src/cassini/apps/vimscal/vimscal.cpp index 863550c79bde34c3363afa6ac5698e1dd760a9cf..bca5152cfff56df68fba46adf7916e19c7402cdb 100644 --- a/isis/src/cassini/apps/vimscal/vimscal.cpp +++ b/isis/src/cassini/apps/vimscal/vimscal.cpp @@ -1,5 +1,8 @@ #include "Isis.h" +#include +#include + #include #include @@ -8,14 +11,18 @@ #include "Camera.h" #include "EndianSwapper.h" +#include "iTime.h" #include "IException.h" #include "IString.h" #include "LeastSquares.h" #include "LineManager.h" #include "PolynomialUnivariate.h" #include "ProcessByLine.h" +#include "ProcessByBrick.h" #include "ProgramLauncher.h" +#include "Pvl.h" #include "PvlGroup.h" +#include "Spice.h" #include "Statistics.h" #include "Table.h" #include "UserInterface.h" @@ -29,18 +36,45 @@ map< pair, double > sampleBasedDarkCorrections; //! map from to dark correction value map< pair, double > lineBasedDarkCorrections; +QString yearString; +QString timeString; + //! specific energy corrections for each band of the cube vector specificEnergyCorrections; +//! Bandwidth centers +vector bandwidthVector; +vector averageBandwidthVector; + //! list of temp files that need deleted vector tempFiles; //! solar remove coefficient double solarRemoveCoefficient; +//! The calibration file containing multiplier information. +static Pvl g_configFile; + +//! Calibration multipliers +static double g_solar(1.0); +static double g_ir(1.0); +static double g_vis(1.0); +static double g_wavecal(1.0); + +//! The calibration version. It's the name of the directory +//! in $cassini/calibration/vims where all of the radiometric +//! calibration cubes are kept. +QString calVersion; +QString g_startTime; + //! Output in I/F units bool iof; +//! +bool g_visBool; + +QString g_oCubeName; + void calculateDarkCurrent(Cube *); void calculateVisDarkCurrent(Cube *); void calculateIrDarkCurrent(Cube *); @@ -49,7 +83,12 @@ void chooseFlatFile(Cube *, ProcessByLine *); void calculateSpecificEnergy(Cube *); void calculateSolarRemove(Cube *, ProcessByLine *); +void loadCalibrationValues(); +void updateWavelengths(Cube *icube); + +void normalize(Buffer &in,Buffer &out); +void normalize1(Buffer &out); void calibrate(vector &in, vector &out); QString createCroppedFile(Cube *icube, QString cubeFileName, bool flatFile = false); @@ -61,20 +100,27 @@ PvlGroup calibInfo; void IsisMain() { UserInterface &ui = Application::GetUserInterface(); - const QString calVersion = "RC17"; - + //load the appropriate multipliers and the correct calibration version + tempFiles.clear(); specificEnergyCorrections.clear(); + bandwidthVector.clear(); + averageBandwidthVector.clear(); sampleBasedDarkCorrections.clear(); lineBasedDarkCorrections.clear(); solarRemoveCoefficient = 1.0; iof = (ui.GetString("UNITS") == "IOF"); calibInfo = PvlGroup("RadiometricCalibration"); - calibInfo += PvlKeyword("CalibrationVersion", calVersion); + + loadCalibrationValues(); ProcessByLine p; Cube *icube = p.SetInputCube("FROM"); + PvlGroup &inst = icube->group("Instrument"); + + + g_visBool = (inst["Channel"][0] != "IR"); bool isVims = true; @@ -86,13 +132,33 @@ void IsisMain() { isVims = false; } + + try { + timeString = QString(inst["StartTime"]); + + } + catch(IException &e) { + + QString msg = "The label for the input cube [" + QString(ui.GetAsString("FROM")) + + "] does not have a start time in the Instrument group."; + throw IException(IException::User,msg,_FILEINFO_); + + } + + iTime startTime(timeString); + //Determine the year string to access the appropriate calibration file + yearString= QString::number(startTime.Year() ); + + if(!isVims) { - QString msg = "The input cube [" + QString(ui.GetAsString("FROM")) + "] is not a Cassini VIMS cube"; + QString msg = "The input cube [" + QString(ui.GetAsString("FROM")) + + "] is not a Cassini VIMS cube"; throw IException(IException::User, msg, _FILEINFO_); } if(icube->label()->findObject("IsisCube").hasGroup("AlphaCube")) { - QString msg = "The input cube [" + QString(ui.GetAsString("FROM")) + "] has had its dimensions modified and can not be calibrated"; + QString msg = "The input cube [" + QString(ui.GetAsString("FROM")) + + "] has had its dimensions modified and can not be calibrated"; throw IException(IException::User, msg, _FILEINFO_); } @@ -106,16 +172,37 @@ void IsisMain() { chooseFlatFile(icube, &p); calculateSpecificEnergy(icube); + updateWavelengths(icube); Cube *outCube = p.SetOutputCube("TO"); + g_oCubeName = outCube->fileName(); + p.StartProcess(calibrate); + outCube->putGroup(calibInfo); // Rename group to Results for writing to Log calibInfo.setName("Results"); Application::Log(calibInfo); p.EndProcess(); + + + //This is used to create normalized spectral plots +#if 0 + ProcessByBrick p1; + CubeAttributeInput iatt; + CubeAttributeOutput oatt; + p1.SetBrickSize(1,1,icube->bandCount()); + p1.SetInputCube(outCube); + p1.SetOutputCube(g_oCubeName+"_norm.cub",oatt,outCube->sampleCount(),outCube->lineCount(), + outCube->bandCount()); + p1.StartProcess(normalize); + p.EndProcess(); + p1.EndProcess(); + +#endif + for(unsigned int i = 0; i < tempFiles.size(); i++) { QFile::remove(tempFiles[i]); @@ -124,6 +211,26 @@ void IsisMain() { tempFiles.clear(); } + +void normalize(Buffer &in,Buffer &out) { + + double normalizer = in[54]; + + + for (int i =0; i < in.size(); i++) { + + if (!IsSpecial(in[i])) { + + out[i] = in[i]/normalizer; + + } + else{ + out[i]=in[i]; + } + } +} + + /** * This applies the calculated calibration coefficients to the file. * @@ -135,7 +242,8 @@ void calibrate(vector &inBuffers, vector &outBuffers) { Buffer *flatFieldBuffer = inBuffers[1]; Buffer *solarRemoveBuffer = NULL; // this is optional - if(inBuffers.size() > 2) { + + if (inBuffers.size() > 2) { inBuffer = inBuffers[0]; solarRemoveBuffer = inBuffers[1]; flatFieldBuffer = inBuffers[2]; @@ -143,7 +251,7 @@ void calibrate(vector &inBuffers, vector &outBuffers) { Buffer *outBuffer = outBuffers[0]; - for(int i = 0; i < inBuffer->size(); i++) { + for (int i = 0; i < inBuffer->size(); i++) { (*outBuffer)[i] = (*inBuffer)[i]; if(IsSpecial((*outBuffer)[i])) continue; @@ -151,42 +259,55 @@ void calibrate(vector &inBuffers, vector &outBuffers) { map< pair, double>::iterator darkCorrection = sampleBasedDarkCorrections.find(pair(i + 1, inBuffer->Band())); - if(darkCorrection != sampleBasedDarkCorrections.end()) { + //Darkfield correction + if (darkCorrection != sampleBasedDarkCorrections.end()) { (*outBuffer)[i] -= darkCorrection->second; } - darkCorrection = lineBasedDarkCorrections.find(pair(inBuffer->Line(), inBuffer->Band())); + darkCorrection = lineBasedDarkCorrections.find(pair(inBuffer->Line(), inBuffer->Band())); + - if(darkCorrection != lineBasedDarkCorrections.end()) { - if(!IsSpecial(darkCorrection->second)) + if (darkCorrection != lineBasedDarkCorrections.end()) { + if (!IsSpecial(darkCorrection->second)) (*outBuffer)[i] -= darkCorrection->second; else (*outBuffer)[i] = Null; } - if(!IsSpecial((*flatFieldBuffer)[i]) && !IsSpecial((*outBuffer)[i])) { + //Flatfield correction + if (!IsSpecial((*flatFieldBuffer)[i]) && !IsSpecial((*outBuffer)[i])) { (*outBuffer)[i] /= (*flatFieldBuffer)[i]; } - if(inBuffer->Band() <= (int)specificEnergyCorrections.size() && !IsSpecial((*outBuffer)[i])) { + + //(1) Convert from DN/sec to photons/sec using RC19 + //(2) Then convert from photons/sec to specific intensity + if (inBuffer->Band() <= (int)specificEnergyCorrections.size() && !IsSpecial((*outBuffer)[i])) + { (*outBuffer)[i] *= specificEnergyCorrections[inBuffer->Band()-1]; } - if(iof && solarRemoveBuffer && !IsSpecial((*outBuffer)[i])) { - (*outBuffer)[i] = (*outBuffer)[i] / ((*solarRemoveBuffer)[i] / solarRemoveCoefficient) * Isis::PI; + + //Convert to I/F/ Equation (3) in the white paper + if (iof && solarRemoveBuffer && !IsSpecial((*outBuffer)[i])) { + (*outBuffer)[i] = (*outBuffer)[i] /( g_solar*(*solarRemoveBuffer)[i] + / solarRemoveCoefficient) * Isis::PI ; } + } } + /** * This calculates the values necessary to convert from * specific energy to I/F. A cube is used as part of the - * equation (which probably* just contains a vector of values) + * equation (which probably just contains a vector of values) * so p->SetInputCube(...) will be called with the appropriate * filename. * - * @param icube - * @param p + * @param *icube A pointer to the input cube + * @param *p A pointer to the ProcessByLine object */ void calculateSolarRemove(Cube *icube, ProcessByLine *p) { UserInterface &ui = Application::GetUserInterface(); @@ -261,13 +382,13 @@ void calculateSolarRemove(Cube *icube, ProcessByLine *p) { */ } - bool vis = (icube->label()-> - findGroup("Instrument", Pvl::Traverse)["Channel"][0] != "IR"); + //bool vis = (icube->label()-> + // findGroup("Instrument", Pvl::Traverse)["Channel"][0] != "IR"); QString attributes; // vis is bands 1-96, ir is bands 97-352 in this calibration file - if(vis) { + if(g_visBool) { attributes = "+1-96"; } else { @@ -276,7 +397,12 @@ void calculateSolarRemove(Cube *icube, ProcessByLine *p) { CubeAttributeInput iatt(attributes); - FileName solarFileName("$cassini/calibration/vims/solar_v????.cub"); + //QString solarFilePath = "$cassini/calibration/vims/solar_v????.cub"; + QString solarFilePath = "$cassini/calibration/vims/"+calVersion+ + "/solar-spectrum/"+"solar."+yearString+"_v????.cub"; + + FileName solarFileName(solarFilePath); + solarFileName = solarFileName.highestVersion(); calibInfo += PvlKeyword("SolarColorFile", @@ -287,46 +413,225 @@ void calculateSolarRemove(Cube *icube, ProcessByLine *p) { /** - * This calculates the coefficients for specific energy corrections + * @brief Loads the approrpriate constants which need to be multiplied by + * the values in the calibration cubes during the calibration phase. + * Also loads the current radiometric calibration version. */ -void calculateSpecificEnergy(Cube *icube) { +void loadCalibrationValues() { + + FileName calibFile("$cassini/calibration/vims/vimsCalibration????.trn"); + calibFile = calibFile.highestVersion(); + + //Pvl configFile; + g_configFile.read(calibFile.expanded()); + PvlGroup &multipliers = g_configFile.findGroup("CalibrationMultipliers"); + + calVersion = (QString)multipliers["version"]; + + g_solar = multipliers["solar"][0].toDouble(); + + g_ir = multipliers["IR"][0].toDouble(); + + g_vis = multipliers["VIS"][0].toDouble(); + + g_wavecal = multipliers["wave-cal"][0].toDouble(); + + + + calibInfo += PvlKeyword("CalibrationVersion", calVersion); + calibInfo += PvlKeyword("SolarMultiplier",QString::number(g_solar,'f',2)); + calibInfo += PvlKeyword("IR_Multiplier",QString::number(g_ir,'f',2)); + calibInfo += PvlKeyword("VIS_Multiplier",QString::number(g_vis,'f',2)); + calibInfo += PvlKeyword("Wave-CalMultiplier",QString::number(g_wavecal,'f',2)); + + +} + + +/** + * @brief Updates the BandBin::Center keyword value in the input cube's label + * with new wavelength values for RC 19 (Radiometric Calibration version 19). + * This is due to the wavelength calibration drift. + * @param icube The original input cube prior to calibration + */ +void updateWavelengths(Cube *icube) { + PvlGroup &inst = icube->label()->findGroup("Instrument", Pvl::Traverse); bool vis = (inst["Channel"][0] != "IR"); + + PvlGroup &bandBin = icube->label()->findGroup("BandBin",Pvl::Traverse); + + QString bandwidthFile = "$cassini/calibration/vims/"+calVersion+"/band-wavelengths/wavelengths."+ + yearString+"_v????.cub"; + + QString averageBandwidthFile = "$cassini/calibration/vims/"+calVersion+"/band-wavelengths/"+ + "wavelengths_average_v????.cub"; + + + FileName bandwidthFileName = FileName(bandwidthFile); + FileName averageBandwidthFileName = FileName(averageBandwidthFile); + bandwidthFileName =bandwidthFileName.highestVersion(); + averageBandwidthFileName = averageBandwidthFileName.highestVersion(); + + Cube averageBandwidthCube; + Cube bandwidthCube; + bandwidthCube.open(bandwidthFileName.expanded()); + averageBandwidthCube.open(averageBandwidthFileName.expanded()); + + calibInfo += PvlKeyword("BandwidthFile", + bandwidthFileName.originalPath() + "/" + bandwidthFileName.name()); + + calibInfo += PvlKeyword("AverageBandwidthFile", + averageBandwidthFileName.originalPath() + "/" + + averageBandwidthFileName.name()); + + LineManager bandwidthMgr(bandwidthCube); + LineManager averageBandwidthMgr(averageBandwidthCube); + + for (int i =0; i < icube->bandCount();i++) { + + Statistics bandwidthStats; + Statistics averageBandwidthStats; + + if (vis) { + averageBandwidthMgr.SetLine(1,i+1); + bandwidthMgr.SetLine(1, i + 1); + } + else { + // ir starts at band 97 + averageBandwidthMgr.SetLine(1,i+97); + bandwidthMgr.SetLine(1, i + 97); + } + + bandwidthCube.read(bandwidthMgr); + bandwidthStats.AddData(bandwidthMgr.DoubleBuffer(), bandwidthMgr.size()); + bandwidthVector.push_back(bandwidthStats.Average()); + + averageBandwidthCube.read(averageBandwidthMgr); + averageBandwidthStats.AddData(averageBandwidthMgr.DoubleBuffer(), averageBandwidthMgr.size()); + averageBandwidthVector.push_back(averageBandwidthStats.Average()); + } + + QString bandbinCenterString("("); + QString averageBandbinString("("); + + for (unsigned int i =0; i < bandwidthVector.size()-1; i++) { + bandbinCenterString+=QString::number(bandwidthVector[i]); + bandbinCenterString+=","; + + averageBandbinString+=QString::number(averageBandwidthVector[i]); + averageBandbinString+=","; + } + + bandbinCenterString+=QString::number(bandwidthVector[bandwidthVector.size()-1]); + bandbinCenterString+=")"; + + averageBandbinString+=QString::number(averageBandwidthVector[averageBandwidthVector.size()-1]); + averageBandbinString+=")"; + + + + PvlKeyword ¢erBand = bandBin.findKeyword("Center"); + centerBand.setValue(bandbinCenterString); + + PvlKeyword averageBand("MissionAverage"); + averageBand.setValue(averageBandbinString); + bandBin.addKeyword(averageBand); + centerBand.setValue(bandbinCenterString); + +} + + +/** + * @brief This calculates the coefficients for specific energy corrections + */ +void calculateSpecificEnergy(Cube *icube) { + PvlGroup &inst = icube->label()->findGroup("Instrument", Pvl::Traverse); + //bool vis = (inst["Channel"][0] != "IR"); + + + double multiplier = 1.0; double coefficient = 1.0; if(inst["GainMode"][0] == "HIGH") { coefficient /= 2; } - if(vis && inst["SamplingMode"][0] == "HI-RES") { + if(g_visBool && inst["SamplingMode"][0] == "HI-RES") { coefficient *= 3; } - if(vis) { + if(g_visBool) { coefficient /= toDouble(inst["ExposureDuration"][1]) / 1000.0; } else { + + //Discrepancies between the VIMS and Spacecraft clock necessitated a + //conversion multiplier, which is in the USGS: ISIS3 version of vimscal + //but was not part of the University of Arizona pipeline. Below is the + //text describing this problem: + /** + I. VIMS ISIS Camera Model - Three subtasks were included in this work: + Timing Discrepancy - The first involved accounting for a timing discrepancy recorded in + the VIMS EDRs. In 2012 (following an inquiry from Mark Showalter) we identified a + timing error that arose because the S/C clock and VIMS internal clock run at slightly + different rates (the VIMS internal clock rate is 1.01725 slower than the + S/C USO-driven clock). The instrument timing reported in the VIMS_IR EDR labels + includes exposure duration, interline delay, and intercube delay. We had been under the + misimpression that these times had been converted to S/C clock units at JPL during the + creation of the EDRs. This was not the case and the labels are, in fact, in units of + the VIMS internal clock. This error propagates into errors in geometric reconstruction + that become particularly severe for very long IR exposures. During reconstruction, + each VIMS IR spectral sample (pixel) is assigned an acquisition time (based on timing + data in the labels) that is used to index into the SPICE kernel data bases in order to + derived necessary geometric information for that pixel. As a result of the use of the wrong + time base, the geometric parameters so derived were in error. + + Prior to making any changes the VIMS internal clock rate was remeasured using inflight + sequences in which both the VIMS and S/C clock times were recorded for each VIMS_IR pixel. + These results showed that the VIMS internal clock rate was the same as measured prelaunch + to a precision of 10-6. We then made changes to ISIS S/W to convert these erroneous times + reported in the EDR headers to UTC time. This required modifying the VIMS IR Camera model + in ISIS-3 (as well as in ISIS-2, used in the VIMS data processing pipeline at the + University of Arizona). Bob Brown is preparing a document for inclusion in PDS EDR + deliveries describing the problem and procedure to convert the time parameters as given in + EDR labels (EXPOSURE_DURATION, INTERLINE_DELAY_DURATION, and INTERFRAME_DELAY_DURATION). + */ + + //USGS coefficient /= (toDouble(inst["ExposureDuration"][0]) * 1.01725) / 1000.0 - 0.004; - } - QString specEnergyFile = "$cassini/calibration/vims/"; - if(vis) { - specEnergyFile += "vis_perf_v????.cub"; - } - else { - specEnergyFile += "ir_perf_v????.cub"; + //University of Arizona + //coefficient /= (toDouble(inst["ExposureDuration"][0]) ) / 1000.0 - 0.004; } - QString waveCalFile = "$cassini/calibration/vims/wavecal_v????.cub"; + + + //QString specEnergyFile = "$cassini/calibration/vims/ir_perf_v????.cub"; + + + + QString specEnergyFile = "$cassini/calibration/vims/"+calVersion+"/RC19-mults/RC19." + +yearString+"_v????.cub"; + + + //B multiplier + //QString waveCalFile = "$cassini/calibration/vims/wavecal_v????.cub"; + + QString waveCalFile = "$cassini/calibration/vims/"+calVersion+"/wave-cal/wave.cal."+ + yearString+"_v????.cub"; + FileName specEnergyFileName(specEnergyFile); specEnergyFileName = specEnergyFileName.highestVersion(); + FileName waveCalFileName(waveCalFile); waveCalFileName = waveCalFileName.highestVersion(); + Cube specEnergyCube; specEnergyCube.open(specEnergyFileName.expanded()); @@ -345,14 +650,18 @@ void calculateSpecificEnergy(Cube *icube) { Statistics specEnergyStats; Statistics waveCalStats; - if(vis) { + if(g_visBool) { specEnergyMgr.SetLine(1, i + 1); waveCalMgr.SetLine(1, i + 1); + multiplier=g_vis; + } else { - specEnergyMgr.SetLine(1, i + 1); + //specEnergyMgr.SetLine(1, i + 1); //vimscalold + specEnergyMgr.SetLine(1,i+96+1); // ir starts at band 97 waveCalMgr.SetLine(1, i + 96 + 1); + multiplier = g_ir; } specEnergyCube.read(specEnergyMgr); @@ -361,12 +670,24 @@ void calculateSpecificEnergy(Cube *icube) { specEnergyStats.AddData(specEnergyMgr.DoubleBuffer(), specEnergyMgr.size()); waveCalStats.AddData(waveCalMgr.DoubleBuffer(), waveCalMgr.size()); - double bandCoefficient = coefficient * specEnergyStats.Average() * waveCalStats.Average(); + + //Determine Specific Intensity + // I = [(Raw_{DN} = Dark)/flatfield]*B*C + // B = waveCalStats.Average() + // C = specEnergyStats.Average() + //Equation 1 in the white paper (C = specificEnergyStats.Average(), + //B = waveCalStats.Average() ) + + double bandCoefficient = coefficient * (multiplier*specEnergyStats.Average()) + *(g_wavecal*waveCalStats.Average() ); + specificEnergyCorrections.push_back(bandCoefficient); } + } + /** * This decides if we have a VIS or IR dark current correction and calls the * appropriate method. @@ -387,6 +708,7 @@ void calculateDarkCurrent(Cube *icube) { } } + /** * This populates darkCorrections with the result of the equation: * dark = a + x * b @@ -482,7 +804,8 @@ void calculateVisDarkCurrent(Cube *icube) { // now set the values to the average for(int setIndex = 0; setIndex < 8; setIndex ++) { pair index = pair(sample, band+setIndex); - if(!setIndex) printf("Changing %.4f to %.4f\n", sampleBasedDarkCorrections.find(index)->second, stats.Average()); + if(!setIndex) printf("Changing %.4f to %.4f\n", + sampleBasedDarkCorrections.find(index)->second, stats.Average()); sampleBasedDarkCorrections.find(index)->second = stats.Average(); } } @@ -490,6 +813,7 @@ void calculateVisDarkCurrent(Cube *icube) { }*/ } + /** * This calculates the dark current corrections for IR. If * IRDARKAVG is false, then it translates the sideplane data @@ -619,17 +943,47 @@ void calculateIrDarkCurrent(Cube *icube) { } /** - * This calls p->SetInputCube with the appropriate flat file needed for + * @brief This calls p->SetInputCube with the appropriate flat file needed for * icube. * * @param icube * @param p */ void chooseFlatFile(Cube *icube, ProcessByLine *p) { + + UserInterface &ui = Application::GetUserInterface(); + + QString flatField= ui.GetString("FLATFIELD"); + QString signature=""; + PvlGroup &inst = icube->label()->findGroup("Instrument", Pvl::Traverse); bool vis = (inst["Channel"][0] != "IR"); bool hires = ((inst["SamplingMode"][0] == "HIGH") || (inst["SamplingMode"][0] == "HI-RES")); +//#if 0 + +if (!vis) { + if (flatField == "2006FLAT") { + signature="352_"; + + } + + else if (flatField == "2006SSFLAT") { + signature = "ss_352_"; + + } + + else if (flatField == "2013FLAT") { + + signature = "2013_"; + } + + } + + +//#endif + + QString calFile = "$cassini/calibration/vims/flatfield/"; if(vis) { @@ -640,21 +994,27 @@ void chooseFlatFile(Cube *icube, ProcessByLine *p) { } if(hires) { - calFile += "hires_flatfield_v????.cub"; + + //calFile += "hires_flatfield_v????.cub"; + calFile += "hires_flatfield_"+signature+"v????.cub"; } else { - calFile += "flatfield_v????.cub"; + //calFile += "ss_flat_352_v????.cub"; + calFile += "flatfield_"+signature+"v????.cub"; + } FileName calibrationFileName(calFile); calibrationFileName = calibrationFileName.highestVersion(); - calibInfo += PvlKeyword("FlatFile", calibrationFileName.originalPath() + "/" + calibrationFileName.name()); + calibInfo += PvlKeyword("FlatFile", calibrationFileName.originalPath() + + "/" + calibrationFileName.name()); CubeAttributeInput iatt; p->SetInputCube(createCroppedFile(icube, calibrationFileName.expanded(), true), iatt); } + /** * This makes our calibration files match the input cube described * by the swath keywords. @@ -689,6 +1049,7 @@ QString createCroppedFile(Cube *icube, QString cubeFileName, bool flatFile) { return tempFile.expanded(); } + void GetOffsets(const Pvl &lab, int &finalSampOffset, int &finalLineOffset) { const PvlGroup &inst = lab.findGroup("Instrument", Pvl::Traverse); diff --git a/isis/src/cassini/apps/vimscal/vimscal.xml b/isis/src/cassini/apps/vimscal/vimscal.xml index 0935588690d8cc2809554f6bffbb5d6e4ebde52f..82aafa62e00163ded2e651bf795017d01f69af3d 100644 --- a/isis/src/cassini/apps/vimscal/vimscal.xml +++ b/isis/src/cassini/apps/vimscal/vimscal.xml @@ -1,25 +1,30 @@ - + Radiometric correction of Cassini VIMS camera images. - This program applies a dark current and a flat field correction to images, then converts the output units - to either specific energy or I/F. + This program applies a dark current and a flat field correction to images, + then converts the output units to either specific energy or I/F.

Dark Current:
- The dark current correction for VIS consists of reading a binary ".tab" file from $cassini/calibration/vims and subtracting - derived values from this file.
- - The dark current correction for IR consists of reading the sideplane data (stored in a SideplaneIr table in the cube) and - subtracting this from the input cube. If "CompressorId" is available then the sideplane data was already subtracted from - the file, but the linear fit capabilities are still available to re-do the dark current with a linear fit instead of the - default subtraction. If spectral summing is on then no dark current can be applied. If spectral editing is on then the linear - fit on the dark current can not be applied. Sideplane keywords for IR are as follows: + The dark current correction for VIS consists of reading a + binary ".tab" file from $cassini/calibration/vims and subtracting derived values from + this file.
+ + The dark current correction for IR consists of reading the sideplane data (stored in a + SideplaneIr table in the cube) and subtracting this from the input cube. If "CompressorId" is + available then the sideplane data was already subtracted from the file, but the linear fit + capabilities are still available to re-do the dark current with a linear fit instead of the + default subtraction. If spectral summing is on then no dark current can be applied. + If spectral editing is on then the linear fit on the dark current can not be applied. + Sideplane keywords for IR are as follows:
  • None = No dark current subtraction (applied by the instrument)
  • Sideplane = Sideplane was subtracted only without fitting a line
    • @@ -30,12 +35,14 @@

    Flat Field:
    - For both VIS and IR this determines the correct file from $cassini/calibration/vims/flatfield and divides the input data by the - flat field data.

    + For both VIS and IR this determines the correct file from $cassini/calibration/vims/flatfield + and divides the input data by the flat field data.

    Subareas
    - The offset and swath keywords will be respected by running "crop" on the calibration files appropriately and using the cropped - calibration files. + The offset and swath keywords will be respected by running "crop" on the calibration + files appropriately and using the cropped calibration files. + + @@ -71,9 +78,21 @@ clock. The Ir exposure duration needs a correction factor of 1.01725 applied before using. References #1759. - - Added RadiometricCalibration group to output cube labels, which contains calibration files - and other calibration parameters. Uses new performance model calibration file (RC17). Fixes #2055. + + Updated vimscal to make use of RC19 files. Instead of having one calibration + cube for solar/specific energy/wavecal data, there are now 14 cubes (one for each year in + the range 2004:2017). This is because of the wavelength calibration shift as + a function of time described in "The VIMS Wavelength and Radiometric Calibration + White Paper", Roger N. Clark, Robert H. Brown, Dyer M. Lytle. Draft submitted to the + NASA Planetary Data System: 07/19/2016. Changes + to the application are minimal. The BandBin:Center keyword value was also updated + for all calibrated cubes to reflect the new knowledge concerning wavelength shifts. + Fixes #4370. + + + Added the ability for users to select which flatfield file they want to use during + calibration. The default option is to continue using the original flatfield files. + References #4370. @@ -141,6 +160,35 @@ + + string + Flatfield file + + + 2006Flat + + + + + + + + boolean Do not smooth IR Dark Current diff --git a/isis/src/cassini/apps/vimscal/vimscalUtil.h b/isis/src/cassini/apps/vimscal/vimscalUtil.h new file mode 100644 index 0000000000000000000000000000000000000000..516c20ff1d3b2d27c9eb3d676a9e69e5c9bd372d --- /dev/null +++ b/isis/src/cassini/apps/vimscal/vimscalUtil.h @@ -0,0 +1,4 @@ +#ifndef VIMSCALUTIL_H +#define VIMSCALUTIL_H + +#endif // VIMSCALUTIL_H diff --git a/isis/src/clementine/apps/clem2isis/bitstrm.cpp b/isis/src/clementine/apps/clem2isis/bitstrm.cpp index 70f190bbd5bcb7525475de3517111f56ebbec38a..9b2f565e1c7e134746c6b11d5223087eec756c88 100644 --- a/isis/src/clementine/apps/clem2isis/bitstrm.cpp +++ b/isis/src/clementine/apps/clem2isis/bitstrm.cpp @@ -1,13 +1,13 @@ /* - * THIS ROUTINE IS PART OF THE CLEMENTINE PDS FILE READER PROGRAM. - * IT WAS WRITTEN BY ACT CORP. IN DIRECT SUPPORT TO THE - * CLEMENTINE (DSPSE) PROGRAM. + * THIS ROUTINE IS PART OF THE CLEMENTINE PDS FILE READER PROGRAM. + * IT WAS WRITTEN BY ACT CORP. IN DIRECT SUPPORT TO THE + * CLEMENTINE (DSPSE) PROGRAM. * - * IF YOU FIND A PROBLEM OR MAKE ANY CHANGES TO THIS CODE PLEASE CONTACT - * Dr. Erick Malaret at ACT Corp. - * tel: (703) 742-0294 - * (703) 683-7431 - * email: nrlvax.nrl.navy.mil + * IF YOU FIND A PROBLEM OR MAKE ANY CHANGES TO THIS CODE PLEASE CONTACT + * Dr. Erick Malaret at ACT Corp. + * tel: (703) 742-0294 + * (703) 683-7431 + * email: nrlvax.nrl.navy.mil * * */ @@ -129,13 +129,13 @@ void *dByteStream(ByteStream *Bs) { short ByteStream_read(ByteStream *Bs) { short c; - char cval; - int n; + char cval; + int n; if(Bs->mode == INPUT) { /* c = fgetc( Bs->file ); */ n = fread(&cval, sizeof(char), 1, Bs->file); - c = cval; + c = cval; if(n != 1) Bs->stat = EOF; return c; } diff --git a/isis/src/clementine/apps/clem2isis/decomp.cpp b/isis/src/clementine/apps/clem2isis/decomp.cpp index ef8559e6f3c21931f1e75cdf0d9c5770ff0d27e1..10c05261e9ff727303abc15a85de477ab9a9087b 100644 --- a/isis/src/clementine/apps/clem2isis/decomp.cpp +++ b/isis/src/clementine/apps/clem2isis/decomp.cpp @@ -1,20 +1,20 @@ /* - * THIS ROUTINE IS PART OF THE CLEMENTINE PDS FILE READER PROGRAM. - * IT WAS WRITTEN BY ACT CORP. IN DIRECT SUPPORT TO THE - * CLEMENTINE (DSPSE) PROGRAM. + * THIS ROUTINE IS PART OF THE CLEMENTINE PDS FILE READER PROGRAM. + * IT WAS WRITTEN BY ACT CORP. IN DIRECT SUPPORT TO THE + * CLEMENTINE (DSPSE) PROGRAM. * - * IF YOU FIND A PROBLEM OR MAKE ANY CHANGES TO THIS CODE PLEASE CONTACT - * Dr. Erick Malaret at ACT Corp. - * tel: (703) 742-0294 - * (703) 683-7431 - * email: nrlvax.nrl.navy.mil + * IF YOU FIND A PROBLEM OR MAKE ANY CHANGES TO THIS CODE PLEASE CONTACT + * Dr. Erick Malaret at ACT Corp. + * tel: (703) 742-0294 + * (703) 683-7431 + * email: nrlvax.nrl.navy.mil * * Dec 11 2006 KJB Changed malloc.h to stdlib.h for the Mac port again. * malloc.h is deprecated. * */ /* - Program to calculate the Discrete Cosine Transform of a 8x8 block of data + Program to calculate the Discrete Cosine Transform of a 8x8 block of data */ #include @@ -30,13 +30,13 @@ #define TRUE 1 #define FALSE 0 -long *DCTHist[64]; -float *Rn[64]; -float Q[64]; -float q_table[64]; +long *DCTHist[64]; +float *Rn[64]; +float Q[64]; +float q_table[64]; float U[64]; short ULS[64]; -int zzseq[] = {0, 1, 8, 16, 9, 2, 3, 10, 17, 24, 32, 25, 18, 11, 4, 5, 12, 19, 26, 33, 40, +int zzseq[] = {0, 1, 8, 16, 9, 2, 3, 10, 17, 24, 32, 25, 18, 11, 4, 5, 12, 19, 26, 33, 40, 48, 41, 34, 27, 20, 13, 6, 7, 14, 21, 28, 35, 42, 49, 56, 57, 50, 43, 36, 29, 22, 15, 23, 30, 37, 44, 51, 58, 59, 52, 45, 38, 31, 39, 46, 53, 60, 61, 54, 47, 55, 62, 63 @@ -134,8 +134,8 @@ void decomp(BitStream *bs, CHARH *Image, long rows, long cols) { } void getDCTHist(BitStream *bs, long rows, long cols) { - short Pred, i; - long nblocks; + short Pred, i; + long nblocks; nblocks = (rows * cols) / 64; Pred = 0; @@ -153,9 +153,9 @@ void getDCTHist(BitStream *bs, long rows, long cols) { } void getRn() { - short i, j; - float lb, ub, a, b, num, den, phi; - float m, pa, pap, pb, pbp, pm, pmp; + short i, j; + float lb, ub, a, b, num, den, phi; + float m, pa, pap, pb, pbp, pm, pmp; for(i = 0; i < 64; i++) { Rn[i][-256] = (float) - 256; diff --git a/isis/src/clementine/apps/clem2isis/huffman.cpp b/isis/src/clementine/apps/clem2isis/huffman.cpp index 244c6f662ef8a6615f1cd0f3b4a78773e169771a..51ef4efbbeb4ae7a522fa8eade195c5cfc0bd81b 100644 --- a/isis/src/clementine/apps/clem2isis/huffman.cpp +++ b/isis/src/clementine/apps/clem2isis/huffman.cpp @@ -1,13 +1,13 @@ /* - * THIS ROUTINE IS PART OF THE CLEMENTINE PDS FILE READER PROGRAM. - * IT WAS WRITTEN BY ACT CORP. IN DIRECT SUPPORT TO THE - * CLEMENTINE (DSPSE) PROGRAM. + * THIS ROUTINE IS PART OF THE CLEMENTINE PDS FILE READER PROGRAM. + * IT WAS WRITTEN BY ACT CORP. IN DIRECT SUPPORT TO THE + * CLEMENTINE (DSPSE) PROGRAM. * - * IF YOU FIND A PROBLEM OR MAKE ANY CHANGES TO THIS CODE PLEASE CONTACT - * Dr. Erick Malaret at ACT Corp. - * tel: (703) 742-0294 - * (703) 683-7431 - * email: nrlvax.nrl.navy.mil + * IF YOU FIND A PROBLEM OR MAKE ANY CHANGES TO THIS CODE PLEASE CONTACT + * Dr. Erick Malaret at ACT Corp. + * tel: (703) 742-0294 + * (703) 683-7431 + * email: nrlvax.nrl.navy.mil * * */ @@ -25,20 +25,20 @@ void genehuf(short *, short *, short *, char *, char *, short); void gendectbls(short *, short *, short *, short *, short *); -short dcbits[16], acbits[16]; -char dchuffval[12], achuffval[162]; +short dcbits[16], acbits[16]; +char dchuffval[12], achuffval[162]; -short dcehufco[16]; -short dcehufsi[16]; -short dcmincode[16]; -short dcmaxcode[16]; -short dcvalptr[16]; +short dcehufco[16]; +short dcehufsi[16]; +short dcmincode[16]; +short dcmaxcode[16]; +short dcvalptr[16]; -short acehufco[256]; -short acehufsi[256]; -short acmincode[16]; -short acmaxcode[16]; -short acvalptr[16]; +short acehufco[256]; +short acehufsi[256]; +short acmincode[16]; +short acmaxcode[16]; +short acvalptr[16]; /******************* Initialization of Huffman tables ********************/ void inithuffcode() { @@ -49,15 +49,15 @@ void inithuffcode() { /* generate dc Huffman codes */ genhuffsize(dchuffsize, dcbits, &dclastk); genhuffcode(dchuffcode, dchuffsize); -// fprintf(qparm,"dc huffman tables:\n"); //removed qparm references BMG 2006-07-18 -// fprintf(qparm,"(symbol length code)\n"); //removed qparm references BMG 2006-07-18 +// fprintf(qparm,"dc huffman tables:\n"); //removed qparm references BMG 2006-07-18 +// fprintf(qparm,"(symbol length code)\n"); //removed qparm references BMG 2006-07-18 genehuf(dcehufco, dcehufsi, dchuffcode, dchuffsize, dchuffval, dclastk); /* generate ac Huffman codes */ genhuffsize(achuffsize, acbits, &aclastk); genhuffcode(achuffcode, achuffsize); -// fprintf(qparm,"ac huffman tables:\n"); //removed qparm references BMG 2006-07-18 -// fprintf(qparm,"(symbol length code)\n"); //removed qparm references BMG 2006-07-18 +// fprintf(qparm,"ac huffman tables:\n"); //removed qparm references BMG 2006-07-18 +// fprintf(qparm,"(symbol length code)\n"); //removed qparm references BMG 2006-07-18 genehuf(acehufco, acehufsi, achuffcode, achuffsize, achuffval, aclastk); /* generate decoding tables */ @@ -111,9 +111,9 @@ void genehuf(short *ehufco, short *ehufsi, short *huffcode, char *huffsize, value = ((short)huffvalue[k]) & 0x00ff; ehufco[value] = huffcode[k]; ehufsi[value] = huffsize[k]; -// fprintf(qparm,"%#.2x\t%d\t%#x\n", //removed qparm reference, BMG 2006-07-18 -// huffvalue[k]&0x00ff, -// ehufsi[value], +// fprintf(qparm,"%#.2x\t%d\t%#x\n", //removed qparm reference, BMG 2006-07-18 +// huffvalue[k]&0x00ff, +// ehufsi[value], // ehufco[value] ); } } diff --git a/isis/src/clementine/apps/clem2isis/jpeg_c.h b/isis/src/clementine/apps/clem2isis/jpeg_c.h index 176b44ba241b0236a5edc984784738388dc654f1..e6a54bdfc15d3ef8b3e4f70952e4fe174148468b 100644 --- a/isis/src/clementine/apps/clem2isis/jpeg_c.h +++ b/isis/src/clementine/apps/clem2isis/jpeg_c.h @@ -19,25 +19,25 @@ extern short ByteStream_status(ByteStream *); #define MEMORY 1 #define DISK 0 #if defined(__BORLANDC__) && !defined(__WIN32__) -#define MALLOC farmalloc -#define FREE farfree -#define CHARH unsigned char huge -#define FAR far +#define MALLOC farmalloc +#define FREE farfree +#define CHARH unsigned char huge +#define FAR far #else -#define MALLOC malloc -#define FREE free -#define CHARH unsigned char +#define MALLOC malloc +#define FREE free +#define CHARH unsigned char #define FAR #endif struct BitStreamDef { - ByteStream bytestream; - short BitBuffer; /* Bit I/O buffer */ - short BitBuffMask; /* Bit I/O buffer mask */ - CHARH *outstring; + ByteStream bytestream; + short BitBuffer; /* Bit I/O buffer */ + short BitBuffMask; /* Bit I/O buffer mask */ + CHARH *outstring; char mode; - unsigned long bytesout; - unsigned short bitmask[17]; + unsigned long bytesout; + unsigned short bitmask[17]; }; typedef struct BitStreamDef BitStream; @@ -47,10 +47,10 @@ extern short BitStream_write(BitStream *, short bits, short width); extern short BitStream_read(BitStream *, short bits); /* Global Tables */ -extern float q_table[64]; -extern int zzseq[64]; -extern short dcbits[16], acbits[16]; -extern char dchuffval[12], achuffval[162]; +extern float q_table[64]; +extern int zzseq[64]; +extern short dcbits[16], acbits[16]; +extern char dchuffval[12], achuffval[162]; /* Function Declarations */ extern void inithuffcode(); diff --git a/isis/src/clementine/apps/clem2isis/pds.h b/isis/src/clementine/apps/clem2isis/pds.h index decc13d4ee0f53a5f305ec68da637ff6f2d05853..42f8d4adf4827f03f2d6d29627262b04ab3c6dac 100644 --- a/isis/src/clementine/apps/clem2isis/pds.h +++ b/isis/src/clementine/apps/clem2isis/pds.h @@ -1,19 +1,19 @@ #if defined(__BORLANDC__) && !defined(__WIN32__) -#define CHARH unsigned char huge +#define CHARH unsigned char huge #else #define CHARH unsigned char #endif typedef struct { - char *text; /* pointer to text header */ - long *hist; /* pointer to histogram */ + char *text; /* pointer to text header */ + long *hist; /* pointer to histogram */ unsigned char *brw_imag; /* pointer to browse image (if available) */ - int browse_nrows; /* number of rows in browse image */ - int browse_ncols; /* number of columns in browse image */ + int browse_nrows; /* number of rows in browse image */ + int browse_ncols; /* number of columns in browse image */ CHARH *image; /* pointer to decompressed or uncompressed image */ - int image_nrows; /* number of rows in the image */ - int image_ncols; /* number of columns in the image */ + int image_nrows; /* number of rows in the image */ + int image_ncols; /* number of columns in the image */ } PDSINFO; //extern FILE *qparm; //removed qparm references BMG 2006-07-18 diff --git a/isis/src/control/apps/cnetcheck/cnetcheck.cpp b/isis/src/control/apps/cnetcheck/cnetcheck.cpp index 4c30fff63679e8420e21e02575009c0867c4be26..1f76338ca0af559262ab1ead917b24f2b7e40e8e 100644 --- a/isis/src/control/apps/cnetcheck/cnetcheck.cpp +++ b/isis/src/control/apps/cnetcheck/cnetcheck.cpp @@ -73,7 +73,6 @@ QString g_delimiter; // Main program void IsisMain() { - Progress progress; UserInterface &ui = Application::GetUserInterface(); diff --git a/isis/src/control/apps/cnetcombinept/ControlPointCloudPt.h b/isis/src/control/apps/cnetcombinept/ControlPointCloudPt.h deleted file mode 100644 index 83b14a95dbf3b8f6cb8cb83e39db98ce2798c37d..0000000000000000000000000000000000000000 --- a/isis/src/control/apps/cnetcombinept/ControlPointCloudPt.h +++ /dev/null @@ -1,310 +0,0 @@ -#ifndef ControlPointCloudPt_h -#define ControlPointCloudPt_h -/** - * @file - * $Revision: 1.0 $ - * $Date: 2014/02/27 18:49:25 $ - * - * Unless noted otherwise, the portions of Isis written by the USGS are public - * domain. See individual third-party library and package descriptions for - * intellectual property information,user agreements, and related information. - * - * Although Isis has been used by the USGS, no warranty, expressed or implied, - * is made by the USGS as to the accuracy and functioning of such software - * and related material nor shall the fact of distribution constitute any such - * warranty, and no responsibility is assumed by the USGS in connection - * therewith. - * - * For additional information, launch - * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see - * the Privacy & Disclaimers page on the Isis website, - * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on - * http://www.usgs.gov/privacy.html. - */ - -#include - -#include -#include -#include -#include - -#include "ControlPoint.h" -#include "ControlMeasure.h" - - -namespace Isis { - -/** - * @brief 3-D ControlPoint class for use in PointCloud datasets - * - * The ControlPoint container is required to not change its content for the - * duration of use of the nanoflann kd-tree built from the points. - * - * @author 2015-10-11 Kris Becker - * - * @internal - * @history 2015-10-11 Kris Becker - Original Version - */ - -class ControlPointCloudPt { - public: - enum CoordinateType { Image, Ground }; - enum Ownership { Shared, // Indicates creator of ControlPoint retains - // ownership. take() provides a unique clone - // of ControlPoint. - Exclusive // Creator gives ownership to ControlPointCloudPt - // take() will give up pointer interally. - }; - - ControlPointCloudPt() : m_xyz(), m_type(Image), m_serialno(), - m_data( new ControlPointData() ), - m_merged() { - m_data->getImageCoordinates(m_xyz); - } - - ControlPointCloudPt(ControlPoint *point, const CoordinateType &ptype, - const Ownership owner, - const QString &serialno = "", - const double &weight = 1.0) : - m_xyz( ), m_type(ptype), m_serialno(serialno), - m_data(new ControlPointData(point, owner, weight)), - m_merged() { - if ( Image == ptype ) { - m_data->setReference(serialno); - if ( !selectImageCoordinates() ) { - m_data->disable(); - } - } - else { // ( Ground == ptype ) - if ( !selectGroundCoordinates() ) { - m_data->disable(); - } - } - } - - virtual ~ControlPointCloudPt() { } - - inline bool isValid() const { - return ( !m_data->isDisabled() ); - } - - inline void disable() { - return ( m_data->disable() ); - } - - inline int size() const { - return ( m_data->size() ); - } - - Ownership owner() const { - return ( m_data->m_owner ); - } - - ControlPoint *take() const { - return ( m_data->take() ); - } - - inline bool selectGroundCoordinates() { - m_type = Ground; - return ( m_data->getGroundCoordinates(m_xyz) ); - } - - inline bool selectImageCoordinates() { - m_type = Image; - return ( m_data->getImageCoordinates(m_xyz) ); - } - - inline CoordinateType getCoordinateType() const { - return ( m_type ); - } - - inline QString id() const { - return ( m_data->m_point->GetId() ); - } - - inline const ControlPoint *getPoint() const { - return ( m_data->m_point ); - } - - inline ControlPoint &getPoint() { - return ( *m_data->m_point ); - } - - inline QString getSerialNumber() const { - return ( m_serialno ); - } - - inline ControlMeasure *getMeasure(const QString &serialno) const { - if ( !isValid() ) { return (0); } - if (m_data->m_point->HasSerialNumber(serialno) ) { - return ( m_data->m_point->GetMeasure(serialno) ); - } - - return (0); - } - - // Convenient retrieval coordinates - inline double x() const { return ( m_xyz[0] ); } - inline double y() const { return ( m_xyz[1] ); } - inline double z() const { return ( m_xyz[2] ); } - inline double w() const { return ( m_xyz[3] ); } - inline const double *array() const { return ( m_xyz ); } - - inline bool operator==(const ControlPointCloudPt &other) const { - return ( m_data->m_point == other.m_data->m_point ); - } - - inline bool operator!=(const ControlPointCloudPt &other) const { - return ( m_data->m_point != other.m_data->m_point ); - } - - private: - /** - * Shared ControlPoint data pointer - * @author 2015-10-11 Kris Becker - * - * @internal - * @history 2015-10-11 Kris Becker - Original Version - */ - class ControlPointData : public QSharedData { - typedef ControlPointCloudPt::Ownership Ownership; - public: - ControlPointData() : QSharedData(), m_point(0), m_reference(0), - m_weight(1.0), m_initial(0), - m_owner(Exclusive){ } - ControlPointData(ControlPoint *point, const Ownership owner, - const double weight = 1.0) : - QSharedData(), m_point(point), - m_reference(point->GetRefMeasure()), - m_weight(weight), - m_initial(point->GetNumValidMeasures()), - m_owner(owner) { } - ControlPointData(const ControlPointData &other) : QSharedData(other), - m_point(other.m_point), - m_reference(other.m_reference), - m_weight(other.m_weight), - m_initial(other.m_initial), - m_owner(Shared) { } - ~ControlPointData() { - if ( Exclusive == m_owner ) { - delete (m_point); - m_point = 0; - } - } - - inline int size() const { - if ( 0 == m_point ) { return (0); } - return ( m_point->GetNumValidMeasures() ); - } - - inline bool setReference(const QString &serialno) { - if ( 0 == m_point ) { return ( false); } - m_reference = 0; - - if ( serialno.isEmpty() ) { - m_reference = m_point->GetRefMeasure(); - } - else { - if ( m_point->HasSerialNumber(serialno) ) { - m_reference = m_point->GetMeasure(serialno); - } - } - - return ( 0 != m_reference ); - } - - /** This approach allows use of 2 and 3 dimensional Euclidean - * distances */ - inline bool getImageCoordinates(double coords[4]) const { - (void) getNoPointData(coords); - if ( 0 == m_reference ) { return (false); } - if ( 0 == m_point ) { return ( false ); } - - // ControlMeasure *refm = m_point->GetRefMeasure(); - coords[0] = m_reference->GetSample(); - coords[1] = m_reference->GetLine(); - coords[2] = 0.0; - coords[3] = m_weight; - return ( true ); - } - - - /** This approach assumes 3 dimensional Euclidean distances */ - inline bool getGroundCoordinates(double coords[4]) const { - (void) getNoPointData(coords); - if ( 0 == m_point ) { return ( false ); } - - // Always get the best surface point (2015-10-27) - SurfacePoint surfpt = m_point->GetBestSurfacePoint(); - if ( !surfpt.Valid() ) { return (false); } - - // Get the location and convert to meters! - surfpt.ToNaifArray(&coords[0]); - coords[0] *= 1000.0; - coords[1] *= 1000.0; - coords[2] *= 1000.0; - return (true); - } - - inline bool isDisabled() const { - if ( 0 == m_point ) return ( true ); - return ( - m_point->IsInvalid() || - m_point->IsIgnored() || - m_point->IsRejected() || - m_point->IsEditLocked() || - ( 0 == m_reference ) - ); - } - - inline void disable() { - if ( !isDisabled() ) { - m_point->SetIgnored( true ); - } - return; - } - - ControlPoint *take() { - ControlPoint *p(m_point); - if ( 0 == m_point ) { return (p); } - - // If someone else owns the point, clone it - if ( Shared == m_owner ) { - p = new ControlPoint(*m_point); - } - else { - // Exclusive == Ownership - // Relinquish ownership - m_point = 0; - } - - return ( p ); - } - - // Data.... - ControlPoint *m_point; - ControlMeasure *m_reference; - double m_weight; - int m_initial; - Ownership m_owner; - - - private: - inline bool getNoPointData(double coords[4]) const { - coords[0] = coords[1] = coords[2] = 0.0; - coords[3] = m_weight; - return ( false ); - } - }; - - // Variables... - double m_xyz[4]; - CoordinateType m_type; - QString m_serialno; - QExplicitlySharedDataPointer m_data; - QList m_merged; -}; - -}; // namespace Isis -#endif diff --git a/isis/src/control/apps/cnetcombinept/ControlPointMerger.cpp b/isis/src/control/apps/cnetcombinept/ControlPointMerger.cpp new file mode 100644 index 0000000000000000000000000000000000000000..5cc795fedea44f673de9c30fbc5e67a03811584e --- /dev/null +++ b/isis/src/control/apps/cnetcombinept/ControlPointMerger.cpp @@ -0,0 +1,212 @@ +/** + * @file + * $Revision: 1.0 $ + * $Date: 2014/02/27 18:49:25 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "ControlPointMerger.h" + +#include + +namespace Isis { + + /** + * Constructs a default ControlPointMerger. + * The tolerance defaults to DBL_MAX. + */ + ControlPointMerger::ControlPointMerger() : m_image_tolerance(DBL_MAX), m_merged() { } + + + /** + * Constructs a ControlPointMerger with a given tolerance. + * + * @param image_tolerance The tolerance used to determine if points will be merged. + */ + ControlPointMerger::ControlPointMerger(const double image_tolerance) : + m_image_tolerance(image_tolerance), m_merged() { } + + + /** + * Destroys a ControlPointMerger. + */ + ControlPointMerger::~ControlPointMerger() { } + + + /** + * Returns the number of points that have been merged. + * + * @return @b int The number of points that have been merged. + */ + int ControlPointMerger::size() const { + return ( m_merged.size() ); + } + + + /** + * Clears the list of merged points. + */ + void ControlPointMerger::clear() { + m_merged.clear(); + return; + } + + + /** + * @brief Merges control points that satisfy image coordinate constraints + * + * Evaluates a list of candidate points to determine if they should be merged + * into a source point. For each candidate point, the image space distance + * between its measures and the source point's measures on shared images are + * averaged. If this average is less than the ControlPointMerger's tolerance + * the candidate point is merged into the source point. + * + * @author 2016-10-25 Kris Becker + * + * @param point Source point to merge candidates into + * @param candidates List of point candidates + * + * @return @b int Number of measures merged + */ + int ControlPointMerger::apply(ControlPoint *point, QList &candidates) { + + QList measures = point->getMeasures( true ); + QList v_processed; + clear(); + + int nMerged(0); + BOOST_FOREACH ( MeasurePoint &measure, candidates ) { + ControlPoint *v_p = measure.getPoint(); + if ( point != v_p) { // Don't process the same point! + if (measure.isValid() && (!v_processed.contains(v_p))) { + v_processed.append(v_p); + + // Compute distance statistics of common measures in two points + Statistics stats; + BOOST_FOREACH ( ControlMeasure *m, measures ) { + if ( v_p->HasSerialNumber( m->GetCubeSerialNumber() ) ) { + ControlMeasure *c = v_p->GetMeasure( m->GetCubeSerialNumber() ); + if ( isValid(*c) ) { + stats.AddData( image_distance(*m, *c) ); + } + } + } + + // Test for conditions of a merger. If there are common image measures, + // use the statistics. + if ( stats.ValidPixels() > 0 ) { + if (stats.Average() <= m_image_tolerance) { + nMerged += merge(point, v_p, stats); + measure.disable(); + m_merged.append(measure); + } + } + } + } + } + return (nMerged); + } + + + /** + * @brief Merges measures from one control point into another. + * + * Merges measures on shared images from a candidate point into a source + * point. If a reference measure is merged, then its residual and goodness + * of fit are set to the average and standard deviation of the distance + * between the source and candidate points' measures. + * + * @param source The source point that measueres are merged into. + * @param candidate The candidate point that measures are merged from. + * @param stats Statistics object containing the distances between + * measures in the source and candidate points on + * common images. + * + * @return @b int The number of measures merged from the candidate point + * into the source point. + * + * @see ControlPointMerger::apply + */ + int ControlPointMerger::merge(ControlPoint *source, ControlPoint *candidate, + const Statistics &stats) { + int nMerged(0); + + // Gut check to ensure we don't merge into ourself + if ( source != candidate ) { + + // Set up for merging a reference measure. Expectation is the tolerance + // is <= 1, but don't assume that. + double residual = stats.Average(); + double goodnessoffit = qMin(qMax(0.0, stats.StandardDeviation()), 1.0); + ControlMeasureLogData data(ControlMeasureLogData::GoodnessOfFit, + goodnessoffit); + + // Consider only valid measures + QList measures = candidate->getMeasures(true); + BOOST_FOREACH ( ControlMeasure *m, measures ) { + if ( !source->HasSerialNumber(m->GetCubeSerialNumber()) ) { + QScopedPointer p_m(new ControlMeasure(*m)); + + // Handle the transfer of a reference measure from the candidate + if ( candidate->GetRefMeasure() == m ) { + p_m->SetResidual(residual, residual); + p_m->SetLogData(data); + } + + source->Add( p_m.take() ); + nMerged++; + } + } + // Essentially disables this point meaning this point is already merged + // with another + if (nMerged > 0) candidate->SetIgnored(true); + } + + return ( nMerged ); + } + + + /** + * Determines if a measure is valid. + * + * @param m The measure to check. + * + * @return @b bool If the measure is ignored or rejected. + */ + bool ControlPointMerger::isValid(const ControlMeasure &m) const { + return ( !( m.IsIgnored() || m.IsRejected() ) ); + } + + /** + * Computes the distance, in image, between two measures. + * Note that this returns the squared distance because that + * is what the nanoflann library expects. + * + * @param source A measure from the source point. + * @param candidate A measure from the candidate point. + * + * @return @b double The squared distance between the measures. + */ + inline double ControlPointMerger::image_distance(const ControlMeasure &source, + const ControlMeasure &candidate) const { + double dx = source.GetSample() - candidate.GetSample(); + double dy = source.GetLine() - candidate.GetLine(); + return ( std::sqrt( dx*dx + dy*dy ) ); + } + +} // namespace Isis diff --git a/isis/src/control/apps/cnetcombinept/ControlPointMerger.h b/isis/src/control/apps/cnetcombinept/ControlPointMerger.h index c9b8a8328eb93873789afc2b3993854e6176a075..666de50c5670dc2cd78639b00ede3de5a668bac0 100644 --- a/isis/src/control/apps/cnetcombinept/ControlPointMerger.h +++ b/isis/src/control/apps/cnetcombinept/ControlPointMerger.h @@ -22,13 +22,17 @@ * http://www.usgs.gov/privacy.html. */ +#include #include #include +#include #include #include +#include -#include "ControlPointCloudPt.h" +#include "ControlMeasureLogData.h" +#include "MeasurePoint.h" #include "Statistics.h" namespace Isis { @@ -45,137 +49,32 @@ namespace Isis { * @author 2015-10-11 Kris Becker * * @internal - * @history 2015-10-11 Kris Becker - Original Version + * @history 2015-10-11 Kris Becker - Original Version + * @history 2016-12-06 Jesse Mapel - Updated documentation. References #4558. + * @history 2016-12-06 Jesse Mapel - Moved implementation to cpp file. References #4558. */ class ControlPointMerger { public: - ControlPointMerger() : m_image_tolerance(DBL_MAX), - m_ground_tolerance(DBL_MAX), - m_ground_distance(DBL_MAX), - m_source(), m_candidates() { } - ControlPointMerger(const double image_tolerance, - const double ground_tolerance = -1.0) : - m_image_tolerance(image_tolerance), - m_ground_tolerance(ground_tolerance), - m_ground_distance(DBL_MAX), - m_source(), m_candidates() { } - virtual ~ControlPointMerger() { } + ControlPointMerger(); + ControlPointMerger(const double image_tolerance); + virtual ~ControlPointMerger(); - int size() const { - return ( m_candidates.size() ); - } - - Statistics getImageStatistics(int index) const { - Q_ASSERT( index >= 0 ); - Q_ASSERT ( index < size() ); - return ( m_candidates[index].second ); - } - - double getGroundDistance() const { - return ( m_ground_distance ); - } - - void clear() { - m_candidates.clear(); - return; - } - - void apply(ControlPointCloudPt &source, ControlPointCloudPt &candidate, - const double distance) { - - if ( !source.isValid() ) { return; } - if ( !candidate.isValid() ) { return; } - m_source = source; - - ControlPoint &point = source.getPoint(); - m_ground_distance = ground_distance( point, candidate.getPoint() ); - - QList measures = point.getMeasures( true ); - Statistics stats; - BOOST_FOREACH ( ControlMeasure *m, measures ) { - if ( isValid(*m) ) { - ControlMeasure *c = candidate.getMeasure(m->GetCubeSerialNumber()); - if ( (0 != c) ) { - if ( isValid(*c) ) { stats.AddData(image_distance(*m, *c)); } - } - } - } - - // Test for conditions of a merger. If there are common image measures, - // use the statistics. If no common measures, use the ground distance. - if ( stats.ValidPixels() > 0 ) { - if (stats.Average() <= m_image_tolerance) { - m_candidates.append( qMakePair (candidate, stats)); - } - } - else if ( m_ground_distance <= m_ground_tolerance ) { - m_candidates.append( qMakePair (candidate, stats)); - } - return; - } - - int merge() { - int nMerged(0); - ControlPoint &source = m_source.getPoint(); - for ( int i = 0 ; i < m_candidates.size() ; i++) { - ControlPointCloudPt &cpt = m_candidates[i].first; - ControlPoint &candidate = cpt.getPoint(); - QList ms = candidate.getMeasures(true); - for ( int m = 0 ; m < ms.size() ; m++) { - if ( !source.HasSerialNumber(ms[m]->GetCubeSerialNumber()) ) { - source.Add( new ControlMeasure(*ms[m]) ); - nMerged++; - } - } - // Essentially disables this point - cpt.disable(); - } - - return ( nMerged ); - } + int size() const; + void clear(); + int apply(ControlPoint *point, QList &candidates); + int merge(ControlPoint *source, ControlPoint *candidate, const Statistics &stats); private: - - double m_image_tolerance; - double m_ground_tolerance; - double m_ground_distance; - ControlPointCloudPt m_source; - QList > m_candidates; - - inline bool isValid(const ControlMeasure &m) const { - return ( !( m.IsIgnored() || m.IsRejected() ) ); - } + double m_image_tolerance; /**!< The image distance tolerance for determining + if control points should be merged.*/ + QList m_merged; /**!< The number of control points that have been + merged by the ControlPointMerger.*/ + inline bool isValid(const ControlMeasure &m) const; inline double image_distance(const ControlMeasure &source, - const ControlMeasure &candidate) const { - double dx = source.GetSample() - candidate.GetSample(); - double dy = source.GetLine() - candidate.GetLine(); - return ( std::sqrt( dx*dx + dy*dy ) ); - } - - inline double ground_distance(const ControlPoint &source, - const ControlPoint &candidate) const { - double spts[3], cpts[3]; - getGroundVector(source, spts); - getGroundVector(candidate, cpts); - - double dx = spts[0] - cpts[0]; - double dy = spts[1] - cpts[1]; - double dz = spts[2] - cpts[2]; - return ( std::sqrt( dx*dx + dy*dy + dz*dz ) ); - } - - /** Compute ground point in meters */ - inline void getGroundVector(const ControlPoint &point, double v[3]) const { - // Always use the best surface point available - point.GetBestSurfacePoint().ToNaifArray(v); - v[0] *= 1000.0; - v[1] *= 1000.0; - v[2] *= 1000.0; - return; - } + const ControlMeasure &candidate) const; }; } // namespace Isis diff --git a/isis/src/control/apps/cnetcombinept/Makefile b/isis/src/control/apps/cnetcombinept/Makefile index 1c608f574d6c4a29bc6e87f64ecabe90e1c6e48f..7578f0b21d038db6a5042c095cda9b34b6bb2570 100644 --- a/isis/src/control/apps/cnetcombinept/Makefile +++ b/isis/src/control/apps/cnetcombinept/Makefile @@ -1,3 +1,7 @@ -include $(ISISROOT)/make/isismake.apps - -ISISCPPFLAGS += -frounding-math +ifeq ($(ISISROOT), $(BLANK)) +.SILENT: +error: + echo "Please set ISISROOT"; +else + include $(ISISROOT)/make/isismake.apps +endif \ No newline at end of file diff --git a/isis/src/control/apps/cnetcombinept/MeasurePoint.h b/isis/src/control/apps/cnetcombinept/MeasurePoint.h new file mode 100644 index 0000000000000000000000000000000000000000..682b6475cdf2241173281f7926e9f82eb85aeeb4 --- /dev/null +++ b/isis/src/control/apps/cnetcombinept/MeasurePoint.h @@ -0,0 +1,330 @@ +#ifndef MeasurePoint_h +#define MeasurePoint_h +/** + * @file + * $Revision: 1.0 $ + * $Date: 2014/02/27 18:49:25 $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include + +#include +#include +#include +#include + +#include "ControlPoint.h" +#include "ControlMeasure.h" + + +namespace Isis { + +/** + * @brief ControlPoint class for use in PointCloud datasets + * + * The ControlPoint container is required to not change its content for the + * duration of use of the nanoflann kd-tree built from the points. + * + * @author 2015-10-11 Kris Becker + * + * @internal + * @history 2015-10-11 Kris Becker - Original Version + * @history 2016-12-06 Jesse Mapel - Updated documentation. References #4558. + */ +class MeasurePoint { + public: + + /** + * Constructs an empty MeasurePoint. + */ + MeasurePoint() : m_data( new ControlMeasureData() ) { } + + + /** + * Constructs a MeasurePoint from a measure. + * + * @param measure The measure that the MeasurePoint represents. + * @param weight The weight of the MeasurePoint in the + */ + MeasurePoint(ControlMeasure *measure, const double &weight = 1.0) : + m_data(new ControlMeasureData(measure, weight) ) { + m_data->m_isvalid = validMeasure(); + } + + + /** + * Destroys a MeasurePoint. + */ + virtual ~MeasurePoint() { } + + + /** + * Determines if the MeasurePoint's parent control point is valid. + * + * @return @b bool If the measure's parent control point is valid. + */ + inline bool validPoint() const { + ControlMeasure *m = m_data->m_measure; + BOOST_ASSERT ( m != 0 ); + ControlPoint *p = m->Parent(); + BOOST_ASSERT ( p != 0 ); + return (!(p->IsIgnored() || p->IsRejected() || p->IsEditLocked() || p->IsInvalid()) ); + } + + + /** + * If the MeasurePoint and parent control point are valid. + * + * @return @b bool If the MeasurePoint and parent control point are both valid. + */ + inline bool isValid() const { + return ( m_data->m_isvalid && validPoint() ); + } + + + /** + * Flags the MeasurePoint as invalid. + */ + inline void disable() { + m_data->m_isvalid = false; + return; + } + + + /** + * Returns the size of the MeasurePoint. + * + * @return @b int Always one. + */ + inline int size() const { + return ( 1 ); + } + + + /** + * Returns the measure's point ID + * + * @return @b QString The point ID of the measure's parent control point. + */ + inline QString id() const { + return ( m_data->m_measure->GetPointId() ); + } + + + /** + * Returns the MeasurePoint's measure. + * + * @return @b ControlMeasure* A pointer to the contained measure. + */ + inline const ControlMeasure *data() const { + return ( m_data->m_measure ); + } + + + /** + * Returns the parent control point. + * + * @return @b ControlPoint* A pointer to the parent control point. + */ + inline ControlPoint *getPoint() const { + return ( m_data->m_measure->Parent() ); + } + + + /** + * Returns the serial number of the cube the measure is on. + * + * @return @b QString The serial number of the cube the measure is on. + */ + inline QString getSerialNumber() const { + return ( m_data->m_measure->GetCubeSerialNumber() ); + } + + + /** + * Returns the MeasurePoint's x coordinate. + * + * @return @b double the MeasurePoint's x coordinate. + */ + inline double x() const { + return ( m_data->m_xyz[0] ); + } + + + /** + * Returns the MeasurePoint's y coordinate. + * + * @return @b double the MeasurePoint's y coordinate. + */ + inline double y() const { + return ( m_data->m_xyz[1] ); + } + + + /** + * Returns the MeasurePoint's z coordinate. + * + * @return @b double the MeasurePoint's z coordinate. + */ + inline double z() const { + return ( m_data->m_xyz[2] ); + } + + + /** + * Returns the MeasurePoint's weight. + * + * @return @b double the MeasurePoint's weight. + */ + inline double w() const { + return ( m_data->m_xyz[3] ); + } + + + /** + * Returns the coordinates and weight of the MeasurePoint. + * + * @return @b double* A pointer to an array containing (in order) + * the x, y, z, and weight of the MeasurePoint. + */ + inline const double *array() const { + return ( m_data->m_xyz ); + } + + + /** + * Determines if the measures contained by this MeasurePoint and + * another MeasurePoint are the same. + * + * @param other The MeasurePoint to compare against. + * + * @return @b bool If the measures are the same. + */ + inline bool operator==(const MeasurePoint &other) const { + return ( m_data->m_measure == other.m_data->m_measure); + } + + + /** + * Determines if the measures contained by this MeasurePoint and + * another MeasurePoint are not the same. + * + * @param other The MeasurePoint to compare against. + * + * @return @b bool If the measures are not the same. + */ + inline bool operator!=(const MeasurePoint &other) const { + return ( m_data->m_measure != other.m_data->m_measure ); + } + + private: + + /** + * Data wrapper class for ControlMeasures. + * + * @see QSharedData + * + * @author 2015-10-11 Kris Becker + * + * @internal + * @history 2015-10-11 Kris Becker - Original Version + * @history 2016-12-06 Jesse Mapel - Updated documentation. References #4558. + */ + class ControlMeasureData : public QSharedData { + public: + + /** + * Constructs and empty ControlMeasureData. + */ + ControlMeasureData() : QSharedData(), m_measure(0), + m_weight(1.0), m_xyz(), m_isvalid(false) { + getImageCoordinates(); + } + + + /** + * Constructs a ControlMeasureData from a measure. + * + * @param measure The ControlMeasure to wrap. + * @param weight The weight for the measure. Defaults to 1.0. + */ + ControlMeasureData(ControlMeasure *measure, const double &weight = 1.0) : + QSharedData(), m_measure(measure), m_weight(weight), + m_xyz(), m_isvalid(false) { + getImageCoordinates(); + } + + + /** + * Destroys a ControlMeasureData. + */ + ~ControlMeasureData() { } + + + /** + * Retrives and stores the coordinates and weights from the wrapped measure. + * If the measure has not been set, then all values are set to 0.0. + */ + inline void getImageCoordinates() { + + if ( !m_measure ) { + m_xyz[0] = 0.0; + m_xyz[1] = 0.0; + m_xyz[2] = 0.0; + m_xyz[3] = 0.0; + } + else { + // ControlMeasure *refm = m_point->GetRefMeasure(); + m_xyz[0] = m_measure->GetSample(); + m_xyz[1] = m_measure->GetLine(); + m_xyz[2] = 0.0; + m_xyz[3] = m_weight; + } + return; + } + + ControlMeasure *m_measure; //!< Wrapped ControlMeasure + double m_weight; //!< The measure's weight. + double m_xyz[4]; /**!< The x, y, z, and weight for the measure. + The x and y coordinates are the sample and + line coordinates of the wrapped measure.*/ + bool m_isvalid; //!< If the data is valid. + }; + + QExplicitlySharedDataPointer m_data; /**!< The internal data containing + a pointer to the measure along + with its coordinates and + weight.*/ + + + /** + * Returns if the internal measure is valid. + * + * @return @b bool If the internal measure is valid. + */ + inline bool validMeasure() const { + ControlMeasure *m = m_data->m_measure; + BOOST_ASSERT ( m != 0 ); + return (!(m->IsIgnored() || m->IsRejected()) ); + } + +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/cnetcombinept/PointCloud.h b/isis/src/control/apps/cnetcombinept/PointCloud.h index 3f94f8a738a9a298e5593aae88da72d32cd17905..77a1fbb8d7c05c66a512fbc3ba5630283b41d652 100644 --- a/isis/src/control/apps/cnetcombinept/PointCloud.h +++ b/isis/src/control/apps/cnetcombinept/PointCloud.h @@ -27,64 +27,65 @@ namespace Isis { -/** - * Functor to compute 3-d Euclidean distances - * - * @author 2014-02-17 Kris Becker - * - * @internal - * @history 2014-02-17 Kris Becker - Original Version - * - */ -template class Dist3d { -public: - enum { Dimension = 3 }; - Dist3d() { } - ~Dist3d() { } - - inline int dimension() const { - return ( Dimension ); - } - - inline double operator()(const T &datum1, const T &datum2) const { - double dx = datum1.x() - datum2.x(); - double dy = datum1.y() - datum2.y(); - double dz = datum1.z() - datum2.z(); - return ( dx*dx + dy*dy + dz*dz ); - } - - inline double operator()(const double *datum1, const T &datum2) const { - double dx = datum1[0] - datum2.x(); - double dy = datum1[1] - datum2.y(); - double dz = datum1[2] - datum2.z(); - return ( dx*dx + dy*dy + dz*dz ); - } -}; - /** * Functor to compute 2-d Euclidean distances * * @author 2014-02-17 Kris Becker * * @internal - * @history 2014-02-17 Kris Becker - Original Version + * @history 2014-02-17 Kris Becker - Original Version + * @history 2016-12-06 Jesse Mapel - Updated documentation. References #4558. */ template class Dist2d { public: - enum { Dimension = 2 }; + enum { Dimension = 2 //!< The dimension of the distance metric. + }; + + /** + * Constructs a Dist2d functor. + */ Dist2d() { } + + + /** + * Destroys a Dist2d functor. + */ ~Dist2d() { } + + /** + * Returns the dimension of the distance metric. + * + * @return @b int Always 2. + */ inline int dimension() const { return ( Dimension ); } + + /** + * Computes the two dimensional distance between two points. + * + * @param datum1 The first point + * @param datum2 The second point + * + * @return @b double The distance between the two points. + */ inline double operator()(const T &datum1, const T &datum2) const { double dx = datum1.x() - datum2.x(); double dy = datum1.y() - datum2.y(); return ( dx*dx + dy*dy ); } + + /** + * Computes the two dimensional distance between two points. + * + * @param datum1 The first point as a double array + * @param datum2 The second point + * + * @return @b double The distance between the two points. + */ inline double operator()(const double *datum1, const T &datum2) const { double dx = datum1[0] - datum2.x(); double dy = datum1[1] - datum2.y(); @@ -92,36 +93,6 @@ public: } }; -/** - * Functor to compute 1-d Manhattan distances - * - * @author 2014-02-17 Kris Becker - * - * @internal - * @history 2014-02-17 Kris Becker - Original Version - */ -template class Dist1d { -public: - enum { Dimension = 1 }; - Dist1d() { } - ~Dist1d() { } - - inline int dimension() const { - return ( Dimension ); - } - - - inline double operator()(const T &datum1, const T &datum2) const { - double dx = datum1.x() - datum2.x(); - return ( dx*dx ); - } - - inline double operator()(const double *datum1, const T &datum2) const { - double dx = datum1[0] - datum2.x(); - return ( dx*dx ); - } -}; - /** * @brief Point cloud adapter class for nanoflann kd-tree interface @@ -136,12 +107,12 @@ public: * In addition, this class accesses individual points from PointCloud using a * vector component operator so as to standardize and complete this interface: * - * @code + * @code * double x() const; // X component of point * double y() const; // Y component of point * double z() const; // Z component of point * double w() const; // Optional weight of point (default should be 1.0) - * @endcode + * @endcode * * The point container is required to not change its content for the duration * of use of the nanoflann kd-tree built from the points. Because of this, @@ -172,43 +143,135 @@ public: * @internal * @history 2014-02-17 Kris Becker - Original Version */ -template > class PointCloud { +template class PointCloud { public: - PointCloud() : m_points() { } - PointCloud(const int &npoints) : m_points() { + + /** + * Constructs a default PointCloud. + */ + PointCloud() : m_id("PointCloud"), m_points(), m_distance() { } + + + /** + * Constructs a PointCloud with a given ID. + * + * @param id The ID of the PointCloud. + */ + explicit PointCloud(const QString &id) : m_id(id), m_points(), m_distance() { } + + + /** + * Constructs a PointCloud with a given ID and + * space for a given number of points reserved. + * + * @param npoints The number of points to reserve space for. + * @param id The ID of the PointCloud. Defaults to "PointCloud". + */ + PointCloud(const int &npoints, const QString &id = "PointCloud") : + m_id(id), m_points(), m_distance() { m_points.reserve(npoints); } - PointCloud(const QVector &points) : m_points(points) { } + + /** + * Constructs a PointCloud with a given ID and set of points. + * + * @param points The set of points to add to the PointCloud. + * @param id The ID of the PointCloud. Defaults to "PointCloud". + */ + PointCloud(const QVector &points, const QString &id = "PointCloud") : + m_id(id), m_points(points), m_distance() { } + + + /** + * Constructs a PointCloud with a given ID and set measures. + * The measures will be used to construct the internal set of points. + * + * @param points The set of measures to add to the PointCloud. + * @param id The ID of the PointCloud. Defaults to "PointCloud". + */ + PointCloud(const QList &points, + const QString &id = "PointCloud") : + m_id(id), m_points(), m_distance() { + for (int i = 0 ; i < points.size() ; i++ ) { + m_points.push_back( T(points[i]) ); + } + } + + + /** + * Desctroys the PointCloud. + */ virtual ~PointCloud() { } - /** Standard size method */ + /** + * Returns the size of the PointCloud. + * + * @return @b int The number of points in the PointCloud. + */ inline int size() const { return ( m_points.size() ); } - /** Add a new point to the list */ + + /** + * Returns the PointCloud's ID. + * + * @return @b QString The PointCloud's ID. + */ + inline QString identifier() const { + return (m_id); + } + + + /** + * Adds a new point to the list + * + * @param point The point to add. + */ inline void addPoint(const T &point) { m_points.push_back(point); } - /** Return a reference to the point at index idx */ + + /** + * Return a reference to the point at a given index. + * + * @param idx The index of the point to return. + * + * @return @b T& A constant reference to the point. + */ inline const T &point(const size_t idx) const { Q_ASSERT( idx >= 0 ); Q_ASSERT( idx < (size_t) size() ); return (m_points[idx]); } + + /** + * Returns the Euclidean distance between two points. + * + * @param first The first point. + * @param second The second point. + * + * @return @b double The squared Euclidean distance between first and second. + */ inline double distance( const T &first, const T &second ) const { return ( m_distance(first, second) ); } - /** Return number of points in cloud */ + + /** + * Returns the number of points in the PointCloud. + * + * @return @b size_t The number of points in the PointCloud. + */ inline size_t kdtree_get_point_count() const { return ( m_points.size() ); } + /** * @brief Return Euclidean distance from a source point to the indexed point * @@ -221,7 +284,7 @@ template > class PointCloud { * @param p1 3-vector of the source point * @param idx_p2 Index into point data set contained herein * - * @return double Returns the squared distance - not the square root! + * @return @b double Returns the squared distance - not the square root! */ inline double kdtree_distance(const double *p1, const size_t idx_p2, size_t p_size) const { @@ -230,6 +293,7 @@ template > class PointCloud { return ( m_distance(p1, point(idx_p2)) ); } + /** * @brief Returns a value for a single dimemsion of a vector * @@ -241,7 +305,7 @@ template > class PointCloud { * @param idx Index of the point to get element from * @param dim The index (0 - 2)of the ith element of the vector * - * @return double Value at the specfied vector point index + * @return @b double Value at the specfied vector point index */ inline double kdtree_get_pt(const size_t idx, int dim) const { if ( dim == 0 ) return ( point(idx).x() ); @@ -249,6 +313,7 @@ template > class PointCloud { return ( point(idx).z() ); } + /** * Let nanoflann range algorithm compute the bounding box * @@ -262,8 +327,10 @@ template > class PointCloud { } private: - QVector m_points; ///!< points in the point cloud - Distance m_distance; ///!< Instantiation of distance functor + + QString m_id; ////! Identifier. + QVector m_points; ///!< Points in the point cloud. + Dist2d m_distance; ///!< Instantiation of distance functor. }; diff --git a/isis/src/control/apps/cnetcombinept/PointCloudSearchResult.h b/isis/src/control/apps/cnetcombinept/PointCloudSearchResult.h deleted file mode 100644 index be2ad2c40a84ef7de87df4c65e45ded3d27aca78..0000000000000000000000000000000000000000 --- a/isis/src/control/apps/cnetcombinept/PointCloudSearchResult.h +++ /dev/null @@ -1,182 +0,0 @@ -#ifndef PointCloudSearchResult_h -#define PointCloudSearchResult_h -/** - * @file - * $Revision: 1.0 $ - * $Date: 2014/02/27 18:49:25 $ - * - * Unless noted otherwise, the portions of Isis written by the USGS are public - * domain. See individual third-party library and package descriptions for - * intellectual property information,user agreements, and related information. - * - * Although Isis has been used by the USGS, no warranty, expressed or implied, - * is made by the USGS as to the accuracy and functioning of such software - * and related material nor shall the fact of distribution constitute any such - * warranty, and no responsibility is assumed by the USGS in connection - * therewith. - * - * For additional information, launch - * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see - * the Privacy & Disclaimers page on the Isis website, - * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on - * http://www.usgs.gov/privacy.html. - */ - -#include -#include -#include - -namespace Isis { - -template class PointCloud; - -/** - * @brief Point cloud query result container - * - * This class provides a convenient and efficent implementation to contain the - * results of a PointCloudTree search result. - * - * Contained in this object is all the ControlPoints resulting from a radial or - * neighbor proximity search. - * - * It is up to the calling enviroment to use the results whilst preserving the - * content of the PointCloud elements as they are provided via a reference into - * the original point cloud. - * - * Care is taken to filter out the source, as it will likely be included in - * every search query, and any invalid points since the status of the points - * could change during processing. - * - * For any type T, here are only two required methods - and operator!=() and an - * isValid() method. Well I suppose the only other required is a default - * constructor as well. - * - * @author 2015-10-11 Kris Becker - * - * @internal - * @history 2015-10-11 Kris Becker - Original Version - */ - -template -class PointCloudSearchResult { - public: - enum SearchType { UnDefined, Radius, NearestNeighbor }; - PointCloudSearchResult() { - m_search_type = UnDefined; - m_source = T(); - m_neighbors = 0; - m_search_radius = 0.0; - m_matches.clear(); - m_pc = QSharedPointer (0); - } - - PointCloudSearchResult(const T &source, int neighbors, - QVector &indices, QVector &distances, - QSharedPointer > &pc) { - Q_ASSERT ( indices.size() == distances.size() ); - Q_ASSERT ( neighbors == indices.size() ); - - m_search_type = NearestNeighbor; - m_source = source; - m_neighbors = neighbors; - m_search_radius = 0.0; - m_pc = pc; - for (int i = 0 ; i < indices.size() ; i++ ) { - T &p = m_pc->point(indices[i]); - if ( m_source != p) { - if ( p.isValid() ) { - m_matches.push_back(qMakePair(p, std::sqrt(distances[i]))); - } - } - } - } - - PointCloudSearchResult(const T &source, const double radius_sq, - std::vector< std::pair > &matches, - const QSharedPointer > &pc, - const int nfound = 0) { - m_search_type = Radius; - m_source = source; - m_neighbors = nfound; - m_search_radius = std::sqrt(radius_sq); - m_pc = pc; - for (unsigned int i = 0 ; i < matches.size() ; i++ ) { - const T &p = m_pc->point(matches[i].first); - if ( m_source != p) { - if ( p.isValid() ) { - m_matches.push_back(qMakePair(p, std::sqrt(matches[i].second))); - } - } - } - } - - virtual ~PointCloudSearchResult() { } - - inline bool isValid() const { - return ( !(UnDefined == m_search_type) ); - } - - inline SearchType type() const { - return ( m_search_type ); - } - - /** Return number of points from the cloud search */ - inline int size() const { - return ( m_matches.size() ); - } - - inline double search_radius() const { - return ( m_search_radius ); - } - - inline double neighbors() const { - return ( m_neighbors ); - } - - inline const T &source() const { - return ( m_source ); - } - - inline const T &point(const size_t idx) const { - // Fetch the point from the PointCloud - return ( m_pc->point(m_matches[idx].first) ); - } - - /** Return search distance in search units */ - inline double distance(const size_t idx) const { - return ( m_matches[idx].second ); - } - - /** - * - * @param process - * - * @return @b int - * - * @author 2015-10-11 Kris Becker - * @internal - * @history 2015-10-11 Kris Becker - Original version. - */ - template int forEachPair( P &process ) { - int npairs( 0 ); - for ( int m = 0 ; m < m_matches.size() ; m++) { - process.apply(m_source, m_matches[m].first, m_matches[m].second); - npairs++; - } - return ( npairs ); - } - - - private: - SearchType m_search_type; - T m_source; - int m_neighbors; - double m_search_radius; - - QVector< QPair > m_matches; - QSharedPointer > m_pc; - -}; - -}; // namespace Isis -#endif diff --git a/isis/src/control/apps/cnetcombinept/PointCloudTree.h b/isis/src/control/apps/cnetcombinept/PointCloudTree.h index 0f311d6aa80573cf3a75bef83e2c2eb1ec0ceaed..4fdb116b26b4a6076e7c3bcb75cb2eef0cdabcdb 100644 --- a/isis/src/control/apps/cnetcombinept/PointCloudTree.h +++ b/isis/src/control/apps/cnetcombinept/PointCloudTree.h @@ -31,7 +31,6 @@ #include #include "PointCloud.h" -#include "PointCloudSearchResult.h" namespace Isis { @@ -71,10 +70,11 @@ namespace Isis { * @author 2014-02-17 Kris Becker * * @internal - * @history 2014-02-17 Kris Becker - Original Version + * @history 2014-02-17 Kris Becker - Original Version + * @history 2016-12-06 Jesse Mapel - Updated documentation. References #4558. */ -template class PointCloudTree { +template class PointCloudTree { private: // Declaration of the Nanoflann interface for our PointCloud. Note the @@ -82,10 +82,11 @@ template class PointCloudTree { // function type so the dimensionality of the distance can be // specified at compile time typedef nanoflann::KDTreeSingleIndexAdaptor< - nanoflann::L2_Simple_Adaptor >, - PointCloud, D::Dimension > PcKdTree_t; + nanoflann::L2_Simple_Adaptor >, + PointCloud, 2 > PcKdTree_t; public: + /** * @brief Constructor of PointCloudTree for the kd-tree point representaion * @@ -102,42 +103,80 @@ template class PointCloudTree { * * @param pc Pointer to PointCloud to build the kd-tree from. This * object takes complete ownership of the PointCloud pointer. - * @param leafNodes Maximum number of leaves stored at each kd-tree node + * @param leafNodes Maximum number of leaves stored at each kd-tree node. + * Defaults to 10 leaves. */ - PointCloudTree(PointCloud *pc, const int &leafNodes = 10) : m_pc(pc), - m_kd_index(D::Dimension, *pc, nanoflann::KDTreeSingleIndexAdaptorParams(leafNodes)) { + PointCloudTree(PointCloud *pc, const int &leafNodes = 10) : m_pc(pc), + m_kd_index(2, *pc, nanoflann::KDTreeSingleIndexAdaptorParams(leafNodes)) { m_kd_index.buildIndex(); } - /** Destructor */ + + /** + * Destroys a PointCloudTree. + */ virtual ~PointCloudTree() { } - /** Perform radius query for points in kilometer units */ - PointCloudSearchResult radius_query(const T &point, - const double &radius_sq) { + + /** + * Performs a radius query for points in kilometer units. + * + * @param point The point to search around. + * @param radius_sq The square of the radius to search around point. + * + * @return @b QList A list of all the points within the radius. + */ + QList radius_query(const T &point, const double &radius_sq) { std::vector > matches; - int n = m_kd_index.radiusSearch(point.array(), radius_sq, matches, - nanoflann::SearchParams()); - return (PointCloudSearchResult(point, radius_sq, matches, m_pc, n)); + (void) m_kd_index.radiusSearch(point.array(), radius_sq, matches, + nanoflann::SearchParams()); + + QList points; + for ( int i = 0 ; i < (int) matches.size() ; i++ ) { + points.push_back( m_pc->point(matches[i].first) ); + } + + return (points); } - /** Perform nearest set of points from its neighbors */ - PointCloudSearchResult neighbor_query(const T &point, - const int &neighbors) { + + /** + * Performs a query for the nearest neighbors to a point. + * + * @param point The point to find neighbors around. + * @param neighbors The number of neighbors to find. + * + * @return @b QList A list of the neighbors. + */ + QList neighbor_query(const T &point, const int &neighbors) { QVector indices(neighbors); QVector distances(neighbors); m_kd_index.knnSearch(point.array(), neighbors, indices.data(), distances.data()); - return (PointCloudSearchResult(point, neighbors, indices, distances)); + + QList points; + for ( int i = 0 ; i < indices.size() ; i++ ) { + points.push_back( m_pc->point(indices[i]) ); + + } + + return (points); } - /** Returns a reference to the point cloud */ - inline const PointCloud &cloud() const { return ( *m_pc ); } + + /** + * Returns a reference to the point cloud. + * + * @return @b A PointCloud& A constant reference to the point cloud. + */ + inline const PointCloud &cloud() const { + return ( *m_pc ); + } private: - QSharedPointer > m_pc; - PcKdTree_t m_kd_index; + QSharedPointer > m_pc; //!< The point cloud. + PcKdTree_t m_kd_index; //!< The kd-tree. }; diff --git a/isis/src/control/apps/cnetcombinept/cnetcombinept.cpp b/isis/src/control/apps/cnetcombinept/cnetcombinept.cpp index 57cba74e9474ea0d4dc77c385892dcb2665588da..1d9c4007867fce8e1c1cf36a83425c4a20b3a136 100644 --- a/isis/src/control/apps/cnetcombinept/cnetcombinept.cpp +++ b/isis/src/control/apps/cnetcombinept/cnetcombinept.cpp @@ -7,11 +7,12 @@ // boost library #include +#include #include "nanoflann/nanoflann.hpp" #include "ControlNet.h" -#include "ControlPointCloudPt.h" +#include "MeasurePoint.h" #include "ControlPointMerger.h" #include "FileList.h" #include "FileName.h" @@ -28,32 +29,39 @@ using namespace std; using namespace Isis; -/** Format an incoming 3-point vector to a string */ -inline QString formatVector(const double *v, const QString &sep = "") { - QString s(sep); - QString data; - for ( int i = 0 ; i < 3 ; i++) { - data += (s + QString::number(v[i])); - s = ","; - } - return (data); + + +/** Check point for validity */ +inline bool isValid(const ControlPoint *point ) { + if ( !point ) { return ( false ); } + return ( !(point->IsIgnored() || point->IsInvalid() || point->IsRejected()) ); +} + + +/** Check point for merging worthiness */ +inline bool isWorthy(const ControlPoint *point ) { + if ( !point ) { return ( false ); } + return ( isValid(point) && !point->IsEditLocked() ); +} + +/** Check measure for validity */ +inline bool isValid(const ControlMeasure *m) { + return ( !( m->IsIgnored() || m->IsRejected() ) ); } // Control network manager typedef QList > ControlNetList; -// ControlNet point cloud types. Dist3d distance works for all types. -typedef ControlPointCloudPt PointType; -typedef Dist3d DistanceType; - -typedef PointCloud CNetPointCloud; -typedef PointCloudTree CNetPointCloudTree; -typedef PointCloudSearchResult ResultType; +// ControlNet point cloud types. +typedef MeasurePoint PointType; +typedef PointCloud CNetPointCloud; +typedef PointCloudTree CNetPointCloudTree; +typedef QSharedPointer CubeMeasureTree; void IsisMain() { // We will be processing by line - ProcessByLine p; + ProcessByLine pbl; UserInterface &ui = Application::GetUserInterface(); QStringList cnetfiles; @@ -78,6 +86,7 @@ void IsisMain() { mess += "] is empty."; throw IException(IException::User, mess, _FILEINFO_); } + BOOST_FOREACH ( FileName cfile, list_o_nets ) { cnetfiles.append( cfile.original() ); nList++; @@ -91,43 +100,33 @@ void IsisMain() { throw IException(IException::User, mess, _FILEINFO_); } - // Ok, if we end up with one net, it must be entered in CNETBASE. - if ( (cnetfiles.size() == 1) && (1 != nBase) ) { - QString mess = "It appears you are attempting to merge points from a " - "single network, which is fine, but it must be specified " - "in CNETBASE. Try again if that is your intent!"; - throw IException(IException::User, mess, _FILEINFO_); - } - - // Now establish the type of processing mode we are dealing with. Can be - // IMAGE or GROUND. - QString cmode = ui.GetString("MODE").toLower(); - ControlPointCloudPt::CoordinateType ctype = ( "image" == cmode) ? - ControlPointCloudPt::Image : - ControlPointCloudPt::Ground ; - - // If image node is requested, get the image to use as a reference - QString serialno; - if ( "image" == cmode ) { - if ( ui.WasEntered("REFERENCE")) { - serialno = SerialNumber::Compose(ui.GetAsString("REFERENCE")); - } - } - - // Create the point cloud container and load the control networks - QScopedPointer cloud(new CNetPointCloud()); - // ControlNetList cnetlist; + //--------------------------------------------------------------------------- + // Load all the input control networks + //--------------------------------------------------------------------------- + Progress progress; + progress.SetText("Loading"); + progress.SetMaximumSteps(cnetfiles.size() ); + progress.CheckStatus(); // Collect some stuff from input nets for the output net QString netid; QString target; QString description; QVector radii; + BigInt allPoints(0); + BigInt validPoints(0); + QHash > cube_measures; + QList all_points; + BOOST_FOREACH ( QString cfile, cnetfiles ) { +#if defined(DEBUG) std::cout << "\nLoading " << cfile << "...\n"; - Progress c_progress; - QScopedPointer cnet( new ControlNet(cfile, &c_progress) ); + Progress cnet_progress; + QScopedPointer cnet( new ControlNet(cfile, &cnet_progress) ); +#else + QScopedPointer cnet( new ControlNet(cfile) ); +#endif if ( netid.isEmpty() ) { netid = cnet->GetNetworkId(); } @@ -141,176 +140,284 @@ void IsisMain() { radii = QVector::fromStdVector(cnet->GetTargetRadii()); } - // Get all control points by taking ownership from the control net - int npoints(0); - QList points = cnet->take(); - BOOST_FOREACH ( ControlPoint *point, points) { - ControlPointCloudPt cpt(point, ctype, ControlPointCloudPt::Exclusive, serialno); - if ( cpt.isValid() ) { - cloud->addPoint(cpt); - npoints++; + // Now get list of all cube serials and add all to list + QList serials = cnet->GetCubeSerials(); + BOOST_FOREACH ( QString sn, serials) { + QList measures = cnet->GetMeasuresInCube(sn); + BOOST_ASSERT( measures.size() > 0 ); + + // Eliminate ignored measures (and its assocaited point) + QList goods; + BOOST_FOREACH (ControlMeasure *m, measures ) { + if ( isValid(m) ) { + ControlPoint *point = m->Parent(); + if ( isWorthy(point) ) { + goods.append(m); + } + } + } + + // Now insert valid measures associated with serial (cube) if we have any + if ( goods.size() > 0 ) { + cube_measures[sn].append(goods); + allPoints += goods.size(); // Measures count } } - std::cout << "Added " << npoints << " of " << points.size() << "\n"; - allPoints += points.size(); - // Instead of having to save the ControlNet instances, we take ownership - // of all the points from ControlNet and turn it over to the cloud... - // - // cnetlist.append( QSharedPointer ( cnet.take() ) ); + // Take ownership of all points and let the cnet file close + validPoints += cnet->GetNumValidPoints(); + all_points.append( cnet->take() ); + progress.CheckStatus(); } - std::cout << "\nTotal " << cloud->size() << " of " << allPoints << "\n"; - // Set up conditions for search - double image_tolerance = ui.GetDouble("IMAGETOL"); - double ground_tolerance = ui.GetDouble("GROUNDTOL"); - double search_distance = ui.GetDouble("DISTANCE"); - double search_radius_sq = search_distance * search_distance; + // Report status of network + int cube_measures_size = cube_measures.size(); + std::cout << "\nTotal Points: " << all_points.size() << "\n"; + std::cout << "Valid Points: " << validPoints << "\n"; + std::cout << "Total Measures: " << allPoints << "\n"; + std::cout << "Total Cubes: " << cube_measures_size << "\n\n"; + + // Now write out the list of SNs if requested + if ( ui.WasEntered("TOSN") ) { + + FileName filename( ui.GetFileName("TOSN") ); + QFile logfile(filename.expanded()); + if ( !logfile.open(QIODevice::WriteOnly | QIODevice::Truncate | + QIODevice::Text | QIODevice::Unbuffered) ) { + QString mess = "Unable to open/create serial number file " + filename.name(); + throw IException(IException::User, mess, _FILEINFO_); + } - std::cout << "\nCreating cloud kd-tree..\n"; + QTextStream lout(&logfile); + QHashIterator > sns(cube_measures); + while ( sns.hasNext() ) { + sns.next(); + lout << sns.key() << "\n"; + } + + logfile.close(); + } + + + //--------------------------------------------------------------------------- + // Construct the kd-trees that assocate all the measures with points for + // each cube. + //--------------------------------------------------------------------------- + progress.SetText("making trees"); + progress.SetMaximumSteps( cube_measures.size() ); + progress.CheckStatus(); + + // Create the kd-tree lookup for each measure in each cube + QHash measure_clouds; + QHashIterator > sn_m(cube_measures); int kd_nodes = ui.GetInteger("KDNODES"); - CNetPointCloudTree cloud_t( cloud.take(), kd_nodes ); + while ( sn_m.hasNext() ) { + sn_m.next(); - // Get the cloud back to use in subsequent processing - const CNetPointCloud &v_cloud = cloud_t.cloud(); - Progress progress; + // Generate a kd-tree for all measures in each cube for distance comparisons + QScopedPointer cloud(new CNetPointCloud(sn_m.value(), sn_m.key())); + CubeMeasureTree cloud_t(new CNetPointCloudTree(cloud.take(), kd_nodes ) ); + measure_clouds.insert(sn_m.key(), cloud_t); + + progress.CheckStatus(); + } + + // Retain for future reference. We intend to release the trees when we are + // done with them as we may need the memory. + // int measure_clouds_size = measure_clouds.size(); + + //--------------------------------------------------------------------------- + // Now perform the merge. Iterate through all points evaluating each + // measure to see if same measure exists in any other point within + // the IMAGETOL limit. + //--------------------------------------------------------------------------- progress.SetText("merging"); - progress.SetMaximumSteps( v_cloud.size() ); + progress.SetMaximumSteps( all_points.size() ); progress.CheckStatus(); + // Measure distance tolerance + double image_tolerance = ui.GetDouble("IMAGETOL"); + double search_radius_sq = image_tolerance * image_tolerance; // Run through all valid points. Note they may be invalided as processing - // is done through mergers, so validity must be checked!!! + // is done through mergers, so validity must be checked at each point. BigInt nfound(0); BigInt nMerged(0); - for (int n = 0 ; n < v_cloud.size() ; n++) { - const ControlPointCloudPt &point = v_cloud.point(n); - if ( point.isValid() ) { - ResultType results = cloud_t.radius_query(point, search_radius_sq); - nfound += results.size(); - ControlPointMerger merger(image_tolerance, ground_tolerance); - results.forEachPair(merger); - nMerged += merger.merge(); + BOOST_FOREACH ( ControlPoint *point, all_points ) { + // Don't consider ignored or edit locked points + if ( isWorthy( point ) ) { + + // Get all valid measures only in the point + QList v_measures = point->getMeasures( true ); + + int p_merged(0); + BOOST_FOREACH ( ControlMeasure *v_m, v_measures ) { + PointType m_p(v_m); // This associates the measure to its point + if ( m_p.isValid() ) { // Valid point? If not, its likely merged already + CubeMeasureTree m_cloud = measure_clouds[v_m->GetCubeSerialNumber()]; + BOOST_ASSERT( m_cloud != 0 ); + QList m_points = m_cloud->radius_query(m_p, search_radius_sq); + ControlPointMerger merger(image_tolerance); + p_merged += merger.apply(point, m_points); + nfound += merger.size(); + } + } + nMerged += p_merged; } progress.CheckStatus(); } - // Now check all remaining points by ignoring all points with less than - // MINMEASURES. - BigInt nMinMeasures(0); - bool setaprioribest = ui.GetBoolean("SETAPRIORIBEST"); - QString rejectedmeasures = ui.GetString("REJECTEDMEASURES").toLower(); - bool ignoreRejected = ( "ignore" == rejectedmeasures); - bool removeRejected = ( "remove" == rejectedmeasures); + // All done with the heavy lifting, so free resources as memory may be + // needed later. + cube_measures.clear(); + measure_clouds.clear(); + + //--------------------------------------------------------------------------- + // Screen the control points for reduction of content in the output network + // file but don't create it in this loop - its very expensive. + //--------------------------------------------------------------------------- + progress.SetText("screening/cleaning/building network"); + progress.SetMaximumSteps( all_points.size() ); + progress.CheckStatus(); + // User options + bool cleannet = ui.GetBoolean("CLEANNET"); + bool cleanmeasures = ui.GetBoolean("CLEANMEASURES"); int minmeasures = ui.GetInteger("MINMEASURES"); - bool savemins = ui.GetBoolean("SAVEMINS"); - // Now create the output control network - BigInt oPoints(0); - BigInt nRejected(0); + // Set up control net here so we can complete all processing in this step + QScopedPointer cnet; + if ( ui.WasEntered("ONET") ) { + // std::cout << "\nWriting network...\n"; + // Set up the output control network + cnet.reset( new ControlNet() ); + if ( ui.WasEntered("NETWORKID") ) { + netid = ui.GetString("NETWORKID"); + } - ControlNet cnet; - if ( ui.WasEntered("NETWORKID") ) { - netid = ui.GetString("NETWORKID"); - } + cnet->SetNetworkId(netid); + cnet->SetUserName(Application::UserName()); - cnet.SetNetworkId(netid); - cnet.SetUserName(Application::UserName()); + if ( ui.WasEntered("DESCRIPTION") ) { + description = ui.GetString("DESCRIPTION"); + } - if ( ui.WasEntered("DESCRIPTION") ) { - description = ui.GetString("DESCRIPTION"); + cnet->SetDescription(description); + cnet->SetCreatedDate(Application::DateTime()); + cnet->SetTarget(target, radii); +#if defined(HAS_WRITE_ONLY_OPTION) + cnet->setWriteOnly(); +#endif } - cnet.SetDescription(description); - cnet.SetCreatedDate(Application::DateTime()); - cnet.SetTarget(target, radii); + // Check to see if we want to reset the apriori surface to the best + // available measure in the point + bool setaprioribest = ui.GetBoolean("SETAPRIORIBEST"); - // Gotta transfer all points/measures - for ( int i = 0 ; i < v_cloud.size() ; i++) { - ControlPointCloudPt point = v_cloud.point(i); + BigInt oPoints(0); + BigInt nRemoved(0); + BigInt nMinMeasures(0); + BigInt vPoints(0); + QHash pointIds; // To protect against redundant point ids + for ( int i = 0 ; i < all_points.size() ; i++) { + + ControlPoint *m_p = all_points[i]; + + // Check for redunant point id here + QString pid = m_p->GetId(); + if ( pointIds.contains( pid ) ) { + int pcount = pointIds.value(pid); + QString id = pid + "_" + QString::number(pcount); + m_p->SetId(id); + pointIds[pid] = ++pcount; + } + else { + pointIds.insert(pid, 1); + } - if ( point.isValid() ) { + if ( isValid(m_p) ) { + vPoints++; - // Set up a reference for convenience - ControlPoint &cp = point.getPoint(); - // Processes measures if requested - if ( true == removeRejected ) { - - QList measures = cp.getMeasures( false ); - ControlMeasure *refm = cp.GetRefMeasure(); - bool removedRef = ( 0 == refm ) ? true : false; + if ( true == cleanmeasures ) { + QList measures = m_p->getMeasures( false ); BOOST_FOREACH ( ControlMeasure *m, measures) { - if ( m->IsRejected() ) { - if ( (0 != refm) && (*m == *refm)) { - removedRef = true; - refm = 0; - } - cp.Delete(m); - nRejected++; - } - } - - // If we removed the reference, simply set to the first measure - if ( removedRef && (cp.GetNumValidMeasures() > 0 ) ) { - cp.SetRefMeasure(0); - } - } - // Set rejected points to ignore - else if ( true == ignoreRejected ) { - QList measures = cp.getMeasures( false ); - BOOST_FOREACH ( ControlMeasure *m, measures) { - if ( m->IsRejected() ) { - m->SetIgnored( true ); - nRejected++; + if ( !isValid(m) ) { + m_p->Delete(m); + nRemoved++; } } } - // Check to see if we want to reset the apriori surface to the best - // available measure. - if ( true == setaprioribest) { - cp.SetAdjustedSurfacePoint(cp.GetBestSurfacePoint()); + // Check for valid measure constraints + if ( (m_p->GetNumValidMeasures() < minmeasures) && (!m_p->IsEditLocked()) ) { + m_p->SetIgnored( true ); + nMinMeasures++; } + } - // Now save point if valid - if (point.size() < minmeasures) { - point.disable(); - nMinMeasures++; - // Check if we are to save points that are less than the valid minimum - // measures. - if ( true == savemins ) { - cnet.AddPoint( point.take() ); + // Save invalid points? We are not going to create the network if only if + // requested by the user with the good points as its a very expensive + // operation. + if ( true == cleannet ) { + if ( isValid(m_p) ) { // Handle valid points + if ( !cnet.isNull() ) { + if ( (true == setaprioribest) && !m_p->IsEditLocked() ) { + m_p->SetAdjustedSurfacePoint(m_p->GetBestSurfacePoint()); + } + cnet->AddPoint(m_p); oPoints++; } + else { // If not creating control network, ensure points are deleted + delete (m_p); + } + } + else { // Not a valid point, delete it + delete (m_p); } - else { - cnet.AddPoint( point.take() ); + } + else { // Handle points when not cleaning + if ( !cnet.isNull() ) { + if ( (true == setaprioribest) && !m_p->IsEditLocked() ) { + m_p->SetAdjustedSurfacePoint(m_p->GetBestSurfacePoint()); + } + + cnet->AddPoint(m_p); oPoints++; } + else { // If not creating control network, ensure points are deleted + delete (m_p); + } } - } + progress.CheckStatus(); + } - // Write the resulting control network to the specfied ONET file + //--------------------------------------------------------------------------- + // Write the resulting control network to the specfied ONET file. We will now + // create the network formally. If not requested, don't forget to free all + // remaining points (done by ControlNet otherwise). + //--------------------------------------------------------------------------- if ( ui.WasEntered("ONET") ) { - cnet.Write( ui.GetAsString("ONET") ); + // Make it so! + cnet->Write( ui.GetAsString("ONET") ); } // Write out a report - int pMerged = v_cloud.size() - oPoints; + int pMerged = validPoints - vPoints; PvlGroup summary("Summary"); - summary += PvlKeyword("TotalInputPoints", toString(v_cloud.size())); + summary += PvlKeyword("TotalCubes", toString(cube_measures_size)); + summary += PvlKeyword("TotalInputPoints", toString(all_points.size())); summary += PvlKeyword("TotalOutputPoints", toString(oPoints)); - summary += PvlKeyword("PointsEliminated", toString(pMerged)); + summary += PvlKeyword("PointsMerged", toString(pMerged)); summary += PvlKeyword("PointsEvaluated", toString(nfound)); - summary += PvlKeyword("RejectedMeasures", toString(nRejected)); + summary += PvlKeyword("TotalMeasures", toString(allPoints)); summary += PvlKeyword("MeasuresMerged", toString(nMerged)); + summary += PvlKeyword("MeasuresDeleted", toString(nRemoved)); summary += PvlKeyword("MinimumMeasures", toString(nMinMeasures)); Application::Log(summary); - p.EndProcess(); + pbl.EndProcess(); } diff --git a/isis/src/control/apps/cnetcombinept/cnetcombinept.xml b/isis/src/control/apps/cnetcombinept/cnetcombinept.xml index ffce7c59ba3226131c89de6c6a4719cae2a463fe..5bffc118eb64114c71fb660e11fb46d3f74dd79a 100644 --- a/isis/src/control/apps/cnetcombinept/cnetcombinept.xml +++ b/isis/src/control/apps/cnetcombinept/cnetcombinept.xml @@ -9,24 +9,18 @@

    This program will create a control network by combining control points - from one or more control networks into single points that satisfy either - ground or image distance criteria. It employs a more robust technique than - cnetmerge. This technique evaluates - each control point in the combined network by applying a search of radial - spatial distance (in meters) to collect all points that may be of the same feature. - This search will find a list of candidate control points, i.e. points - that the algorithm has found might be matches. Distance statistics of common - control measures from the image are computed using the source point and each - candidate control point. The MODE parameter for this program specifies the - maximum distance, in IMAGE (pixel units) or GROUND (meter units), allowed - to determine whether the two control points are measurements of the same - image feature. If the average of all common measures is less than or equal to - the distance (in the given IMAGE or GROUND units), then all control - measures from the candidate control point are copied to the source control - point (increasing image match depth) and the candidate control point is - disabled so that it will never be considered for another merger. The now - augmented control point is added back to the search pool for further merger - considerations. + from one or more control networks into single points that satisfy image + distance criteria. It employs a more robust/direct technique than + cnetmerge. This technique evaluates each control point in all + input networks by finding all candidate merger control points who have a + measure within IMAGETOL. Then, for each candidate point, the average + distance of the measures in the candidate to a measure in the source + point is computed. If the average distance to any measure in the source + point is less than IMAGETOL, then the candidate point and source point + are merged. The candidate control point is disabled so that it will + never be considered for another merger and the now augmented control + point is added back to the search pool for further merger considerations, + which can occur when other common measures are considered.

    When all control points have been searched and all mergers have taken @@ -65,6 +59,12 @@ Modified to set the new control net's target and radii by using the input control net's values. References #3892 + + Modified merging algorithm and parameters. Fixes #4558. + + + Created new tests and updated documentation. References #4558. + @@ -106,18 +106,6 @@ *.lis *.txt - - - - cube - input - None - Cube file to use as a reference image for IMAGE mode - - The reference cube for matching by image. - - *.cub - @@ -135,6 +123,21 @@ *.net *.cnet *.ctl + + filename + output + None + + Write a list of all serial numbers contained in the network + + + Provided with a filename in this option, all the cube serial numbers + that are contained in the network are written to this file as soon as + it is determined in the processing. + + *.lis + + string None @@ -159,65 +162,6 @@ - - string - GROUND - Type of control point merger to apply - - The MODE parameter indicates whether to use ground or image coordinates to determine - merge points. - - - - - - - - - double - - Specifies the radial search distance for merge candidates - - - The radial search range from the source control point to find all - candidate control points to consider for merging. This distance is - specified in meters. Users must carefully consider this value as - it must be large enough to include the maximum uncertainity in the - SPICE ephemeris data for all images. Note if the adjusted - latitude/longitude coordiate exists in the point, it will be used - to determine the ground coordinate, otherwise apriori - latitude/longitudes are used to compute distances from each - control point. It also should not be so small that it will not - find all the points of the same feature. - - - double 1.0 @@ -227,23 +171,12 @@ - - double - 0.0 - - Specifies distance on ground to merge point if no common image measures . - - - The acceptable distance, in ground measurements, for merging points. - - - integer 10 Specify the leaf size of the kd-tree - Number of leafs in the kd-tree structure. + Number of leaves in the kd-tree structure. @@ -260,62 +193,67 @@ false - - string - NOACTION - Tweek rejected measures - - Determeines how to deal with rejected measures. - - - - - - + + boolean + true + Remove all invalid or ignored control points/measures + +

    + When true, all invalid or ignored control points and measures + are removed from the output control network as one of + the main objectives of this application is to remove + redundancies and mimimize the size of networks. However, for + evaluation purposes, you can set this to false, which will + preserve all control points. +

    +

    + When specifying the minimum number of measures/control point + using the MINMEASURES parameter, any control point that does + not meet this criteria will also be removed from the netwrk + when CLEANNET=true, otherwise these points will be set to + ignored. +

    +     +     + + + boolean + true + Remove all invalid or ignored control measures + +

    + When true, all invalid or ignored control points and measures + are removed from the output control network as one of + the main objectives of this application is to remove + redundancies and mimimize the size of networks. However, for + evaluation purposes, you can set this to false, which will + preserve all control points. +

    +

    + When specifying the minimum number of measures/control point + using the MINMEASURES parameter, any control point that does + not meet this criteria will also be removed from the netwrk + when CLEANNET=true, otherwise these points will be set to + ignored. +

    +     integer 0 - Select minimim number of measures that are valid + Select minimim number of valid measures/point - This allows users to disable (by setting measures as ignored) - points that have less than MINMEASURES control - measures/control point. For example, if you want to flag all - points as ignored with 2 measures or less, set MINMEASURES=3. + This allows users to disable points that have less than + MINMEASURES control measures/control point. For example, if you + want to flag all points as ignored with 2 measures or less, set + MINMEASURES=3. Points that don't meet this critieria are set to + ignore and are subject to the CLEANNET action requested by the + user (i.e., all ignored points are removed from the network if + CLEANNET=true). - - - boolean - - Save points that have less than the mininum measures - - - When TRUE, all points found to have the minimum number of - measures are set to ignore and written to the output control - network. When FALSE, they are excluded(removed) from the output - network. - - false - + diff --git a/isis/src/control/apps/cnetcombinept/tsts/messenger/Makefile b/isis/src/control/apps/cnetcombinept/tsts/messenger/Makefile index 9a52f9b5cd16cc533d1129d6658026b1add41986..36676e4069d9d3a22ff8d9a562c18c5215ce345b 100644 --- a/isis/src/control/apps/cnetcombinept/tsts/messenger/Makefile +++ b/isis/src/control/apps/cnetcombinept/tsts/messenger/Makefile @@ -7,12 +7,8 @@ commands: $(APPNAME) cnetlist=$(OUTPUT)/networks.lis \ onet=$(OUTPUT)/Equi065S355ED10.net \ networkid=Equi065S355ED10 \ - description="Messenger data test" \ - mode=image \ - distance=3000.0 \ - imagetol=1 \ - setaprioribest=true \ - rejectedmeasures=remove \ + description="Messenger data test" \ + imagetol=3000.0 \ > /dev/null; $(RM) $(OUTPUT)/networks.lis; diff --git a/isis/src/control/apps/cnetcombinept/tsts/noclean/Makefile b/isis/src/control/apps/cnetcombinept/tsts/noclean/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..3b786209219cebc5734f21c170288e5eb92db873 --- /dev/null +++ b/isis/src/control/apps/cnetcombinept/tsts/noclean/Makefile @@ -0,0 +1,16 @@ +APPNAME = cnetcombinept + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(LS) $(INPUT)/*.net > $(OUTPUT)/networks.lis; + $(APPNAME) cnetlist=$(OUTPUT)/networks.lis \ + onet=$(OUTPUT)/Equi065S355ED10.net \ + networkid=Equi065S355ED10 \ + description="Messenger data test" \ + imagetol=3000.0 \ + cleannet=false \ + cleanmeasures=false \ + > /dev/null; + + $(RM) $(OUTPUT)/networks.lis; diff --git a/isis/src/control/apps/cnetcombinept/tsts/setapriori/Makefile b/isis/src/control/apps/cnetcombinept/tsts/setapriori/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..4bc27ec747c75ecd4f3c6c018898658cc57f92a7 --- /dev/null +++ b/isis/src/control/apps/cnetcombinept/tsts/setapriori/Makefile @@ -0,0 +1,15 @@ +APPNAME = cnetcombinept + +include $(ISISROOT)/make/isismake.tsts + +commands: + $(LS) $(INPUT)/*.net > $(OUTPUT)/networks.lis; + $(APPNAME) cnetlist=$(OUTPUT)/networks.lis \ + onet=$(OUTPUT)/Equi065S355ED10.net \ + networkid=Equi065S355ED10 \ + description="Messenger data test" \ + imagetol=1000.0 \ + setaprioribest=true \ + > /dev/null; + + $(RM) $(OUTPUT)/networks.lis; diff --git a/isis/src/control/apps/cnetedit/cnetedit.cpp b/isis/src/control/apps/cnetedit/cnetedit.cpp index 366e4e3929a8b2079ec217482cc455d6409cc37b..65ae762af7b8e54b5ce284a9dfcefcb140254bf2 100644 --- a/isis/src/control/apps/cnetedit/cnetedit.cpp +++ b/isis/src/control/apps/cnetedit/cnetedit.cpp @@ -104,6 +104,11 @@ ControlNetValidMeasure *validator; // Main program void IsisMain() { + // 2016-12-08 Ian Humphrey - Set the QHash seed, otherwise output is ALWAYS slightly + // different. Note that in Qt4, the seed was constant, but in Qt5, the seed is + // created differently for each process. Fixes #4206. + qSetGlobalQHashSeed(1031); + // Reset the counts of points and measures deleted numPointsDeleted = 0; numMeasuresDeleted = 0; @@ -177,7 +182,7 @@ void IsisMain() { QString line = in.readLine(); QStringList results = line.split(","); if (results.size() < 2) { - QString msg = "Line " + QString(lineNumber) + " in the MEASURELIST does " + QString msg = "Line " + QString::number(lineNumber) + " in the MEASURELIST does " "not contain a Point ID and a cube filename separated by a comma"; throw IException(IException::User, msg, _FILEINFO_); } diff --git a/isis/src/control/apps/cnetmerge/cnetmerge.cpp b/isis/src/control/apps/cnetmerge/cnetmerge.cpp index 762710f08c2c0240d117d7f5d5ff522993e31e1f..aa767110c2e60a6a4cc97cd046e6430636ed289d 100644 --- a/isis/src/control/apps/cnetmerge/cnetmerge.cpp +++ b/isis/src/control/apps/cnetmerge/cnetmerge.cpp @@ -20,7 +20,8 @@ using namespace Isis; ControlNet * mergeNetworks(FileList &filelist, PvlObject &conflictLog, QString networkId, QString description); -void mergeNetwork(ControlNet &baseNet, ControlNet &newNet, PvlObject &cnetLog); +void mergeNetwork(ControlNet &baseNet, ControlNet &newNet, + PvlObject &cnetLog, Progress progress); ControlPoint * mergePoint( ControlPoint *basePoint, ControlPoint *newPoint, @@ -210,27 +211,26 @@ ControlNet * mergeNetworks(FileList &filelist, PvlObject &conflictLog, } } - // Creates a Progress bar for the entire merging process + // Show progress using "File X of N" and progress bar for each file. Progress progress; - progress.SetMaximumSteps(filelist.size()); + progress.SetText("Loading base network"); progress.CheckStatus(); // The original base network is the first in the list, all successive // networks will be added to the base in descending order - ControlNet *baseNet = new ControlNet(filelist[0].toString()); + ControlNet *baseNet = new ControlNet(filelist[0].toString(), &progress); baseNet->SetNetworkId(networkId); baseNet->SetUserName(Isis::Application::UserName()); baseNet->SetCreatedDate(Isis::Application::DateTime()); baseNet->SetModifiedDate(Isis::iTime::CurrentLocalTime()); baseNet->SetDescription(description); - progress.CheckStatus(); // Loop through each network in the list and attempt to merge it into the // base for (int cnetIndex = 1; cnetIndex < (int) filelist.size(); cnetIndex++) { FileName currentCnetFileName(filelist[cnetIndex]); - ControlNet newNet(currentCnetFileName.expanded()); + ControlNet newNet(currentCnetFileName.expanded(), &progress); // Networks can only be merged if the targets are the same if (baseNet->GetTarget().toLower() != newNet.GetTarget().toLower()) { @@ -243,19 +243,21 @@ ControlNet * mergeNetworks(FileList &filelist, PvlObject &conflictLog, PvlObject cnetLog = createNetworkLog(newNet); // Merge the network, add the resulting conflicts to the log - mergeNetwork(*baseNet, newNet, cnetLog); + progress.SetText("Merging file " + QString::number(cnetIndex+1) + + " of " + QString::number(filelist.size())); + mergeNetwork(*baseNet, newNet, cnetLog, progress); addLog(conflictLog, cnetLog); - progress.CheckStatus(); } return baseNet; } -void mergeNetwork(ControlNet &baseNet, ControlNet &newNet, PvlObject &cnetLog) { +void mergeNetwork(ControlNet &baseNet, ControlNet &newNet, PvlObject &cnetLog, Progress progress) { // Loop through all points in the new network, looking for new points to add // and conflicting points to resolve + progress.SetMaximumSteps(newNet.GetNumPoints()); for (int newIndex = 0; newIndex < newNet.GetNumPoints(); newIndex++) { ControlPoint *newPoint = newNet.GetPoint(newIndex); if (baseNet.ContainsPoint(newPoint->GetId())) { @@ -274,6 +276,7 @@ void mergeNetwork(ControlNet &baseNet, ControlNet &newNet, PvlObject &cnetLog) { ControlPoint *outPoint = new ControlPoint(*newPoint); baseNet.AddPoint(outPoint); } + progress.CheckStatus(); } } diff --git a/isis/src/control/apps/cnetref/CnetRefByResolution.cpp b/isis/src/control/apps/cnetref/CnetRefByResolution.cpp index c970bb6261b787bb0685e7ac5204ee4654b4b1a7..cdadb2f4bea05682647e640ef0cb3a10eecb93d0 100644 --- a/isis/src/control/apps/cnetref/CnetRefByResolution.cpp +++ b/isis/src/control/apps/cnetref/CnetRefByResolution.cpp @@ -137,7 +137,8 @@ namespace Isis { pvlMeasureGrp += Isis::PvlKeyword("UnIgnored", "Failed Validation Test but not Ignored as Measure EditLock is True"); } else { - pvlMeasureGrp += Isis::PvlKeyword("Ignored", "Failed Validation Test"); + pvlMeasureGrp += Isis::PvlKeyword("Ignored", "For point [" + newPnt->GetId() + "] and measure [" + sn + + "], point failed to intersect body."); newMsr->SetIgnored(true); iNumIgnore++; } diff --git a/isis/src/control/apps/cnetref/CnetRefByResolution.h b/isis/src/control/apps/cnetref/CnetRefByResolution.h index b482e0ccd38433a9d0ea52246424551277772201..fef1089f5ae5b36020d2e51b0bd8c6337ceb641b 100644 --- a/isis/src/control/apps/cnetref/CnetRefByResolution.h +++ b/isis/src/control/apps/cnetref/CnetRefByResolution.h @@ -72,6 +72,9 @@ namespace Isis { * @history 2011-06-07 Debbie A. Cook and Tracie Sucharski - Modified point types * Ground ------> Fixed * Tie----------> Free + * @history 2016-07-13 Adam Paquette - Updated Ignored keyword in pvlMeasureGrp to a + * more accurate error messages as to whythe measure + * is being ignored */ class CnetRefByResolution : public ControlNetValidMeasure { public: diff --git a/isis/src/control/apps/cnetref/tsts/resolutionHigh/Makefile b/isis/src/control/apps/cnetref/tsts/resolutionHigh/Makefile index 9be47e9ab8218eb1555dadf4b1e94ef5229de5a3..caf88e7ea4b635fe99c050ef059492f681b79da7 100644 --- a/isis/src/control/apps/cnetref/tsts/resolutionHigh/Makefile +++ b/isis/src/control/apps/cnetref/tsts/resolutionHigh/Makefile @@ -14,4 +14,10 @@ commands: onet=$(OUTPUT)/truth.net \ networkid=DefaultTruth \ Description=RefByResolutionHigh > /dev/null; + $(APPNAME) fromlist=$(OUTPUT)/cube.lis \ + cnet=$(INPUT)/autoseed_edit.pvl \ + criteria=resolution \ + type=high \ + onet=$(OUTPUT)/autoseed_edit_truth.net \ + Description=RefByResolutionHighFail > /dev/null; $(RM) $(OUTPUT)/cube.lis; diff --git a/isis/src/control/apps/cnettable/cnettable.cpp b/isis/src/control/apps/cnettable/cnettable.cpp index ff0302477119a61d13987a1d336b1f7a5e67f5fe..0197197049979b5a969df282db17051395960fd4 100644 --- a/isis/src/control/apps/cnettable/cnettable.cpp +++ b/isis/src/control/apps/cnettable/cnettable.cpp @@ -1,5 +1,10 @@ #include "Isis.h" +#include + +#include +#include +#include #include "CameraPointInfo.h" #include "ControlMeasure.h" @@ -21,13 +26,6 @@ #include "SurfacePoint.h" #include "TextFile.h" #include "UserInterface.h" -//#include "LocalPointInfo.h" - -#include -#include -#include - -#include using namespace std; using namespace Isis; @@ -62,7 +60,7 @@ void IsisMain() { SerialNumberList serials(ui.GetFileName("FROMLIST")); append = ui.GetBoolean("APPEND"); - if(cnet.GetNumMeasures() == 0) { + if (cnet.GetNumMeasures() == 0) { string msg = "Your control network must contain at least one point"; throw IException(IException::User, msg, _FILEINFO_); } @@ -192,11 +190,15 @@ void IsisMain() { measureInfo += QString(CheckValue(Asp.GetLatSigma().degrees())) + ","; measureInfo += QString(CheckValue(Asp.GetLonSigma().degrees())) + ","; measureInfo += QString(CheckValue(Asp.GetLocalRadiusSigma().kilometers())) + ","; - try { measureInfo += QString(CheckValue(Asp.GetLatSigmaDistance().kilometers())) + ","; } + try { + measureInfo += QString(CheckValue(Asp.GetLatSigmaDistance().kilometers())) + ","; + } catch (IException &) { measureInfo += ","; } - try { measureInfo += QString(CheckValue(Asp.GetLonSigmaDistance().kilometers())) + ","; } + try { + measureInfo += QString(CheckValue(Asp.GetLonSigmaDistance().kilometers())) + ","; + } catch (IException &) { measureInfo += ","; } @@ -214,11 +216,15 @@ void IsisMain() { measureInfo += QString(CheckValue(sp.GetLatSigma().degrees())) + ","; measureInfo += QString(CheckValue(sp.GetLonSigma().degrees())) + ","; measureInfo += QString(CheckValue(sp.GetLocalRadiusSigma().kilometers())) + ","; - try { measureInfo += QString(CheckValue(sp.GetLatSigmaDistance().kilometers())) + ","; } + try { + measureInfo += QString(CheckValue(sp.GetLatSigmaDistance().kilometers())) + ","; + } catch (IException &e) { measureInfo += ","; } - try { measureInfo += QString(CheckValue(sp.GetLonSigmaDistance().kilometers())) + ","; } + try { + measureInfo += QString(CheckValue(sp.GetLonSigmaDistance().kilometers())) + ","; + } catch (IException &e) { measureInfo += ","; } @@ -271,7 +277,7 @@ void IsisMain() { ControlMeasureLogData::GoodnessOfFit).Average())) + ","; // Loop through all measures in controlpoint - for(int j = 0; j < cpoint->GetNumMeasures(); j++) { + for (int j = 0; j < cpoint->GetNumMeasures(); j++) { const ControlMeasure * cmeasure = (*cpoint)[j]; @@ -280,7 +286,7 @@ void IsisMain() { grp = camPoint.SetImage(cmeasure->GetSample(), cmeasure->GetLine(), outside, errors); // Shouldn't ever happen, but, being safe... - if(grp == NULL) { + if (grp == NULL) { string msg = "You shouldn't have gotten here. Errors in CameraPointInfo class"; throw IException(IException::Programmer, msg, _FILEINFO_); } @@ -295,7 +301,7 @@ void IsisMain() { // All done, clean up prog.CheckStatus(); - if(txt != NULL) { + if (txt != NULL) { delete txt; txt = NULL; } @@ -339,7 +345,7 @@ void Write(PvlGroup *point, const ControlMeasure &cm) { // Do we have errors? int maxCount = 0; bool errors = point->hasKeyword("Error"); - if(errors) { + if (errors) { maxCount = point->keywords() - 1; } else { @@ -347,7 +353,7 @@ void Write(PvlGroup *point, const ControlMeasure &cm) { } // If its first and not appending, write the column labels - if(isFirst && !append) { + if (isFirst && !append) { QList< QStringList > printableMeasureData = cm.PrintableClassData(); QStringList nameValuePair; @@ -356,8 +362,8 @@ void Write(PvlGroup *point, const ControlMeasure &cm) { } // point information - for(int i = 0; i < maxCount; i++) { - if((*point)[i].size() == 3) { + for (int i = 0; i < maxCount; i++) { + if ((*point)[i].size() == 3) { output += QString((*point)[i].name()) + "X,"; output += QString((*point)[i].name()) + "Y,"; output += QString((*point)[i].name()) + "Z,"; @@ -367,16 +373,13 @@ void Write(PvlGroup *point, const ControlMeasure &cm) { } } - // control measure information - //dataNames = cm.GetMeasureDataNames(); - //for(int i = 0; i < dataNames.size(); i++) { - // output += IString(dataNames[i] + ","); - //} - - - if(errors) output += QString((*point)[maxCount].name()); + if (errors) output += QString((*point)[maxCount].name()); isFirst = false; measureLabels += output; + // In some cases, we need to trim a trailing comma: + if (measureLabels.endsWith(",")) { + measureLabels.chop(1); + } txt->PutLine(measureLabels); } output.clear(); @@ -390,31 +393,28 @@ void Write(PvlGroup *point, const ControlMeasure &cm) { // Write out date values // point information - for(int i = 0; i < maxCount; i++) { - if((*point)[i].size() == 3) { + for (int i = 0; i < maxCount; i++) { + if ((*point)[i].size() == 3) { output += QString(CheckValue((*point)[i][0])) + ","; output += QString(CheckValue((*point)[i][1])) + ","; output += QString(CheckValue((*point)[i][2])) + ","; - } + } else { output += QString(CheckValue((*point)[i][0])) + ","; } } - //dataNames = cm.GetMeasureDataNames(); - //for(int i = 0; i < dataNames.size(); i++) { - // output += IString(cm.GetMeasureData(dataNames[i])) + ","; - //} - - + if (errors) output += QString((*point)[maxCount][0]); - if(errors) output += QString((*point)[maxCount][0]); - - // Meaure info comes first + // Measure info comes first QString pri = ""; pri += measureInfo; pri += output; + // In some cases, we need to trim a trailing comma: + if (pri.endsWith(",")) { + pri.chop(1); + } txt->PutLine(pri); output.clear(); diff --git a/isis/src/control/apps/cnettable/cnettable.xml b/isis/src/control/apps/cnettable/cnettable.xml index 03717ef93da2f4ca6dc4dc8f42cd8e8b274851e6..226184a603b2aac2d2662087992d2d9527d2847b 100644 --- a/isis/src/control/apps/cnettable/cnettable.xml +++ b/isis/src/control/apps/cnettable/cnettable.xml @@ -129,7 +129,10 @@ xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Applica Updated application truth data due to modifications in CameraPointInfo class. References #476. - + + + Trimmed extra commas from label and data. + References #4657. diff --git a/isis/src/control/apps/cnettable/tsts/append/Makefile b/isis/src/control/apps/cnettable/tsts/append/Makefile index 7fe9c37a826836bb153b5ea72e985c027eb8b91d..f8cdc14f225a3869dc446eb0909ec79041d0cac1 100644 --- a/isis/src/control/apps/cnettable/tsts/append/Makefile +++ b/isis/src/control/apps/cnettable/tsts/append/Makefile @@ -3,18 +3,24 @@ APPNAME = cnettable include $(ISISROOT)/make/isismake.tsts commands: - cp $(INPUT)/appendTo.txt $(OUTPUT); \ + # This test is for the append function with data as of 2017-04-21 find $(INPUT)/*.cub > $(OUTPUT)/cubeList.lst; \ - $(APPNAME) fromlist=$(OUTPUT)/cubeList.lst \ - cnet=$(INPUT)/testNet.net \ - flatfile=$(OUTPUT)/appendTo.txt \ - append=true > /dev/null; + $(APPNAME) FROMLIST=$(OUTPUT)/cubeList.lst \ + CNET=$(INPUT)/testNet.net \ + FLATFILE=$(OUTPUT)/cnetstats.txt \ + > /dev/null; + # Run again with append mode = true, using same files as above. This should duplicate the same + # data in the output file. + $(APPNAME) FROMLIST=$(OUTPUT)/cubeList.lst \ + CNET=$(INPUT)/testNet.net \ + FLATFILE=$(OUTPUT)/cnetstats.txt APPEND=TRUE \ + > /dev/null; rm -f $(OUTPUT)/cubeList.lst > /dev/null; - cat $(OUTPUT)/appendTo.txt | sed s/,\[^,]\*\.cub,/,file.cub,/ \ - | sed 's/\([0-9][0-9]*\.[0-9]\)\([0-9][0-9]*\)/\1/g' \ - | sed s/`date +%Y-%m-%dT`\[0-2\]\[0-9\]:\[0-5\]\[0-9\]:\[0-5\]\[0-9\]/date/ \ + cat $(OUTPUT)/cnetstats.txt | $(SED) s/,\[^,]\*\.cub,/,file.cub,/ \ + | $(SED) 's/\([0-9][0-9]*\.[0-9]\)\([0-9][0-9]*\)/\1/g' \ + | $(SED) s/`date +%Y-%m-%dT`\[0-2\]\[0-9\]:\[0-5\]\[0-9\]:\[0-5\]\[0-9\]/date/ \ > $(OUTPUT)/output.txt - rm -f $(OUTPUT)/appendTo.txt + rm -f $(OUTPUT)/cnetstats.txt > /dev/null; # To comment what is going on: # The 3 seds do as follows: # 1. remove cube filenames diff --git a/isis/src/control/apps/cnetthinner/CnetManager.cpp b/isis/src/control/apps/cnetthinner/CnetManager.cpp new file mode 100644 index 0000000000000000000000000000000000000000..0bcfc4236daa88619c4118c1e754fbe77a57191d --- /dev/null +++ b/isis/src/control/apps/cnetthinner/CnetManager.cpp @@ -0,0 +1,305 @@ +/** + * @file + * $Revision: 6565 $ + * $Date: 2016-02-10 17:15:35 -0700 (Wed, 10 Feb 2016) $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "CnetManager.h" +#include "ControlNet.h" +#include "ControlPoint.h" +#include "ControlMeasure.h" +#include "ControlMeasureLogData.h" + +#include "tnt/tnt_array2d.h" +#include "tnt/tnt_array2d_utils.h" + +///#define DEBUG 1 + +namespace Isis { + +// KPoint implementation + +/** + * Empty Constructor. Disabled at runtime. + * + */ + KPoint::KPoint() { + m_point = 0; + m_strength = -3; + m_index = -1; + m_selected = false; + BOOST_ASSERT ( m_point != 0 ); + } + + +/** + * Constructs a KPoint. + * + * @param point The control point to make a KPoint from. + * @param index The source index. + * @param weight The point's weight. + * + */ + KPoint::KPoint(ControlPoint *point, const int &index, const double &weight) { + BOOST_ASSERT ( point != 0 ); + m_point = point; + m_strength = calculateStrength(m_point, weight); + m_sourceIndex = m_index = index; + m_selected = false; + } + + +/** + * Set the status of the KPoint to true for selected or + * false for unselected. + * + * @param state If true, the KPoint is set to selected. + */ + void KPoint::select(const bool &state) { + m_selected = state; + } + + +/** + * Calculate the strength of a control point. A negative return value indicates + * an invalid result. + * + * @param point + * @param weight + * + * @return double + */ + double KPoint::calculateStrength(const ControlPoint *point, + const double &weight) const { + // Gut check for validity + if ( !point ) return (-2.0); + + // Don't use points which have only 1 valid measure or fewer, since + // we don't use refIncides in the strength calculation. + if ( point->GetNumValidMeasures() < 2.0 ) return (-1.0); + + // Got some good ones, compute strength + double sum(0.0); + int count(0); + int refIndex = point->IndexOfRefMeasure(); + for ( int i = 0 ; i < point->GetNumMeasures() ; i++) { + if ( i != refIndex ) { // Check all but the reference measure + const ControlMeasure *m = point->GetMeasure(i); + if ( !m->IsIgnored() && m->HasLogData(ControlMeasureLogData::GoodnessOfFit) ) { + sum += m->GetLogData(ControlMeasureLogData::GoodnessOfFit).GetNumericalValue(); + count++; + } + } + } + + // Compute the weighted strength + BOOST_ASSERT ( count > 0 ); + double v_count(count); + double v_strength = sum / v_count; + return ( v_strength * ( 1.0 + (qLn(v_count) * weight) ) ); + } + +// CnetManager implementation + +/** + * Constructs an emtpy CnetManager. + * + */ + CnetManager::CnetManager() : m_kpts() { } + + +/** + * Constructs a CnetManager using an input control network and a weight. + * + * @param cnet Input control network to be managed. + * @param weight Weights to apply to the control network. + */ + CnetManager::CnetManager(ControlNet &cnet, const double &weight) { + load(cnet.GetPoints(), weight); + } + + +/** + * + * Default Destructor + * + */ + CnetManager::~CnetManager() { } + + +/** + * The number of points managed by CnetManager. + * + * @return @b int The number of points in this CnetManager. + */ + int CnetManager::size() const { + return ( m_kpts.size() ); + } + + +/** + * Loads a list of control points into the CnetManager. + * + * @param pts The QList of ControlPoints to load into the CnetManager. + * @param weight The weight to apply to each ControlPoint in the list. + * + * @return @b int The number of ControlPoints loaded into the CnetManager. + */ + int CnetManager::load(const QList &pts, const double &weight) { + m_kpts.clear(); + + for (int i = 0; i < pts.size(); i++) { + ControlPoint *p = pts[i]; + if ( !(p->IsInvalid() || p->IsIgnored()) ) { + m_kpts.append(KPoint(p, i, weight)); + } + } + + // Sort the points based upon strength + qSort(m_kpts.begin(), m_kpts.end(), SortStrengthDescending()); + +#if defined(DEBUG) + for (int p = 0 ; p < qMin(m_kpts.size(), 5) ; p++) { + std::cout << "Point: " << p << " - Strength: " << m_kpts[p].strength() << "\n"; + } +#endif + + // Now have to set the real sorted indexes + for (int i = 0; i < m_kpts.size(); i++) { + m_kpts[i].m_index = i; + } + + return ( size() ); + } + + +/** + * Get a list of control points in this CnetManager. + * + * @return @b const QList List of control points in CnetManager. + */ + const QList CnetManager::getControlPoints() const { + QList pts; + BOOST_FOREACH ( const KPoint &p, m_kpts ) { + pts.append( p.point() ); + } + return (pts); + } + + +/** + * Return a map of the number of measures per cube. + * + * @return @b QMap Serial number, number of measures per that serial number (cube) + */ + QMap CnetManager::getCubeMeasureCount() const { + QMap k_map; + BOOST_FOREACH ( const KPoint &p, m_kpts ) { + QList measures = p.point()->getMeasures(true); + BOOST_FOREACH ( const ControlMeasure *m, measures ) { + QString cn = m->GetCubeSerialNumber(); + if ( k_map.contains(cn) ) { k_map[cn] += 1; } + else { k_map.insert(cn, 1); } + } + } + return (k_map); + } + + +/** + * Returns control measures and their associated indicies for a given cube (serial number.) + * + * @param serialNo Serial number (indicates a specific cube) to get the measure indicies for. + * + * @return @b CnetManager::PointSet Data structure containing the calculated index and measure. + */ + CnetManager::PointSet CnetManager::getCubeMeasureIndices(const QString &serialNo) const { + PointSet cubeNdx; + BOOST_FOREACH ( const KPoint &p, m_kpts ) { + int index = p.point()->IndexOf(serialNo, false); + if ( index >= 0 ) { + cubeNdx.append( qMakePair(p.index(), p.point()->GetMeasure(index)) ); + } + } + return ( cubeNdx ); + } + + +/** + * Will return the KPoint at an input index. + * + * @return @b const KPoint& The KPoint at the requested index. + */ + const KPoint &CnetManager::operator()(const int index) const { + BOOST_ASSERT ( index < m_kpts.size() ); + return ( m_kpts.at(index) ); + } + + +/** + * + * Get a point at a specificed index. + * + * @param index Index of the point to get. + * + * @return @b const ControlPoint* The point at the requested index. + */ + const ControlPoint *CnetManager::point(const int &index) const { + BOOST_ASSERT ( index < m_kpts.size() ); + return ( m_kpts.at(index).point() ); + } + + +/** + * Gets the list of KPoints managed by this CubeManager. + * + * @return @b const QList& List of KPoints managed by this CnetManager. + */ + const QList &CnetManager::pointList() const { + return ( m_kpts ); + } + + +/** + * Get a point at a specificed index. + * + * @param index Index of the point. + * + * @return @b ControlPoint* The point at the requested index. + */ + ControlPoint *CnetManager::point(const int index) { + BOOST_ASSERT ( index < m_kpts.size() ); + return ( m_kpts.at(index).point() ); + } + +} // namespace Isis diff --git a/isis/src/control/apps/cnetthinner/CnetManager.h b/isis/src/control/apps/cnetthinner/CnetManager.h new file mode 100644 index 0000000000000000000000000000000000000000..867166e712187d108983a8b451ca3bfc35064e0e --- /dev/null +++ b/isis/src/control/apps/cnetthinner/CnetManager.h @@ -0,0 +1,190 @@ +#ifndef CnetManager_h +#define CnetManager_h +/** + * @file + * $Revision: 6565 $ + * $Date: 2016-02-10 17:15:35 -0700 (Wed, 10 Feb 2016) $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "ControlNet.h" +#include "ControlPoint.h" +#include "ControlMeasure.h" +#include "ControlMeasureLogData.h" + + +#include "tnt/tnt_array2d.h" +#include "tnt/tnt_array2d_utils.h" + +namespace Isis { + + class CnetManager; + +/** + * Class to store control points with a weight and computed strength for CnetManager. + * + * @author 2016-09-30 Kris Becker + * + * @internal + * @history 2016-09-30 Kris Becker - Original Version + * @history 2016-12-28 Kristin Berry - Added documentation and tests for checkin + * + */ + class KPoint { + + friend class CnetManager; + + public: + KPoint(); + KPoint(ControlPoint *point, const int &index, const double &weight = 0.0); + + void select(const bool &state = true); + + //definitions of inline functions + + /** + * Get the control point the KPoint was constructed from. + * + * @return @b ControlPoint* The original control point. + */ + inline ControlPoint *point() const { + BOOST_ASSERT ( m_point != 0 ); + return ( m_point ); + } + + + /** + * Gets the calculated strength of this KPoint. + * + * @return @b double The calculated strength of this KPoint. + */ + inline double strength() const { + return ( m_strength ); + } + + + /** + * Gets the index of this KPoint. + * + * @return @b int The index of this KPoint. + */ + inline int index () const { + return ( m_index ); + } + + + /** + * Gets the original index of this KPoint. + * + * @return @b int The original or source index of this KPoint. + */ + inline int sourceIndex() const { + return (m_sourceIndex); + } + + private: + ControlPoint *m_point; //! The original ControlPoint used to construct the KPoint. + double m_strength; //! The calulated strength of this KPoint. + int m_sourceIndex; //! The original index of this KPoint. + int m_index; //! The calculated index of this KPoint. + bool m_selected; //! Flag to indicated whether to use this KPoint or not. + + double calculateStrength(const ControlPoint *point, const double &weight) const; + + }; + + +/** + * Container class for the network and suppression data. + * + * @author 2016-09-30 Kris Becker + * + * @internal + * @history 2016-09-30 Kris Becker - Original Version + * @history 2016-12-28 Kristin Berry - Added documentation and tests for checkin + */ + class CnetManager { + public: + typedef QPair IndexPoint; //! + typedef QVector PointSet; //! + + CnetManager(); + CnetManager(ControlNet &cnet, const double &weight = 0.0); + virtual ~CnetManager(); + + int size() const; + int load(const QList &pts, const double &weight = 0.0); + + QMap getCubeMeasureCount() const; + const QList getControlPoints() const; + PointSet getCubeMeasureIndices(const QString &serialNo) const; + + const KPoint &operator()(const int index) const; + const ControlPoint *point(const int &index) const; + const QList &pointList() const; + + protected: + ControlPoint *point(const int index); + + private: + QList m_kpts; //! List of KPoints managed by this class + + /** + * @brief Ascending order sort functor + * + * This is a comparison class used to sort lists of KPoint objects by strength, in + * ascending order. + * + * @author 2016-09-30 Kris Becker + * + * @internal + * @history 2016-09-30 Kris Becker - Original Version + * + */ + class SortStrengthDescending { + public: + SortStrengthDescending() { } + ~SortStrengthDescending() { } + inline bool operator()(const KPoint &a, const KPoint &b) const { + return ( a.strength() > b.strength() ); + } + }; + + + }; + + +} // namespace Isis +#endif diff --git a/isis/src/control/apps/cnetthinner/CnetSuppression.cpp b/isis/src/control/apps/cnetthinner/CnetSuppression.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d76409c90125c048712bf927695ab4af9a5171d2 --- /dev/null +++ b/isis/src/control/apps/cnetthinner/CnetSuppression.cpp @@ -0,0 +1,711 @@ +/** + * @file + * $Revision: 6565 $ + * $Date: 2016-02-10 17:15:35 -0700 (Wed, 10 Feb 2016) $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "Application.h" +#include "CnetSuppression.h" +#include "CnetManager.h" +#include "Progress.h" + +#include "tnt/tnt_array2d.h" +#include "tnt/tnt_array2d_utils.h" + +#define EARLY_TERMINATION true +#define RADIUS_CELLS 100 + +///#define DEBUG 1 + +namespace Isis { + +/** + * Constructs an empty CnetSuppression object. + * + */ + CnetSuppression::CnetSuppression() : CnetManager(), m_cnet(), m_points(), m_results(), + m_early_term(EARLY_TERMINATION), + m_area() { } + +/** + * Constructs a CentSuppression object using a filename and a weight. + * + * @param cnetfile Filename of the controlnet file. + * @param weight Weight to apply to all points in controlnet. + * + * @throws IException::User "Control Net filename [FILENAME] is invalid." + */ + CnetSuppression::CnetSuppression(const QString &cnetfile, const double &weight) : + CnetManager( ), m_cnet(), m_points(), m_results(), + m_early_term(EARLY_TERMINATION), + m_area() { + + Progress progress; + m_cnet.reset(new ControlNet(cnetfile, &progress)); + + if (!m_cnet->IsValid()) { + QString msg = QString("Control Net filename [%1] is invalid.").arg(cnetfile); + throw IException(IException::User, msg, _FILEINFO_); + } + + m_points = m_cnet->take(); + load(m_points, weight); + } + + +/** + * Constructs a CnetSuppression object using a CnetManager + * + * @param cman CnetManager used to construct a CnetSuppression. + */ + CnetSuppression::CnetSuppression(const CnetManager &cman) : + CnetManager(cman), + m_cnet(), m_points(), + m_results(), + m_early_term(EARLY_TERMINATION), + m_area() { } + +/** + * + * Destructor. Cleans up dynamically allocated control points. + * + */ + CnetSuppression::~CnetSuppression() { + BOOST_FOREACH ( ControlPoint *p, m_points ) { + delete p; + } + } + + +/** + * Sets the early termiation flag + * + * @param state Will terminate early if true + */ + void CnetSuppression::setEarlyTermination(const bool &state) { //TODO this is not used right now at all? + m_early_term = state; + return; + } + + +/** + * Performs a suppression on all cubes associated with the CnetSuppression object and returns the + * results as a Results object. An input bitmask will be used to mask all pointsets associated with + * all cubes before running the suppression. + * + * @param minpts minimum points to keep in the result set + * @param maxpts maximum points to keep in the result set. + * @param min_radius The minimum radius to use for the suppression calculation. + * @param tolerance A multiplicative tolerance on the number of maxpoints to return. + * @param bm A BitMask to apply to the input point set. + * + * @return @b CnetSuppression::Results The Results set for the suppression run. + */ + CnetSuppression::Results CnetSuppression::suppress(const int &minpts, const int &maxpts, + const double &min_radius, + const double &tolerance, + const CnetSuppression::BitMask &bm) { + + QMap cubePnts = getCubeMeasureCount(); + + QMapIterator cubeset(cubePnts); + QVector > pntcount; + while ( cubeset.hasNext() ) { + cubeset.next(); + pntcount.append(qMakePair(cubeset.key(), cubeset.value())); + } + + // Sort to find the image with the highest measure count as a starting point + qSort(pntcount.begin(), pntcount.end(), SortSerialsByPntSize()); + +#if defined(DEBUG) + for (int i = 0; i < pntcount.size() ; i++) { + std::cout << pntcount[i].first << "\t" << pntcount[i].second << "\n"; + } +#endif + + // Suppress points in highest to lowest count + m_results.clear(); + BitMask myBm = bm; + Results final; + for ( int p = 0 ; p < pntcount.size() ; p++) { + QString serialno = pntcount[p].first; + +#if defined(DEBUG) +// int pts = pntcount[p].second; + std::cout << "\n--> Serial: " << serialno.toStdString() << "\n"; +#endif + + Results r = suppress(serialno, minpts, maxpts, min_radius, + tolerance, myBm); + m_results.append(r); + +#if defined(DEBUG) + std::cout << " Total Saved: " << r.size() << " at cell radius " + << r.m_radius << "\n"; +#endif + + final = merge(r,final); + myBm = final.m_selected; + } + + return (final); + } + + +/** + * Performs a suppression on the PointSet associated with a single cube as indicated by + * its serial number and returns the results as a new PointSet. An input bitmask will + * be used to mask the input pointset before running the suppression. + * + * @param serialno The serial number for the image/cube to run suppression on. + * @param minpts The minimum possible points to keep after a suppression run. + * @param maxpts The maximum possible points to keep after a suppression run. + * @param min_radius The minimum radius to use for the suppression calculation. + * @param tolerance A multiplicative tolerance on the number of maxpoints to return. + * @param bm A BitMask to apply to the input point set. + * + * @return @b CnetSuppression::Results The Result set for the suppression run. + */ + CnetSuppression::Results CnetSuppression::suppress(const QString &serialno, const int minpts, + const int &maxpts, const double &min_radius, + const double &tolerance, + const CnetSuppression::BitMask &bm) { + PointSet cubeset = getCubeMeasureIndices(serialno); + +#if defined(DEBUG) + std::cout << " PointSetSize: " << cubeset.size() << "\n"; +#endif + + return ( suppress(cubeset, minpts, maxpts, min_radius, tolerance, bm) ); + } + + +/** + * Performs a suppression on the input PointSet and returns the result as a new PointSet. + * An input bitmask will be used to mask the input pointset before running the suppression. + * + * @param points The point set to run suppression on. + * @param minpts The minimum possible points to keep after a suppression run. + * @param maxpts The maximum possible points to keep after a suppression run. + * @param min_radius The minimum radius to use for the suppression calculation. + * @param tolerance A tolerance factor which scales the size of the search space for suppression. + * @param bm A BitMask to apply to the input point set. + * + * @return @b CnetSuppression::Results The Result set for the suppression run. + */ + CnetSuppression::Results CnetSuppression::suppress(const CnetSuppression::PointSet &points, + const int &minpts, const int &maxpts, + const double &min_radius, + const double &tolerance, + const CnetSuppression::BitMask &bm) { + + // Bounding box of control points + QRectF d = domain(points); + + double max_radius = qMax(d.width(), d.height()); + int num = qMax(qFloor(max_radius - min_radius), 11); //TODO not sure where the 11 came from...? + QVector radii = linspace(min_radius, max_radius, num, + 1.0/qSqrt(2.0) ); + + QPointF botR = d.bottomRight(); + +#if defined(DEBUG) + QPointF topL = d.topLeft(); + std::cout << " Domain((x), (y)): (" << topL.x() << "," << botR.x() + << "), (" << topL.y() << "," << botR.y() << ")\n"; + std::cout << " Min.Max, count Radius: " << min_radius << ", " + << max_radius << " ," << num << "\n"; +#endif + + // Get scaled points to save + int v_maxpts = int ( (double) maxpts * getScale( d.size() ) ); + v_maxpts = qMax(v_maxpts, minpts); + int pnttol = qFloor( (v_maxpts * tolerance) + 0.5 ); + + + // Determine if any previously selected points are contained in this set + PointSet fixed( contains(bm, points) ); + +#if defined(DEBUG) + std::cout << " FixedPoints: " << fixed.size() << " - ToSave: " + << v_maxpts << " (scaled) - Pnttol: " << pnttol << "\n"; +#endif + + Results result(size(), d, 1.0); + result.add(fixed); + + // Check for a termination condition on input + if ( result.size() > (v_maxpts - pnttol) ) { + +#if defined(DEBUG) + std::cout << " ++> Initial condition met - return input set\n"; +#endif + + m_results.append(result); + return (result); + } + + // Binary loop around cell radius list + int bmin = 0; + int bmax = radii.size() - 1; + while ( (bmax-bmin) > 1 ) { + int bmid = (bmin + bmax) / 2; + +#if defined(DEBUG) +// std::cout << " \nBSearchIndx: (" << bmin << "," << bmid << "," << bmax << ")\n"; +#endif + + double cell_size = radii[bmid]; + int n_x_cells = qCeil(botR.x() / cell_size); + int n_y_cells = qCeil(botR.y() / cell_size); + BOOST_ASSERT ( n_x_cells > 0 ); + BOOST_ASSERT ( n_y_cells > 0 ); + +#if defined(DEBUG) + std::cout << " CellRadius(x,y): " << cell_size << " - " + << "Grid(" << n_x_cells << "," << n_y_cells << ")\n"; +#endif + + // Create initial coverage grid with fixed points + GridMask grid(n_x_cells, n_y_cells, false); + result = Results(size(), d, cell_size); + result.add(fixed); + cover(grid, fixed, cell_size); + +#if defined(DEBUG) + int nIcov = cover(grid, fixed, cell_size); + std::cout << " InitialCoverage: " << nIcov << "\n"; +#endif + + // Evaluate all points + int x_center, y_center; + for ( int i = 0 ; i < points.size() ; i++) { + + cellIndex(points[i], cell_size, x_center, y_center); + BOOST_ASSERT ( x_center < n_x_cells ); + BOOST_ASSERT ( y_center < n_y_cells ); + + // Got one, update result state + if ( false == grid[x_center][y_center] ) { + + // First check to see if we have exceeded the requested results set + result.add(points[i]); + if ( m_early_term ) { + if ( result.size() > (v_maxpts + pnttol) ) { + bmin = bmid; + break; + } + } + + // Compute cell coverage + cover(grid, x_center, y_center, cell_size); + +#if defined(DEBUG) + int ncov = cover(grid, x_center, y_center, cell_size); + std::cout << " TotalCovered: " << ncov << "(" << nCovered(grid) + << ") of " << (n_x_cells*n_y_cells) << "\n"; +#endif + + } + } + + // Results of search... +// std::cout << " PointsFound: " << result.size() << "\n"; + + // Now determine if we have enough points to call it good + if ( (result.size() >= (v_maxpts - pnttol) ) && + (result.size() <= (v_maxpts + pnttol) ) ) { + bmax = bmin; // This will terminate the binary search + } + else { + if ( result.size() < v_maxpts ) { + bmax = bmid; + } + else { + bmin = bmid; + } + + // Test failure condition? Not sure yet if we need to do anything + } + } + + // Caller should check to determine if success + return (result); + } + + +/** + * Write out a Results object to an output control network. + * + * @param onetfile Filename for output control network + * @param result Object containin the results of a suppression calculation + * @param saveall If true, copies all points to the output control net, even if ignored. + * @param netid Control networkd id + */ + void CnetSuppression::write(const QString &onetfile, const Results &result, + const bool saveall, const QString &netid) { + // Create new network + QScopedPointer onet; + if ( m_cnet.isNull() ) { + onet.reset( new ControlNet() ); + onet->SetNetworkId("cnetsuppress"); + onet->SetUserName(Application::UserName()); + onet->SetDescription("Network created from suppression of control point set"); + onet->SetCreatedDate(Application::DateTime()); + } + else { + onet.reset( new ControlNet(*m_cnet) ); + } + + if ( !netid.isEmpty() ) { onet->SetNetworkId(netid); } + + // Set states from result set and add points if + for ( int i = 0 ; i < size() ; i++ ) { + ControlPoint *p = point(i); + p->SetIgnored( !result.m_selected[i] ); + if ( (!saveall) && result.m_selected[i] ) { onet->AddPoint(p); } + } + + // Save all original points with altered ignored status + if ( saveall ) { + for ( int i = 0; i < m_points.size(); i++ ) { //TODO: is this the same as size() + onet->AddPoint( m_points[i] ); + } + } + + // Write the points + onet->Write(onetfile); + (void) onet->take(); // Not necessary to retain these points + return; + } + + +/** + * Gets the control net associated with the CnetSuppresssion. + * + * @return @b const ControlNet* The control net for this CnetSuppression + */ + const ControlNet *CnetSuppression::net() const { + return ( m_cnet.data() ); + } + + +/** + * Gets the index of an input IndexPoint + * + * @param p An IndexPoint to get the index of. + * + * @return @b int The index of the input index point. + */ + int CnetSuppression::index(const CnetSuppression::IndexPoint &p) const { + return (p.first); + } + + +/** + * Gets the control measure from the input IndexPoint. + * + * @param p The IndexPoint to get the control measure from + * + * @return @b ControlMeasure* The control measure of the input IndexPoint + */ + ControlMeasure *CnetSuppression::measure(const CnetSuppression::IndexPoint &p) const { + return ( p.second ); + } + + +/** + * Create a BitMask of a specified size for an input PointSet. + * + * @param nbits The size of a BitMask to create. + * @param p The PointSet used to create a BitMask. + * + * @return @b CnetSuppression::BitMask A bit mask with entires set to true if their index is in the + * input PointSet. + */ + CnetSuppression::BitMask CnetSuppression::maskPoints(int nbits, + const CnetSuppression::PointSet &p) + const { + BOOST_ASSERT (nbits > 0); + BitMask bm(nbits, false); + for (int i = 0 ; i < p.size() ; i++) { + BOOST_ASSERT(p[i].first < nbits); + bm[p[i].first] = true; + } + return (bm); + } + + +/** + * Use an input BitMask to mask the input PointSet, and return the results. + * + * @param bm BitMask contining true for indices to keep and false for indicies to get rid of. + * @param pset The PointSet to apply the BitMask to. + * + * @return @b CnetSuppression::PointSet A PointSet containing only the points not masked out. + */ + CnetSuppression::PointSet CnetSuppression::contains(const CnetSuppression::BitMask &bm, + const CnetSuppression::PointSet &pset) const { + PointSet result; + if ( bm.dim1() == 0 ) { return (result); } + + + BOOST_FOREACH ( const IndexPoint &p, pset) { + BOOST_ASSERT ( index(p) < bm.dim1() ); + if ( bm[index(p)] == true) { + result.append(p); + } + } + return (result); + } + + +/** + * Calculates the (x,y) coordinates for an IndexPoint inside of a cell + * of input size. + * + * @param p The index point to calculate the x_center and y_center of. + * @param cell_size Size of the cell. + * @param x_center The x-coordinate of the center of the cell (Result). + * @param y_center The y-coordinate of the center of the cell (Result). + */ + void CnetSuppression::cellIndex(const CnetSuppression::IndexPoint &p, + const double &cell_size, + int &x_center, int &y_center) const { + x_center = int((measure(p)->GetSample()) / cell_size); + y_center = int((measure(p)->GetLine()) / cell_size); + return; + } + + +/** + * Determine the number of (x,y) positions in the input grid which are set to true. + * + * @param grid The grid to calculate the number of covered points from. + * + * @return @b int The number of convered points; the number of (x,y) positions for which the bitmask + * is set to true. + */ + int CnetSuppression::nCovered(const CnetSuppression::GridMask &grid) const { + int ncov(0); + for ( int x = 0 ; x < grid.dim1() ; x++) { + for ( int y = 0 ; y < grid.dim2() ; y++) { + if ( grid[x][y] == true) ncov++; + } + } + return (ncov); + } + + +/** + * Update a grid to contain true values where it is covered by cells as defined by the input + * PointSet. + * + * @param grid The grid to update by setting to true grid entries which are contained within cells + * definted by the input PointSet. + * @param points The input PointSet to use to update the grid. + * @param cell_size The size of a cell. + * + * @return @b int The number of grid entries updated. + */ + int CnetSuppression::cover(CnetSuppression::GridMask &grid, + const CnetSuppression::PointSet &points, + const double &cell_size) const { + + int x_center, y_center, ncov(0); + BOOST_FOREACH ( const IndexPoint &p, points ) { + cellIndex(p, cell_size, x_center, y_center); + ncov = cover(grid, x_center, y_center, cell_size); + } + return (ncov); //ncov should be += for _all_ covered? + } + + +/** + * Update a grid to contain true values where it overlaps a rectangle defined by the + * input paramters and return the number of values contained in this rectange. + * + * @param grid The grid to update by setting to true grid entries contained within the + * rectangle defined by the paramters passed to this function. + * @param x_center The x-coordinate of the center of the grid. + * @param y_center The y-coordinate of the center of the grid. + * @param cell_size The size of a cell. + * + * @return @b int The number of covered cells. + */ + int CnetSuppression::cover(CnetSuppression::GridMask &grid, + const int &x_center, const int &y_center, + const double &cell_size) const { + + int n_x_cells = grid.dim1(); + int n_y_cells = grid.dim2(); + + // Compute the cover. NOTE this is a rectangle, NOT euclidean distance!!! + int g_x_min = qMax(x_center - int(cell_size+0.5), 0); + int g_x_max = qMin(x_center + int(cell_size+0.5), n_x_cells-1); + int g_y_min = qMax(y_center - int(cell_size+0.5), 0); + int g_y_max = qMin(y_center + int(cell_size+0.5), n_y_cells-1); + +#if defined(DEBUG) + std::cout << " CellCover: (" << g_x_min << "," << g_x_max << ")(" + << g_y_min << "," << g_y_max << ")\n"; +#endif + + grid.subarray(g_x_min, g_x_max, g_y_min, g_y_max) = true; + int ncov = (g_x_max-g_x_min+1) * (g_y_max-g_y_min+1); + return ( ncov ); + } + + +/** + * Merge two PointSets together and return the result. + * + * @param s1 The first PointSet to be merged. + * @param s2 The second PointSet to be merged. + * + * @return @b CnetSuppression::PointSet The merged PointSet. + */ + CnetSuppression::PointSet CnetSuppression::merge(const CnetSuppression::PointSet &s1, + const CnetSuppression::PointSet &s2) const { + BitMask bm2 = maskPoints(size(), s2); + PointSet merged = s2; + for ( int i = 0 ; i < s1.size() ; i++) { + if ( !bm2[s1[i].first] ) { + merged.append(s1[i]); + } + } + return (merged); + } + + +/** + * Merge two CnetSuppression::Results objects together and return the result. + * + * @param r1 The first Results to be merged. + * @param r2 The second Results to be merged. + * + * @return @b CnetSuppression::Results The merged Results. + */ + CnetSuppression::Results CnetSuppression::merge(const CnetSuppression::Results &r1, + const CnetSuppression::Results &r2) const { + if ( !r1.isValid() ) { return (r2); } + if ( !r2.isValid() ) { return (r1); } + + // Both are good, merge them + Results merged; + merged.m_candidates = orMasks(r1.m_candidates, r2.m_candidates); + merged.m_selected = orMasks(r1.m_selected, r2.m_selected); + merged.m_points = merge(r1.m_points, r2.m_points); + return ( merged ); + } + + QRectF CnetSuppression::domain(const CnetSuppression::PointSet &pts) const { + QPointF topL(DBL_MAX, DBL_MAX); + QPointF botR(-DBL_MAX, -DBL_MAX); + BOOST_FOREACH ( IndexPoint p, pts) { + topL.setX(qMin(topL.x(), measure(p)->GetSample()) ); + topL.setY(qMin(topL.y(), measure(p)->GetLine()) ); + + botR.setX(qMax(botR.x(), measure(p)->GetSample()) ); + botR.setY(qMax(botR.y(), measure(p)->GetLine()) ); + + } + return ( QRectF(topL, botR) ); + } + + +/** + * Calculates the ratio between the area contained in a square of side-length d and the area + * of the CnetSuppression. + * + * @param d The length of a side of a square. + * + * @return @b double The fraction: area of a square of size d / the area of the CnetSuppression. + */ + double CnetSuppression::getScale(const QSizeF &d) const { + if ( m_area.isEmpty() ) { m_area = d; } + double area = d.width() * d.height(); + double pcnt = area / (m_area.width() * m_area.height()); + return ( pcnt ); + } + + +/** + * Computes and returns the bitwise 'or' of the two input bitmasks. + * + * @param b1 First input BitMask + * @param b2 Second input BitMask + * + * @return @b CnetSuppression::BitMask A BitMask which is the bitwise result of 'b1 or b2' + */ + CnetSuppression::BitMask CnetSuppression::orMasks(const CnetSuppression::BitMask &b1, + const CnetSuppression::BitMask &b2) const { + BOOST_ASSERT ( b1.dim1() == b2.dim1() ); + BitMask omask(b1.dim1()); + for (int i = 0 ; i < b1.dim1() ; i++) { + omask[i] = b1[i] | b2[i]; + } + return (omask); + } + + +/** + * Creates and returns a vector which contains num entries, starting at dmin and ending at dmax. + * The entires in-between span the space between dmin and dmax with equal steps each time. The + * entire vector is multiplied by an input scale factor. + * + * @param dmin The minimum value of the vector. + * @param dmax The maximum value of the vector. + * @param num The number of entries that should be in the returned vector. + * @param scale Multiplicative scale factor to multiply the entire vector by. + * + * @return @b QVector A vector of size num with entries starting at dmin and ending + * at dmax with values of equal increment spanning the space between them and + * with all entries multiplied by scale. + */ + QVector CnetSuppression::linspace(const double dmin, + const double dmax, + const int num, + const double &scale) const { + double inc = (dmax - dmin) / (double) (num - 1); + QVector ndarray(num); + for (int i = 0 ; i < num ; i++) { + ndarray[i] = (dmin + (inc * (double) i)) * scale; + } + ndarray[num-1] = dmax * scale; + return ( ndarray ); + } + + +} // namespace Isis + diff --git a/isis/src/control/apps/cnetthinner/CnetSuppression.h b/isis/src/control/apps/cnetthinner/CnetSuppression.h new file mode 100644 index 0000000000000000000000000000000000000000..cacdea7cb2c08b868117dad879c2b3b1b80ed6c5 --- /dev/null +++ b/isis/src/control/apps/cnetthinner/CnetSuppression.h @@ -0,0 +1,221 @@ +#ifndef CnetSuppression_h +#define CnetSuppression_h +/** + * @file + * $Revision: 6565 $ + * $Date: 2016-02-10 17:15:35 -0700 (Wed, 10 Feb 2016) $ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +#include +#include + +#include "CnetManager.h" +#include "Progress.h" + +#include "tnt/tnt_array2d.h" +#include "tnt/tnt_array2d_utils.h" + +namespace Isis { + +/** + * Container class for CnetManager + * + * @author 2016-09-30 Kris Becker + * + * @internal + * @history 2016-09-30 Kris Becker - Original Version + * @history 2016-12-28 Kristin Berry - Added documentation and tests for checkin + * + */ + class CnetSuppression : public CnetManager { + public: + typedef CnetManager::IndexPoint IndexPoint; + typedef CnetManager::PointSet PointSet; + + typedef TNT::Array2D GridMask; + typedef TNT::Array1D BitMask; + + /** + * Results of a particular suppression + * + * @author 2016-09-30 Kris Becker + * + * @internal + * @history 2016-09-30 Kris Becker - Original Version + * + */ + class Results { + public: + Results() : m_candidates(), m_selected(), m_points(), + m_domain(), m_radius(0) { } + Results(const int n, const QRectF domain, const double &radius) : + m_candidates(n, false), m_selected(n, false), + m_points(), m_domain(domain),m_radius(radius) { + } + + + /** + * True if the Results are valid. + * + * @return @b bool True if results are valid. + */ + inline bool isValid() const { + return (m_candidates.dim() > 0); + } + + + /** + * The number of points in the Result. + * + * @return @b int Number of points in the Result. + */ + inline int size() const { + return ( m_points.size() ); + } + + + /** + * Add a PointSet to the Results. + * + * @param points The points to add to the Result set. + */ + inline void add(const PointSet &points) { + BOOST_FOREACH (const IndexPoint &p, points) { add(p); } + return; + } + + + /** + * Add a single point to the Result. + * + * @param point The point to add to the Result. + */ + inline void add(const IndexPoint &point) { + m_points.append(point); + int index = point.first; + BOOST_ASSERT (index < m_selected.dim1() ); + m_selected[index] = true; + return; + } + + BitMask m_candidates; //! + BitMask m_selected; //! + PointSet m_points; //! + QRectF m_domain; //! + double m_radius; //! + }; + + CnetSuppression(); + CnetSuppression(const QString &cnetfile, const double &weight = 0.0); + CnetSuppression(const CnetManager &cman); + + virtual ~CnetSuppression(); + + void setEarlyTermination(const bool &state = true); + + Results suppress(const int &minpts, const int &maxpts, + const double &min_radius = 1.5, + const double &tolerance = 0.1, + const BitMask &bm = BitMask()); + + Results suppress(const QString &serialno, const int minpts, + const int &maxpts, const double &min_radius, + const double &tolerance, + const BitMask &bm = BitMask()); + + Results suppress(const PointSet &points, const int &minpts, + const int &maxpts, const double &min_radius, + const double &tolerance, + const BitMask &bm = BitMask()); + + + void write(const QString &onetfile, const Results &result, + const bool saveall = false, const QString &netid = ""); + + protected: + const ControlNet *net() const; + + private: + QScopedPointer m_cnet; //! + QList m_points; //! + BitMask m_saved; //! + QVector m_results; //! + bool m_early_term; //! Will terminate early if true + mutable QSizeF m_area; //! + + int index(const IndexPoint &p) const; + ControlMeasure *measure(const IndexPoint &p) const; + BitMask maskPoints(int nbits, const PointSet &p) const; + PointSet contains(const BitMask &bm, const PointSet &pset) const; + + + void cellIndex(const IndexPoint &p, const double &cell_size, + int &x_center, int &y_center) const; + int nCovered(const GridMask &grid) const; + int cover(GridMask &grid, const PointSet &points, + const double &cell_size) const; + int cover(GridMask &grid, const int &x_center, const int &y_center, + const double &cell_size) const; + + PointSet merge(const PointSet &s1, const PointSet &s2) const; + Results merge(const Results &r1, const Results &r2) const; + + QRectF domain(const PointSet &pts) const; + double getScale(const QSizeF &d) const; + BitMask orMasks(const BitMask &b1, const BitMask &b2) const; + QVector linspace(const double dmin, const double dmax, + const int num, const double &scale = 1.0) const; + + + /** + * @brief Descending order sort functor + * + * This is a comparison class used to sort lists of objects, + * where the QPair.second datum is a number in descending order. + * + * @author 2016-09-30 Kris Becker + * + * @internal + * @history 2016-09-30 Kris Becker - Original Version + * + */ + class SortSerialsByPntSize { + public: + SortSerialsByPntSize() { } + ~SortSerialsByPntSize() { } + inline bool operator()(const QPair &a, + const QPair &b) const { + return ( a.second > b.second ); + } + }; + }; + + +} // namespace Isis +#endif diff --git a/isis/src/control/apps/cnetthinner/Makefile b/isis/src/control/apps/cnetthinner/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..80ccbb3008877eeb67ee7b36e85c3b40f48bf149 --- /dev/null +++ b/isis/src/control/apps/cnetthinner/Makefile @@ -0,0 +1 @@ +include $(ISISROOT)/make/isismake.apps diff --git a/isis/src/control/apps/cnetthinner/cnetthinner.cpp b/isis/src/control/apps/cnetthinner/cnetthinner.cpp new file mode 100644 index 0000000000000000000000000000000000000000..82c07ed5feceb4a4e2c3c32211a72dbf8109645e --- /dev/null +++ b/isis/src/control/apps/cnetthinner/cnetthinner.cpp @@ -0,0 +1,64 @@ +#include "Isis.h" + +#include +#include + +#include "CnetManager.h" +#include "CnetSuppression.h" +#include "ControlNet.h" +#include "ProcessByLine.h" + +using namespace std; +using namespace Isis; + +void IsisMain() { + + // We will be processing by line + ProcessByLine p; + UserInterface &ui = Application::GetUserInterface(); + + QString cnetfrom = ui.GetAsString("CNET"); + double weight = ui.GetDouble("WEIGHT"); + double tolerance = ui.GetDouble("TOLERANCE"); + int maxpoints = ui.GetDouble("MAXPOINTS"); + int minpoints = ui.GetDouble("MINPOINTS"); + QString suppressed = ui.GetString("SUPPRESSED").toLower(); + + if (tolerance < 0.0 || tolerance > 1.0) { + QString msg = "TOLERANCE must be between 0.0 and 1.0"; + throw IException(IException::User, msg, _FILEINFO_); + } + + QScopedPointer suppressor(new CnetSuppression(cnetfrom, weight)); + // suppression->setEarlyTermination(true); NOTE: early termination is currently set by a hard-coded + // flag + + // Suppress the points + int totalLoaded = suppressor->size(); + CnetSuppression::Results result = suppressor->suppress(minpoints, maxpoints, + 1.5, tolerance); + int nsaved = result.size(); + int nremoved = totalLoaded - nsaved; + double efficiency = ( (double) nremoved/(double) totalLoaded ) * 100.0; + + if ( ui.WasEntered("ONET") ) { + bool saveall = ( "ignore" == suppressed ); + QString netid; + if ( ui.WasEntered("NETWORKID") ) { + netid = ui.GetString("NETWORKID"); + } + suppressor->write(ui.GetAsString("ONET"), result, saveall, netid); + } + + // Report results + PvlGroup results("Results"); + results += PvlKeyword("Points", toString(totalLoaded) ); + results += PvlKeyword("Saved", toString(nsaved) ); + results += PvlKeyword("Suppressed", toString(nremoved) ); + results += PvlKeyword("Efficiency", toString(efficiency, 4), "percent" ); + Application::Log(results); + + p.EndProcess(); + +} + diff --git a/isis/src/control/apps/cnetthinner/cnetthinner.xml b/isis/src/control/apps/cnetthinner/cnetthinner.xml new file mode 100644 index 0000000000000000000000000000000000000000..84d3f6c8c8ef468f884bd11f208d3a2feaaa3e9f --- /dev/null +++ b/isis/src/control/apps/cnetthinner/cnetthinner.xml @@ -0,0 +1,174 @@ + + + + + + Generate an updated control network with fewer points, with efficient spatial distributed across images. + + + +

    + cnetthinner will compute the most efficient spatial control + point distribution for each image in the control network using an input number of maximum points. This would typically + be used for very densely populated control networks that could be processed + more quickly if some of the less-useful control points or measures were ignored or removed. cnetthinner's goal is to decrease the total number + of control points without compromising their spatial coverage, as much as is possible. +

    +

    + cnetthinner accomplishes this goal using an algorithm called Suppression via Disk Covering (SDC) [1] to select + the most spacially-efficient control points to retain. +

    +

    + The maximum and minimum number of Control Points to keep in the output Control Network can + be specified with the MAXPOINTS and MINPOINTS parameters. MAXPOINTS must be specified by the user and should be determined by examining the current size and density of the Control Network. Suppressed Control Points can either be set to Ignored or Removed entirely from the output + Control Network using the SUPPRESSED parameter. The results can also be adjusted using the WEIGHT and TOLERANCE + parameters. The TOLERANCE parameter adjusts how flexible the number of output points allowed from the suppression + calculation is around the MAXPOINTS value and the WEIGHT parameter adjusts how much each input control point's strength is weighted in the algorithm, specifically based on the number of valid measures with "goodness of fit" it has. +

    +

    +cnetthinner will output a Control Network and also output a Results PVL group. The Results group provides the following information about the results: +

    +Group = Results
+  Points = (Original Number of Points)
+  Saved = (Number Of Points Retained)
+  Suppressed = (Number of Points Ignored or Removed) 
+  Efficiency = (Number of Points Removed / Original Number of Points) * 100 percent
+End_Group
+
    +

    +

    References

    + +     Efficiently selecting spatially distributed keypoints for visual tracking + S Gauglitz, L Foschini, M Turk, T Höllerer + Image Processing (ICIP), 18th IEEE International Conference on, 1869-1872 + +
    + + + + + + Original Version + + + Add documentation, error-checking, and updates to meet ISIS coding standards and get checked in. Changed application name from cnetsuppress to cnetthinner on Kris's request. + + + + + Control Networks + + + + + + + filename + input + None + Input + + The input Control Network to calculate a spacially-efficient subset of. + + *.net + + + + filename + output + None + + Output + + + The output Control Network, which is the result of the suppression calculation on the input Control + Network. + + + *.ctl *.pvl *.net + + + + + + + double + 0.0 + Weight applied to control point + + A weight factor of the natural LOG(#Measures) * WEIGHT is applied + to the AVERAGE(GoodnessOfFit) of all the measures to produce the + strength of a control point for purposes of selecting the best + points of spatial distribution accross the images in the control + network. The equation is: + 
    +                 AVERAGE(GoodnessOfFit of all Measures) * (1 + LOG(#Measures) * WEIGHT) 
+
    +     +     + + + double + 0.1 + Point count tolerance + + This tolerance factor adjusts the range of acceptable point count output results. + Valid range is: 0.0 - 1.0. (Though 1.0 will result in only 1 output point.) + + + + + double + Number of points to retain per image + + Specify the number of control points per image to retain. + Typically, the absolute minimum points would be 3, but more are + better. In some cases, you may hundreds or perhaps 25 or so. + + + + + double + 3.0 + Select minimum number of points to save + + For non-reference images that may have very little overlap, + this is the minimum number of control points to retain regardless + of the total points contained in the overlap. This is intended to + retain the minimum number of points jigsaw requires to produce an + acceptable bundle adjustment. + + + + + string + REMOVE + Disposition of removed points + + + + + + + + + + string + None + Name of the resulting network + + Users have the option to rename the output control network. + + + +     +     + diff --git a/isis/src/control/apps/cnetthinner/tsts/Makefile b/isis/src/control/apps/cnetthinner/tsts/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..46d84c74c297304e943452a44e06b111f179a92b --- /dev/null +++ b/isis/src/control/apps/cnetthinner/tsts/Makefile @@ -0,0 +1,4 @@ +BLANKS = "%-6s" +LENGTH = "%-40s" + +include $(ISISROOT)/make/isismake.tststree diff --git a/isis/src/control/apps/cnetthinner/tsts/badInput/Makefile b/isis/src/control/apps/cnetthinner/tsts/badInput/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..70f4008aca56256066fcddb6e6266ef2ed4f2716 --- /dev/null +++ b/isis/src/control/apps/cnetthinner/tsts/badInput/Makefile @@ -0,0 +1,13 @@ +APPNAME = cnetthinner + +include $(ISISROOT)/make/isismake.tsts + +# History comments + +commands: + if [ `$(APPNAME) cnet=$(INPUT)/FakeFile.net to=$(OUTPUT)/fail.net \ + maxpoints = 20 >& $(OUTPUT)/error.txt` ]; \ + then \ + true; \ + fi; + diff --git a/isis/src/control/apps/cnetthinner/tsts/default/Makefile b/isis/src/control/apps/cnetthinner/tsts/default/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..c1b8b0c253f1d3bb990908932362175aa34fd7f3 --- /dev/null +++ b/isis/src/control/apps/cnetthinner/tsts/default/Makefile @@ -0,0 +1,12 @@ +APPNAME = cnetthinner + +include $(ISISROOT)/make/isismake.tsts + +# History comments + +commands: + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/output.net maxpoints=20000 \ + suppressed=ignore >& /dev/null; + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/thinned.net maxpoints=20000 \ + suppressed=ignore networkid=testID >& /dev/null; + diff --git a/isis/src/control/apps/cnetthinner/tsts/ignoreOrRemove/Makefile b/isis/src/control/apps/cnetthinner/tsts/ignoreOrRemove/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..000664e9c288ab492292b6b27bf348f577e32004 --- /dev/null +++ b/isis/src/control/apps/cnetthinner/tsts/ignoreOrRemove/Makefile @@ -0,0 +1,20 @@ +APPNAME = cnetthinner +APPNAME2 = cnetedit +APPNAME3 = cnetdiff + +include $(ISISROOT)/make/isismake.tsts + +# History comments + +commands: + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/ignored.net maxpoints=200 \ + suppressed=ignore >& /dev/null; + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/removed.net maxpoints=200 \ + suppressed=remove >& /dev/null; + $(APPNAME2) cnet=$(OUTPUT)/ignored.net onet=$(OUTPUT)/ignored_removed.net \ + delete=yes >& /dev/null; + $(APPNAME3) from=$(OUTPUT)/ignored_removed.net from2=$(OUTPUT)/removed.net report=full \ + >& $(OUTPUT)/cnetdiff.txt; \ + $(RM) $(OUTPUT)/ignored_removed.net >& /dev/null; + + diff --git a/isis/src/control/apps/cnetthinner/tsts/minMaxPoints/Makefile b/isis/src/control/apps/cnetthinner/tsts/minMaxPoints/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..9241b6d22c991b7163034363e9e8e29b3445026f --- /dev/null +++ b/isis/src/control/apps/cnetthinner/tsts/minMaxPoints/Makefile @@ -0,0 +1,20 @@ +APPNAME = cnetthinner + +include $(ISISROOT)/make/isismake.tsts + +# History comments + +commands: + #MAXPOINTS + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/400.net \ + maxpoints=400 >& /dev/null; \ + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/200.net \ + maxpoints=200 >& /dev/null; \ + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/50.net \ + maxpoints=50 >& /dev/null; \ + grep -a NumberOfPoints $(OUTPUT)/50.net >& $(OUTPUT)/50.txt; \ + grep -a NumberOfPoints $(OUTPUT)/200.net >& $(OUTPUT)/200.txt; \ + grep -a NumberOfPoints $(OUTPUT)/400.net >& $(OUTPUT)/400.txt; + + #MINPOINTS + diff --git a/isis/src/control/apps/cnetthinner/tsts/tolerance/Makefile b/isis/src/control/apps/cnetthinner/tsts/tolerance/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..f16ddf23be8ff680dd6111cfa0203f08e8c69e8b --- /dev/null +++ b/isis/src/control/apps/cnetthinner/tsts/tolerance/Makefile @@ -0,0 +1,16 @@ +APPNAME = cnetthinner +include $(ISISROOT)/make/isismake.tsts + +# History comments + +commands: + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/tolSmall.net maxpoints=200 \ + tolerance = 0.0 >& /dev/null; \ + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/tolMedium.net maxpoints=200 \ + tolerance = 0.5 >& /dev/null; \ + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/tolLarge.net maxpoints=200 \ + tolerance=1.0 >& /dev/null; \ + grep -a NumberOfPoints $(OUTPUT)/tolSmall.net >& $(OUTPUT)/sm.txt; \ + grep -a NumberOfPoints $(OUTPUT)/tolMedium.net >& $(OUTPUT)/med.txt; \ + grep -a NumberOfPoints $(OUTPUT)/tolLarge.net >& $(OUTPUT)/large.txt; + diff --git a/isis/src/control/apps/cnetthinner/tsts/weight/Makefile b/isis/src/control/apps/cnetthinner/tsts/weight/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..df6e84393be9f575f135dd03b4c1ed6bc613a0e7 --- /dev/null +++ b/isis/src/control/apps/cnetthinner/tsts/weight/Makefile @@ -0,0 +1,20 @@ +APPNAME = cnetthinner +include $(ISISROOT)/make/isismake.tsts + +# History comments +# Right now, these will all be identical... + +commands: + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/Small.net maxpoints=200 \ + weight = 0.0 >& /dev/null; + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/Medium.net maxpoints=200 \ + weight = 0.5 >& /dev/null; + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/Large.net maxpoints=200 \ + weight = 1.0 >& /dev/null; + $(APPNAME) cnet=$(INPUT)/customPointsTruth.net onet=$(OUTPUT)/XLarge.net maxpoints=200 \ + weight = 10000.0 >& /dev/null; + grep -a NumberOfPoints $(OUTPUT)/Small.net >& $(OUTPUT)/sm.txt; \ + grep -a NumberOfPoints $(OUTPUT)/Medium.net >& $(OUTPUT)/med.txt; \ + grep -a NumberOfPoints $(OUTPUT)/Large.net >& $(OUTPUT)/large.txt; \ + grep -a NumberOfPoints $(OUTPUT)/XLarge.net >& $(OUTPUT)/Xlarge.txt; + diff --git a/isis/src/control/apps/findfeatures/AKAZEAlgorithm.cpp b/isis/src/control/apps/findfeatures/AKAZEAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..0fc63cce2669c3a6aa3a5835e11347774f3124e3 --- /dev/null +++ b/isis/src/control/apps/findfeatures/AKAZEAlgorithm.cpp @@ -0,0 +1,253 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "AKAZEAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + AKAZEAlgorithm::AKAZEAlgorithm() : + Feature2DAlgorithm("AKAZE", "Feature2D", + AKAZEType::create()) { + setupMaps(); + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + AKAZEAlgorithm::AKAZEAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("AKAZE", "Feature2D", + AKAZEType::create(), cvars) { + setupMaps(); + setConfig(config); + setAlgorithmVariables(cvars); + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Destroys the algorithm + */ + AKAZEAlgorithm::~AKAZEAlgorithm() { } + + + /** + * Fills the maps for converting the DescriptorType & Diffusivity variable. + */ + void AKAZEAlgorithm::setupMaps() { + // DescriptorType map. Int values are from OpenCV's API. + m_descriptorTypeMap.left.insert(std::pair("DESCRIPTOR_KAZE_UPRIGHT", 2)); + m_descriptorTypeMap.left.insert(std::pair("DESCRIPTOR_KAZE", 3)); + m_descriptorTypeMap.left.insert(std::pair("DESCRIPTOR_MLDB_UPRIGHT", 4)); + m_descriptorTypeMap.left.insert(std::pair("DESCRIPTOR_MLDB", 5)); + + // Diffusivity map. Int values are from OpenCV's API. + m_diffusivityMap.left.insert(std::pair("DIFF_PM_G1", 0)); + m_diffusivityMap.left.insert(std::pair("DIFF_PM_G2", 1)); + m_diffusivityMap.left.insert(std::pair("DIFF_WEICKERT", 2)); + m_diffusivityMap.left.insert(std::pair("DIFF_CHARBONNIER", 3)); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString AKAZEAlgorithm::description() const { + QString desc = "The OpenCV AKAZE Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d8/d30/classcv_1_1AKAZE.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *AKAZEAlgorithm::create(const PvlFlatMap &vars, + const QString &config) { + return ( new AKAZEAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool AKAZEAlgorithm::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool AKAZEAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool AKAZEAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap AKAZEAlgorithm::getAlgorithmVariables( ) const { + AKAZEPtr algorithm = m_algorithm.dynamicCast(); + PvlFlatMap variables; + variables.add("DescriptorType", m_descriptorTypeMap.right.at( + algorithm->getDescriptorType())); + variables.add("DescriptorSize", toString(algorithm->getDescriptorSize())); + variables.add("DescriptorChannels", toString(algorithm->getDescriptorChannels())); + variables.add("Threshold", toString(algorithm->getThreshold())); + variables.add("NOctaves", toString(algorithm->getNOctaves())); + variables.add("NOctaveLayers", toString(algorithm->getNOctaveLayers())); + variables.add("Diffusivity", m_diffusivityMap.right.at( + algorithm->getDiffusivity())); + return (variables); + } + + +/** + * Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Number of variables actually set + * + * @throws IException::User "The input value is not valid for AKAZE's [DescriptorType] variable" + * @throws IException::User "The input value is not valid for AKAZE's [Diffusivity] variable" + */ + int AKAZEAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + + AKAZEPtr algorithm = m_algorithm.dynamicCast(); + + int numSet(0); + if ( variables.exists("DescriptorType") ) { + QString value = variables.get("DescriptorType"); + bool isInt; + // Check if the value is an integer + int intValue = value.toInt(&isInt); + try { + if (isInt) { + // If it is an integer make sure it is a valid option + m_descriptorTypeMap.right.at(intValue); + } + else { + // If it is a string, then convert it to an integer + intValue = m_descriptorTypeMap.left.at(value); + } + } + catch (std::exception &e) { + QString msg = "The input value [" + value + + "] is not valid for AKAZE's [DescriptorType] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + algorithm->setDescriptorType(intValue); + numSet++; + } + + if ( variables.exists("DescriptorSize") ) { + algorithm->setDescriptorSize(toInt(variables.get("DescriptorSize"))); + numSet++; + } + + if ( variables.exists("DescriptorChannels") ) { + algorithm->setDescriptorChannels(toInt(variables.get("DescriptorChannels"))); + numSet++; + } + + if ( variables.exists("Threshold") ) { + algorithm->setThreshold(toInt(variables.get("Threshold"))); + numSet++; + } + + if ( variables.exists("NOctaves") ) { + algorithm->setNOctaves(toInt(variables.get("NOctaves"))); + numSet++; + } + + if ( variables.exists("NOctaveLayers") ) { + algorithm->setNOctaveLayers(toInt(variables.get("NOctaveLayers"))); + numSet++; + } + + if ( variables.exists("Diffusivity") ) { + QString value = variables.get("Diffusivity"); + bool isInt; + // Check if the value is an integer + int intValue = value.toInt(&isInt); + try { + if (isInt) { + // If it is an integer make sure it is a valid option + m_diffusivityMap.right.at(intValue); + } + else { + // If it is a string, then convert it to an integer + intValue = m_diffusivityMap.left.at(value); + } + } + catch (std::exception &e) { + QString msg = "The input value [" + value + + "] is not valid for AKAZE's [Diffusivity] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + algorithm->setDiffusivity(intValue); + numSet++; + } + + return (numSet); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/AKAZEAlgorithm.h b/isis/src/control/apps/findfeatures/AKAZEAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..e35307f6d5104531af31edb1dc7c70dabc956378 --- /dev/null +++ b/isis/src/control/apps/findfeatures/AKAZEAlgorithm.h @@ -0,0 +1,81 @@ +#ifndef AKAZEAlgorithm_h +#define AKAZEAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "FeatureAlgorithm.h" +#include "opencv2/features2d.hpp" + +#include +#include + +namespace Isis { + +/** + * @brief AKAZE Feature matcher algorithm + * + * This class provides the OpenCV3 AKAZE Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-07 Jesse Mapel + * + * @internal + * @history 2016-12-07 Jesse Mapel - Original Version + */ + +class AKAZEAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + AKAZEAlgorithm(); + AKAZEAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); + virtual ~AKAZEAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + // Provide information about the abilities of the algorithm + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + void setupMaps(); + + boost::bimap m_descriptorTypeMap; /**!< Bi-directional map for converting + DescriptorType values.*/ + boost::bimap m_diffusivityMap; /**!< Bi-directional map for converting + Diffusivity values.*/ + + + private: + typedef cv::AKAZE AKAZEType; + typedef cv::Ptr AKAZEPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/AgastAlgorithm.cpp b/isis/src/control/apps/findfeatures/AgastAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..f22c4a9ca1686eddcecfbbb4d10bbfec70059ca5 --- /dev/null +++ b/isis/src/control/apps/findfeatures/AgastAlgorithm.cpp @@ -0,0 +1,194 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "AgastAlgorithm.h" + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + AgastAlgorithm::AgastAlgorithm() : + Feature2DAlgorithm("AGAST", "Feature2D", + AgastType::create()) { + setupTypeMap(); + m_variables.merge( getAlgorithmVariables() ); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + AgastAlgorithm::AgastAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("AGAST", "Feature2D", + AgastType::create(), cvars) { + setupTypeMap(); + setConfig(config); + setAlgorithmVariables(cvars); + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Destroys the algorithm + */ + AgastAlgorithm::~AgastAlgorithm() { } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString AgastAlgorithm::description() const { + QString desc = "The OpenCV AGAST Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d7/d19/classcv_1_1AgastFeatureDetector.html"; + return (desc); + } + + + /** + * Fills the map for converting the type variable. + */ + void AgastAlgorithm::setupTypeMap() { + m_typeMap.left.insert(std::pair("AGAST_5_8", 0)); + m_typeMap.left.insert(std::pair("AGAST_7_12D", 1)); + m_typeMap.left.insert(std::pair("AGAST_7_12S", 2)); + m_typeMap.left.insert(std::pair("OAST_9_16", 3)); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *AgastAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new AgastAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool AgastAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool AgastAlgorithm::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool AgastAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap AgastAlgorithm::getAlgorithmVariables( ) const { + AgastPtr algorithm = m_algorithm.dynamicCast(); + PvlFlatMap variables; + variables.add("NonmaxSuppression", toString(algorithm->getNonmaxSuppression())); + variables.add("Threshold", toString(algorithm->getThreshold())); + variables.add("Type", m_typeMap.right.at(algorithm->getType())); + return (variables); + } + + +/** + * Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Number of variables actually set + * + * @throws IException::User "The input value is not valid for AGAST's [Type] variable" + */ + int AgastAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + + AgastPtr algorithm = m_algorithm.dynamicCast(); + + int numSet(0); + if ( variables.exists("NonmaxSuppression") ) { + algorithm->setNonmaxSuppression(toInt(variables.get("NonmaxSuppression"))); + numSet++; + } + + if ( variables.exists("Threshold") ) { + algorithm->setThreshold(toInt(variables.get("Threshold"))); + numSet++; + } + + if ( variables.exists("Type") ) { + QString value = variables.get("Type"); + bool isInt; + // Check if the value is an integer + int intValue = value.toInt(&isInt); + try { + if (isInt) { + // If it is an integer make sure it is a valid option + m_typeMap.right.at(intValue); + } + else { + // If it is a string, then convert it to an integer + intValue = m_typeMap.left.at(value.toUpper()); + } + } + catch (std::exception &e) { + QString msg = "The input value [" + value + + "] is not valid for AGAST's [Type] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + algorithm->setType(intValue); + numSet++; + } + + return (numSet); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/AgastAlgorithm.h b/isis/src/control/apps/findfeatures/AgastAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..154d0064162161f2c0c14c08d3bd71c2cb4c7924 --- /dev/null +++ b/isis/src/control/apps/findfeatures/AgastAlgorithm.h @@ -0,0 +1,77 @@ +#ifndef AgastAlgorithm_h +#define AgastAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" + +#include + +#include "opencv2/core.hpp" +#include "opencv2/features2d.hpp" + +namespace Isis { + +/** + * @brief AGAST Feature matcher algorithm + * + * This class provides the OpenCV3 AGAST Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-07 Jesse Mapel + * + * @internal + * @history 2016-12-07 Jesse Mapel - Original Version + */ + +class AgastAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + AgastAlgorithm(); + AgastAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); + virtual ~AgastAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + // Provide information about the abilities of the algorithm + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + void setupTypeMap(); + + boost::bimap m_typeMap; //!< Bi-directional map for converting type values. + + private: + typedef cv::AgastFeatureDetector AgastType; + typedef cv::Ptr AgastPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/AlgorithmParameters.cpp b/isis/src/control/apps/findfeatures/AlgorithmParameters.cpp deleted file mode 100644 index 9338c76c854884a88d8746f3aa5f62dacc9593c9..0000000000000000000000000000000000000000 --- a/isis/src/control/apps/findfeatures/AlgorithmParameters.cpp +++ /dev/null @@ -1,611 +0,0 @@ -/** - * @file - * $Revision: 6598 $ - * $Date: 2016-03-08 11:22:39 -0700 (Tue, 08 Mar 2016) $ - * $Id: AlgorithmParameters.cpp 6598 2016-03-08 18:22:39Z kbecker@GS.DOI.NET $ - * - * Unless noted otherwise, the portions of Isis written by the USGS are - * public domain. See individual third-party library and package descriptions - * for intellectual property information, user agreements, and related - * information. - * - * Although Isis has been used by the USGS, no warranty, expressed or - * implied, is made by the USGS as to the accuracy and functioning of such - * software and related material nor shall the fact of distribution - * constitute any such warranty, and no responsibility is assumed by the - * USGS in connection therewith. - * - * For additional information, launch - * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html - * in a browser or see the Privacy & Disclaimers page on the Isis website, - * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on - * http://www.usgs.gov/privacy.html. - */ - - -#include -#include -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include - -#include - -#include - -#include -#include - -#include "AlgorithmParameters.h" -#include "FileName.h" -#include "IString.h" -#include "IException.h" -#include "PvlKeyword.h" -#include "PvlObject.h" - -using namespace std; - -namespace Isis { - - -/* Constructor */ -AlgorithmParameters::AlgorithmParameters() { } - -/* Destructor */ -AlgorithmParameters::~AlgorithmParameters() { } - -/** - * @brief Get a PVL Object style description of Algorithm and its parameters - * - * @param algorithm Pointer to algorithm to generate a PVL Object for its - * parameters - * @param aType Specifies the type of algorithm - * - * @return PvlObject - */ -PvlObject AlgorithmParameters::getDescription(const cv::Algorithm *algorithm, - const QString &aType) - const { - - checkPtr(algorithm, "Null Algorithm pointer - cannot get description", - _FILEINFO_); - - PvlObject description("Algorithm"); - if ( !aType.isEmpty() ) { - description.addKeyword(PvlKeyword("Type", aType)); - } - - description.addKeyword(PvlKeyword("Name", toQt(algorithm->name())) ); - - vector parameters; - algorithm->getParams(parameters); - for (unsigned int i = 0 ; i < parameters.size() ; i++) { - QString name = toQt(parameters[i]); - PvlKeyword key = PvlKeyword(name, getParameter(algorithm, name) ); - description.addKeyword(key); - } - return (description); -} - -/** - * @brief Get a type of an OpenCV Algorithm parameters - * - * The returned value is an OpenCV internal type code that is used in the - * proper translation of the parameter. Valid return types vary - see the - * OpenCV documentation for type codes. - * - * @param algorithm Algorithm to get parameter type from - * @param parameter Name of parameter to get type for - * - * @return int - */ -int AlgorithmParameters::getParameterType(const cv::Algorithm *algorithm, - const QString ¶meter) const { - - - checkPtr(algorithm, "Null Algorithm pointer - cannot get parameter type for " + parameter, - _FILEINFO_); - - string name = getParameterName(algorithm, parameter); - return (algorithm->paramType(name.c_str())); -} - - -/** - * @brief Determine if a parameter exists in the given algorithm - * - * This method accepts a case insensitive string naming a potential parameter - * within the given algorithm. - * - * @param algorithm Algorithm to look up parameter for - * @param parameter Name of parameter to look up. - * - * @return bool True if the parameter exists in the given Algorithm - */ -bool AlgorithmParameters::hasParameter(const cv::Algorithm *algorithm, - const QString ¶meter) const { - vector names; - algorithm->getParams(names); - QString target(parameter.toLower()); - BOOST_FOREACH ( string name, names ) { - if ( toQt(name).toLower() == target) return ( true ); - } - return ( false ); - -} - -/** - * @brief Get the value of a named parameter in an Algorithm - * - * This method will retrieve the value of a named parameter in the given - * Algorithm and return it as a string. - * - * Matrices, vectors and Algorithms are not supported value types in this - * method. - * - * @param algorithm Algorithm to get parameter from - * @param parameter Name of parameter to get value for - * - * @return QString String representation of the value of the parameter. - * @see getParameterVariant() - */ -QString AlgorithmParameters::getParameter(const cv::Algorithm *algorithm, - const QString ¶meter) - const { - - checkPtr(algorithm, "Null Algorithm pointer - cannot get parameter " + parameter, - _FILEINFO_); - - QString value("Null"); - try { - int argType = getParameterType(algorithm, parameter); - switch ( argType ) { - case cv::Param::BOOLEAN: - value = toString(algorithm->getBool(toStd(parameter))); - break; - - case cv::Param::INT: - case cv::Param::SHORT: - case cv::Param::UNSIGNED_INT: - case cv::Param::UCHAR: - case cv::Param::UINT64: - value = toString(algorithm->getInt(toStd(parameter))); - break; - - case cv::Param::REAL: - case cv::Param::FLOAT: - value = toString(algorithm->getDouble(toStd(parameter))); - break; - - case cv::Param::STRING: - value = toQt(algorithm->getString(toStd(parameter))); - break; - - case cv::Param::MAT: - value = "cv::Mat"; - break; - - case cv::Param::MAT_VECTOR: - value = "cv::Mat_Vector"; - break; - - case cv::Param::ALGORITHM: { - cv::Ptr subalgo = getAlgorithm(algorithm, parameter); - if ( !subalgo.empty() ) { value = toQt(subalgo->name()); } - else { value = "Null"; } - } - break; - - default: - value = "Null"; - break; - } - } - catch (cv::Exception &e) { - QString mess = "Cannot get parameter " + parameter + ", OpenCV::Error - " + - toQt(e.what()); - throw IException(IException::Programmer, mess, _FILEINFO_); - } - - return (value); -} - -/** - * @brief Get the value of a named parameter in an Algorithm - * - * This method will retrieve the value of a named parameter in the given - * Algorithm and return it as a generic QVariant type. - * - * All OpenCV parameter types are supported by this method. - * - * @param algorithm Algorithm to get parameter from - * @param parameter Name of parameter to get value for - * - * @return QVariant Returns the value as a QVariant - * @see getParameter() - */ -QVariant AlgorithmParameters::getParameterVariant(const cv::Algorithm *algorithm, - const QString ¶meter) const { - - - checkPtr(algorithm, "Null Algorithm pointer - cannot get parameter variant " + parameter, - _FILEINFO_); - - QVariant value; - try { - int argType = getParameterType(algorithm, parameter); - switch ( argType ) { - case cv::Param::BOOLEAN: - value = QVariant(algorithm->getBool(toStd(parameter))); - break; - - case cv::Param::INT: - case cv::Param::SHORT: - case cv::Param::UNSIGNED_INT: - case cv::Param::UCHAR: - case cv::Param::UINT64: - value = QVariant(algorithm->getInt(toStd(parameter))); - break; - - case cv::Param::REAL: - case cv::Param::FLOAT: - value = QVariant(algorithm->getDouble(toStd(parameter))); - break; - - case cv::Param::STRING: - value = QVariant(toQt(algorithm->getString(toStd(parameter)))); - break; - - case cv::Param::MAT: - value = QVariant::fromValue(algorithm->getMat(toStd(parameter))); - break; - - case cv::Param::MAT_VECTOR: - value = QVariant::fromValue(algorithm->getMatVector(toStd(parameter))); - break; - - case cv::Param::ALGORITHM: - value = QVariant::fromValue(getAlgorithm(algorithm, parameter)); - break; - - default: - break; - } - } - catch (cv::Exception &e) { - QString mess = "Cannot get parameter to variant " + parameter + ", OpenCV::Error - " + - toQt(e.what()); - throw IException(IException::Programmer, mess, _FILEINFO_); - } - - return (value); -} - -/** - * @brief Set an Algorithm parameter with the given value string representation - * - * This method will take a string representation of an Algorithm parameter - * value, convert it to the proper internal representation and set in the given - * algorithm. - * - * Matrices, vectors and algorithm types are not supported in this method - * - * @param algorithm Algorithm to set the parameter - * @param parameter Name of the paramter to set - * @param value String of the value to convert and set in the algorithm - * - * @return bool True if successful, false if failed - * @see setParameterVariant() - */ -bool AlgorithmParameters::setParameter(cv::Algorithm *algorithm, - const QString ¶meter, - const QString &value) const { - - - checkPtr(algorithm, "Null Algorithm pointer - cannot set parameter " + parameter, - _FILEINFO_); - - try { - string name = getParameterName(algorithm, parameter); - int argType = getParameterType(algorithm, parameter); - switch ( argType ) { - case cv::Param::BOOLEAN: - algorithm->set(name, toBool(value)); - break; - - case cv::Param::UCHAR: { - unsigned char uval = cv::saturate_cast(toInt(value)); - algorithm->set(name, uval); - } - break; - - case cv::Param::INT: - case cv::Param::SHORT: - case cv::Param::UNSIGNED_INT: - case cv::Param::UINT64: - algorithm->set(name, toInt(value)); - break; - - case cv::Param::REAL: - case cv::Param::FLOAT: - algorithm->set(name, toDouble(value)); - break; - - case cv::Param::STRING: - algorithm->set(name, toStd(value)); - break; - - case cv::Param::MAT: - case cv::Param::MAT_VECTOR: - case cv::Param::ALGORITHM: - default: { - QString mess = "Data type " + QString::number(argType) + - " not supported in this method for parameter " + parameter; - throw IException(IException::Programmer, mess, _FILEINFO_); - } - } - } - catch (cv::Exception &e) { - QString mess = "Cannot set parameter " + parameter + ", OpenCV::Error - " + - toQt(e.what()); - throw IException(IException::Programmer, mess, _FILEINFO_); - } - return (true); -} - -/** - * @brief Set an Algorithm parameter with value in QVariant - * - * This method will take a QVariant representation of an Algorithm parameter - * value and set in the given algorithm. All types are assumed to be of the - * cooresponding type if the parameter - * - * All OpenCV paremeter types are supported. Exception are thrown if the - * QVairiant type cannot be converted to the parameter type. - * - * @param algorithm Algorithm to set the parameter - * @param parameter Name of the paramter to set - * @param value QVarint value to set in the algorithm - * - * @return bool True if successful, false if failed - * @see setParameter() - */ -bool AlgorithmParameters::setParameterVariant(cv::Algorithm *algorithm, - const QString ¶meter, - const QVariant &value) const { - - checkPtr(algorithm, "Null Algorithm pointer - cannot set parameter variant " + parameter, - _FILEINFO_); - - try { - string name = getParameterName(algorithm, parameter); - int argType = getParameterType(algorithm, parameter); - switch ( argType ) { - case cv::Param::BOOLEAN: - algorithm->set(name, value.toBool()); - break; - - case cv::Param::UCHAR: { - unsigned char uval = cv::saturate_cast(value.toInt()); - algorithm->set(name, uval); - } - break; - - case cv::Param::INT: - case cv::Param::SHORT: - case cv::Param::UNSIGNED_INT: - case cv::Param::UINT64: - algorithm->set(name, value.toInt()); - break; - - case cv::Param::REAL: - case cv::Param::FLOAT: - algorithm->set(name, value.toDouble()); - break; - - case cv::Param::STRING: - algorithm->set(name, toStd(value.toString())); - break; - - case cv::Param::MAT: - if ( value.canConvert() ) { - algorithm->set(name, value.value()); - } - else { - QString mess = "Cannot convert " + parameter + " parameter to cv::Mat"; - throw IException(IException::Programmer, mess, _FILEINFO_); - } - break; - - case cv::Param::MAT_VECTOR: - if ( value.canConvert >() ) { - algorithm->set(name, value.value >()); - } - else { - QString mess = "Cannot convert " + parameter + " parameter to vector"; - throw IException(IException::Programmer, mess, _FILEINFO_); - } - break; - - case cv::Param::ALGORITHM: - if ( value.canConvert >() ) { - algorithm->set(name, value.value >()); - } - else { - QString mess = "Cannot convert " + parameter + " parameter to cv::Prt"; - throw IException(IException::Programmer, mess, _FILEINFO_); - } - break; - - default: { - QString mess = "Data type " + QString::number(argType) + - " not supported in this method for parameter " + parameter; - throw IException(IException::Programmer, mess, _FILEINFO_); - } - } - } - catch (cv::Exception &e) { - QString mess = "Cannot set parameter w/variant " + parameter + ", OpenCV::Error - " + - toQt(e.what()); - throw IException(IException::Programmer, mess, _FILEINFO_); - } - return (true); -} - -/** - * @brief Retrieve an Algorithm type parameter from an Algorithm - * - * This method will get the Algorithm type from a parameter in the given - * Algorithm. - * - * @param algorithm Algorithm to get the parameter for - * @param parameter Name of the algorithm in the Algorithm - * - * @return cv::Ptr Pointer to Algorithm if sucessful - */ -cv::Ptr AlgorithmParameters::getAlgorithm(const cv::Algorithm *algorithm, - const QString ¶meter) const { - checkPtr(algorithm, "Null Algorithm pointer - cannot get parameter " + parameter, - _FILEINFO_); - int argType = getParameterType(algorithm, parameter); - if ( argType != cv::Param::ALGORITHM ) { - throw IException(IException::Programmer, - "Parameter " + parameter + " is not an algorithm", - _FILEINFO_); - } - return (algorithm->getAlgorithm(toStd(parameter))); -} - -/** - * @brief Retrieve a Matrix type parameter from an Algorithm - * - * This method will get the matrix type from a parameter in the given - * Algorithm. - * - * @param algorithm Algorithm to get the parameter for - * @param parameter Name of the matrix in the Algorithm - * @return cv::Mat Returns the matrix in the given parameter - */ -cv::Mat AlgorithmParameters::getMat(const cv::Algorithm *algorithm, - const QString ¶meter) const { - - checkPtr(algorithm, "Null Algorithm pointer - cannot get cv::Mat " + parameter, - _FILEINFO_); - int argType = getParameterType(algorithm, parameter); - if ( argType != cv::Param::MAT ) { - throw IException(IException::Programmer, - "Parameter " + parameter + " is not an cv::Mat", - _FILEINFO_); - } - return (algorithm->getMat(toStd(parameter))); -} - -/** - * @brief Retrieve a Matrix Vector type parameter from an Algorithm - * - * This method will get the matrix vector type from a parameter in the given - * Algorithm. - * - * @param algorithm Algorithm to get the parameter for - * @param parameter Name of the matrix vector in the Algorithm - * @return cv::Mat Returns the matrix ivector n the given parameter - */ -vector AlgorithmParameters::getMatVector(const cv::Algorithm *algorithm, - const QString ¶meter) const { - - checkPtr(algorithm, "Null Algorithm pointer - cannot get cv::MatVector " + parameter, - _FILEINFO_); - int argType = getParameterType(algorithm, parameter); - if ( argType != cv::Param::MAT_VECTOR ) { - throw IException(IException::Programmer, - "Parameter " + parameter + " is not an cv::MatVector", - _FILEINFO_); - } - return (algorithm->getMatVector(toStd(parameter))); -} - -/** - * @brief Check the validity of an Algorithm pointer - * - * If the pointer given is invalid an error is thrown. - * - * @param algorithm Algorithm pointer to check - * @param mess Message to include in exception - * @param sourceFile File data for error message formatting - * @param lineno File line for error message formatting - */ -void AlgorithmParameters::checkPtr(const cv::Algorithm *algorithm, - const QString &mess, - const char *sourceFile,int lineno) const { - if ( algorithm == 0 ) { - throw IException(IException::Programmer, mess, sourceFile, lineno); - } - return; -} - -/** - * @brief Determine real parameter name from case insensitive version - * - * @param algorithm Algorithm to look for parameter name - * @param name Name of parameter without regard to case - * - * @return string Real name of the algorithm parameter - */ -string AlgorithmParameters::getParameterName(const cv::Algorithm *algorithm, - const QString &name) const { - - checkPtr(algorithm, "Null Algorithm pointer - cannot get real parameter name for " + name, - _FILEINFO_); - - vector params; - algorithm->getParams(params); - QString target(name.toLower()); - BOOST_FOREACH ( string realParm, params ) { - if ( toQt(realParm).toLower() == target ) { - return (realParm); - } - } - - return ( string() ); -} - - -/** - * @brief Sets a parameter in an Algorithm with formatted parameter/value - * - * This method accepts a formatted parameter/value string and sets all - * parameters found in the string. The string should be of the form - * "@parameter:value@parameter:value@...". - * - * @param algorithm Algorithm to set the parameters - * @param parameters String of formatted paramaters - */ -void AlgorithmParameters::setFormattedParameter(cv::Algorithm *algorithm, - const QStringList ¶meters) - const { - checkPtr(algorithm, "Null Algorithm pointer - cannot get set formatted parameter list", - _FILEINFO_); - - BOOST_FOREACH ( QString param, parameters ) { - QStringList parts = param.split(":", QString::SkipEmptyParts); - if ( parts.size() != 2 ) { - QString mess = "Bad parameter/value form (" + param + ") for algorithm " - + toQt(algorithm->name()); - throw IException(IException::User, mess, _FILEINFO_); - } - - setParameter(algorithm, parts[0], parts[1]); - } - return; -} - - -} // namespace Isis diff --git a/isis/src/control/apps/findfeatures/AlgorithmParameters.h b/isis/src/control/apps/findfeatures/AlgorithmParameters.h deleted file mode 100644 index e4c12000f0e16ae820fb798be3785bd7031ab386..0000000000000000000000000000000000000000 --- a/isis/src/control/apps/findfeatures/AlgorithmParameters.h +++ /dev/null @@ -1,146 +0,0 @@ -#ifndef AlgorithmParameters_h -#define AlgorithmParameters_h -/** - * @file - * $Revision $ - * $Date: 2016-03-08 11:22:39 -0700 (Tue, 08 Mar 2016) $ - * - * Unless noted otherwise, the portions of Isis written by the USGS are public - * domain. See individual third-party library and package descriptions for - * intellectual property information,user agreements, and related information. - * - * Although Isis has been used by the USGS, no warranty, expressed or implied, - * is made by the USGS as to the accuracy and functioning of such software - * and related material nor shall the fact of distribution constitute any such - * warranty, and no responsibility is assumed by the USGS in connection - * therewith. - * - * For additional information, launch - * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see - * the Privacy & Disclaimers page on the Isis website, - * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on - * http://www.usgs.gov/privacy.html. - */ -#include -#include -#include - -#include - -#include -#include -#include - -#include "IException.h" -#include "PvlObject.h" - -namespace Isis { -/** - * @brief Provides parameterization of OpenCV Algorithms - * - * This class provides a generic interface to OpenCV Algorithms. THere are - * getter and setter methods that will retrieve and set, respectively, - * named parameters in an OpenCV Algorithm object. Note that matrices, vectors - * and Algorithm types contained within Algorithms are not yet suppported, - * - * Parameters in OpenCV algorithms are case sensitive, bur this class does not - * require to know the case. All parameters in the given algorithm are available - * in the OpenCV API so they are retrieved and a case insensitive lookup is - * performed to determine the requested algorithm. - * - * In general, algorithm parameters can be specified in a string in the - * following genral format: - * - * @code - * [type.]algorithm[@parameter:value@...] - * @endcode - * - * The name of each parameter to modify is provided right after the @ and a - * colon (:) separates the value from the parameter name. - * - * Example: - * @code - * algorithm=surf@hessianThreshold:100/surf - * @endcode - * - * The above example selects a SURF detector that sets the SURF parameter - * HessianThreshHold to 100 and also selects a SUFR extractor with no parameter - * changes. The extractor is also set to a SURF algorithm. - * - * @author 2015-08-18 Kris Becker - * @internal - * @history 2015-08-18 Kris Becker - Original Version - * @history 2016-04-12 Kris Becker Added class documentation - * @history 2016-10-05 Ian Humphrey & Makayla Shepherd - Changed headers back to OpenCV2. - */ -class AlgorithmParameters { - public: - AlgorithmParameters(); - virtual ~AlgorithmParameters(); - - PvlObject getDescription(const cv::Algorithm *algorithm, - const QString &aType = "") const; - - int getParameterType(const cv::Algorithm *algorithm, - const QString ¶meter) const; - - bool hasParameter(const cv::Algorithm *algorithm, - const QString ¶meter) const; - - QString getParameter(const cv::Algorithm *algorithm, - const QString ¶meter) const; - QVariant getParameterVariant(const cv::Algorithm *algorithm, - const QString ¶meter) const; - - bool setParameter(cv::Algorithm *algorithm, const QString ¶meter, - const QString &value) const; - bool setParameterVariant(cv::Algorithm *algorithm, const QString ¶meter, - const QVariant &value) const; - - cv::Ptr getAlgorithm(const cv::Algorithm *algorithm, - const QString ¶meter) const; - - cv::Mat getMat(const cv::Algorithm *algorithm, - const QString ¶meter) const; - std::vector getMatVector(const cv::Algorithm *algorithm, - const QString ¶meter) const; - - void checkPtr(const cv::Algorithm *algorithm, - const QString &mess = "Null pointer detected!", - const char *sourceFile = __FILE__, - int lineno = __LINE__) const; - - protected: - std::string getParameterName(const cv::Algorithm *algorithm, - const QString &name) const; - - void setFormattedParameter(cv::Algorithm *algorithm, - const QStringList ¶meters) const; - - /* Efficent conversion of standard string to Qt QString */ - inline QString toQt(const std::string &s) const { - return (QString::fromStdString(s)); - } - - /* Efficient conversion of QString to standard string */ - inline std::string toStd(const QString &s) const { - return (s.toStdString()); - } - - /* Efficient conversion of string to float value */ - inline float toFloat(const QString &value) const { - return ( value.toFloat() ); - } - -}; - -} // namespace Isis - -// Declarations so they can be stored as QVariants -Q_DECLARE_METATYPE(cv::Mat); -Q_DECLARE_METATYPE(std::vector); -Q_DECLARE_METATYPE(cv::Ptr); - -#endif - - diff --git a/isis/src/control/apps/findfeatures/BRISKAlgorithm.cpp b/isis/src/control/apps/findfeatures/BRISKAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..14e286a6b79c4b87387ec22ec73b57858a337abc --- /dev/null +++ b/isis/src/control/apps/findfeatures/BRISKAlgorithm.cpp @@ -0,0 +1,197 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "BRISKAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + BRISKAlgorithm::BRISKAlgorithm() : + Feature2DAlgorithm("BRISK", "Feature2D", + BRISKType::create()) { + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + BRISKAlgorithm::BRISKAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("BRISK", "Feature2D", + BRISKType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + + // Constructs the algorithm for a custom pattern + if (variables.exists("RadiusList") && variables.exists("NumberList")) { + std::vector radiusList; + QStringList radiusStrings = variables.get("RadiusList").split(","); + BOOST_FOREACH(QString radius, radiusStrings) { + radiusList.push_back(radius.toFloat()); + } + + std::vector numberList; + QStringList numberStrings = variables.get("NumberList").split(","); + BOOST_FOREACH(QString number, numberStrings) { + numberList.push_back(toInt(number)); + } + const float dMax = variables.get("DMax", "5.85").toFloat(); + const float dMin = variables.get("DMin", "8.2").toFloat(); + + std::vector indexChange; + if (!variables.get("IndexChange", "").isEmpty()) { + QStringList indexStrings = variables.get("IndexChange").split(","); + BOOST_FOREACH(QString index, indexStrings) { + indexChange.push_back(toInt(index)); + } + } + m_algorithm = BRISKType::create(radiusList, numberList, dMax, dMin, indexChange); + } + // Constructs the algorithm with the input variables + else { + const int thresh = toInt(variables.get("Threshold")); + const int octaves = toInt(variables.get("NOctaves")); + const float patternScale = variables.get("PatternScale").toFloat(); + + m_algorithm = BRISKType::create(thresh, octaves, patternScale); + } + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + BRISKAlgorithm::~BRISKAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap BRISKAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("Threshold", "30"); + variables.add("NOctaves", "3"); + variables.add("PatternScale", "1.0"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString BRISKAlgorithm::description() const { + QString desc = "The OpenCV BRISK Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/de/dbf/classcv_1_1BRISK.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *BRISKAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new BRISKAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool BRISKAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool BRISKAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool BRISKAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap BRISKAlgorithm::getAlgorithmVariables( ) const { + return (variables()); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "BRISKAlgorithm does not have the ability + * to set algorithm parameters." + */ + int BRISKAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "BRISKAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/BRISKAlgorithm.h b/isis/src/control/apps/findfeatures/BRISKAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..295cf07fa15b0b381a07d45a7dc2f30fdf07abd3 --- /dev/null +++ b/isis/src/control/apps/findfeatures/BRISKAlgorithm.h @@ -0,0 +1,72 @@ +#ifndef BRISKAlgorithm_h +#define BRISKAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/features2d.hpp" + +#include + +namespace Isis { + +/** + * @brief BRISK Feature matcher algorithm + * + * This class provides the OpenCV3 BRISK Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-12 Jesse Mapel + * + * @internal + * @history 2016-12-12 Jesse Mapel - Original Version + */ + +class BRISKAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + BRISKAlgorithm(); + BRISKAlgorithm( const PvlFlatMap &cvars, const QString &config = QString() ); + virtual ~BRISKAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create( const PvlFlatMap &vars, + const QString &config = QString() ); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::BRISK BRISKType; + typedef cv::Ptr BRISKPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/BlobDetectionAlgorithm.cpp b/isis/src/control/apps/findfeatures/BlobDetectionAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..a015fa79e7222c28ba7c9d989c813c12723ed4fb --- /dev/null +++ b/isis/src/control/apps/findfeatures/BlobDetectionAlgorithm.cpp @@ -0,0 +1,202 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" + +#include "BlobDetectionAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + BlobDetectionAlgorithm::BlobDetectionAlgorithm() : + Feature2DAlgorithm("Blob", "Feature2D", + BLOBType::create()) { + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + BlobDetectionAlgorithm::BlobDetectionAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("Blob", "Feature2D", + BLOBType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + cv::SimpleBlobDetector::Params params; + params.thresholdStep = variables.get("ThresholdStep").toFloat(); + params.minThreshold = variables.get("MinThreshold").toFloat(); + params.maxThreshold = variables.get("MaxThreshold").toFloat(); + params.minRepeatability = variables.get("MinRepeatability").toUInt(); + params.minDistBetweenBlobs = variables.get("MinDistance").toFloat(); + params.filterByColor = toBool(variables.get("FilterByColor")); + params.blobColor = (unsigned char) toInt(variables.get("BlobColor")); + params.filterByArea = toBool(variables.get("FilterByArea")); + params.minArea = variables.get("MinArea").toFloat(); + params.maxArea = variables.get("MaxArea").toFloat(); + params.filterByCircularity = toBool(variables.get("FilterByCircularity")); + params.minCircularity = variables.get("MinCircularity").toFloat(); + params.maxCircularity = variables.get("maxCircularity").toFloat(); + params.filterByInertia = toBool(variables.get("FilterByInertia")); + params.minInertiaRatio = variables.get("MinInertiaRatio").toFloat(); + params.maxInertiaRatio = variables.get("MaxInertiaRatio").toFloat(); + params.filterByConvexity = toBool(variables.get("FilterByConvexity")); + params.minConvexity = variables.get("MinConvexity").toFloat(); + params.maxConvexity = variables.get("MaxConvexity").toFloat(); + + m_algorithm = BLOBType::create(params); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + BlobDetectionAlgorithm::~BlobDetectionAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap BlobDetectionAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("ThresholdStep", "10"); + variables.add("MinThreshold", "50"); + variables.add("MaxThreshold", "220"); + variables.add("MinRepeatability", "2"); + variables.add("MinDistance", "10"); + variables.add("FilterByColor", "true"); + variables.add("BlobColor", "0"); + variables.add("FilterByArea", "true"); + variables.add("MinArea", "25"); + variables.add("MaxArea", "5000"); + variables.add("FilterByCircularity", "false"); + variables.add("MinCircularity", "0.8"); + variables.add("maxCircularity", "inf"); + variables.add("FilterByInertia", "true"); + variables.add("MinInertiaRatio", "0.1"); + variables.add("MaxInertiaRatio", "inf"); + variables.add("FilterByConvexity", "true"); + variables.add("MinConvexity", "0.95"); + variables.add("MaxConvexity", "inf"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString BlobDetectionAlgorithm::description() const { + QString desc = "The OpenCV simple blob detection algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d0/d7a/classcv_1_1SimpleBlobDetector.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *BlobDetectionAlgorithm::create(const PvlFlatMap &vars, + const QString &config) { + return ( new BlobDetectionAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool BlobDetectionAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool BlobDetectionAlgorithm::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool BlobDetectionAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap BlobDetectionAlgorithm::getAlgorithmVariables( ) const{ + return ( variables() ); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "BlobDetectionAlgorithm does not have the ability + * to set algorithm parameters." + */ + int BlobDetectionAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "BlobDetectionAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/BlobDetectionAlgorithm.h b/isis/src/control/apps/findfeatures/BlobDetectionAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..3f855b27878a19e639ddc92a7da6194bbcc347f9 --- /dev/null +++ b/isis/src/control/apps/findfeatures/BlobDetectionAlgorithm.h @@ -0,0 +1,75 @@ +#ifndef BlobDetectionAlgorithm_h +#define BlobDetectionAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/features2d.hpp" + +#include + +namespace Isis { + +/** + * @brief Blob detection algorithm + * + * This class provides the OpenCV3 Simple Blob Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-07 Jesse Mapel + * + * @internal + * @history 2016-12-07 Jesse Mapel - Original Version + * @history 2016-12-23 Kristin Berry - Added hasDetector, hasExtractor, hasMatcher and reorganized + * constructor/create code. + */ + +class BlobDetectionAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + BlobDetectionAlgorithm(); + BlobDetectionAlgorithm( const PvlFlatMap &cvars, const QString &config = QString() ); + + virtual ~BlobDetectionAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create( const PvlFlatMap &vars, + const QString &config = QString() ); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::SimpleBlobDetector BLOBType; + typedef cv::Ptr BLOBPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/BriefDescriptorAlgorithm.cpp b/isis/src/control/apps/findfeatures/BriefDescriptorAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..e03b37ed288707a631f8117a07ca3a18ac3b26a7 --- /dev/null +++ b/isis/src/control/apps/findfeatures/BriefDescriptorAlgorithm.cpp @@ -0,0 +1,171 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "BriefDescriptorAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + BriefDescriptorAlgorithm::BriefDescriptorAlgorithm() : + Feature2DAlgorithm("Brief", "Feature2D", + BriefType::create()) { + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + BriefDescriptorAlgorithm::BriefDescriptorAlgorithm(const PvlFlatMap &cvars, + const QString &config) : + Feature2DAlgorithm("Brief", "Feature2D", + BriefType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + int bytes = toInt(variables.get("Bytes")); + bool useOrientation = toBool(variables.get("UseOrientation")); + + m_algorithm = BriefType::create(bytes, useOrientation); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + BriefDescriptorAlgorithm::~BriefDescriptorAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap BriefDescriptorAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("Bytes", "32"); + variables.add("UseOrientation", "true"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString BriefDescriptorAlgorithm::description() const { + QString desc = "The OpenCV simple blob detection algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d0/d7a/classcv_1_1SimpleBlobDetector.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *BriefDescriptorAlgorithm::create(const PvlFlatMap &vars, + const QString &config) { + + return ( new BriefDescriptorAlgorithm(vars, config) ); + } + + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool BriefDescriptorAlgorithm::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool BriefDescriptorAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool BriefDescriptorAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap BriefDescriptorAlgorithm::getAlgorithmVariables( ) const{ + return ( variables() ); + } + + + /** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "BriefDescriptorAlgorithm does not have the ability + * to set algorithm parameters." + */ + int BriefDescriptorAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "BriefDescriptorAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/BriefDescriptorAlgorithm.h b/isis/src/control/apps/findfeatures/BriefDescriptorAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..476068820bc7feba5e9eeff0ea301bcb29c82d43 --- /dev/null +++ b/isis/src/control/apps/findfeatures/BriefDescriptorAlgorithm.h @@ -0,0 +1,71 @@ +#ifndef BriefDescriptorAlgorithm_h +#define BriefDescriptorAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/xfeatures2d.hpp" + +#include + +namespace Isis { + +/** + * @brief Brief descriptor algorithm + * + * This class provides the OpenCV3 Brief Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-09 Jesse Mapel + * + * @internal + * @history 2016-12-09 Jesse Mapel - Original Version + */ + +class BriefDescriptorAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + BriefDescriptorAlgorithm(); + BriefDescriptorAlgorithm( const PvlFlatMap &cvars, const QString &config = QString() ); + virtual ~BriefDescriptorAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create( const PvlFlatMap &vars, + const QString &config = QString() ); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::BriefDescriptorExtractor BriefType; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/BruteForceMatcher.cpp b/isis/src/control/apps/findfeatures/BruteForceMatcher.cpp new file mode 100644 index 0000000000000000000000000000000000000000..dd715650f56461bb5862e9855d0c4ac04b843114 --- /dev/null +++ b/isis/src/control/apps/findfeatures/BruteForceMatcher.cpp @@ -0,0 +1,220 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "PvlFlatMap.h" + +#include + +#include "BruteForceMatcher.h" + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + BruteForceMatcher::BruteForceMatcher() : + DescriptorMatcherAlgorithm("BFMatcher", "DecriptorMatcher", + cv::makePtr()) { + m_normTypeMap = setupNormTypeMap(); + PvlFlatMap variables; + variables.add("NormType", "NORM_L2"); + variables.add("CrossCheck", "false"); + m_variables.merge(variables); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + * @param normType The type of norm to use. Options are + * 2: The L1 norm, + * 4: The L2 norm (DEFAULT), + * 6: The Hamming norm, or + * 7: The Hamming 2 norm. + * @param crossCheck If true; when j, the nearest neightbor to a point i, is + * found it will be checked that i is the nearest neighbor + * to j. Defaults to false. + * + * @throws IException::User "The input value is not valid for + * BruteForceMatcher's [NormType] variable" + * + * @see cv::NormTypes + */ + BruteForceMatcher::BruteForceMatcher(const PvlFlatMap &cvars, const QString &config, + const int normType, const bool crossCheck) : + DescriptorMatcherAlgorithm("BFMatcher", "DecriptorMatcher", + cv::makePtr(normType, crossCheck), cvars) { + m_normTypeMap = setupNormTypeMap(); + setConfig(config); + PvlFlatMap variables; + try { + variables.add("NormType", m_normTypeMap.right.at(normType)); + } + catch (std::exception &e){ + QString msg = "The input value [" + toString(normType) + + "] is not valid for BruteForceMatcher's [NormType] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + variables.add("CrossCheck", toString(crossCheck)); + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + BruteForceMatcher::~BruteForceMatcher() { } + + + /** + * Sets up and returns the bi-directional map for norm type. + * + * @return @b boost:bimap The map between name and int for norm type. + * + * @see cv::NormTypes + */ + boost::bimap BruteForceMatcher::setupNormTypeMap() { + boost::bimap normTypeMap; + + normTypeMap.left.insert(std::pair("NORM_L1", 2)); + normTypeMap.left.insert(std::pair("NORM_L2", 4)); + normTypeMap.left.insert(std::pair("NORM_HAMMING", 6)); + normTypeMap.left.insert(std::pair("NORM_HAMMING2", 7)); + + return ( normTypeMap ); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString BruteForceMatcher::description() const { + QString desc = "The OpenCV BFMatcher DescriptorMatcher matcher algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d3/da1/classcv_1_1BFMatcher.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + * + * @throws IException::User "The input value is not valid for + * BruteForceMatcher's [NormType] variable" + */ + DescriptorMatcherAlgorithm *BruteForceMatcher::create(const PvlFlatMap &vars, + const QString &config) { + boost::bimap normTypeMap = setupNormTypeMap(); + const QString norm = vars.get("NormType", "NORM_L2"); + bool isInt; + int normType = norm.toInt(&isInt); + try { + if (isInt) { + normTypeMap.right.at(normType); + } + else { + normType = normTypeMap.left.at(norm); + } + } + catch (std::exception &e) { + QString msg = "The input value [" + norm + + "] is not valid for BruteForceMatcher's [NormType] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + + const bool crossCheck = toBool(vars.get("CrossCheck", "false")); + + return ( new BruteForceMatcher(vars, config, normType, crossCheck) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool BruteForceMatcher::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool BruteForceMatcher::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool BruteForceMatcher::hasMatcher() const { + return true; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap BruteForceMatcher::getAlgorithmVariables( ) const { + return ( variables() ); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "BruteForceMatcher does not have the ability + * to set algorithm parameters." + */ + int BruteForceMatcher::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "BruteForceMatcher does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/BruteForceMatcher.h b/isis/src/control/apps/findfeatures/BruteForceMatcher.h new file mode 100644 index 0000000000000000000000000000000000000000..cf994d55d6cde5059747e98465374d24da7c3131 --- /dev/null +++ b/isis/src/control/apps/findfeatures/BruteForceMatcher.h @@ -0,0 +1,71 @@ +#ifndef BruteForceMatcher_h +#define BruteForceMatcher_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "FeatureAlgorithm.h" +#include + +namespace Isis { + +/** + * @brief Brute Force Feature matcher algorithm + * + * This class provides the OpenCV3 BFMatcher DescriptorMatcher algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-08 Jesse Mapel + * + * @internal + * @history 2016-12-08 Jesse Mapel - Original Version + */ + +class BruteForceMatcher : public DescriptorMatcherAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + BruteForceMatcher(); + BruteForceMatcher(const PvlFlatMap &cvars, const QString &config = QString(), + const int normType = 4, const bool crossCheck = false); + virtual ~BruteForceMatcher(); + + QString description() const; + + // Required for all algorithms + static DescriptorMatcherAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + static boost::bimap setupNormTypeMap(); + + boost::bimap m_normTypeMap; /**!< Bi-directional map for converting + NormType values.*/ +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/CropTransform.cpp b/isis/src/control/apps/findfeatures/CropTransform.cpp index ff140b27baa539431affa1d17354edb9480072f5..5902b5484a8d1435452d025a8312d12b88c9513e 100644 --- a/isis/src/control/apps/findfeatures/CropTransform.cpp +++ b/isis/src/control/apps/findfeatures/CropTransform.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision: 6598 $ - * $Date: 2016-03-08 11:22:39 -0700 (Tue, 08 Mar 2016) $ - * $Id: CropTransform.cpp 6598 2016-03-08 18:22:39Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/control/apps/findfeatures/CropTransform.h b/isis/src/control/apps/findfeatures/CropTransform.h index bd3b3d8a27aa413ac0489e46b3ca15986a0fb429..91a4c6d24e138c72e1c9bb303dfb909809e9e699 100644 --- a/isis/src/control/apps/findfeatures/CropTransform.h +++ b/isis/src/control/apps/findfeatures/CropTransform.h @@ -2,8 +2,8 @@ #define CropTransform_h /** * @file - * $Revision: 6598 $ - * $Date: 2016-03-08 11:22:39 -0700 (Tue, 08 Mar 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/DaisyAlgorithm.cpp b/isis/src/control/apps/findfeatures/DaisyAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..ee2f8a55e20339e15f588d48f7b092538f458d66 --- /dev/null +++ b/isis/src/control/apps/findfeatures/DaisyAlgorithm.cpp @@ -0,0 +1,238 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "DaisyAlgorithm.h" + +#include +#include +#include + +namespace Isis { + + /** + * Constructs a default DaisyAlgorithm with default variables. Note the OpenCV + * Daisy algorithm does not provide direct parameter access after construction + * so all variable values must be know when constructed. + */ + DaisyAlgorithm::DaisyAlgorithm() : Feature2DAlgorithm("DAISY", "Feature2D", + DAISYType::create()) { + setupTypeMap(); + setupParameters(); + } + + + /** + * Constructs a DaisyAlgorithm with input variables. + * + * This constuctor provides a custom Daisy algorithm that allows users to + * provide specfic values for all algorithm parameters. + * + * H is an optional 3x3 homography matrix used to warp the grid of Daisy. If + * not entereted, it will default to the identity matrix. + * + * + * @throws IException::Programmer "Homography matrix, H, was not input as a string of the form + * \"d,d,d,d,d,d,d,d,d\" where d is a double or integer numerical value." + * + * @param cvars Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + DaisyAlgorithm::DaisyAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("DAISY", "Feature2D", DAISYType::create()) { + setupTypeMap(); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + setConfig(config); + + float radius = (float) toDouble(variables.get("radius")); + int q_radius = toInt(variables.get("q_radius")); + int q_theta = toInt(variables.get("q_theta")); + int q_hist = toInt(variables.get("q_hist")); + int norm = m_typeMap.left.at(variables.get("norm")); + cv::Mat H = cv::Mat::eye(3,3,CV_64FC1); + if ( variables.exists("H")) { + // Convert H-string to a 3x3 matrix represented by a std::vector (opencv will accept this + // as an alternative to a cv::InputArray) + QString Hparm = QString(variables.get("H")); + QStringList elts = Hparm.split( "," ); + + if (elts.size() != 9 ) { + QString mess = "Homography matrix, H, was not input as a string of the form \"d,d,d,d,d,d,d," + "d,d\" where d is a double or integer numerical value."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + // potentially add a try/catch around this for failed .at's or .toDoubles + for (int row = 0; row < 3; row++) { + double* Hi = H.ptr(row); + for (int column = 0 ; column < 3 ; column++) { + Hi[column] = elts.value( column + (row * 3)).toDouble(); + } + } + } + bool interpolation = toBool(variables.get("interpolation")); + bool use_orientation = toBool(variables.get("use_orientation")); + + // Direct creation of DAISY algorithm, replacing default in constructor + // initialization in FeatureAlgorithm::m_algorithm + m_algorithm = DAISYType::create(radius, q_radius, q_theta, q_hist, norm, H, + interpolation, use_orientation); + + // Set the input parameter conditions + m_variables.merge(variables); + } + + +/** + * Default Destructor + */ + DaisyAlgorithm::~DaisyAlgorithm() { } + + + /** + * Returns a description of the DaisyAlgorithm. + * + * @return @b QString A description of the algorithm. + */ + QString DaisyAlgorithm::description() const { + QString desc = "The OpenCV DAISY Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d9/d37/classcv_1_1xfeatures2d_1_1DAISY.html"; + return (desc); + } + + + /** + * Fills the map for converting the type variable. + */ + void DaisyAlgorithm::setupTypeMap() { + m_typeMap.left.insert(std::pair("NRM_NONE", (int) DAISYType::NRM_NONE)); + m_typeMap.left.insert(std::pair("NRM_PARTIAL", (int) DAISYType::NRM_PARTIAL)); + m_typeMap.left.insert(std::pair("NRM_FULL", (int) DAISYType::NRM_FULL)); + m_typeMap.left.insert(std::pair("NRM_SIFT", (int) DAISYType::NRM_SIFT)); + } + + +/** + * Creates and returns an instance of DaisyAlgorithm. + * + * @param vars PvlFlatMap containing algorithm parameters and their values + * @param config A configuration string input by the user + * + * @return @b Feature2DAlgorithm A DaisyAlgorithm instance + */ + Feature2DAlgorithm *DaisyAlgorithm::create(const PvlFlatMap &vars, + const QString &config) { + return ( new DaisyAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool DaisyAlgorithm::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool DaisyAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool DaisyAlgorithm::hasMatcher() const { + return false; + } + + +/** + * Get and return DAISY's parameters and what they're set to as a PvlFlatMap. + * + * @return PvlFlatMap A PvlFlatMap of DAISY's currently set variables and their values. + */ + PvlFlatMap DaisyAlgorithm::getAlgorithmVariables( ) const { + return ( variables() ); + } + + +/** + * @brief Set parameters as provided by the variables, does not work for the + * DAISY algorithm in OpenCV3, so calling this will throw an exception. + * + * @param variables Container of parameters to set + * + * @return int Number of variables actually set + */ + int DaisyAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString message = "DAISY does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, message, _FILEINFO_); + + return (-1); + } + + +/** + * @brief Initiolize the Daisy default parameters according to documentation + * + * This methiod provides the Daisy algorithm parameter defaults according to the + * OpenCV documentation found at + * http://docs.opencv.org/3.1.0/d9/d37/classcv_1_1xfeatures2d_1_1DAISY.html. + * + * This will reset the Daisy parameters to the default conditions and cotnained + * in FeatureAlgorithm::m_variables. + * + * @author Kris Becker 2016-12-18 + * + * @return PvlFlatMap Container of all Daisy parameters + */ + PvlFlatMap DaisyAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("radius", "15"); + variables.add("q_radius", "3"); + variables.add("q_theta", "8"); + variables.add("q_hist", "8"); + variables.add("norm", "NRM_NONE"); + variables.add("H", "1,0,0,0,1,0,0,0,1"); + variables.add("interpolation", "true"); + variables.add("use_orientation", "false"); + m_variables = variables; + return (m_variables); + } + +}; +// namespace Isis + diff --git a/isis/src/control/apps/findfeatures/DaisyAlgorithm.h b/isis/src/control/apps/findfeatures/DaisyAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..69cae4faec825e4815b88e9bdfe51521dbb1a2f3 --- /dev/null +++ b/isis/src/control/apps/findfeatures/DaisyAlgorithm.h @@ -0,0 +1,86 @@ +#ifndef DaisyAlgorithm_h +#define DaisyAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "DaisyExtractor.h" +#include "FeatureAlgorithm.h" +#include "opencv2/xfeatures2d.hpp" + +#include + +#include +#include + +namespace Isis { + +/** + * @brief Daisy Feature matcher algorithm + * + * This class provides the OpenCV3 SURF Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-11-30 Kristin Berry + * + * @internal + * @history 2016-11-30 Kristin Berry - Original Version + */ + +class DaisyAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + DaisyAlgorithm(); + DaisyAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); +#if 0 + DaisyAlgorithm(float radius=15, int q_radius=3, int q_theta=8, int q_hist=8, + int norm=DAISY::NRM_NONE, InputArray H=noArray(), + bool interpolation=true, bool use_orientation=false); +#endif + virtual ~DaisyAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + +protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + void setupTypeMap(); + PvlFlatMap setupParameters(); + + boost::bimap m_typeMap; //!< Bi-directional map for converting type values. + + private: + typedef DaisyExtractor DAISYType; + typedef cv::Ptr DAISYPtr; + +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/DaisyExtractor.cpp b/isis/src/control/apps/findfeatures/DaisyExtractor.cpp new file mode 100644 index 0000000000000000000000000000000000000000..bc937aa89ebaf5ab5cd06e5266b6fc522c9fe06c --- /dev/null +++ b/isis/src/control/apps/findfeatures/DaisyExtractor.cpp @@ -0,0 +1,133 @@ +#include "DaisyExtractor.h" +#include "IException.h" + +#include + +namespace Isis { + +/** + * Always throws an exception. This function is not actually implemented. + * + * @param image image + * @param keypoints keypoints + * @param descriptors descriptors + * + * @throws IException::Programmer "Daisy is unable to run compute with these arguments." + */ + void DaisyExtractor::compute( cv::InputArray image, std::vector& keypoints, + cv::OutputArray descriptors ) { + QString mess = "Daisy is unable to run compute with these arguments."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + +/** + * Always throws an exception. This function is not actually implemented. + * + * @param image image + * @param roi region of interest + * @param descriptors descriptors + * + * @throws IException::Programmer "Daisy is unable to run compute with these arguments." + */ + void DaisyExtractor::compute( cv::InputArray image, cv::Rect roi, cv::OutputArray descriptors ){ + QString mess = "Daisy is unable to run compute with these arguments."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + +/** + * + * Always throws an exception. This function is not actually implemented. + * + * @param image image + * @param descriptors descriptors + * + * @throws IException::Programmer "Daisy is unable to run compute with these arguments." + */ + void DaisyExtractor::compute( cv::InputArray image, cv::OutputArray descriptors ){ + QString mess = "Daisy is unable to run compute with these arguments."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + +/** + * Always throws an exception. This function is not actually implemented. + * + * @param y y coordinate for descriptor + * @param x x coordinate for descriptor + * @param orientation orientation + * @param descriptor descriptor + * + * @throws IException::Programmer "Daisy cannot run GetDescriptor." + */ + void DaisyExtractor::GetDescriptor( double y, double x, int orientation, + float* descriptor ) const { + QString mess = "Daisy cannot run GetDescriptor"; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + +/** + * Always throws an exception. This function is not actually implemented. + * + * + * @param y y coordinate + * @param x x coordinate + * @param orientation orientation + * @param descriptor descriptor + * @param H transformation matrix + * + * @throws IException::Programmer "Daisy cannot run GetDescriptor." + * + * @return @b bool Always false. + */ + bool DaisyExtractor::GetDescriptor( double y, double x, int orientation, float* descriptor, + double* H ) const { + QString mess = "Daisy cannot run GetDescriptor."; + throw IException(IException::Programmer, mess, _FILEINFO_); + return false; + } + +/** + * + * Always throws an exception. This function is not actually implemented. + * + * @param y y coordinate + * @param x x coordinate + * @param orientation orientation + * @param descriptor descriptor + * + * @throws IException::Programmer "Daisy cannot run GetUnnormalizedDescriptor." + */ + + void DaisyExtractor::GetUnnormalizedDescriptor( double y, double x, int orientation, + float* descriptor ) const { + QString mess = "Daisy cannot run GetUnnormalizedDescriptor."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + +/** + * Always throws an exception. This function is not actually implemented. * + * + * @param y y coordinate + * @param x x coordinate + * @param orientation orientation + * @param descriptor descriptor + * @param H transformation matrix + * + * @throws IException::Programmer "Daisy cannot run GetUnnormalizedDescriptor." + * + * @return @b bool Always false. + */ + bool DaisyExtractor::GetUnnormalizedDescriptor( double y, double x, int orientation, + float* descriptor , double *H ) const { + QString mess = "Daisy cannot run GetUnnormalizedDescriptor."; + throw IException(IException::Programmer, mess, _FILEINFO_); + return false; + } + +}; + + diff --git a/isis/src/control/apps/findfeatures/DaisyExtractor.h b/isis/src/control/apps/findfeatures/DaisyExtractor.h new file mode 100644 index 0000000000000000000000000000000000000000..5a8a7652586180207a46ac8d82693529731f4969 --- /dev/null +++ b/isis/src/control/apps/findfeatures/DaisyExtractor.h @@ -0,0 +1,46 @@ +#ifndef DaisyExtractor_h +#define DaisyExtractor_h + +#include "opencv2/xfeatures2d.hpp" +#include "opencv2/opencv.hpp" + +namespace Isis { + +/** + * @brief Wrap of OpenCV3 DAISY algorithm to implement pure virtual functions. + * + * This class wraps the abstract DAISY algorithm so it can be used. + * + * @author 2016-12-20 Kristin Berry + * + * @internal + * @history 2016-12-20 Kristin Berry - Original Version + * + */ + +class DaisyExtractor : public cv::xfeatures2d::DAISY { + +public: + + virtual void compute( cv::InputArray image, std::vector& keypoints, + cv::OutputArray descriptors ); + + virtual void compute( cv::InputArray image, cv::Rect roi, cv::OutputArray descriptors ); + + virtual void compute( cv::InputArray image, cv::OutputArray descriptors ); + + virtual void GetDescriptor( double y, double x, int orientation, float* descriptor ) const; + + virtual bool GetDescriptor( double y, double x, int orientation, float* descriptor, + double* H ) const; + + virtual void GetUnnormalizedDescriptor( double y, double x, int orientation, + float* descriptor ) const; + + virtual bool GetUnnormalizedDescriptor( double y, double x, int orientation, + float* descriptor , double *H ) const; +}; + +} +#endif + diff --git a/isis/src/control/apps/findfeatures/FASTAlgorithm.cpp b/isis/src/control/apps/findfeatures/FASTAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..b9e55efe62d27cd92f50a73a8d27e400433d28c1 --- /dev/null +++ b/isis/src/control/apps/findfeatures/FASTAlgorithm.cpp @@ -0,0 +1,198 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" + +#include "FASTAlgorithm.h" + +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + FASTAlgorithm::FASTAlgorithm() : + Feature2DAlgorithm("FAST", "Feature2D", + FASTType::create()) { + setupTypeMap(); + m_variables.merge( getAlgorithmVariables() ); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + FASTAlgorithm::FASTAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("FAST", "Feature2D", + FASTType::create(), cvars) { + setupTypeMap(); + setConfig(config); + setAlgorithmVariables(cvars); + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Destroys the algorithm + */ + FASTAlgorithm::~FASTAlgorithm() { } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString FASTAlgorithm::description() const { + QString desc = "The OpenCV FAST Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/df/d74/classcv_1_1FASTFeatureDetector.html"; + return (desc); + } + + + /** + * Fills the map for converting the type variable. + */ + void FASTAlgorithm::setupTypeMap() { + m_typeMap.left.insert(std::pair("TYPE_5_8", 0)); + m_typeMap.left.insert(std::pair("TYPE_7_12", 1)); + m_typeMap.left.insert(std::pair("TYPE_9_16", 2)); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *FASTAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new FASTAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool FASTAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool FASTAlgorithm::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool FASTAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap FASTAlgorithm::getAlgorithmVariables( ) const { + FASTPtr algorithm = m_algorithm.dynamicCast(); + PvlFlatMap variables; + variables.add("NonmaxSuppression", toString(algorithm->getNonmaxSuppression())); + variables.add("Threshold", toString(algorithm->getThreshold())); + variables.add("Type", m_typeMap.right.at(algorithm->getType())); + return (variables); + } + + +/** + * Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Number of variables actually set + * + * @throws IException::User "The input value is not valid for FAST's [Type] variable" + */ + int FASTAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + + FASTPtr algorithm = m_algorithm.dynamicCast(); + + int numSet(0); + if ( variables.exists("NonmaxSuppression") ) { + algorithm->setNonmaxSuppression(toInt(variables.get("NonmaxSuppression"))); + numSet++; + } + + if ( variables.exists("Threshold") ) { + algorithm->setThreshold(toInt(variables.get("Threshold"))); + numSet++; + } + + if ( variables.exists("Type") ) { + QString value = variables.get("Type"); + bool isInt; + // Check if the value is an integer + int intValue = value.toInt(&isInt); + try { + if (isInt) { + // If it is an integer make sure it is a valid option + m_typeMap.right.at(intValue); + } + else { + // If it is a string, then convert it to an integer + intValue = m_typeMap.left.at(value); + } + } + catch (std::exception &e) { + QString msg = "The input value [" + value + + "] is not valid for FAST's [Type] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + algorithm->setType(intValue); + numSet++; + } + + return (numSet); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/FASTAlgorithm.h b/isis/src/control/apps/findfeatures/FASTAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..bd39917c78c0686559f770d8ea6cba4caaedce32 --- /dev/null +++ b/isis/src/control/apps/findfeatures/FASTAlgorithm.h @@ -0,0 +1,76 @@ +#ifndef FASTAlgorithm_h +#define FASTAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "FeatureAlgorithm.h" +#include "opencv2/features2d.hpp" + +#include +#include + +namespace Isis { + +/** + * @brief FAST Feature matcher algorithm + * + * This class provides the OpenCV3 FAST Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-07 Jesse Mapel + * + * @internal + * @history 2016-12-07 Jesse Mapel - Original Version + */ + +class FASTAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + FASTAlgorithm(); + FASTAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); + virtual ~FASTAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + void setupTypeMap(); + + boost::bimap m_typeMap; //!< Bi-directional map for converting type values. + + private: + typedef cv::FastFeatureDetector FASTType; + typedef cv::Ptr FASTPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/FREAKAlgorithm.cpp b/isis/src/control/apps/findfeatures/FREAKAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..419e631def8d12d784b19e3b2b15b504b9a0fc3e --- /dev/null +++ b/isis/src/control/apps/findfeatures/FREAKAlgorithm.cpp @@ -0,0 +1,180 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "FREAKAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + FREAKAlgorithm::FREAKAlgorithm() : + Feature2DAlgorithm("FREAK", "Feature2D", + FREAKType::create()) { + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + FREAKAlgorithm::FREAKAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("FREAK", "Feature2D", + FREAKType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + const bool orientationNormalized = toBool(variables.get("OrientationNormalized")); + const bool scaleNormalized = toBool(variables.get("ScaleNormalized")); + const float patternScale = variables.get("PatternScale").toFloat(); + const int nOctaves = toInt(variables.get("NOctaves")); + std::vector selectedPairs; + if (!variables.get("SelectedPairs").isEmpty()) { + QStringList pairList = variables.get("SelectedPairs").split(","); + BOOST_FOREACH(QString pair, pairList) { + selectedPairs.push_back(toInt(pair)); + } + } + + m_algorithm = FREAKType::create(orientationNormalized, scaleNormalized, patternScale, + nOctaves, selectedPairs); + + m_variables.merge(variables); + } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap FREAKAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("OrientationNormalized", "true"); + variables.add("ScaleNormalized", "true"); + variables.add("PatternScale", "22.0"); + variables.add("NOctaves", "4"); + variables.add("SelectedPairs", ""); + m_variables = variables; + return (m_variables); + } + + + /** + * Destroys the algorithm + */ + FREAKAlgorithm::~FREAKAlgorithm() { } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString FREAKAlgorithm::description() const { + QString desc = "The OpenCV FREAK Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/df/db4/classcv_1_1xfeatures2d_1_1FREAK.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *FREAKAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new FREAKAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool FREAKAlgorithm::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool FREAKAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool FREAKAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap FREAKAlgorithm::getAlgorithmVariables( ) const { + return ( variables() ); + } + + + /** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "FREAKAlgorithm does not have the ability + * to set algorithm parameters." + */ + int FREAKAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "FREAKAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/FREAKAlgorithm.h b/isis/src/control/apps/findfeatures/FREAKAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..eae8a5db659e97709001a4c73f726bb79cb59bc3 --- /dev/null +++ b/isis/src/control/apps/findfeatures/FREAKAlgorithm.h @@ -0,0 +1,70 @@ +#ifndef FREAKAlgorithm_h +#define FREAKAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include + +namespace Isis { + +/** + * @brief FREAK Feature matcher algorithm + * + * This class provides the OpenCV3 FREAK Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-12 Jesse Mapel + * + * @internal + * @history 2016-12-12 Jesse Mapel - Original Version + */ + +class FREAKAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + FREAKAlgorithm(); + FREAKAlgorithm(const PvlFlatMap &cvars, const QString &config = QString() ); + virtual ~FREAKAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create( const PvlFlatMap &vars, + const QString &config = QString() ); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::FREAK FREAKType; + typedef cv::Ptr FREAKPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/FastGeom.cpp b/isis/src/control/apps/findfeatures/FastGeom.cpp index dd9c7d5d3bf1452810a0fb45772788313a878bc8..638d90bbaabeb9ceed6a9ad574bd1dc8684941bd 100644 --- a/isis/src/control/apps/findfeatures/FastGeom.cpp +++ b/isis/src/control/apps/findfeatures/FastGeom.cpp @@ -1,7 +1,7 @@ /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/FastGeom.h b/isis/src/control/apps/findfeatures/FastGeom.h index 973f27248f09ac7fd4eff7e50a04401f291d115d..1725feecb909061eba33bd140db1847a3b957d5c 100644 --- a/isis/src/control/apps/findfeatures/FastGeom.h +++ b/isis/src/control/apps/findfeatures/FastGeom.h @@ -2,8 +2,8 @@ #define FastGeom_h /** * @file - * $Revision: 6598 $ - * $Date: 2016-03-08 11:22:39 -0700 (Tue, 08 Mar 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/FeatureAlgorithm.h b/isis/src/control/apps/findfeatures/FeatureAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..fcd06684fb77ffaf081fa2c1c37e8aac0032f0de --- /dev/null +++ b/isis/src/control/apps/findfeatures/FeatureAlgorithm.h @@ -0,0 +1,425 @@ +#ifndef FeatureAlgorithm_h +#define FeatureAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "IException.h" +#include "PvlFlatMap.h" +#include "PvlKeyword.h" +#include "PvlObject.h" + +#include +#include + +// boost library +#include + +#include "opencv2/core.hpp" +#include "opencv2/features2d.hpp" + +namespace Isis { + +/** + * @brief Wrapper for generic algorithm OpenCV3 feature matcher algorithms + * + * This class provides a generic wrapper that is intended to restore some of the + * functionality for these algorithms that were lost in the upgrade from version + * 2. Hence, the class T is intended to be an OpenCV Ptr type that contains + * either a Feature2D or DescriptorMatcher algorithm pointer. + * + * However, the design does lend itself to overide some the OpenCV specifics + * if needed. + * + * The OpenCV implementation can simply extract and populate the + * the PvlFlatMap variable structure to allow the default + * implementation to serve up the algorithm variables to the + * calling environment - or provide a specific implementation if + * inadequate. + * + * The config variable provides a direct way to store how the + * invocation string in the form of + * "algorithmname@var:value@var:value...". + * + * @author 2016-11-30 Kris Becker + * + * @internal + * @history 2016-11-30 Kris Becker - Original Version + */ + +template class FeatureAlgorithm { + public: + FeatureAlgorithm(); + FeatureAlgorithm(const QString &name, const QString &type); + FeatureAlgorithm(const QString &name, const QString &type, + const T algorithm, + const PvlFlatMap &variables = PvlFlatMap()); + virtual ~FeatureAlgorithm(); + + virtual bool isValid() const; + + QString name() const; + QString type() const; + + /** Deriving classes must provide a description of the algorithm */ + virtual QString description() const; + + // Setter/getter for config string + void setConfig(const QString &config); + QString config() const; + + // Setter/getter for algorithm variable + virtual bool setVariable(const QString &var, const QString &value); + virtual QString getVariable(const QString &var, + const QString &separator = ","); + + // Setter/getter for specialized variant variable + virtual bool setVariable(const QString &name, const QVariant &var); + virtual bool getVariable(const QString &var, QVariant &value); + + const PvlFlatMap &variables() const; + + /** Pointer operator - designed for a T shared pointer thus the oddness */ + T algorithm() { return ( m_algorithm ); } + T algorithm() const { return ( m_algorithm ); } + + // Return algorithm information in PVL form + virtual PvlObject info(const QString &objname = "Algorithm") const; + + // Provide information about the abilities of the algorithm + virtual bool hasDetector() const { return false; } + virtual bool hasExtractor() const { return false; } + virtual bool hasMatcher() const { return false; } + + protected: + QString m_name; + QString m_type; + QString m_config; + T m_algorithm; + PvlFlatMap m_variables; + + /** Inheritor must provide implementation of variable + * manipulators */ + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); +}; + + + +//----------------------------------------------------------------------------- +// Implementation of template methods +//----------------------------------------------------------------------------- + +/** + * @brief Default constructor, which is likely needed but useless + * + * @author 2016-12-07 Kris Becker + */ +template FeatureAlgorithm::FeatureAlgorithm() : + m_name("FeatureAlgorithm"), + m_type("Algorithm"), m_config(), + m_algorithm(), m_variables() { } + + +/** + * @brief Construct a named feature algorithm + * + * This constructor is partially valid but assumes the deriving class defines + * the algoritm after construction + * + * @author 2016-12-07 Kris Becker + * + * @param name Name of algorithm + * @param type Type of Algorithm, typically "Feature2D" or "DecriptorMatcher" + */ +template FeatureAlgorithm::FeatureAlgorithm(const QString &name, + const QString &type) : + m_name(name), + m_type(type), + m_config(), + m_algorithm(), + m_variables() { } + +/** + * @brief Construct a complete algorithm + * + * This constructor will provide a complete algorithm with the parameters + * provided. + * + * @author 2016-12-07 Kris Becker + * + * @param name Name of algorithm + * @param type Type of Algorithm, typically "Feature2D" or "DecriptorMatcher" + * @param algorithm Algorithm (assumed to be a cv::Ptr-type parameter + * @param variables Optional list of variables that accompany the algorithm + */ +template FeatureAlgorithm::FeatureAlgorithm(const QString &name, + const QString &type, + const T algorithm, + const PvlFlatMap &variables) : + m_name(name), + m_type(type), + m_config(), + m_algorithm(algorithm), + m_variables(variables) { } + +/** Destructor */ +template FeatureAlgorithm::~FeatureAlgorithm() { } + +/** + * @brief Check validity of algorithm + * + * The default implementation is to simply test if the cv::Ptr is valid. + * Derived classes can reimplement this method if needed. + * + * @author 2016-12-07 Kris Becker + * + * @return bool Returns true if all is well, false if not + */ +template bool FeatureAlgorithm::isValid() const { + return ( !m_algorithm.empty() ); +} + +/** Return the name of the algorithm */ +template QString FeatureAlgorithm::name() const { + return ( m_name ); +} + +/** Returns the type of the algorithm */ +template QString FeatureAlgorithm::type() const { + return ( m_type ); +} + +/** Returns the description of the algorithm */ +template QString FeatureAlgorithm::description() const { + return ( QString("-- Description not provided ---") ); +} + +/** Set the config string if appropriate (typically seen at higher level) */ +template void FeatureAlgorithm::setConfig(const QString &config) { + m_config = config; +} + +/** Return the config string */ +template QString FeatureAlgorithm::config() const { + return ( m_config ); +} + +/** + * @brief Set an algorithm variable to a specific value + * + * The parameters provided in this method are deferred to the + * setAlgorithmVariables() method that derived classes must implement. A + * PvlFlatMap of the value is constructed and passed into the derived routine + * that implenents the setting of all variables. The derived class must return + * the number of valid variables set, which in this case is expected to be 1, + * which is tested for success. If it fails, an exception is thrown. The + * deriving class can also throw an exception if indicated, which is trapped + * and propagated up the call chain. + * + * If the setting succeeds the value is added to the existing Pvl container to + * maintain consistent states of the algorithm variable settings. + * + * If the needed, the deriving class can reimplement this method if the + * behavior is not acceptable. + * + * @author 2016-12-07 Kris Becker + * + * @param var Name of variable to set. Deriving classes should not expect + * case insensitive variable names. Note PvlFlatMap is case + * insensitive. + * @param value String value to set + * + * @return bool True if the variable was successfully set. A false condition + * will never be returned as an exception is thrown on failure. + */ +template bool FeatureAlgorithm::setVariable(const QString &var, + const QString &value) { + PvlFlatMap variable; + variable.add(var, value); + try { + if (0 >= setAlgorithmVariables(variable)) { + QString mess = "Setting of variable " + var + " failed in " + name(); + throw IException(IException::Programmer, mess, _FILEINFO_); + } + } + catch (IException &ie) { + QString mess = "Error setting variable " + var + " in " + name(); + throw IException(ie, IException::Programmer, mess, _FILEINFO_); + } + + m_variables.merge(variable); + return (true); + } + +/** + * @brief Return the values of an algorithm parameter + * + * This method returns the value of an algorithm as it is currently set. + * + * @author 2016-12-12 Kris Becker + * + * @param var Name of variable to retrieve + * + * @return QString The value of the variable. Multiple values are separateed by + * commas. + */ +template QString FeatureAlgorithm::getVariable(const QString &var, + const QString &separator) { + if ( m_variables.exists(var) ) { + return (m_variables.allValues(var).join(separator)); + } + return (QString()); + } + +/** + * @brief Set variable with value contained in a QVariant + * + * This method is for those algorithm uncommon variable types that are not + * suitable to be represented as a string or may require special consideration + * (such as higher precision of doubles). The default implementation, however, + * attempts to convert the QVariant content to a string and apply it using the + * setAlgorithmnVariables() method. + * + * Deriving classes can reimplement this method should it need specialized + * value treatment. + * + * @author 2016-12-07 Kris Becker + * + * @param name Name of variable to set + * @param var QVariant containing the value to appy in the algorithm + * + * @return bool True if successful, however failures result in a thrown + * exception + */ +template bool FeatureAlgorithm::setVariable(const QString &vname, + const QVariant &var) { + QString value = var.toString(); + if ( value.isEmpty() ) { + QString mess = "Variant/variable " + vname + + " cannot be converted in " + name(); + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + PvlFlatMap variable; + variable.add(vname, value); + if ( 0 >= setAlgorithmVariables(variable) ) { + QString mess = "Setting of variable " + vname + " failed in " + name(); + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + m_variables.merge(variable); + return (true); + } + +/** + * @brief Retreive an algorithm variable in a QVariant + * + * This method is provided for algorithm variable types that are not well + * suited for representation in strings. One such example may be a cv::Mat + * variable type. + * + * This method should be reimplemented by deriving classes with special + * variable types if needed. The deffault behavior is to convert the parameter + * data to a QStringList. + * + * @author 2016-12-07 Kris Becker + * + * @param var Name of variable to retrieve its value from + * @param value A QVariont to return the value in + * + * @return bool True if successful, however failures result in a thrown + * exception + */ +template bool FeatureAlgorithm::getVariable(const QString &var, + QVariant &value) { + value = QVariant(QStringList()); + if ( m_variables.exists(var) ) { + if ( m_variables.count(var) > 0 ) { + value = QVariant(m_variables.allValues(var)); + } + return (true); + } + return (false); + } + +/** Returns the PvlFlatMap containing all the variable/values as + * keyword/values */ +template const PvlFlatMap &FeatureAlgorithm::variables() const { + return ( m_variables ); +} + +/** + * @brief Create an object structure of algorithm definition + * + * @author 2016-12-07 Kris Becker + * + * @param objname Optional name for the PvlObject of the description + * + * @return PvlObject PvlObject containing a description of the algorithm + */ +template PvlObject FeatureAlgorithm::info(const QString &objname) const { + PvlObject data(objname); + data.addKeyword(PvlKeyword("CVVersion", CV_VERSION)); + data.addKeyword(PvlKeyword("Name", name())); + data.addKeyword(PvlKeyword("Type", type())); + + PvlKeyword options("Features"); + if ( hasDetector() ) { options += "Detector"; } + if ( hasExtractor() ) { options += "Extractor"; } + if ( hasMatcher() ) { options += "Matcher"; } + data.addKeyword(options); + + data.addKeyword(PvlKeyword("Description", description())); + data.addKeyword(PvlKeyword("CreatedUsing", config())); + + QList values = m_variables.values(); + PvlGroup parameters("Parameters"); + BOOST_FOREACH(PvlKeyword &key, values ) { + parameters.addKeyword(key); + } + data.addGroup(parameters); + return (data); + } + +template PvlFlatMap FeatureAlgorithm::getAlgorithmVariables() const { + return ( m_variables ); +} + + +template int FeatureAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + throw IException(IException::Programmer, "Derived classes must reimplement this method", + _FILEINFO_); + + return (0); +} + + + +// A couple of convenient typedefs for types we know will be need +typedef FeatureAlgorithm > Feature2DAlgorithm; +typedef FeatureAlgorithm > DescriptorMatcherAlgorithm; + +// Shared pointers for convenience +typedef cv::Ptr FeatureAlgorithmPtr; +typedef cv::Ptr MatcherAlgorithmPtr; +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.cpp b/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.cpp index 1d466a36e212cab80a390b953a5f67c7df23a65f..a3e225f3b6a2fb781279de9f0a6ae45c4d7bfd53 100644 --- a/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.cpp +++ b/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision: 6600 $ - * $Date: 2016-03-09 10:30:30 -0700 (Wed, 09 Mar 2016) $ - * $Id: FeatureAlgorithmFactory.cpp 6600 2016-03-09 17:30:30Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -31,6 +31,7 @@ #include #include +#include #include #include #include @@ -39,9 +40,6 @@ #include -#include -#include - #include "FileName.h" #include "IString.h" #include "IException.h" @@ -50,6 +48,29 @@ #include "PvlObject.h" #include "RobustMatcher.h" +// List all the known algorithms +#include "AgastAlgorithm.h" +#include "AKAZEAlgorithm.h" +#include "BlobDetectionAlgorithm.h" +#include "BriefDescriptorAlgorithm.h" +#include "BRISKAlgorithm.h" +#include "DaisyAlgorithm.h" +#include "FASTAlgorithm.h" +#include "FREAKAlgorithm.h" +#include "GFTTAlgorithm.h" +#include "KAZEAlgorithm.h" +#include "LATCHAlgorithm.h" +#include "LUCIDAlgorithm.h" +#include "MSDAlgorithm.h" +#include "MSERAlgorithm.h" +#include "ORBAlgorithm.h" +#include "SIFTAlgorithm.h" +#include "StarAlgorithm.h" +#include "SURFAlgorithm.h" + +#include "BruteForceMatcher.h" +#include "FlannBasedMatcher.h" + using namespace std; namespace Isis { @@ -66,36 +87,23 @@ FeatureAlgorithmFactory *FeatureAlgorithmFactory::m_maker = 0; * handler to an ISIS handler method, and enabling all OpenCV algorithms for * parsing and resolving algorithms. */ -FeatureAlgorithmFactory::FeatureAlgorithmFactory() : AlgorithmParameters() { +FeatureAlgorithmFactory::FeatureAlgorithmFactory() { // This ensures this singleton is shut down when the application exists qAddPostRoutine(DieAtExit); m_nMade = 0; - m_Feature2DModuleName = "Feature2D"; - m_DetectorModuleName = "Detector"; - m_ExtractorModuleName = "Extractor"; - m_MatcherModuleName = "Matcher"; - // Disable OpenCV's error handler by default to suppress text on screen disableOpenCVErrorHandler(); - // List here all those that require something other than uppercase names - // (OpenCV is very case-sensitive when it comes to algorithm names) - m_algorithmNameMap << "SimpleBlob" << "Dense" << "FlannBased" - << "BruteForce-Hamming(2)" << "BruteForce-Hamming" - << "BruteForce-L1" << "BruteForce" << "BFMatcher"; - - m_parameters = PvlFlatMap(); + // Collection of global parameters + m_globalParameters = PvlFlatMap(); // Initialize algorithms - cv::initModule_contrib(); - cv::initModule_ml(); - cv::initModule_video(); - cv::superres::initModule_superres(); - cv::initModule_nonfree(); // Initialize non-free algorithms + (void) initialize(); return; } + /** * @brief Destructor * @@ -105,6 +113,7 @@ FeatureAlgorithmFactory::FeatureAlgorithmFactory() : AlgorithmParameters() { */ FeatureAlgorithmFactory::~FeatureAlgorithmFactory() { } + /** * @brief Retrieve reference to Singleton instance of this object * @@ -122,6 +131,40 @@ FeatureAlgorithmFactory *FeatureAlgorithmFactory::getInstance() { return (m_maker); } + +int FeatureAlgorithmFactory::initialize() { + + int numAliases(0); + + // The detector/extractor Feature2D + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.add("FASTX", FASTAlgorithm::create); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + numAliases += m_algorithmInventory.addFeatureAlgorithm(); + + // The matchers + numAliases += m_algorithmInventory.addMatcherAlgorithm(); + numAliases += m_algorithmInventory.addMatcherAlgorithm(); + + return ( numAliases ); +} + + /** * @brief Disable the OpenCV error handler and replace with ISIS exceptions * @@ -138,6 +181,7 @@ void FeatureAlgorithmFactory::disableOpenCVErrorHandler() { return; } + /** * @brief Re-enable OpenCV error handling * @@ -150,6 +194,7 @@ void FeatureAlgorithmFactory::enableOpenCVErrorHandler() { return; } + /** * @brief Retrieve a list of all available algorithms from OpenCV * @@ -159,35 +204,9 @@ void FeatureAlgorithmFactory::enableOpenCVErrorHandler() { * @return QStringList List of all OpenCV algorithms */ QStringList FeatureAlgorithmFactory::getListAll() const { - vector algorithms; - cv::Algorithm::getList(algorithms); - - QStringList qsAlgos; - BOOST_FOREACH ( string a, algorithms ) { - qsAlgos.push_back(QString::fromStdString(a)); - } - return (qsAlgos); -} - -/** Return a list of all OpenCV Feature2D algorithms */ -QStringList FeatureAlgorithmFactory::getListFeature2D() const { - return (findWithPattern(getListAll(), m_Feature2DModuleName)); -} - -/** Return list of all OpenCV feature detector algorithms */ -QStringList FeatureAlgorithmFactory::getListDetectors() const { - return (findWithPattern(getListAll(), m_DetectorModuleName)); -} - -/** Return list of all OpenCV feature extractor algorithms */ -QStringList FeatureAlgorithmFactory::getListExtractors() const { - return (findWithPattern(getListAll(), m_ExtractorModuleName)); + return ( m_algorithmInventory.allNames() ); } -/** Return list of all OpenCV feature matcher algorithms */ -QStringList FeatureAlgorithmFactory::getListMatchers() const { - return (findWithPattern(getListAll(), m_MatcherModuleName)); -} /** * @brief Return reference to global matcher parameters @@ -197,10 +216,11 @@ QStringList FeatureAlgorithmFactory::getListMatchers() const { * * @return const PvlFlatMap& Reference to matcher algorithms */ -const PvlFlatMap &FeatureAlgorithmFactory::getGlobalParameters() const { - return ( m_parameters ); +const PvlFlatMap &FeatureAlgorithmFactory::globalParameters() const { + return ( m_globalParameters ); } + /** * @brief Set the global parameters to use in all matchers created * @@ -211,9 +231,10 @@ const PvlFlatMap &FeatureAlgorithmFactory::getGlobalParameters() const { * @param globals Global parameters to set for all RobustMatcher algorithms */ void FeatureAlgorithmFactory::setGlobalParameters(const PvlFlatMap &globals) { - m_parameters = globals; + m_globalParameters = globals; } + /** * @brief Add parameters to the global set of RobustMatcher parameters * @@ -224,9 +245,10 @@ void FeatureAlgorithmFactory::setGlobalParameters(const PvlFlatMap &globals) { * @param globals Set of new parameters to add to exist global parameters */ void FeatureAlgorithmFactory::addGlobalParameters(const PvlFlatMap &globals) { - m_parameters = PvlFlatMap(m_parameters, globals); + m_globalParameters = PvlFlatMap(m_globalParameters, globals); } + /** * @brief Add a single parameter to the global RobustMatcher parameters * @@ -238,52 +260,31 @@ void FeatureAlgorithmFactory::addGlobalParameters(const PvlFlatMap &globals) { */ void FeatureAlgorithmFactory::addParameter(const QString &name, const QString &value) { - m_parameters.add(name, value); + m_globalParameters.add(name, value); } + /** * @brief Provide Pvl Object describing parameters of an OpenCV algorithm * * The complete parameter list of the specified OpenCV algorithm is retrieved - * and a Pvl Object is created that contains this description. In some cases, - * callers may want to simplify ore replace the real name. Use of the - * genericName parameter will be used as the name of the PvlObject return by - * this method rather than the full name (which may cause Pvl parse problems). + * and a Pvl Object is created that contains this description. * - * @param name Name of the OpenCV algorithm to return parameters for - * @param genericName Optional name to use instead of real algorithm name + * @param name Name of the OpenCV algorithm to return parameters for * * @return PvlObject Contains all parameters and values for the named algorithm */ -PvlObject FeatureAlgorithmFactory::info(const QString &name, - const QString &genericName) const { -// cout << "Creating algorithm parameter info for " << name << "\n"; - QStringList candidates = getListAll().filter(name); - if ( (candidates.size() < 1) || ( name.isEmpty() ) ) { - QString mess = "Algorithm \"" + name + "\" does not exist or is invalid"; - throw IException(IException::Programmer, mess, _FILEINFO_); - } - - // If there is more than one algorithm that matches this name, defer it to - // the method for this purpose - if ( candidates.size() > 1 ) return ( info(candidates, name) ); - - cv::Ptr a = cv::Algorithm::create(candidates[0].toStdString()); - if ( a.empty() ) { - QString mess = "Failed to create algorithm " + name; - throw IException(IException::Programmer, mess, _FILEINFO_); - } - - return ( getDescription(a, genericName) ); +PvlObject FeatureAlgorithmFactory::info(const QString &name) const { + return ( m_algorithmInventory.info( name ) ); } + /** * @brief Create Pvl Objects with parameters for list of OpenCV algorithms * * This method creates objects for each algorithm that contains parameters and * current default values. Each algorithm object is contained in the top level - * object named "Algorithms". If a value is provided in genericName, it is added - * as a keyword in the top level Algoriths object. + * object named "Algorithms". * * If an error should occur, the algorithm object is created but the name and a * description of the error (in the Error keyword) is recorded instead of @@ -292,46 +293,16 @@ PvlObject FeatureAlgorithmFactory::info(const QString &name, * The OpenCV version is recorded in the "OpenCVVersion" keyword in the * Algorithms object. * - * @param algorithms List of algorithms to create parameter/value objects - * @param genericName Optional name of top level object + * @param algorithms List of algorithms to create parameter/value objects * * @return PvlObject Top level Algorithms object contain algorithm * parameter/value objects */ -PvlObject FeatureAlgorithmFactory::info(const QStringList &algorithms, - const QString &genericName) const { - PvlObject pvlAlgo("Algorithms"); - pvlAlgo.addKeyword(PvlKeyword("OpenCVVersion", CV_VERSION)); - if ( !genericName.isEmpty() ) pvlAlgo.addKeyword(PvlKeyword("GenericName", - genericName)); - - BOOST_FOREACH ( QString name, algorithms ) { -// cout << "Getting list info for algorithm " << name << "\n"; - try { - cv::Ptr a = cv::Algorithm::create(name.toStdString()); - // Check success here if an exception is not thrown - if ( a.empty() ) { - QString mess = "Failed to create algorithm - returned null pointer"; - PvlObject errout("Algorithm"); - errout.addKeyword(PvlKeyword("Name", name)); - errout.addKeyword(PvlKeyword("Error", mess)); - pvlAlgo.addObject(errout); - } - else { - pvlAlgo.addObject( getDescription(a) ); - } - } - catch (cv::Exception &e) { - PvlObject errout("Algorithm"); - errout.addKeyword(PvlKeyword("Name", name)); - errout.addKeyword(PvlKeyword("Error", toQt(e.what()) )); - pvlAlgo.addObject(errout); - continue; - } - } - return ( pvlAlgo ); +PvlObject FeatureAlgorithmFactory::info(const QStringList &algorithms) const { + return ( m_algorithmInventory.info( algorithms, "Algorithms" ) ); } + /** * @brief Create Pvl object of parameter/values for RobustMatcher algorithms * @@ -346,24 +317,23 @@ PvlObject FeatureAlgorithmFactory::info(const QStringList &algorithms, * algorithm (Specification) are also added to the object. These algorithms are * added to a top level object called "FeatureAlgorithms". * - * @param algorithms List of RobustMatcher algorithms to generate info for - * @param genericName Genric name of the top level PvlObject + * @param algorithmList List of RobustMatcher algorithms to generate info for * * @return PvlObject Top level FeatureAlgorithms object containing current * parameter/values for each RobustMatcher algorithm */ -PvlObject FeatureAlgorithmFactory::info(const RobustMatcherList &algorithms, - const QString &genericName) const { - PvlObject pvlAlgo("FeatureAlgorithms"); - if ( !genericName.isEmpty() ) pvlAlgo.addKeyword(PvlKeyword("GenericName", - genericName)); - - BOOST_FOREACH ( SharedRobustMatcher a, algorithms ) { - pvlAlgo.addObject( a->info() ); +PvlObject FeatureAlgorithmFactory::info(const RobustMatcherList &algorithmList) + const { + PvlObject listPvl("FeatureAlgorithms"); + + BOOST_FOREACH(SharedRobustMatcher algorithms, algorithmList) { + listPvl += algorithms->info(); } - return ( pvlAlgo ); + + return ( listPvl ); } + /** * @brief Create a series of feature-based RobustMatcher algorithms * @@ -399,13 +369,12 @@ PvlObject FeatureAlgorithmFactory::info(const RobustMatcherList &algorithms, * algorithms */ RobustMatcherList FeatureAlgorithmFactory::create(const QString &specs, - const bool &errorIfEmpty) - const { + const bool &errorIfEmpty) + const { RobustMatcherList algoList; // Individual algorithm specifications are separated by vertical bars QStringList algorithms = specs.split("|", QString::SkipEmptyParts); - // cout << "create: got " << algorithms.size() << " algorithms...\n"; if ( algorithms.size() == 0 ) { if ( errorIfEmpty ) { QString mess = "No feature matcher algorithms provided!"; @@ -414,19 +383,19 @@ RobustMatcherList FeatureAlgorithmFactory::create(const QString &specs, return (algoList); } - // Make all feature algorithms - BOOST_FOREACH ( QString matcher, algorithms ) { - // cout << " making " << matcher << " algorithm...\n"; - SharedRobustMatcher algo( make(matcher) ); + // Make all feature algorithms + BOOST_FOREACH ( QString matcherSpec, algorithms ) { + SharedRobustMatcher algo( make(matcherSpec) ); if ( algo.isNull() ) { - QString mess = "Failed to create feature matcher from spec " + matcher; + QString mess = "Failed to create feature matcher from spec " + matcherSpec + "."; throw IException(IException::User, mess, _FILEINFO_); } - algoList.push_back(algo); + algoList.append(algo); } return (algoList); } + /** * @brief Create OpenCV feature-based RobustMatcher algorithm from string spec * @@ -445,250 +414,279 @@ RobustMatcherList FeatureAlgorithmFactory::create(const QString &specs, * * @return RobustMatcher* Pointer to a RobustMatcher algorithm */ -RobustMatcher *FeatureAlgorithmFactory::make(const QString &definition) const { - - cv::Ptr detector; - cv::Ptr extractor; - cv::Ptr matcher; - - QStringList featureName; - QString description(definition); - - QStringList parts = definition.split("/", QString::SkipEmptyParts); - if ( (parts.size() < 2) || (parts.size() > 4) ) { - QString mess = "Feature algorithm (" + definition + - ") specification is ill-formed. Must be of the form: " - "Detector/Extractor[/Matcher][/parameters@...] where " - "Detector and Extractor can be a Feature2D algorithm or " - "of its own type. The Matcher is optional and an " - "appropriate one will be allocated based upon the type of " - "Extractor descriptor. Parameters that pertain to the " - "Robust matcher algorithm can be provided in the Parameters " - "option. See findfeatures documentation for what is " - "currently available as parameters."; - throw IException(IException::User, mess, _FILEINFO_); +SharedRobustMatcher FeatureAlgorithmFactory::make(const QString &definition) const { + + // std::cout << "FeatureAlgorithmFactorty::make - Creating feature algorithms from spec: " << definition << "\n"; + FeatureAlgorithmPtr detector; + FeatureAlgorithmPtr extractor; + MatcherAlgorithmPtr matcher; + + QString fullspec(definition); + // Split the full config string up and check formatting + // Output order is always detector, extractor, matcher, parameters + QStringList formattedSpecs = formatSpecifications(fullspec); + + // Merge parameters with global parameters + PvlFlatMap matcherParameters = globalParameters(); + if ( !formattedSpecs[3].isEmpty() ) { + QStringList parametersList = m_algorithmInventory.parse(formattedSpecs[3], "@"); + parametersList.removeFirst(); + matcherParameters.merge( m_algorithmInventory.parameters( parametersList ) ); } - QStringList allOfThem = getListAll(); - int partno(0); - PvlFlatMap algoparms; // Any algorithm parameters are in spec - BOOST_FOREACH ( QString specs, parts ) { - QStringList elements = specs.split("@", QString::SkipEmptyParts); - if ( elements.size() == 0 ) { - QString mess = "Ill-formed \"algorithm[@parameter:value]+]\" ALGORITHM " - "specified in " + specs; - throw IException(IException::User, mess, _FILEINFO_); + // Construct the detector and extractor + try { + if ( !formattedSpecs[0].isEmpty() ) { + // std::cout << "Creating detector with " << formattedSpecs[0]<< "\n"; + detector = m_algorithmInventory.getDetector(formattedSpecs[0]); + if ( formattedSpecs[1].isEmpty() ) { + // std::cout << "Equating extractor to detector\n"; + extractor = detector; + } } - // First check if the spec is the algorithm parameters option and treat it - // special - QString feature = elements.takeFirst(); - if ( "parameters" == feature.toLower() ) { - algoparms = parseParameters(specs); - continue; + if ( !formattedSpecs[1].isEmpty() ) { + // std::cout << "Creating extractor with " << formattedSpecs[1]<< "\n"; + extractor = m_algorithmInventory.getExtractor(formattedSpecs[1]); + if ( formattedSpecs[0].isEmpty() ) { + // std::cout << "Equating detector to extractor\n"; + detector = extractor; + } } - // Its a matcher component so parse it - partno++; - featureName.push_back(feature); - QStringList candidate = findWithPattern(allOfThem, feature); - if ( candidate.size() == 0 ) { - // If its not validated, assume the user knows what they are doing - candidate.push_back(feature); + if ( !formattedSpecs[2].isEmpty() ) { + // std::cout << "Creating matcher with " << formattedSpecs[2]<< "\n"; + matcher = m_algorithmInventory.getMatcher( formattedSpecs[2] ); } + } + catch (IException &e) { + QString mess = "Failed to create algorithms for config:\n" + definition; + throw IException(e, IException::User, mess, _FILEINFO_); + } + + // If no matcher was entered use a BruteForceMatcher + if ( formattedSpecs[2].isEmpty() ) { + // std::cout << "Creating matcher from extractor with " << formattedSpecs[1]<< "\n"; + matcher = createMatcher(extractor); + fullspec += ("/" + matcher->config()); + } + + // Make the algorithms container + MatcherAlgorithms algos(detector, extractor, matcher, matcherParameters); + SharedRobustMatcher falgo( new RobustMatcher(fullspec, algos, matcherParameters) ); + + // Check for validity of matcher that has just been created + try { + falgo->validate(true); + } + catch (IException &ie) { + QString mess = "MatcherAlgorithms were not created successfully!"; + ie.append(IException(IException::User, mess, _FILEINFO_)); + throw ie; + } - // Got a single algorithm. Determine which one - QString ftype = candidate.takeFirst(); - QString realName = mapAlgorithmName(ftype.split(".").takeLast().toUpper()); - string name = toStd(realName); - if ( isFeature2D(ftype) ) { -// cout << "Got a Feature2D engine algorithm: " << ftype -// << ", Name(" << name << ")...\n"; - if ( 1 == partno ) { - detector = cv::Feature2D::create(name); - checkPtr(detector, "Failed to create Feature2D algorithm for " + ftype, - _FILEINFO_); - setFormattedParameter(detector, elements); + m_nMade++; + return ( falgo ); +} + + +/** + * @brief Parses a full specification string for a set of algorithms. + * + * Parses a full specification string for a set of algorithms and checks formatting. + * The specifications will be returned as a QStringList containing, in order: the detector + * specification, the extractor specification, the matcher specification, and the + * parameters specification. If the matcher and/or parameters are not specified they + * will be a null QString. + * + * Upon return, you can expect the following conditions: + * + * 1) All strings have content meaning the specification contained all + * four (detector, extractor, matcher, parameters) algorithm specifications + * 2) Only one of detector *or* extractor was specified and it is a fully + * capable Feature2D algorithm (i.e., it has both valid detector and + * extractor capabilities). + * 3) May not have a matcher, so it must be allocated from the type of the + * extractor which must be determined after it has been initialized (see + * createMatcher(extractor)).. + */ +QStringList FeatureAlgorithmFactory::formatSpecifications(QString specification) const { + QStringList parts = specification.split("/", QString::SkipEmptyParts); + + // Componenet specifications + QString feature2dSpec; + QString detectorSpec; + QString extractorSpec; + QString matcherSpec; + QString parametersSpec; + + QStringList remains; + // Within each part are the values between /'s (i.e., detector, extractor, + // matcher and parameters. + for (int i = 0 ; i < parts.size() ; i++) { + QString part = parts[i].trimmed(); // Remove leading/trailing whitespace + if ( part.contains(QRegularExpression("^feature2d\\.*", QRegularExpression::CaseInsensitiveOption)) ) { + // std::cout << "Setting feature2d: " << part << "\n"; + // If we have a detector and extractor, this is an error + if ( !detectorSpec.isEmpty() && !extractorSpec.isEmpty() ) { + QString mess = "Too many Feature2Ds specified at " + part + " in specification " + + specification; + throw IException(IException::User, mess, _FILEINFO_); } - else if ( 2 == partno ) { - extractor = cv::Feature2D::create(name); - checkPtr(extractor, "Failed to create Feature2D algorithm for " + ftype, - _FILEINFO_); - setFormattedParameter(extractor, elements); + + // Check detector situation + if ( detectorSpec.isEmpty() ) { + detectorSpec = part; } else { - QString mess = "Feature2D type " + ftype + " is not a valid Matcher type"; + // Already have a detector so this must be extractor + extractorSpec = part; + } + // Also sets this for testing purposes + feature2dSpec = part; + } + // Check for explicit settin of detector + else if ( part.contains(QRegularExpression("^detector\\.*", QRegularExpression::CaseInsensitiveOption)) ) { + // std::cout << "Setting detector: " << part << "\n"; + if ( !detectorSpec.isEmpty() ) { + QString mess = "Multiple Detector specs found - have \"" + detectorSpec + "\", but found \"" + + part + "\" in specification: " + specification; throw IException(IException::User, mess, _FILEINFO_); } + detectorSpec = part; } - else if ( isDetector( ftype ) ) { - if ( 1 != partno ) { - QString mess = ftype + " is not a valid detector type"; + // Check for explicit setting of the extractor + else if ( part.contains(QRegularExpression("^extractor\\.*", QRegularExpression::CaseInsensitiveOption)) ) { + // std::cout << "Setting extractor: " << part << "\n"; + if ( !extractorSpec.isEmpty() ) { + QString mess = "Multiple Extractor specs found - have \"" + extractorSpec + "\", but found \"" + + part + "\" in specification: " + specification; throw IException(IException::User, mess, _FILEINFO_); } -// cout << "Making Detector: " << name << "\n"; - detector = cv::FeatureDetector::create(name); - checkPtr(detector, "Failed to create Detector algorithm for " + ftype, - _FILEINFO_); - setFormattedParameter(detector, elements); + extractorSpec = part; } - else if ( isExtractor( ftype ) ) { - if ( 2 != partno ) { - QString mess = ftype + " is not a valid Extractor type"; + // Find matcher alorithm string specification + else if ( part.contains(QRegularExpression("^matcher\\.*", QRegularExpression::CaseInsensitiveOption)) ) { + // std::cout << "Setting matcher: " << part << "\n"; + if ( !matcherSpec.isEmpty() ) { + QString mess = "Multiple Matcher specs found - have \"" + matcherSpec + "\", but found \"" + + part + "\" in specification: " + specification; throw IException(IException::User, mess, _FILEINFO_); } -// cout << "Making Extractor: " << name << "\n"; - extractor = cv::DescriptorExtractor::create(name); - checkPtr(extractor, "Failed to create Extractor algorithm for " + ftype, - _FILEINFO_); - setFormattedParameter(extractor, elements); + matcherSpec = part; } - else if ( isMatcher( ftype) ) { -// cout << "Got a matcher algorithm: " << ftype << " - RealName: " << name << "...\n"; - if ( 3 != partno ) { - QString mess = ftype + " is not a valid in this context must be a " + - (( 1 == partno ) ? "Detector" : "Extractor"); + else if ( part.contains(QRegularExpression("^parameters*", QRegularExpression::CaseInsensitiveOption)) ) { + // std::cout << "Setting paramters: " << part << "\n"; + if ( !parametersSpec.isEmpty() ) { + QString mess = "Multiple Parameter specs found - have \"" + parametersSpec + "\", but found \"" + + part + "\" in specification: " + specification; throw IException(IException::User, mess, _FILEINFO_); } - matcher = cv::DescriptorMatcher::create(name); - checkPtr(matcher, "Failed to create Matcher algorithm for " + ftype, - _FILEINFO_); - setFormattedParameter(matcher, elements); + parametersSpec = part; } else { - QString mess = "Algorithm feature \"" + feature + "\" not a valid feature. " + - "Must be member of one of the following CV modules: " + - m_Feature2DModuleName + ", " + m_DetectorModuleName + ", " + - m_ExtractorModuleName + ", " + m_MatcherModuleName; - throw IException(IException::User, mess, _FILEINFO_); + // std::cout << "Setting algorithm[" << i << "] to " << part << "\n"; + // Can't safely check for ill-formed qualifier, so let the allocation + if ( detectorSpec.isEmpty() ) { + detectorSpec = part; + } + else if ( extractorSpec.isEmpty() ) { + extractorSpec = part; + } + else if ( matcherSpec.isEmpty() ) { + matcherSpec = part; + } + else { + // Should have had parameter already so there are too many parts of + // the specification and its invalid. + QString mess = "Invalid algorithm/part at or near \"" + part + + "\" - too many or invalid algorithm specs detected in specification: " + + specification; + throw IException(IException::User, mess, _FILEINFO_); + } } } - // Verify and construct the RobustMatcher. Parameters specified in each - // algorithm specification take precendence over the globals. - QScopedPointer falgo; - PvlFlatMap mergedParms(m_parameters, algoparms); - if ( matcher.empty() ) { - falgo.reset (new RobustMatcher(featureName.join("+"), detector, extractor, - mergedParms)); - description += falgo->getMatcherDescription(); } - else { - falgo.reset(new RobustMatcher(featureName.join("/"), detector, extractor, - matcher, mergedParms)); - } - - // Check for validity - if ( falgo.isNull() ) { - QString mess = "RobustMatcher::" + featureName.join("/") + - " was not created successfully!"; - throw IException(IException::User, mess, _FILEINFO_); - } - - // Set the specfication string - falgo->setDescription(description); - - m_nMade++; - return ( falgo.take() ); -} - -/** Returns the number of algorithms created by this object */ -unsigned int FeatureAlgorithmFactory::manufactured() const { - return (m_nMade); -} - -/** Find a subset of strings that contain a particular pattern */ -QStringList FeatureAlgorithmFactory::findWithPattern(const QStringList &flist, - const QString &pattern) - const { - return ( flist.filter(pattern, Qt::CaseInsensitive) ); -} - -/** Check for special algorithm cases */ -QString FeatureAlgorithmFactory::mapAlgorithmName(const QString &name) const { - // Ok, special check for a specific case: FlannBasedMatcher = FlannBased - QString target = name.contains("Flann", Qt::CaseInsensitive) ? "Flann" : name; - QStringList algoMap = findWithPattern(m_algorithmNameMap, target); - if ( !algoMap.empty() ) { - return ( algoMap.takeLast() ); + // If a parameter specification was found get it + if ( !parametersSpec.isEmpty() ) { + if ( parametersSpec.split("@", QString::SkipEmptyParts).takeFirst().toLower() != + "parameters" ) { + QString mess = "Invalid specification:\n" + + specification + "\n" + + "Invalid parameters specification:\n" + + parametersSpec; + throw IException(IException::User, mess, _FILEINFO_); + } } - return ( name ); -} - -/** Determine if the string contains an OpenCV Feature2D algorithm spec */ -bool FeatureAlgorithmFactory::isFeature2D(const QString &name) const { - return (name.contains(m_Feature2DModuleName, Qt::CaseInsensitive)); -} - -/** Determine if the string contains an OpenCV detector algorithm spec */ -bool FeatureAlgorithmFactory::isDetector(const QString &name) const { - return (name.contains(m_DetectorModuleName, Qt::CaseInsensitive)); -} - -/** Determine if the string contains an OpemCV extractor algorithm spec */ -bool FeatureAlgorithmFactory::isExtractor(const QString &name) const { - return (name.contains(m_ExtractorModuleName, Qt::CaseInsensitive)); -} - -/** Detemine if the string contains an OpenCV matcher algorithm spec */ -bool FeatureAlgorithmFactory::isMatcher(const QString &name) const { - return (name.contains(m_MatcherModuleName, Qt::CaseInsensitive)); + QStringList formattedSpecs; + formattedSpecs.append(detectorSpec); + formattedSpecs.append(extractorSpec); + formattedSpecs.append(matcherSpec); + formattedSpecs.append(parametersSpec); + + return ( formattedSpecs ); } /** - * @brief Parse a parameter string for values and return in parameter map - * - * This method parses the parameter section of the RobustMatcher specification - * of the matcher algorithm. The general form of the string specification is - * "/parameter@name:value[@name1:value1...]". This will result in a Pvl map - * entry of the form "name = value". - * - * @param parameters Parameter specification part of the feature matcher string - * - * @return PvlFlatMap Pvl map of the parameters parsed from the string + * @brief Allocate a BruteForceMatcher algorithm based upon descriptor extractor + * + * See the OpenCV 3.1 BFMatcher documentation + * http://docs.opencv.org/3.1.0/d3/da1/classcv_1_1BFMatcher.html + * for details on this implementation. + * + * @author 2016-12-19 Jesse Mapel + * @internal + * @history 2016-12-19 Jesse Mapel - Adapted from Kris Becker's RobustMatcher::allocateMatcher */ -PvlFlatMap FeatureAlgorithmFactory::parseParameters(const QString ¶meters) - const { - PvlFlatMap pmap; - - // If the string is empty, return an empty paramter list - QStringList parts = parameters.split("@"); - if ( parts.size() == 0 ) { return (pmap); } - - // Ensure the first part of the parameter list is "parameters" or an error - // is assumed. - QString parmtag = parts.takeFirst(); - if ( "parameters" != parmtag.toLower() ) { - QString mess = "Illformed parameters string [" + parameters + "] - must be " - "of the form \"parameters@parm1:value1@parm2:value2...\""; - throw IException(IException::User, mess, _FILEINFO_); - } +MatcherAlgorithmPtr FeatureAlgorithmFactory::createMatcher(FeatureAlgorithmPtr extractor, + const QString &normalize, + const QString &crossCheck) + const { - // All good so far, parse each parameter string - BOOST_FOREACH ( QString specs, parts ) { + QString name( extractor->name().toLower() ); - // Is it valid? - QStringList parmvaltag = specs.split(":"); - if ( 2 != parmvaltag.size() ) { - QString mess = "Invalid parameter at or near [" + specs + "] in \"" + - parameters + "\" - must be of the form " - "\"parameters@parm1:value1@parm2:value2...\""; - throw IException(IException::User, mess, _FILEINFO_); + QString normType(normalize); + if ( name.contains("SURF", Qt::CaseInsensitive) ) { + normType = "NORM_L2"; + } + else if ( name.contains("SIFT", Qt::CaseInsensitive) ) { + normType = "NORM_L2"; + } + else if (name.contains("ORB", Qt::CaseInsensitive) ) { + normType = "NORM_HAMMING"; + try { + if ( toInt( extractor->getVariable("WTA_K") ) > 2 ) { + normType = "NORM_HAMMING2"; + } + } + catch ( cv::Exception &e ) { + // NOOP - use existing value } - - // Looks good, set the parameters - pmap.add(parmvaltag[0], parmvaltag[1]); + } + else if ( name.contains("BRISK", Qt::CaseInsensitive) ) { + normType = "NORM_HAMMING"; + } + else if ( name.contains("BRIEF", Qt::CaseInsensitive) ) { + normType = "NORM_HAMMING"; } - // All done... - return ( pmap ); + // Create the matcher and return + QString matcherSpecs = "BFMatcher"; + matcherSpecs += ("@NormType:" + normType); + matcherSpecs += ("@CrossCheck:" + crossCheck); + MatcherAlgorithmPtr matcher = m_algorithmInventory.getMatcher(matcherSpecs); + return ( matcher ); } -/* +/** Returns the number of algorithms created by this object */ +unsigned int FeatureAlgorithmFactory::manufactured() const { + return (m_nMade); +} + - */ /** * @brief Method to capture OpenCV exceptions/errors and suppress them * @@ -723,22 +721,22 @@ int FeatureAlgorithmFactory::handleOpenCVErrors( int status, return 0; //Return value is not used } - /** - * @brief Exit termination routine - * - * This (static) method ensure this object is destroyed when Qt exits. - * - * Note that it is error to add this to the system _atexit() routine because - * this object utilizes Qt classes. At the time the atexit call stack is - * executed, Qt is long gone resulting in Very Bad Things. Fortunately, Qt has - * an exit stack function as well. This method is added to the Qt exit call - * stack. - */ - void FeatureAlgorithmFactory::DieAtExit() { - delete m_maker; - m_maker = 0; - return; - } +/** + * @brief Exit termination routine + * + * This (static) method ensure this object is destroyed when Qt exits. + * + * Note that it is error to add this to the system _atexit() routine because + * this object utilizes Qt classes. At the time the atexit call stack is + * executed, Qt is long gone resulting in Very Bad Things. Fortunately, Qt has + * an exit stack function as well. This method is added to the Qt exit call + * stack. + */ +void FeatureAlgorithmFactory::DieAtExit() { + delete m_maker; + m_maker = 0; + return; +} } // namespace Isis diff --git a/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.h b/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.h index 1496690b3cd9ea9cfd9a2ce9e0537c83ddef8481..5423bb472f2ac3129b89c1fb1c3fe01658c38c39 100644 --- a/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.h +++ b/isis/src/control/apps/findfeatures/FeatureAlgorithmFactory.h @@ -3,7 +3,7 @@ /** * @file * $Revision $ - * $Date: 2016-03-09 10:31:51 -0700 (Wed, 09 Mar 2016) $ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for @@ -32,11 +32,11 @@ #include -#include "AlgorithmParameters.h" -#include "RobustMatcher.h" #include "IException.h" +#include "FeatureInventory.h" #include "PvlFlatMap.h" #include "PvlObject.h" +#include "RobustMatcher.h" namespace Isis { @@ -105,7 +105,7 @@ namespace Isis { * @history 2016-03-06 Kris Becker Completed documentation * @history 2016-10-05 Ian Humphrey & Makayla Shepherd - Changed headers to OpenCV2. */ -class FeatureAlgorithmFactory : public AlgorithmParameters { +class FeatureAlgorithmFactory { public: static FeatureAlgorithmFactory *getInstance(); @@ -113,54 +113,39 @@ class FeatureAlgorithmFactory : public AlgorithmParameters { void disableOpenCVErrorHandler(); QStringList getListAll() const; - QStringList getListFeature2D() const; - QStringList getListDetectors() const; - QStringList getListExtractors() const; - QStringList getListMatchers() const; void setGlobalParameters(const PvlFlatMap &globals); void addGlobalParameters(const PvlFlatMap &globals); void addParameter(const QString &name, const QString &value); - const PvlFlatMap &getGlobalParameters() const; + const PvlFlatMap &globalParameters() const; - PvlObject info(const QString &name, - const QString &genericName = "") const; - PvlObject info(const QStringList &algorithms, - const QString &genericName = "") const; - PvlObject info(const RobustMatcherList &algorithms, - const QString &genericName = "") const; + PvlObject info(const QString &name) const; + PvlObject info(const QStringList &algorithms) const; + PvlObject info(const RobustMatcherList &algorithmList) const; RobustMatcherList create(const QString &specifications, const bool &errorIfEmpty = true) const; - RobustMatcher *make(const QString &definition) const; + SharedRobustMatcher make(const QString &definition) const; unsigned int manufactured() const; private: static FeatureAlgorithmFactory *m_maker; mutable unsigned int m_nMade; - - QString m_Feature2DModuleName; - QString m_DetectorModuleName; - QString m_ExtractorModuleName; - QString m_MatcherModuleName; - QStringList m_algorithmNameMap; - PvlFlatMap m_parameters; + FeatureInventory m_algorithmInventory; + PvlFlatMap m_globalParameters; // The Singleton constructor/destructor are private FeatureAlgorithmFactory(); ~FeatureAlgorithmFactory(); + int initialize(); - QStringList findWithPattern(const QStringList &flist, - const QString &pattern) const; - QString mapAlgorithmName(const QString &name) const; + QStringList formatSpecifications(QString specification) const; - bool isFeature2D(const QString &name) const; - bool isDetector(const QString &name) const; - bool isExtractor(const QString &name) const; - bool isMatcher(const QString &name) const; - PvlFlatMap parseParameters(const QString ¶meters) const; + MatcherAlgorithmPtr createMatcher(FeatureAlgorithmPtr extractor, + const QString &normalize = "NORM_L2", + const QString &crossCheck = "false") const; static int handleOpenCVErrors( int status, const char* func_name, const char* err_msg,const char* file_name, diff --git a/isis/src/control/apps/findfeatures/FeatureInventory.cpp b/isis/src/control/apps/findfeatures/FeatureInventory.cpp new file mode 100644 index 0000000000000000000000000000000000000000..9b5eafe64b9380930422141c74f21b073a007153 --- /dev/null +++ b/isis/src/control/apps/findfeatures/FeatureInventory.cpp @@ -0,0 +1,304 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include + +#include +#include +#include + +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "FeatureInventory.h" + +namespace Isis { + FeatureInventory::FeatureInventory() : m_theFeatureCreator(), + m_theMatcherCreator() { } + + + FeatureInventory::~FeatureInventory() { } + + + int FeatureInventory::add(const QString &name, + FeatureInventory::FeatureCreator maker, + const QStringList &aliases) { + + // Add the fundamental + int v_made(0); + // There cannot be withspace at the begging or end of the name - its okay + // to embed them. + QString v_name = name.toLower().trimmed(); + m_theFeatureCreator.insert(v_name, maker); + v_made++; + + // Add all aliases. Expected to of form "detector.name, extractor.name", + // etc.... + BOOST_FOREACH ( QString a_name, aliases ) { + if ( !a_name.isEmpty() ) { + QString l_name = a_name.toLower().trimmed(); + m_theFeatureCreator.insert(l_name, maker); + v_made++; + if ( l_name.contains(QRegularExpression("^detector\\.*", + QRegularExpression::CaseInsensitiveOption) ) ) { + m_detectorNames.append( l_name.toLower() ); + } + if ( a_name.contains(QRegularExpression("^extractor\\.*", + QRegularExpression::CaseInsensitiveOption) ) ) { + m_extractorNames.append( l_name.toLower() ); + } + } + } + + return ( v_made ); + } + + + int FeatureInventory::add(const QString &name, + FeatureInventory::MatcherCreator maker, + const QStringList &aliases) { + int v_made(0); + // There cannot be whitespace at the begining or end of the name - its okay + // to embed them. + QString v_name = name.toLower().trimmed(); + m_theMatcherCreator.insert(v_name, maker); + m_matcherNames.append( name.toLower() ); + v_made++; + + // Add all aliases. Expected to of form "detector.name, extractor.name", + // etc.... + BOOST_FOREACH ( QString a_name, aliases ) { + QString l_name = a_name.toLower().trimmed(); + if ( !l_name.isEmpty() ) { + m_theMatcherCreator.insert(l_name, maker); + } + v_made++; + } + + return ( v_made ); + } + + + FeatureAlgorithmPtr FeatureInventory::getFeature(const QString &config) const { + QStringList parts = parse(config, "@"); + + if ( parts.isEmpty() ) { + QString mess = "No config string provided in FeatureInventory::getFeature"; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + QString name = parts.takeFirst().toLower().trimmed(); + PvlFlatMap variables = parameters(parts); + + if ( m_theFeatureCreator.contains(name) ) { + FeatureCreator creator = m_theFeatureCreator.value(name); + return ( creator( variables, config) ); + } + else { + QString mess = name + "Feature2D not found or invalid"; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + // Shouldn't get here but just in case + return ( FeatureAlgorithmPtr() ); + + } + + + FeatureAlgorithmPtr FeatureInventory::getDetector(const QString &config) const { + FeatureAlgorithmPtr algo = getFeature(config); + if ( !algo->hasDetector() ) { + QString mess = "Specification does not define a detector:\n" + config; + throw IException(IException::User, mess, _FILEINFO_); + } + return ( algo ); + } + + + FeatureAlgorithmPtr FeatureInventory::getExtractor(const QString &config) const { + FeatureAlgorithmPtr algo = getFeature(config); + if ( !algo->hasExtractor() ) { + QString mess = "Specification does not define an extractor:\n" + config; + throw IException(IException::User, mess, _FILEINFO_); + } + return ( algo ); + } + + + MatcherAlgorithmPtr FeatureInventory::getMatcher(const QString &config) const { + QStringList parts = parse(config, "@"); + + if ( parts.isEmpty() ) { + QString mess = "No config string provided in FeatureInventory::getMatcher"; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + QString c_name = parts.takeFirst(); + QString name = c_name.toLower().trimmed(); + PvlFlatMap variables = parameters(parts); + + if ( m_theMatcherCreator.contains(name) ) { + MatcherCreator matcher = m_theMatcherCreator.value(name); + return ( matcher(variables, config)); + } + else { + QString mess = c_name + " Matcher not found or invalid"; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + // Shouldn't get here but just in case + return ( MatcherAlgorithmPtr() ); + + } + + + PvlObject FeatureInventory::info(const QString &name) const { + return ( info( allNames(), name ) ); + } + + + PvlObject FeatureInventory::info(const QStringList algorithms, + const QString &name) const { + PvlObject algos(name); + + BOOST_FOREACH ( QString algorithmName, algorithms ) { + algos += algorithmInfo( algorithmName ); + } + + return ( algos ); + } + + + PvlObject FeatureInventory::algorithmInfo(const QString algorithmName) const { + PvlObject algorithmObject(algorithmName); + QString lowerName = algorithmName.toLower().trimmed(); + + try { + if ( m_theFeatureCreator.contains(lowerName) ) { + algorithmObject = getFeature(lowerName)->info(); + } + else if ( m_theMatcherCreator.contains(lowerName) ) { + algorithmObject = getMatcher(lowerName)->info(); + } + else { + QString mess = "Algorithm [" + algorithmName + + "] is not a supported OpenCV3 algorithm."; + throw IException(IException::User, mess, _FILEINFO_); + } + + algorithmObject += aliases( lowerName ); + } + catch (IException &e) { + algorithmObject.clear(); + algorithmObject += PvlKeyword( "Error", e.toString() ); + } + + return ( algorithmObject ); + } + + + PvlKeyword FeatureInventory::aliases(const QString algorithmName) const { + PvlKeyword aliasKey("Aliases"); + QString lowerName = algorithmName.toLower().trimmed(); + + if ( m_theFeatureCreator.contains( lowerName ) ) { + FeatureCreator creator = m_theFeatureCreator.value(lowerName); + QStringList aliasList = m_theFeatureCreator.keys(creator); + BOOST_FOREACH ( QString alias, aliasList) { + aliasKey += alias; + } + } + else if ( m_theMatcherCreator.contains( lowerName ) ) { + MatcherCreator creator = m_theMatcherCreator.value(lowerName); + QStringList aliasList = m_theMatcherCreator.keys(creator); + BOOST_FOREACH ( QString alias, aliasList) { + aliasKey += alias; + } + } + else { + QString mess = "Algorithm [" + algorithmName + + "] is not a supported OpenCV3 algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + return ( aliasKey ); + } + + + QStringList FeatureInventory::detectorNames() const { + return ( m_detectorNames ); + } + + + QStringList FeatureInventory::extractorNames() const { + return ( m_extractorNames ); + } + + + QStringList FeatureInventory::feature2DNames() const { + QSet nameSet = m_detectorNames.toSet(); + nameSet.intersect( m_extractorNames.toSet() ); + QStringList nameList = QList::fromSet( nameSet ); + + return ( nameList ); + } + + + QStringList FeatureInventory::matcherNames() const { + return ( m_matcherNames ); + } + + + QStringList FeatureInventory::allNames() const { + QStringList fullList = m_detectorNames; + fullList.append(m_extractorNames); + fullList.append(m_matcherNames); + fullList.removeDuplicates(); + + return ( fullList ); + } + + + /** Split the string with the provided separator in individual parts */ + QStringList FeatureInventory::parse(const QString &config, + const QString &sep) const { + return ( config.split(sep, QString::SkipEmptyParts) ); + } + + PvlFlatMap FeatureInventory::parameters(const QStringList &fromConfig) const { + PvlFlatMap parms; + BOOST_FOREACH ( QString parm, fromConfig) { + QStringList parts = parse(parm, ":"); + if ( parts.size() > 0 ) { + PvlKeyword key(parts.takeFirst().trimmed()); + BOOST_FOREACH (QString value, parts) { + key.addValue(value); + } + parms.add(key); + } + } + + return ( parms ); + } + +}; + diff --git a/isis/src/control/apps/findfeatures/FeatureInventory.h b/isis/src/control/apps/findfeatures/FeatureInventory.h new file mode 100644 index 0000000000000000000000000000000000000000..55bcbc167dfcb14912fc8c8e420d93047d28f40a --- /dev/null +++ b/isis/src/control/apps/findfeatures/FeatureInventory.h @@ -0,0 +1,161 @@ +#ifndef FeatureInventory_h +#define FeatureInventory_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "IException.h" +#include "PvlFlatMap.h" +#include "PvlKeyword.h" +#include "PvlObject.h" + +#include +#include + +// boost library +#include + +#include "FeatureAlgorithm.h" + +namespace Isis { + +/** + * @brief Wrapper for generic algorithm OpenCV3 feature matcher algorithms + * + * This class provides a generic wrapper that is intended to restore some of the + * functionality for these algorithms that were lost in the upgrade from version + * 2. Hence, the class T is intended to be an OpenCV Ptr type that contains + * either a Feature2D or DescriptorMatcher algorithm pointer. + * + * However, the design does lend itself to overide some the OpenCV specifics + * if needed. + * + * The OpenCV implementation can simply extract and populate the + * the PvlFlatMap variable structure to allow the default + * implementation to serve up the algorithm variables to the + * calling environment - or provide a specific implementation if + * inadequate. + * + * The config variable provides a direct way to store how the + * invocation string in the form of + * "algorithmname@var:value@var:value...". + * + * @author 2016-11-30 Kris Becker + * + * @internal + * @history 2016-11-30 Kris Becker - Original Version + */ + +class FeatureInventory { + public: + // Creator and storage types + typedef Feature2DAlgorithm* (*FeatureCreator)(const PvlFlatMap &object, + const QString &config); + typedef DescriptorMatcherAlgorithm* (*MatcherCreator)(const PvlFlatMap &object, + const QString &config); + + FeatureInventory(); + virtual ~FeatureInventory(); + + int add(const QString &name, FeatureCreator make, + const QStringList &alias = QStringList()); + + int add(const QString &name, MatcherCreator maker, + const QStringList &alias = QStringList()); + + FeatureAlgorithmPtr getFeature(const QString &config) const; + FeatureAlgorithmPtr getDetector(const QString &config) const; + FeatureAlgorithmPtr getExtractor(const QString &config) const; + MatcherAlgorithmPtr getMatcher(const QString &config) const; + + PvlObject info(const QString &name = "Algorithms") const; + PvlObject info(const QStringList algorithms, + const QString &name = "Algorithms") const; + + QStringList detectorNames() const; + QStringList extractorNames() const; + QStringList feature2DNames() const; + QStringList matcherNames() const; + QStringList allNames() const; + + QStringList parse(const QString &config, const QString &sep) const; + PvlFlatMap parameters(const QStringList &fromConfig) const; + PvlKeyword aliases(const QString algorithmName) const; + PvlObject algorithmInfo(const QString algorithmName) const; + + template int addFeatureAlgorithm() { + int numAliases(0); + FeatureAlgorithmPtr algorithm = T::create( PvlFlatMap() ); + FeatureCreator maker = T::create; + QString algorithmName = algorithm->name().toLower(); + + m_theFeatureCreator.insert(algorithmName, maker); + numAliases++; + if ( algorithm->hasDetector() ) { + m_theFeatureCreator.insert("detector." + algorithmName, maker); + m_detectorNames.append( algorithmName ); + numAliases++; + } + if ( algorithm->hasExtractor() ) { + m_theFeatureCreator.insert("extractor." + algorithmName, maker); + m_extractorNames.append( algorithmName ); + numAliases++; + } + if ( algorithm->hasDetector() && algorithm->hasExtractor() ) { + m_theFeatureCreator.insert("feature2d." + algorithmName, maker); + numAliases++; + } + + return ( numAliases ); + } + + template int addMatcherAlgorithm() { + int numAliases(0); + MatcherAlgorithmPtr algorithm = T::create( PvlFlatMap() ); + MatcherCreator maker = T::create; + QString algorithmName = algorithm->name().toLower(); + + m_theMatcherCreator.insert(algorithmName, maker); + numAliases++; + if ( algorithm->hasMatcher() ) { + m_theMatcherCreator.insert("matcher." + algorithmName, maker); + m_matcherNames.append( algorithmName ); + numAliases++; + } + + return ( numAliases ); + } + + private: + + typedef QMap Features; + typedef QMap Matchers; + + Features m_theFeatureCreator; + Matchers m_theMatcherCreator; + QStringList m_detectorNames; + QStringList m_extractorNames; + QStringList m_matcherNames; + +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/FeatureMatcherTypes.h b/isis/src/control/apps/findfeatures/FeatureMatcherTypes.h index 5bc3e3eb09458444ffa66161593d653fb7592531..8895ce3f9a991a815b3421979dffa2d3e9f4df14 100644 --- a/isis/src/control/apps/findfeatures/FeatureMatcherTypes.h +++ b/isis/src/control/apps/findfeatures/FeatureMatcherTypes.h @@ -2,8 +2,8 @@ #define FeatureMatcherTypes_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/FlannBasedMatcher.cpp b/isis/src/control/apps/findfeatures/FlannBasedMatcher.cpp new file mode 100644 index 0000000000000000000000000000000000000000..91fd9ffe3aa344ddbd5307e9f6298e706f4d8f24 --- /dev/null +++ b/isis/src/control/apps/findfeatures/FlannBasedMatcher.cpp @@ -0,0 +1,165 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include + +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "PvlFlatMap.h" + +#include + +#include "FlannBasedMatcher.h" + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + FlannBasedMatcher::FlannBasedMatcher() : + DescriptorMatcherAlgorithm("FlannBasedMatcher", "DecriptorMatcher", + cv::makePtr()) { + PvlFlatMap variables; + variables.add("Checks", "32"); + variables.add("Epsilon", "0.0"); + variables.add("Sorted", "true"); + m_variables.merge(variables); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + FlannBasedMatcher::FlannBasedMatcher(const PvlFlatMap &cvars, const QString &config, + const int checks, const float epsilon, const bool sorted) : + DescriptorMatcherAlgorithm("FlannBasedMatcher", "DecriptorMatcher", + cv::makePtr( + cv::makePtr(checks, epsilon, sorted))) { + setConfig(config); + PvlFlatMap variables; + variables.add("Checks", toString(checks)); + variables.add("Epsilon", toString(epsilon)); + variables.add("Sorted", toString(sorted)); + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + FlannBasedMatcher::~FlannBasedMatcher() { } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString FlannBasedMatcher::description() const { + QString desc = "The OpenCV FlannBasedMatcher DescriptorMatcher matcher algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/dc/de2/classcv_1_1FlannBasedMatcher.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + DescriptorMatcherAlgorithm *FlannBasedMatcher::create(const PvlFlatMap &vars, + const QString &config) { + const int checks = toInt(vars.get("Checks", "32")); + const float epsilon = vars.get("Epsilon", "0.0").toFloat(); + const bool sorted = toBool(vars.get("Sorted", "true")); + + return ( new FlannBasedMatcher(vars, config, checks, epsilon, sorted) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool FlannBasedMatcher::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool FlannBasedMatcher::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool FlannBasedMatcher::hasMatcher() const { + return true; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap FlannBasedMatcher::getAlgorithmVariables( ) const { + return ( variables() ); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "FlannBasedMatcher does not have the ability + * to set algorithm parameters." + */ + int FlannBasedMatcher::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "FlannBasedMatcher does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/FlannBasedMatcher.h b/isis/src/control/apps/findfeatures/FlannBasedMatcher.h new file mode 100644 index 0000000000000000000000000000000000000000..244fe87f371835d5237f8e02ceb28e5cf417a2b8 --- /dev/null +++ b/isis/src/control/apps/findfeatures/FlannBasedMatcher.h @@ -0,0 +1,66 @@ +#ifndef FlannBasedMatcher_h +#define FlannBasedMatcher_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include + +namespace Isis { + +/** + * @brief Flann Based Feature matcher algorithm + * + * This class provides the OpenCV3 FlannBasedMatcher DescriptorMatcher algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-08 Jesse Mapel + * + * @internal + * @history 2016-12-08 Jesse Mapel - Original Version + */ + +class FlannBasedMatcher : public DescriptorMatcherAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + FlannBasedMatcher(); + FlannBasedMatcher(const PvlFlatMap &cvars, const QString &config = QString(), + const int checks = 32, const float epsilon = 0.0, const bool sorted = true); + virtual ~FlannBasedMatcher(); + + QString description() const; + + // Required for all algorithms + static DescriptorMatcherAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/GFTTAlgorithm.cpp b/isis/src/control/apps/findfeatures/GFTTAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..0cc07ee61590dfb43b535ec40b43e5cf729c783f --- /dev/null +++ b/isis/src/control/apps/findfeatures/GFTTAlgorithm.cpp @@ -0,0 +1,183 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "GFTTAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + GFTTAlgorithm::GFTTAlgorithm() : + Feature2DAlgorithm("GFTT", "Feature2D", + GFTTType::create()) { + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + GFTTAlgorithm::GFTTAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("GFTT", "Feature2D", + GFTTType::create(), cvars) { + setConfig(config); + setAlgorithmVariables(cvars); + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Destroys the algorithm + */ + GFTTAlgorithm::~GFTTAlgorithm() { } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString GFTTAlgorithm::description() const { + QString desc = "The OpenCV GFTT Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/df/d21/classcv_1_1GFTTDetector.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *GFTTAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new GFTTAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool GFTTAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool GFTTAlgorithm::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool GFTTAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap GFTTAlgorithm::getAlgorithmVariables( ) const { + GFTTPtr algorithm = m_algorithm.dynamicCast(); + PvlFlatMap variables; + variables.add("MaxFeatures", toString(algorithm->getMaxFeatures())); + variables.add("QualityLevel", toString(algorithm->getQualityLevel())); + variables.add("MinDistance", toString(algorithm->getMinDistance())); + variables.add("BlockSize", toString(algorithm->getBlockSize())); + variables.add("HarrisDetector", toString(algorithm->getHarrisDetector())); + variables.add("K", toString(algorithm->getK())); + return (variables); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return int Number of variables actually set + */ + int GFTTAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + + GFTTPtr algorithm = m_algorithm.dynamicCast(); + + int nset(0); + if ( variables.exists("MaxFeatures") ) { + algorithm->setMaxFeatures(toInt(variables.get("MaxFeatures"))); + nset++; + } + + if ( variables.exists("QualityLevel") ) { + algorithm->setQualityLevel(toDouble(variables.get("QualityLevel"))); + nset++; + } + + if ( variables.exists("MinDistance") ) { + algorithm->setMinDistance(toDouble(variables.get("MinDistance"))); + nset++; + } + + if ( variables.exists("BlockSize") ) { + algorithm->setBlockSize(toInt(variables.get("BlockSize"))); + nset++; + } + + if ( variables.exists("HarrisDetector") ) { + algorithm->setHarrisDetector(toBool(variables.get("HarrisDetector"))); + nset++; + } + + if ( variables.exists("K") ) { + algorithm->setK(toDouble(variables.get("K"))); + nset++; + } + + return (nset); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/GFTTAlgorithm.h b/isis/src/control/apps/findfeatures/GFTTAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..f722fe509882ddf51916f7856d7fd39b4c317b07 --- /dev/null +++ b/isis/src/control/apps/findfeatures/GFTTAlgorithm.h @@ -0,0 +1,70 @@ +#ifndef GFTTAlgorithm_h +#define GFTTAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/features2d.hpp" + +#include + +namespace Isis { + +/** + * @brief GFTT Feature matcher algorithm + * + * This class provides the OpenCV3 GFTT Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-07 Jesse Mapel + * + * @internal + * @history 2016-12-07 Jesse Mapel - Original Version + */ + +class GFTTAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + GFTTAlgorithm(); + GFTTAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); + virtual ~GFTTAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::GFTTDetector GFTTType; + typedef cv::Ptr GFTTPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/GenericTransform.cpp b/isis/src/control/apps/findfeatures/GenericTransform.cpp index 4f055eff800df7ad4ca6cb5505973eaa2a580871..692b9e4ccb80166a5d1e2ec6b34693f5dc8f40cf 100644 --- a/isis/src/control/apps/findfeatures/GenericTransform.cpp +++ b/isis/src/control/apps/findfeatures/GenericTransform.cpp @@ -1,7 +1,7 @@ /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/GenericTransform.h b/isis/src/control/apps/findfeatures/GenericTransform.h index b8400db107b31a2e6e79eb35c83a7526e95e1814..c1acafc46bc340dba1c69cac3de09edb555a93ec 100644 --- a/isis/src/control/apps/findfeatures/GenericTransform.h +++ b/isis/src/control/apps/findfeatures/GenericTransform.h @@ -2,8 +2,8 @@ #define GenericTransform_h /** * @file - * $Revision: 6601 $ - * $Date: 2016-03-09 10:31:51 -0700 (Wed, 09 Mar 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/ImageSource.cpp b/isis/src/control/apps/findfeatures/ImageSource.cpp index ee98595a402b8efa5c14f41bf9a644ccfe384b8f..3c0d8e792aabef8f44331587f29ed054ae2dc62a 100644 --- a/isis/src/control/apps/findfeatures/ImageSource.cpp +++ b/isis/src/control/apps/findfeatures/ImageSource.cpp @@ -1,8 +1,8 @@ /** 4 @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ - * $Id: ImageSource.cpp 6563 2016-02-10 23:56:52Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/control/apps/findfeatures/ImageSource.h b/isis/src/control/apps/findfeatures/ImageSource.h index d3e16bdfc5005f358a44bef20f89bf4a589b4b02..0f9509273d3d70ffe0ecf3a9cbd5c51ed8cb03c0 100644 --- a/isis/src/control/apps/findfeatures/ImageSource.h +++ b/isis/src/control/apps/findfeatures/ImageSource.h @@ -2,8 +2,8 @@ #define ImageSource_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/ImageTransform.cpp b/isis/src/control/apps/findfeatures/ImageTransform.cpp index ffb7c2bbe78071d36faa9075a07c000cd520b57d..3e93f3ffb81b67fc7b0136720f5e2f633c7817bd 100644 --- a/isis/src/control/apps/findfeatures/ImageTransform.cpp +++ b/isis/src/control/apps/findfeatures/ImageTransform.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ - * $Id: ImageTransform.cpp 6563 2016-02-10 23:56:52Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/control/apps/findfeatures/ImageTransform.h b/isis/src/control/apps/findfeatures/ImageTransform.h index 811191f8fb32072048ee9a57a6fa10dd4d5c1543..c293254a252aa091c1dc92050240b060f9e5e21c 100644 --- a/isis/src/control/apps/findfeatures/ImageTransform.h +++ b/isis/src/control/apps/findfeatures/ImageTransform.h @@ -2,8 +2,8 @@ #define ImageTransform_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/KAZEAlgorithm.cpp b/isis/src/control/apps/findfeatures/KAZEAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..cf03ab8e521586dcf5882ea6a799c725c0674d61 --- /dev/null +++ b/isis/src/control/apps/findfeatures/KAZEAlgorithm.cpp @@ -0,0 +1,212 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "KAZEAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + KAZEAlgorithm::KAZEAlgorithm() : + Feature2DAlgorithm("KAZE", "Feature2D", + KAZEType::create()) { + setupTypeMap(); + m_variables.merge( getAlgorithmVariables() ); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + KAZEAlgorithm::KAZEAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("KAZE", "Feature2D", + KAZEType::create(), cvars) { + setupTypeMap(); + setConfig(config); + setAlgorithmVariables(cvars); + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Destroys the algorithm + */ + KAZEAlgorithm::~KAZEAlgorithm() { } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString KAZEAlgorithm::description() const { + QString desc = "The OpenCV KAZE Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d3/d61/classcv_1_1KAZE.html"; + return (desc); + } + + + /** + * Fills the map for converting the type variable. + */ + void KAZEAlgorithm::setupTypeMap() { + m_typeMap.left.insert(std::pair("DIFF_PM_G1", 0)); + m_typeMap.left.insert(std::pair("DIFF_PM_G2", 1)); + m_typeMap.left.insert(std::pair("DIFF_WEICKERT", 2)); + m_typeMap.left.insert(std::pair("DIFF_CHARBONNIER", 3)); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *KAZEAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new KAZEAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool KAZEAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool KAZEAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool KAZEAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap KAZEAlgorithm::getAlgorithmVariables( ) const { + KAZEPtr algorithm = m_algorithm.dynamicCast(); + PvlFlatMap variables; + variables.add("Diffusivity", m_typeMap.right.at(algorithm->getDiffusivity())); + variables.add("Extended", toString(algorithm->getExtended())); + variables.add("NOctaveLayers", toString(algorithm->getNOctaveLayers())); + variables.add("NOctaves", toString(algorithm->getNOctaves())); + variables.add("Threshold", toString(algorithm->getThreshold())); + variables.add("Upright", toString(algorithm->getUpright())); + return (variables); + } + + +/** + * Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Number of variables actually set + * + * @throws IException::User "The input value is not valid for KAZE's [Type] variable" + */ + int KAZEAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + KAZEPtr algorithm = m_algorithm.dynamicCast(); + + int numSet(0); + if ( variables.exists("Extended") ) { + algorithm->setExtended(toInt(variables.get("Extended"))); + numSet++; + } + + if ( variables.exists("Threshold") ) { + algorithm->setThreshold(toInt(variables.get("Threshold"))); + numSet++; + } + + if ( variables.exists("NOctaveLayers") ) { + algorithm->setNOctaveLayers(toInt(variables.get("NOctaveLayers"))); + numSet++; + } + + if ( variables.exists("NOctaves") ) { + algorithm->setNOctaves(toInt(variables.get("NOctaves"))); + numSet++; + } + + if ( variables.exists("Upright") ) { + algorithm->setUpright(toInt(variables.get("Upright"))); + numSet++; + } + + if ( variables.exists("Diffusivity") ) { + QString value = variables.get("Diffusivity"); + bool isInt; + // Check if the value is an integer + int intValue = value.toInt(&isInt); + try { + if (isInt) { + // If it is an integer make sure it is a valid option + m_typeMap.right.at(intValue); + } + else { + // If it is a string, then convert it to an integer + intValue = m_typeMap.left.at(value); + } + } + catch (std::exception &e) { + QString msg = "The input value [" + value + + "] is not valid for KAZE's [Type] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + algorithm->setDiffusivity(intValue); + numSet++; + } + + return (numSet); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/KAZEAlgorithm.h b/isis/src/control/apps/findfeatures/KAZEAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..4dabc98ae9f84ed0cc75fe3c8c1224dbebef08ea --- /dev/null +++ b/isis/src/control/apps/findfeatures/KAZEAlgorithm.h @@ -0,0 +1,81 @@ +#ifndef KAZEAlgorithm_h +#define KAZEAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + + +#include "FeatureAlgorithm.h" +#include "opencv2/features2d.hpp" + +#include +#include +#include + +#include + +namespace Isis { + +/** + * @brief KAZE Feature matcher algorithm + * + * This class provides the OpenCV3 KAZE Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-09 Kristin Berry + * + * @internal + * @history 2016-12-09 Kristin Berry - Original Version + */ + +class KAZEAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + KAZEAlgorithm(); + KAZEAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); + virtual ~KAZEAlgorithm(); + + virtual QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + void setupTypeMap(); + + boost::bimap m_typeMap; //!< Bi-directional map for converting type values. + + private: + typedef cv::KAZE KAZEType; + typedef cv::Ptr KAZEPtr; + +}; + + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/LATCHAlgorithm.cpp b/isis/src/control/apps/findfeatures/LATCHAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..3c278568dcc2383e6cf3685c4dac53b90afdeefb --- /dev/null +++ b/isis/src/control/apps/findfeatures/LATCHAlgorithm.cpp @@ -0,0 +1,170 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "LATCHAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + LATCHAlgorithm::LATCHAlgorithm() : + Feature2DAlgorithm("LATCH", "Feature2D", + LATCHType::create()) { + + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + LATCHAlgorithm::LATCHAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("LATCH", "Feature2D", + LATCHType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + const int bytes = toInt(variables.get("Bytes")); + const bool rotationInvariance = toBool(variables.get("RotationInvariance")); + const int halfSSDSize = toInt(variables.get("HalfSSDSize")); + + m_algorithm = LATCHType::create(bytes, rotationInvariance, halfSSDSize); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + LATCHAlgorithm::~LATCHAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap LATCHAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("Bytes", "32"); + variables.add("RotationInvariance", "true"); + variables.add("HalfSSDSize", "3"); + m_variables.merge(variables); + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString LATCHAlgorithm::description() const { + QString desc = "The OpenCV LATCH Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d_1_1LATCH.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *LATCHAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new LATCHAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool LATCHAlgorithm::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool LATCHAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool LATCHAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap LATCHAlgorithm::getAlgorithmVariables( ) const { + return (variables()); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "LATCHAlgorithm does not have the ability + * to set algorithm parameters." + */ + int LATCHAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "LATCHAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/LATCHAlgorithm.h b/isis/src/control/apps/findfeatures/LATCHAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..86602cea15ef2a7fb91b76df1cce68f949d289f0 --- /dev/null +++ b/isis/src/control/apps/findfeatures/LATCHAlgorithm.h @@ -0,0 +1,72 @@ +#ifndef LATCHAlgorithm_h +#define LATCHAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/xfeatures2d.hpp" + +#include + +namespace Isis { + +/** + * @brief LATCH Feature matcher algorithm + * + * This class provides the OpenCV3 LATCH Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-12 Jesse Mapel + * + * @internal + * @history 2016-12-12 Jesse Mapel - Original Version + */ + +class LATCHAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + LATCHAlgorithm(); + LATCHAlgorithm(const PvlFlatMap &cvars, const QString &config = QString() ); + virtual ~LATCHAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::LATCH LATCHType; + typedef cv::Ptr LATCHPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/LUCIDAlgorithm.cpp b/isis/src/control/apps/findfeatures/LUCIDAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..6ef700cd740362b61dda8d455fce88cbadad921f --- /dev/null +++ b/isis/src/control/apps/findfeatures/LUCIDAlgorithm.cpp @@ -0,0 +1,167 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "LUCIDAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + LUCIDAlgorithm::LUCIDAlgorithm() : + Feature2DAlgorithm( "LUCID", "Feature2D", + LUCIDType::create(1,1) ) { + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + LUCIDAlgorithm::LUCIDAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("LUCID", "Feature2D", + LUCIDType::create(1,1), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + const int lucidKernel = toInt(variables.get("LucidKernel")); + const int blurKernel = toInt(variables.get("BlurKernel")); + + m_algorithm = LUCIDType::create(lucidKernel, blurKernel); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + LUCIDAlgorithm::~LUCIDAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap LUCIDAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("LucidKernel", "1"); + variables.add("BlurKernel", "1"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString LUCIDAlgorithm::description() const { + QString desc = "The OpenCV LUCID Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d_1_1LUCID.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *LUCIDAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new LUCIDAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool LUCIDAlgorithm::hasDetector() const { + return false; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool LUCIDAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool LUCIDAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap LUCIDAlgorithm::getAlgorithmVariables( ) const { + return ( variables() ); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "LUCIDAlgorithm does not have the ability + * to set algorithm parameters." + */ + int LUCIDAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "LUCIDAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/LUCIDAlgorithm.h b/isis/src/control/apps/findfeatures/LUCIDAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..6a8afc876a7a3f5f30398178eb9f4c9d8edd4fad --- /dev/null +++ b/isis/src/control/apps/findfeatures/LUCIDAlgorithm.h @@ -0,0 +1,70 @@ +#ifndef LUCIDAlgorithm_h +#define LUCIDAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include + +namespace Isis { + +/** + * @brief LUCID Feature matcher algorithm + * + * This class provides the OpenCV3 LUCID Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-12 Jesse Mapel + * + * @internal + * @history 2016-12-12 Jesse Mapel - Original Version + */ + +class LUCIDAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + LUCIDAlgorithm(); + LUCIDAlgorithm(const PvlFlatMap &cvars, const QString &config = QString() ); + virtual ~LUCIDAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create( const PvlFlatMap &vars, + const QString &config = QString() ); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::LUCID LUCIDType; + typedef cv::Ptr LUCIDPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/MSDAlgorithm.cpp b/isis/src/control/apps/findfeatures/MSDAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..af037a1c3c70e641161615b436f6967c788ac98e --- /dev/null +++ b/isis/src/control/apps/findfeatures/MSDAlgorithm.cpp @@ -0,0 +1,184 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "MSDAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + MSDAlgorithm::MSDAlgorithm() : + Feature2DAlgorithm("MSD", "Feature2D", + MSDType::create()) { + setupParameters(); + + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + MSDAlgorithm::MSDAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("MSD", "Feature2D", + MSDType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + const int patchRadius = toInt(variables.get("PatchRadius")); + const int searchAreaRadius = toInt(variables.get("SearchAreaRadius")); + const int nmsRadius = toInt(variables.get("NMSRadius")); + const int nmsScaleRadius = toInt(variables.get("NMSScaleRadius")); + const float thSaliency = variables.get("THSaliency").toFloat(); + const int kNN = toInt(variables.get("KNN")); + const float scaleFactor = variables.get("ScaleFactor").toFloat(); + const int nScales = toInt(variables.get("NScales")); + const bool computeOrientation = toBool(variables.get("ComputeOrientation")); + + m_algorithm = MSDType::create(patchRadius, searchAreaRadius, nmsRadius, nmsScaleRadius, + thSaliency, kNN, scaleFactor, nScales, computeOrientation); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + MSDAlgorithm::~MSDAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap MSDAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("PatchRadius", "3"); + variables.add("SearchAreaRadius", "5"); + variables.add("NMSRadius", "5"); + variables.add("NMSScaleRadius", "0"); + variables.add("THSaliency", "250.0"); + variables.add("KNN", "4"); + variables.add("ScaleFactor", "1.25"); + variables.add("NScales", "-1"); + variables.add("ComputeOrientation", "false"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString MSDAlgorithm::description() const { + QString desc = "The OpenCV MSD Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d_1_1MSD.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *MSDAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + + return ( new MSDAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool MSDAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool MSDAlgorithm::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool MSDAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap MSDAlgorithm::getAlgorithmVariables( ) const { + return (variables()); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "MSDAlgorithm does not have the ability + * to set algorithm parameters." + */ + int MSDAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "MSDAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/MSDAlgorithm.h b/isis/src/control/apps/findfeatures/MSDAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..7cf9fc794eaa492ad1215342600385dbfe8952a8 --- /dev/null +++ b/isis/src/control/apps/findfeatures/MSDAlgorithm.h @@ -0,0 +1,73 @@ +#ifndef MSDAlgorithm_h +#define MSDAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/xfeatures2d.hpp" + +#include + +namespace Isis { + +/** + * @brief MSD Feature matcher algorithm + * + * This class provides the OpenCV3 MSDDetector Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-12 Jesse Mapel + * + * @internal + * @history 2016-12-12 Jesse Mapel - Original Version + */ + +class MSDAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + MSDAlgorithm(); + MSDAlgorithm( const PvlFlatMap &cvars, const QString &config = QString() ); + + virtual ~MSDAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create( const PvlFlatMap &vars, + const QString &config = QString() ); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::MSDDetector MSDType; + typedef cv::Ptr MSDPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/MSERAlgorithm.cpp b/isis/src/control/apps/findfeatures/MSERAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d28c517cd2ce8e3de6ae34c1cc7f772d51f896b7 --- /dev/null +++ b/isis/src/control/apps/findfeatures/MSERAlgorithm.cpp @@ -0,0 +1,182 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "MSERAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + MSERAlgorithm::MSERAlgorithm() : + Feature2DAlgorithm("MSERA", "Feature2D", + MSERType::create()) { + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + MSERAlgorithm::MSERAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("MSERA", "Feature2D", + MSERType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + const int delta = toInt(variables.get("Delta")); + const int minArea = toInt(variables.get("MinArea")); + const int maxArea = toInt(variables.get("MaxArea")); + const double maxVariation = toDouble(variables.get("MaxVariation")); + const double minDiversity = toDouble(variables.get("MinDiversity")); + const int maxEvolution = toInt(variables.get("MaxEvolution")); + const double areaThreshold = toDouble(variables.get("AreaThreshold")); + const double minMargin = toDouble(variables.get("MinMargin")); + const int edgeBlurSize = toInt(variables.get("EdgeBlurSize")); + + m_algorithm = MSERType::create(delta, minArea, maxArea, maxVariation, minDiversity, + maxEvolution, areaThreshold, minMargin, edgeBlurSize); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + MSERAlgorithm::~MSERAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap MSERAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("Delta", "5"); + variables.add("MinArea", "60"); + variables.add("MaxArea", "14400"); + variables.add("MaxVariation", "0.25"); + variables.add("MinDiversity", "0.2"); + variables.add("MaxEvolution", "200"); + variables.add("AreaThreshold", "1.01"); + variables.add("MinMargin", "0.003"); + variables.add("EdgeBlurSize", "5"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString MSERAlgorithm::description() const { + QString desc = "The OpenCV MSERA Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d3/d28/classcv_1_1MSER.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *MSERAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new MSERAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool MSERAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool MSERAlgorithm::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool MSERAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap MSERAlgorithm::getAlgorithmVariables( ) const { + return ( variables() ); + } + + +/** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "BriefDescriptorAlgorithm does not have the ability + * to set algorithm parameters." + */ + int MSERAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "MSERAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/MSERAlgorithm.h b/isis/src/control/apps/findfeatures/MSERAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..4f9ba3aef1b923e6a1598c28913401e72829760e --- /dev/null +++ b/isis/src/control/apps/findfeatures/MSERAlgorithm.h @@ -0,0 +1,74 @@ +#ifndef MSERAlgorithm_h +#define MSERAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "opencv2/features2d.hpp" + +#include + +#include "MSERExtractor.h" +#include "FeatureAlgorithm.h" + +namespace Isis { + +/** + * @brief MSER Feature matcher algorithm + * + * This class provides the OpenCV3 MSER Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-08 Jesse Mapel + * + * @internal + * @history 2016-12-08 Jesse Mapel - Original Version + */ + +class MSERAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + MSERAlgorithm(); + MSERAlgorithm( const PvlFlatMap &cvars, const QString &config = QString() ); + virtual ~MSERAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create( const PvlFlatMap &vars, + const QString &config = QString() ); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef MSERExtractor MSERType; + typedef cv::Ptr MSERPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/MSERExtractor.cpp b/isis/src/control/apps/findfeatures/MSERExtractor.cpp new file mode 100644 index 0000000000000000000000000000000000000000..0b2a3bcfb3d1d812d45485bb232ebf5a37bc22f7 --- /dev/null +++ b/isis/src/control/apps/findfeatures/MSERExtractor.cpp @@ -0,0 +1,136 @@ +#include "MSERExtractor.h" +#include "IException.h" + +#include + +namespace Isis { + + /** + * Always throws an exception. + * + * @param image input image + * @param msers resulting list of point sets + * @param bboxes bounding boxes + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + void MSERExtractor::detectRegions (cv::InputArray image, + std::vector< std::vector< cv::Point > > &msers, + std::vector< cv::Rect > &bboxes) { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @return int (-1) + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + int MSERExtractor::getDelta () const { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @return int (-1) + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + int MSERExtractor::getMaxArea () const { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @return int (-1) + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + int MSERExtractor::getMinArea () const { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @return bool false + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + bool MSERExtractor::getPass2Only () const { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @param delta input delta to set + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + void MSERExtractor::setDelta (int delta) { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @param maxArea input maximum area + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + void MSERExtractor::setMaxArea (int maxArea) { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @param minArea input minimum area + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + void MSERExtractor::setMinArea (int minArea) { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } + + + /** + * Always throws an exception. + * + * @param f input value + * + * @throws IException::Programmer "ISIS does not support this method for the OpenCV MSER + * algorithm." + */ + void MSERExtractor::setPass2Only (bool f) { + QString mess = "ISIS does not support this method for the OpenCV MSER algorithm."; + throw IException(IException::Programmer, mess, _FILEINFO_); + } +}; diff --git a/isis/src/control/apps/findfeatures/MSERExtractor.h b/isis/src/control/apps/findfeatures/MSERExtractor.h new file mode 100644 index 0000000000000000000000000000000000000000..d1311005790da29eaf5ba40992175d8f8c1bec8c --- /dev/null +++ b/isis/src/control/apps/findfeatures/MSERExtractor.h @@ -0,0 +1,44 @@ +#ifndef MSERExtractor_h +#define MSERExtractor_h + +#include "opencv2/xfeatures2d.hpp" +#include "opencv2/opencv.hpp" + +namespace Isis { + +/** + * Wrap of OpenCV3 MSER algorithm to implement pure virtual functions. + * + * @author 2016-12-20 Jesse Mapel + * + * @internal + * @history 2016-12-20 Jesse Mapel - Original Version + * @history 2016-12-27 Kristin Berry - Added documentation + */ + +class MSERExtractor : public cv::MSER { + +public: + virtual void detectRegions (cv::InputArray image, + std::vector< std::vector< cv::Point > > &msers, + std::vector< cv::Rect > &bboxes); + + virtual int getDelta () const; + + virtual int getMaxArea () const; + + virtual int getMinArea () const; + + virtual bool getPass2Only () const; + + virtual void setDelta (int delta); + + virtual void setMaxArea (int maxArea); + + virtual void setMinArea (int minArea); + + virtual void setPass2Only (bool f); +}; + +} +#endif diff --git a/isis/src/control/apps/findfeatures/MatchImage.h b/isis/src/control/apps/findfeatures/MatchImage.h index fc4024ef7f3d88d75b6137b024bee4037ea95b27..63d28983c782f96b9b4b231336a860db6610def3 100644 --- a/isis/src/control/apps/findfeatures/MatchImage.h +++ b/isis/src/control/apps/findfeatures/MatchImage.h @@ -2,8 +2,8 @@ #define MatchImage_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for @@ -73,10 +73,23 @@ class MatchImage { m_data->m_duration = ptime; } + MatchImage(const MatchImage &other): m_data(other.m_data) { } + virtual ~MatchImage() { } + /** + * Creates a copy of this MatchImage object with shared image source + * and a copy of all transformations but empty keypoints, descriptors, + * and duration. + */ + MatchImage clone() { + MatchImage copyImage(*this); + copyImage.m_data.detach(); + return copyImage; + } + inline int size() const { return ( m_data->m_keypoints.size() ); } @@ -173,7 +186,7 @@ class MatchImage { m_duration(0) { } ImageData(const ImageData &other) : QSharedData(other), m_source(other.m_source), - m_transforms(), + m_transforms(other.m_transforms), m_keypoints(), m_descriptors(), m_duration(0) { } diff --git a/isis/src/control/apps/findfeatures/MatchMaker.cpp b/isis/src/control/apps/findfeatures/MatchMaker.cpp index aaf4e266b81db6127fd9e2f46990e1b1785842f9..ebab336e2370cae862cf82a865bd88014c8663a3 100644 --- a/isis/src/control/apps/findfeatures/MatchMaker.cpp +++ b/isis/src/control/apps/findfeatures/MatchMaker.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ - * $Id: MatchMaker.cpp 6563 2016-02-10 23:56:52Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -125,41 +125,32 @@ MatchImage MatchMaker::getGeometrySource() const { return ( MatchImage() ); // Got none } -MatcherSolution *MatchMaker::match(const SharedRobustMatcher &matcher, - const PvlFlatMap ¶meters) { +MatcherSolution *MatchMaker::match(const SharedRobustMatcher &matcher) { // Pass along logging status matcher->setDebugLogger( stream(), isDebug() ); - PvlFlatMap matchParms(m_parameters, parameters); - matcher->setRatio(getParameter("Ratio", matchParms, matcher->getRatio())); - matcher->setEpiTolerance(getParameter("EpiTolerance", matchParms, matcher->getEpiTolerance())); - matcher->setEpiConfidence(getParameter("EpiConfidence", matchParms, matcher->getEpiConfidence())); - matcher->setHmgTolerance(getParameter("HmgTolerance", matchParms, matcher->getHmgTolerance())); - matcher->setMaxPoints(getParameter("MaxPoints", matchParms, matcher->getMaxPoints())); - MatcherSolution *m(0); if ( m_trainers.size() == 1 ) { // Run a pair only matcher m = new MatcherSolution(matcher, matcher->match(m_query, m_trainers[0]), - matchParms, *this /* MatchMaker and/or QLogger */ ); + *this /* MatchMaker and/or QLogger */ ); } else { // Run the multi-matcher m = new MatcherSolution(matcher, matcher->match(m_query, m_trainers), - matchParms, *this /* MatchMaker and/or QLogger */ ); + *this /* MatchMaker and/or QLogger */ ); } return ( m ); } -MatcherSolutionList MatchMaker::match(const RobustMatcherList &matchers, - const PvlFlatMap ¶meters) { +MatcherSolutionList MatchMaker::match(const RobustMatcherList &matchers) { // Thread here!!!! MatcherSolutionList solutions; for (int i = 0 ; i < matchers.size() ; i++) { - solutions.push_back(SharedMatcherSolution( match(matchers[i], parameters) )); + solutions.push_back(SharedMatcherSolution( match(matchers[i]) )); } return ( solutions ); } @@ -306,9 +297,9 @@ int MatchMaker::addMeasure(ControlPoint **cpt, const MatchPair &mpair, // network. Use 2 * homography tolerance as a limit unless the user has added // a ResidualTolerance parameter to the matcher. double residual = std::sqrt( diff.x*diff.x + diff.y*diff.y); - double residTol = solution.matcher()->getHmgTolerance() * 2.0; - residTol = toDouble(solution.matcher()->getParameter("ResidualTolerance", - toString(residTol))); + double residTol = toDouble(solution.matcher()->parameters().get("HmgTolerance")) * 2.0; + residTol = toDouble(solution.matcher()->parameters().get("ResidualTolerance", + toString(residTol))); // Don't add the measure to the point if it exceeds tolerance if ( residual <= residTol ) { @@ -336,8 +327,7 @@ ControlMeasure *MatchMaker::makeMeasure(const MatchImage &image, v_measure->SetCubeSerialNumber(image.id()); // imgpt is unused variable, so it has been commented out - /*cv::Point2f imgpt = */ - image.keypoint(keyindex).pt; + /*cv::Point2f imgpt = image.keypoint(keyindex).pt; */ // std::cout << "ImageCoordinate: " << imgpt << "\n"; cv::Point2f query = image.imageToSource(image.keypoint(keyindex).pt); diff --git a/isis/src/control/apps/findfeatures/MatchMaker.h b/isis/src/control/apps/findfeatures/MatchMaker.h index db3e7f36c828feb009397d5ffbcdd511ae7f7c3e..541481c3f2820f41d376ad286d627981b346818f 100644 --- a/isis/src/control/apps/findfeatures/MatchMaker.h +++ b/isis/src/control/apps/findfeatures/MatchMaker.h @@ -2,8 +2,8 @@ #define MatchMaker_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for @@ -74,6 +74,7 @@ class MatchMaker : public QLogger { const MatchImage &query() const; MatchImage &query(); + const MatchImage &train(const int &index = 0) const; MatchImage &train(const int &index = 0); @@ -99,10 +100,8 @@ class MatchMaker : public QLogger { GeometrySourceFlag getGeometrySourceFlag() const; MatchImage getGeometrySource() const; - MatcherSolution *match(const SharedRobustMatcher &matcher, - const PvlFlatMap ¶meters = PvlFlatMap()); - MatcherSolutionList match(const RobustMatcherList &matchers, - const PvlFlatMap ¶meters = PvlFlatMap()); + MatcherSolution *match(const SharedRobustMatcher &algorithms); + MatcherSolutionList match(const RobustMatcherList &algorithms); PvlGroup network(ControlNet &cnet, const MatcherSolution &solution, ID &pointMaker) const; diff --git a/isis/src/control/apps/findfeatures/MatchPair.h b/isis/src/control/apps/findfeatures/MatchPair.h index 0424dea64faafc6b299830dbdfa79e7c44970aef..5bfccf53d853bd5a2a08ac9eb59b9de1a4b8db1d 100644 --- a/isis/src/control/apps/findfeatures/MatchPair.h +++ b/isis/src/control/apps/findfeatures/MatchPair.h @@ -2,8 +2,8 @@ #define MatchPair_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/MatcherAlgorithms.cpp b/isis/src/control/apps/findfeatures/MatcherAlgorithms.cpp new file mode 100644 index 0000000000000000000000000000000000000000..0e3609b01bcdfb8c9ac7971434c3afab098f845a --- /dev/null +++ b/isis/src/control/apps/findfeatures/MatcherAlgorithms.cpp @@ -0,0 +1,196 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include + +#include + +#include "IException.h" +#include "MatcherAlgorithms.h" + +namespace Isis { + + MatcherAlgorithms::MatcherAlgorithms() { } + + + MatcherAlgorithms::MatcherAlgorithms(FeatureAlgorithmPtr &detector, + FeatureAlgorithmPtr &extractor, + MatcherAlgorithmPtr &matcher, + PvlFlatMap parameters) : + m_detector(detector), + m_extractor(extractor), + m_matcher(matcher), + m_parameters(parameters) { + } + + + MatcherAlgorithms::~MatcherAlgorithms() { } + + + /** Determine validity of the algorithms with robust validation */ + bool MatcherAlgorithms::isValid() const { + return ( validate(false) ); + } + + +/** + * @brief This method throughly vets the matcher algorithms for validity + * + * This method insures the contents of this container is valid for its intend + * operations. This includes ensuring that the detector, extractor and matcher + * algorithms have all been allocated. If this is valid + * + * @author 2016-12-23 Kris Becker + * + * @param throwOnErrors Throw a cummulative exception reporting errors if true + * + * @return bool Returns true if no errors are found. If errors are found and + * the throwOnErrors parameters is false, it will return false. + */ + bool MatcherAlgorithms::validate(const bool &throwOnErrors) const { + // Accumulate errors for a comprehensive list of issues + IException ie; + int nerrors(0); + + // Check the detector algorithm to ensure all are allocated properly + // and it contains the require functionality + if ( m_detector.empty() ){ + ie.append(IException(IException::Programmer, + "Required detector algorithm has not been allocated", + _FILEINFO_)); + nerrors++; + } + else { + if ( !m_detector->isValid() ) { + ie.append(IException(IException::Programmer, + "Required detector algorithm is not present/valid", + _FILEINFO_)); + nerrors++; + } + else { + if ( !m_detector->hasDetector() ) { + QString mess = "Detector " + detector().name() + " does not possess detector capabilities"; + ie.append(IException(IException::Programmer, mess,_FILEINFO_)); + nerrors++; + } + } + } + + // Check the extractor algorithm to ensure all are allocated properly and it + // contains the require functionality + if ( m_extractor.empty() ) { + ie.append(IException(IException::Programmer, + "Required extractor algorithm has not been allocated", + _FILEINFO_)); + nerrors++; + } + else { + if ( !m_extractor->isValid() ) { + ie.append(IException(IException::Programmer, + "Required extractor algorithm is not present", + _FILEINFO_)); + nerrors++; + } + else { + if ( !m_extractor->hasExtractor() ) { + QString mess = "Extractor " + extractor().name() + " does not possess extractor capabilities"; + ie.append(IException(IException::Programmer, mess,_FILEINFO_)); + nerrors++; + } + } + } + + // Check the matcher algorithm to ensure all are allocated properly and it + // contains the require functionality + if ( m_matcher.empty() ) { + ie.append(IException(IException::Programmer, + "Required matcher algorithm has not been allocated", + _FILEINFO_)); + nerrors++; + } + else { + if ( !m_matcher->isValid() ) { + ie.append(IException(IException::Programmer, + "Required matcher algorithm is not present", + _FILEINFO_)); + nerrors++; + } + else { + if ( !m_matcher->hasMatcher() ) { + QString mess = "Matcher " + matcher().name() + " does not possess matcher capabilities"; + ie.append(IException(IException::Programmer, mess,_FILEINFO_)); + nerrors++; + } + } + } + + // Shall we throw an exception to report the issues? + if ( (0 < nerrors) && (true == throwOnErrors)) { + QString mess = "There were " + QString::number(nerrors) + + " errors found in this matcher algorithm set"; + ie.append(IException(IException::Programmer, mess, _FILEINFO_)); + throw ie; + } + + return ( 0 == nerrors ); + } + + + /** Return the detector algorithm */ + Feature2DAlgorithm &MatcherAlgorithms::detector() const { + BOOST_ASSERT ( m_detector.empty() == false); + BOOST_ASSERT ( m_detector->isValid() == true ); + return ( *m_detector ); + } + + /** Return a reference to the OpenCV extractor algorithm */ + Feature2DAlgorithm &MatcherAlgorithms::extractor() const { + BOOST_ASSERT ( m_extractor.empty() == false); + BOOST_ASSERT ( m_extractor->isValid() == true ); + return ( *m_extractor ); + } + + /** Return a reference to the OpenCV matcher algorithm */ + DescriptorMatcherAlgorithm &MatcherAlgorithms::matcher() const { + BOOST_ASSERT ( m_matcher.empty() == false); + BOOST_ASSERT ( m_matcher->isValid() == true ); + return ( *m_matcher ); + } + + + /** Return a const reference to the merge of the RobustMatcher and global + * parameters */ + const PvlFlatMap &MatcherAlgorithms::parameters() const { + return ( m_parameters ); + } + + /** Return a PvlObject containing the chain of algorithm information */ + PvlObject MatcherAlgorithms::info(const QString &name) const { + PvlObject data(name); + data += m_detector->info("Detector"); + data += m_extractor->info("Extractor"); + data += m_matcher->info("Matcher"); + return ( data ); + } + + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/MatcherAlgorithms.h b/isis/src/control/apps/findfeatures/MatcherAlgorithms.h new file mode 100644 index 0000000000000000000000000000000000000000..961716ea3aa97ed6d7cd2f3796137966c1838be6 --- /dev/null +++ b/isis/src/control/apps/findfeatures/MatcherAlgorithms.h @@ -0,0 +1,81 @@ +#ifndef MatcherAlgorithms_h +#define MatcherAlgorithms_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include + +#include + +#include "FeatureAlgorithm.h" +#include "PvlFlatMap.h" +#include "PvlObject.h" + + +namespace Isis { + +/** + * @brief Generic container for ISIS/OpenCV-type feature matcher algorithms + * + * This class provides a container for the three elements of feature-based + * matching: detector, extractor and matcher. An addition container of robust + * matcher outlier detection is added as a "paramters" specification. + * + * @author 2016-11-29 Kris Becker + * + * @internal + * @history 2016-11-29 Kris Becker - Original Version + */ + +class MatcherAlgorithms { + public: + MatcherAlgorithms(); + + MatcherAlgorithms(FeatureAlgorithmPtr &detector, + FeatureAlgorithmPtr &extractor, + MatcherAlgorithmPtr &matcher, + PvlFlatMap parameters = PvlFlatMap()); + + virtual ~MatcherAlgorithms(); + + virtual bool isValid() const; + bool validate(const bool &throwOnErrors = true) const; + + Feature2DAlgorithm &detector() const; + Feature2DAlgorithm &extractor() const; + DescriptorMatcherAlgorithm &matcher() const; + + const PvlFlatMap ¶meters() const; + + PvlObject info(const QString &name = "MatcherAlgorithms") const; + + private: + FeatureAlgorithmPtr m_detector; //!< Detector algorithm + FeatureAlgorithmPtr m_extractor; //!< Extractor algorithm + MatcherAlgorithmPtr m_matcher; //!< Matcher algorithm + PvlFlatMap m_parameters; //!< Parameters for matcher + +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/MatcherSolution.h b/isis/src/control/apps/findfeatures/MatcherSolution.h index 3fe3825a927321a27b11dc850e87d3858c1635bc..03e497addb00788fcdd0ac3ee7d49951b0b3255a 100644 --- a/isis/src/control/apps/findfeatures/MatcherSolution.h +++ b/isis/src/control/apps/findfeatures/MatcherSolution.h @@ -2,8 +2,8 @@ #define MatcherSolution_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for @@ -60,19 +60,16 @@ class MatcherSolution : public QLogger { MatcherSolution() { } MatcherSolution(const SharedRobustMatcher &matcher, - const MatchPair &pair, - const PvlFlatMap ¶meters = PvlFlatMap(), + const MatchPair &pair, const QLogger &logger = QLogger()) : QLogger(logger), - m_matcher(matcher), m_pairs(), m_parameters(parameters) { + m_matcher(matcher), m_pairs() { m_pairs.push_back(pair); } MatcherSolution(const SharedRobustMatcher &matcher, const MatchPairQList &pairs, - const PvlFlatMap ¶meters = PvlFlatMap(), const QLogger &logger = QLogger()) : QLogger(logger), - m_matcher(matcher), m_pairs(pairs), - m_parameters(parameters) { } + m_matcher(matcher), m_pairs(pairs) { } virtual ~MatcherSolution() { } @@ -97,11 +94,7 @@ class MatcherSolution : public QLogger { return ( m_matcher ); } - inline const PvlFlatMap ¶meters() const { - return ( m_parameters ); - } - - Statistics quality() const { + Statistics qualityStatistics() const { Statistics stats; for (int i = 0 ; i < size() ; i++) { stats.AddData( m_pairs[i].efficiency() ); @@ -109,6 +102,10 @@ class MatcherSolution : public QLogger { return ( stats ); } + double quality() const { + return ( qualityStatistics().Average() ); + } + MatchPairIterator begin() { return ( m_pairs.begin() ); } @@ -129,7 +126,7 @@ class MatcherSolution : public QLogger { template int forEachPair( T &process ) { int npairs( 0 ); BOOST_FOREACH ( MatchPair &mpair, m_pairs ) { - process.apply(mpair, *m_matcher, m_parameters, *this); + process.apply(mpair, *m_matcher, *this); npairs++; } return ( npairs ); @@ -138,7 +135,7 @@ class MatcherSolution : public QLogger { template int forEachPair( const T &process ) const { int npairs( 0 ); BOOST_FOREACH ( const MatchPair &mpair, m_pairs ) { - process.apply(mpair, *m_matcher, m_parameters, *this); + process.apply(mpair, *m_matcher, *this); npairs++; } return ( npairs ); @@ -160,7 +157,7 @@ class MatcherSolution : public QLogger { SharedMatcherSolution candidate(matches[0]); for (int i = 1 ; i < matches.size() ; i++) { - if ( matches[i] < candidate ) { + if ( matches[i]->quality() < candidate->quality() ) { candidate = matches[i]; } } diff --git a/isis/src/control/apps/findfeatures/ORBAlgorithm.cpp b/isis/src/control/apps/findfeatures/ORBAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..a6272484ebaf76503bc2c854100ef6f62012812f --- /dev/null +++ b/isis/src/control/apps/findfeatures/ORBAlgorithm.cpp @@ -0,0 +1,239 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "ORBAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the ORB algorithm with default variables. + */ + ORBAlgorithm::ORBAlgorithm() : + Feature2DAlgorithm("ORB", "Feature2D", + ORBType::create()) { + setupTypeMap(); + m_variables.merge( getAlgorithmVariables() ); + } + + + /** + * Constructs the ORB algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + ORBAlgorithm::ORBAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("ORB", "Feature2D", + ORBType::create(), cvars) { + setupTypeMap(); + setConfig(config); + setAlgorithmVariables(cvars); + m_variables.merge(getAlgorithmVariables()); + } + + + /** + * Destroys the ORB algorithm + */ + ORBAlgorithm::~ORBAlgorithm() { } + + + /** + * Returns a description of the ORB algorithm. + * + * @return @b QString A description of the ORB algorithm. + */ + QString ORBAlgorithm::description() const { + QString desc = "The OpenCV ORB Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/db/d95/classcv_1_1ORB.html"; + return (desc); + } + + + /** + * Fills the map for converting the type variable. + */ + void ORBAlgorithm::setupTypeMap() { + m_typeMap.left.insert(std::pair("kBytes", 32)); + m_typeMap.left.insert(std::pair("HARRIS_SCORE", 0)); + m_typeMap.left.insert(std::pair("FAST_SCORE", 1)); + } + + + /** + * Creates an instance of the ORB algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *ORBAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new ORBAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool ORBAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool ORBAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool ORBAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the ORB algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap ORBAlgorithm::getAlgorithmVariables( ) const { + ORBPtr algorithm = m_algorithm.dynamicCast(); + + PvlFlatMap variables; + variables.add("nfeatures", toString(algorithm->getMaxFeatures())); + variables.add("scaleFactor", toString(algorithm->getScaleFactor())); + variables.add("nlevels", toString(algorithm->getNLevels())); + variables.add("edgeThreshold", toString(algorithm->getEdgeThreshold())); + variables.add("firstLevel", toString(algorithm->getFirstLevel())); + variables.add("WTA_K", toString(algorithm->getWTA_K())); + variables.add("scoreType", m_typeMap.right.at(algorithm->getScoreType())); + variables.add("patchSize", toString(algorithm->getPatchSize())); + variables.add("fastThreshold", toString(algorithm->getFastThreshold())); + return (variables); + } + + +/** + * Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Number of variables actually set + * + * @throws IException::User "The input value is not valid for ORB's [scoreType] variable" + */ + int ORBAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + + ORBPtr algorithm = m_algorithm.dynamicCast(); + + int numSet(0); + if ( variables.exists("nfeatures") ) { + algorithm->setMaxFeatures(toInt(variables.get("nfeatures"))); + numSet++; + } + + if ( variables.exists("scaleFactor") ) { + algorithm->setScaleFactor(toDouble(variables.get("scaleFactor"))); + numSet++; + } + + + if ( variables.exists("nlevels") ) { + algorithm->setNLevels(toInt(variables.get("nlevels"))); + numSet++; + } + + if ( variables.exists("edgeThreshold") ) { + algorithm->setEdgeThreshold(toInt(variables.get("edgeThreshold"))); + numSet++; + } + + if ( variables.exists("firstLevel") ) { + algorithm->setFirstLevel(toInt(variables.get("firstLevel"))); + numSet++; + } + + if ( variables.exists("WTA_K") ) { + algorithm->setWTA_K(toInt(variables.get("WTA_K"))); + numSet++; + } + + + if ( variables.exists("scoreType") ) { + QString value = variables.get("scoreType"); + bool isInt; + // Check if the value is an integer + int intValue = value.toInt(&isInt); + try { + if (isInt) { + // If it is an integer make sure it is a valid option + m_typeMap.right.at(intValue); + } + else { + // If it is a string, then convert it to an integer + intValue = m_typeMap.left.at(value); + } + } + catch (std::exception &e) { + QString msg = "The input value [" + value + + "] is not valid for ORB's [Type] variable"; + throw IException(IException::User, msg, _FILEINFO_); + } + + algorithm->setScoreType(intValue); + numSet++; + + if ( variables.exists("patchSize") ) { + algorithm->setPatchSize(toInt(variables.get("patchSize"))); + numSet++; + } + + if ( variables.exists("fastThreshold") ) { + algorithm->setPatchSize(toInt(variables.get("fastThreshold"))); + numSet++; + } + } + return (numSet); + } + +}; // namespace Isis + diff --git a/isis/src/control/apps/findfeatures/ORBAlgorithm.h b/isis/src/control/apps/findfeatures/ORBAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..28c567b5040b6648f775b42bbe42e045334bcc5c --- /dev/null +++ b/isis/src/control/apps/findfeatures/ORBAlgorithm.h @@ -0,0 +1,75 @@ +#ifndef ORBAlgorithm_h +#define ORBAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/features2d.hpp" + +#include +#include + +namespace Isis { + +/** + * @brief ORB Feature matcher algorithm + * + * This class provides the OpenCV3 ORB Feature2D algortithm. + * + * @author 2016-12-08 Kristin Berry + * + * @internal + * @history 2016-12-08 Kristin Berry - Original Version + */ + +class ORBAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + ORBAlgorithm(); + ORBAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); + virtual ~ORBAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + void setupTypeMap(); + + boost::bimap m_typeMap; //!< Bi-directional map for converting type values. + + private: + typedef cv::ORB ORBType; + typedef cv::Ptr ORBPtr; +}; + + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/QDebugLogger.h b/isis/src/control/apps/findfeatures/QDebugLogger.h index 016c5e11b6a38ed138d2525c63bfe26128799f20..60990bde9a4fd0aeed2b58f2cdfd12549c6e6b82 100644 --- a/isis/src/control/apps/findfeatures/QDebugLogger.h +++ b/isis/src/control/apps/findfeatures/QDebugLogger.h @@ -2,8 +2,8 @@ #define QDebugLogger_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/RobustMatcher.cpp b/isis/src/control/apps/findfeatures/RobustMatcher.cpp index 6b743d59ea0f1fb79cadebc223cb2ca1f6453180..156be235b280c97a18c0e005e55546bb42dd5d31 100644 --- a/isis/src/control/apps/findfeatures/RobustMatcher.cpp +++ b/isis/src/control/apps/findfeatures/RobustMatcher.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ - * $Id: RobustMatcher.cpp 6563 2016-02-10 23:56:52Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions @@ -36,14 +36,11 @@ #include #include -#include -#include // boost library #include #include "Application.h" -#include "AlgorithmParameters.h" #include "IException.h" #include "IString.h" #include "FileName.h" @@ -58,308 +55,32 @@ namespace Isis { * @see init(const QString &name, const PvlFlatMap(), const bool * useDefaults(false)). */ -RobustMatcher::RobustMatcher() { - init("RobustMatcher", PvlFlatMap(), true); +RobustMatcher::RobustMatcher() : MatcherAlgorithms(), QLogger(), + m_name("RobustMatcher"), m_parameters() { + init(); } -RobustMatcher::RobustMatcher(const QString &name, - const PvlFlatMap ¶meters ) { - init("RobustMatcher", parameters, true); +RobustMatcher::RobustMatcher(const QString &name) : + MatcherAlgorithms(), + QLogger(),m_name(name), + m_parameters() { + init(); } -/** - * @brief Construct a matcher with specific componets and parameters - * - * @author 2015-08-28 Kris Becker - * - * @param name Name of matcher being created. - * @param detector Feature detector - * @param extractor Feature extractor - * @param bfNormType BFMatcher normalization parameter - * @param crossCheck Do OpenCV ratio test. NOT recommended. - */ -RobustMatcher::RobustMatcher(const QString &name, - cv::Ptr &detector, - cv::Ptr &extractor, +RobustMatcher::RobustMatcher(const QString &name, + const MatcherAlgorithms &algorithms, const PvlFlatMap ¶meters, - const int &bfNormType, - const bool &crossCheck) : - QLogger() { - init(name, parameters, false); - m_detector = detector; - m_extractor = extractor; - setDescriptorMatcher(bfNormType, crossCheck); + const QLogger &logger) : + MatcherAlgorithms(algorithms),QLogger(logger), + m_name(name), m_parameters() { + init(parameters); } -/** - * @brief Construct a matcher with all componets and parameters - * - * @author 2015-08-28 Kris Becker - * - * @param name Name of matcher being created. - * @param detector Feature detector - * @param extractor Feature extractor - * @param matcher Feature matcher - */ -RobustMatcher::RobustMatcher(const QString &name, - cv::Ptr &detector, - cv::Ptr &extractor, - cv::Ptr &matcher, - const PvlFlatMap ¶meters) : - QLogger() { - - init(name, parameters, false); - m_detector = detector; - m_extractor = extractor; - m_matcher = matcher; -} -/** Desctructor requires no actions */ +/** Destructor requires no actions */ RobustMatcher::~RobustMatcher() { } -/** Set the feature detector */ -void RobustMatcher::setFeatureDetector(cv::Ptr& detector) { - m_detector = detector; -} - - -/** Set the descriptor extractor */ -void RobustMatcher::setDescriptorExtractor(cv::Ptr& extractor) { - m_extractor = extractor; -} - -/** Set the descriptor matcher */ -void RobustMatcher::setDescriptorMatcher(cv::Ptr& matcher) { - m_matcher = matcher; - return; -} - -void RobustMatcher::setDescriptorMatcher(const int &normType, - const bool &crossCheck) { - m_matcher = allocateMatcher(m_extractor, normType, crossCheck); - return; -} - -QString RobustMatcher::getMatcherDescription() const { - return ( m_matcherSpec ); -} - - -void RobustMatcher::setDescription(const QString &description) { - m_description = description; - return; -} - -QString RobustMatcher::getDescription() const { - return ( m_description ); -} - - - /** - * @brief Determines whether the PVL keyword with the given name at the given index is null. - * - * This method looks for the PVL keyword in this Resource's PvlFlatMap that is mapped to the - * given name and checks whether the value at the given index is null. If no index is given, by - * default this method checks the first value (i.e. index 0). If the keyword does not exist in - * the map, this method returns true. - * - * @param keywordName Name of the PVL keyword whose values will be accessed. - * @param index Zero-based index for the value to be checked. - * - * @return bool Indicates whether the given PVL keyword is null at the given index. - */ - bool RobustMatcher::isParameterNull(const QString &name, const int index) const { - return ( m_parameters.isNull(name, index) ); - } - - /** - * Adds the PVL keywords from the given map of keywords to this Resource. - * The new keywords are inserted into this Resource's existing PvlFlatMap. - * - * @param keys A PvlFlatMap containing the PvlKeywords to be inserted into the existing - * keyword list. - */ - void RobustMatcher::addParameters(const PvlFlatMap ¶meters, - const bool &precedence) { - if ( true == precedence) { - m_parameters = PvlFlatMap(m_parameters, parameters); - } - else { - m_parameters = PvlFlatMap(parameters, m_parameters); - } - return; - } - - /** - * Adds a PVL keyword with the given name and value to this Resource. A PvlKeyword object - * is created and added to the PvlFlatMap belonging to this Resource. - * - * @param keywordName A string containing the name of the keyword to be added. - * @param keywordValue A string containing the value of the keyword to be added. - */ - void RobustMatcher::addParameter(const QString &name, - const QString &value) { - m_parameters.add(name, value); - return; - } - - - /** - * Adds the given PVL keyword to this Resource. The PvlKeyword object is added to - * the PvlFlatMap belonging to this Resource. - * - * @param keyword A reference to the PvlKeyword object to be added. - */ - void RobustMatcher::addParameter(const PvlKeyword &keyword, - const QString &name) { - if ( name.isEmpty() ) { - m_parameters.add(keyword); - } - else { - PvlKeyword temp = keyword; - temp.setName(name); - m_parameters.add(temp); - } - } - - /** - * Determines whether a PVL keyword with the given name is in this Resource. - * - * @param name A string containing the keyword name. - * - * @return bool Indicates whether a PVL keyword in this RobustMatcher's - * PvlFlatMap is mapped to the given name. - */ - bool RobustMatcher::hasParameter(const QString &name) const { - return ( m_parameters.exists(name) ); - } - - /** - * @brief Gets the value of the PVL keyword with the given name at the given index. - * - * This method looks for the PVL keyword in this RobustMatcher's PvlFlatMap - * that is mapped to the given name and accesses the value at the given - * index. If no index is given, by default this method returns the first - * value (i.e. index 0). - * - * Note: If the keyword does not exist in the map, PvlFlatMap throws an - * exception. To avoid this, the isNull() method can be called before - * invoking this method to verify whether a value exists at the given - * index. Otherwise, the value(QString, QString, int) version of this - * overloaded method can be called. - * - * @see isNull(QString, int) - * @see value(QString, QString, int) - * - * @param keywordName A string containing the name of the PVL keyword in this Resource's - * list of keywords. - * @param index Zero-based index for the value to be accessed. - * - * @return QString A string containing the PVL keyword value at the given index. - */ - QString RobustMatcher::getParameter(const QString &name, const int &index) const { - return ( m_parameters.get(name, index) ); - } - - - /** - * @brief Gets the value of the PVL keyword at the given index, if found; otherwise it returns - * the given default value. - * - * This method looks for the PVL keyword in this RobustMatcher's PvlFlatMap - * that is mapped to the given name and accesses the value at the given - * index. If no index is given, by default this method returns the first - * value (i.e. index 0). - * - * If the keyword does not exist in the map, the given default value will be - * returned. - * - * @see isNull(QString, int) - * @see value(QString, int) - * - * @param name A string containing the name of the PVL keyword in this - * Resource's list of keywords. - * @param defaultValue A string containing the default value for this - * keyword if not found in the PvlFlatMap. - * @param index Zero-based index for the value to be accessed. - * - * @return QString A string containing the PVL keyword value at the - * given index, if it exists; otherwise the given default - * value is returned. - */ - QString RobustMatcher::getParameter(const QString &name, - const QString &defaultValue, - const int &index) const { - QString keywordValue(defaultValue); - if ( !isParameterNull(name, index) ) { - keywordValue = getParameter(name, index); - } - return (keywordValue); - } - - - - /** - * Counts the number of values the PVL keyword with the given name has, if it exists - * in this Resource. Otherwise, it returns 0. - * - * @param keywordName A string containing the keyword name. - * - * @return int The size of the PvlKeyword object mapped to the given name in - * this Resource's PvlFlatMap. - */ - int RobustMatcher::getParameterCount(const QString &name) const { - return ( m_parameters.count(name) ); - } - -void RobustMatcher::setRatio(const double ratio) { - m_ratio = ratio; - return; -} - -void RobustMatcher::setEpiTolerance(const double tolerance) { - m_epiTolerance = tolerance; - return; -} - -void RobustMatcher::setEpiConfidence(const double confidence) { - m_epiConfidence = confidence; - return; -} - -void RobustMatcher::setHmgTolerance(const double tolerance) { - m_hmgTolerance = tolerance; - return; -} - -void RobustMatcher::setMaxPoints(const int maxpoints) { - m_maxpoints = maxpoints; - return; -} - -double RobustMatcher::getRatio() const { - return ( m_ratio ); -} - -double RobustMatcher::getEpiTolerance() const { - return ( m_epiTolerance ); -} - -double RobustMatcher::getEpiConfidence() const { - return ( m_epiConfidence ); -} - -double RobustMatcher::getHmgTolerance() const { - return ( m_hmgTolerance ); -} - - -int RobustMatcher::getMaxPoints() const { - return ( m_maxpoints ); -} - - /** * @brief Construct required interface with match image pairs * @@ -407,23 +128,23 @@ MatchPair RobustMatcher::match(MatchImage &query, MatchImage &train) const { logger() << "\n@@ matcher-pair started on " << Application::DateTime() << "\n"; logger() << "\n+++++++++++++++++++++++++++++\n"; logger() << "Entered RobustMatcher::match(MatchImage &query, MatchImage &trainer)...\n"; - logger() << " Specification: " << getDescription() << "\n"; + logger() << " Specification: " << name() << "\n"; logger().flush(); } const bool onErrorThrow = false; // Conditions for managed matching // Setup - MatchImage &v_query = query; - MatchImage &v_train = train; + MatchImage v_query = query.clone(); + MatchImage v_train = train.clone(); MatchPair v_pair(v_query, v_train); // Render images for matching cv::Mat i_query = v_query.image(); cv::Mat i_train = v_train.image(); - if ( toBool(getParameter("SaveRenderedImages", "false")) ) { - QString savepath = getParameter("SavePath", "$PWD"); + if ( toBool(m_parameters.get("SaveRenderedImages")) ) { + QString savepath = m_parameters.get("SavePath"); FileName qfile(v_query.source().name()); QString qfout = savepath + "/" + qfile.baseName() + "_query.png"; @@ -456,19 +177,20 @@ MatchPair RobustMatcher::match(MatchImage &query, MatchImage &train) const { stime.start(); // 1a. Detection of the features - m_detector->detect(i_query, v_query.keypoints()); - m_detector->detect(i_train, v_train.keypoints()); + detector().algorithm()->detect(i_query, v_query.keypoints()); + detector().algorithm()->detect(i_train, v_train.keypoints()); int v_query_points = v_query.size(); int v_train_points = v_train.size(); int allPoints = v_query_points + v_train_points; // Limit keypoints if requested by user - if ( m_maxpoints > 0 ) { - logger() << " Keypoints restricted by user to " << m_maxpoints << " points...\n"; + int v_maxpoints = toInt(m_parameters.get("MaxPoints")); + if ( v_maxpoints > 0 ) { + logger() << " Keypoints restricted by user to " << v_maxpoints << " points...\n"; logger().flush(); - cv::KeyPointsFilter::retainBest(v_query.keypoints(), m_maxpoints); - cv::KeyPointsFilter::retainBest(v_train.keypoints(), m_maxpoints); + cv::KeyPointsFilter::retainBest(v_query.keypoints(), v_maxpoints); + cv::KeyPointsFilter::retainBest(v_train.keypoints(), v_maxpoints); } double v_time = elapsed(stime); // Event timing @@ -488,13 +210,14 @@ MatchPair RobustMatcher::match(MatchImage &query, MatchImage &train) const { // 1b. Extraction of the descriptors cv::Mat queryDescriptors, trainerDescriptors; - m_extractor->compute(i_query, v_query.keypoints(), v_query.descriptors()); - m_extractor->compute(i_train, v_train.keypoints(), v_train.descriptors()); + extractor().algorithm()->compute(i_query, v_query.keypoints(), v_query.descriptors()); + extractor().algorithm()->compute(i_train, v_train.keypoints(), v_train.descriptors()); double d_time = elapsed(stime) - v_time; v_pair.addTime( v_time + d_time ); // Do root sift normalization if requested - if ( m_doRootSift ) { + bool v_doRootSift = toBool(m_parameters.get("RootSift")); + if ( v_doRootSift ) { if ( isDebug() ) { logger() << " Computing RootSift Descriptors...\n"; } @@ -574,7 +297,7 @@ MatchPairQList RobustMatcher::match(MatchImage &query, logger() << "\n@@ matcher-multi started on " << Application::DateTime() << "\n"; logger() << "\n+++++++++++++++++++++++++++++\n"; logger() << "Entered RobustMatcher::match(MatchImage &query,""MatchImageList &trainer)...\n"; - logger() << " Specification: " << getDescription() << "\n"; + logger() << " Specification: " << name() << "\n"; logger().flush(); } @@ -595,8 +318,8 @@ MatchPairQList RobustMatcher::match(MatchImage &query, // Render images for efficiency cv::Mat i_query = v_query.image(); std::vector i_trainers; - bool saveRendered = toBool(getParameter("SaveRenderedImages", "false")); - QString savepath = getParameter("SavePath", "$PWD"); + bool saveRendered = toBool(m_parameters.get("SaveRenderedImages")); + QString savepath = m_parameters.get("SavePath"); if ( true == saveRendered ) { // Save the query image first @@ -643,8 +366,8 @@ MatchPairQList RobustMatcher::match(MatchImage &query, // 1a. Run detection of features std::vector > trainerKeypoints; - m_detector->detect(i_query, v_query.keypoints()); - m_detector->detect(i_trainers, trainerKeypoints); + detector().algorithm()->detect(i_query, v_query.keypoints()); + detector().algorithm()->detect(i_trainers, trainerKeypoints); int v_query_points = v_query.size(); int allPoints = v_query_points; @@ -655,12 +378,13 @@ MatchPairQList RobustMatcher::match(MatchImage &query, } // Limit keypoints if requested by user - if ( m_maxpoints > 0 ) { - logger() << " Keypoints restricted by user to " << m_maxpoints << " points...\n"; + int v_maxpoints = toInt(m_parameters.get("MaxPoints")); + if ( v_maxpoints > 0 ) { + logger() << " Keypoints restricted by user to " << v_maxpoints << " points...\n"; logger().flush(); - cv::KeyPointsFilter::retainBest(v_query.keypoints(), m_maxpoints); + cv::KeyPointsFilter::retainBest(v_query.keypoints(), v_maxpoints); for (unsigned int i = 0 ; i < trainerKeypoints.size() ; i++) { - cv::KeyPointsFilter::retainBest(trainerKeypoints[i], m_maxpoints); + cv::KeyPointsFilter::retainBest(trainerKeypoints[i], v_maxpoints); } } @@ -694,8 +418,8 @@ MatchPairQList RobustMatcher::match(MatchImage &query, // 1b. Extraction of the descriptors std::vector trainerDescriptors; - m_extractor->compute(i_query, v_query.keypoints(), v_query.descriptors()); - m_extractor->compute(i_trainers, trainerKeypoints, trainerDescriptors); + extractor().algorithm()->compute(i_query, v_query.keypoints(), v_query.descriptors()); + extractor().algorithm()->compute(i_trainers, trainerKeypoints, trainerDescriptors); // Record time to detect features and extract descriptors for all images double e_time = elapsed(stime) - d_time; @@ -705,7 +429,8 @@ MatchPairQList RobustMatcher::match(MatchImage &query, v_query.addTime( (d_time + e_time) * ( v_query.size() / allPoints ) ); // Do root sift normalization if requested - if ( m_doRootSift ) { + bool v_doRootSift = toBool(m_parameters.get("RootSift")); + if ( v_doRootSift ) { if ( isDebug() ) { logger() << " Computing RootSift Descriptors...\n"; } @@ -843,10 +568,10 @@ bool RobustMatcher::removeOutliers(const cv::Mat &queryDescriptors, logger() << " Computing query->train Matches...\n"; logger().flush(); } - m_matcher->knnMatch(queryDescriptors, trainDescriptors, - matches1, // vector of matches (up to 2 per entry) - 2); // return 2 nearest neighbours - } + matcher().algorithm()->knnMatch(queryDescriptors, trainDescriptors, + matches1, // vector of matches (up to 2 per entry) + 2); // return 2 nearest neighbours + } catch (cv::Exception &e) { QString mess = "RobustMatcher::MatcherFailed: "+ QString(e.what()) + " - if its an assertion failure, you may be enabling " @@ -875,7 +600,8 @@ bool RobustMatcher::removeOutliers(const cv::Mat &queryDescriptors, logger() << " Computing train->query Matches...\n"; logger().flush(); } - m_matcher->knnMatch(trainDescriptors, queryDescriptors, + + matcher().algorithm()->knnMatch(trainDescriptors, queryDescriptors, matches2, // vector of matches (up to 2 per entry) 2); // return 2 nearest neighbours v_time = elapsed(stime) - mtime; @@ -919,9 +645,10 @@ bool RobustMatcher::removeOutliers(const cv::Mat &queryDescriptors, // 4) Compute the homography matrix with outlier removal options bool refineHomography(true); + double v_hmgTolerance = toDouble(m_parameters.get("HmgTolerance")); homography = computeHomography(queryKeypoints, trainKeypoints, symMatches, homography_matches, - mtime, CV_FM_RANSAC, getHmgTolerance(), + mtime, CV_FM_RANSAC, v_hmgTolerance, refineHomography, onErrorThrow); // 5) Compute the fundamental matrix with outliers @@ -932,7 +659,7 @@ bool RobustMatcher::removeOutliers(const cv::Mat &queryDescriptors, refineHomography = false; homography = computeHomography(queryKeypoints, trainKeypoints, epipolar_matches, matches, - mtime, CV_FM_RANSAC, getHmgTolerance(), + mtime, CV_FM_RANSAC, v_hmgTolerance, refineHomography, onErrorThrow); @@ -945,10 +672,11 @@ bool RobustMatcher::removeOutliers(const cv::Mat &queryDescriptors, // i.e. size will be 0) int RobustMatcher::ratioTest(std::vector > &matches, double &mtime) const { - + + double v_ratio = toDouble(m_parameters.get("Ratio")); if ( isDebug() ) { logger() << "Entered RobustMatcher::ratioTest(matches[2]) for 2 NearestNeighbors (NN)...\n"; - logger() << " RobustMatcher::Ratio: " << getRatio() << "\n"; + logger() << " RobustMatcher::Ratio: " << v_ratio << "\n"; logger().flush(); } @@ -967,7 +695,7 @@ int RobustMatcher::ratioTest(std::vector > &matches, if (matchIterator->size() > 1) { // check distance ratio if ((*matchIterator)[0].distance/ - (*matchIterator)[1].distance > getRatio()) { + (*matchIterator)[1].distance > v_ratio) { matchIterator->clear(); // remove match removed++; nfailed++; @@ -1072,11 +800,13 @@ cv::Mat RobustMatcher::ransacTest(const std::vector& matches, // Introduce ourselves + double v_epiTolerance = toDouble(m_parameters.get("EpiTolerance")); + double v_epiConfidence = toDouble(m_parameters.get("EpiConfidence")); if ( isDebug() ) { logger() << "Entered EpiPolar RobustMatcher::ransacTest(matches, keypoints1/2...)...\n"; logger() << " -Running EpiPolar Constraints/Fundamental Matrix...\n"; - logger() << " RobustMatcher::EpiTolerance: " << getEpiTolerance() << "\n"; - logger() << " RobustMatcher::EpiConfidence: " << getEpiConfidence() << "\n"; + logger() << " RobustMatcher::EpiTolerance: " << v_epiTolerance << "\n"; + logger() << " RobustMatcher::EpiConfidence: " << v_epiConfidence << "\n"; logger() << " Number Initial Matches: " << matches.size() << "\n"; logger().flush(); } @@ -1087,11 +817,12 @@ cv::Mat RobustMatcher::ransacTest(const std::vector& matches, cv::Mat fundamental = cv::Mat::eye(3,3,CV_64F); // See if enough points to compute fundamental matrix. Minumum number needed - // for RANSAC is 8 points. - if ( (unsigned int) m_minEpiPoints > matches.size() ) { + // for RANSAC is 8 points. + int v_minEpiPoints = toInt(m_parameters.get("MinimumFundamentalPoints")); + if ( (unsigned int) v_minEpiPoints > matches.size() ) { if ( isDebug() ) { logger() << "->ERROR - Not enough points (need at least " - << m_minEpiPoints << ") to proceed - returning identity!\n"; + << v_minEpiPoints << ") to proceed - returning identity!\n"; logger().flush(); } return ( fundamental ); @@ -1117,8 +848,8 @@ cv::Mat RobustMatcher::ransacTest(const std::vector& matches, try { fundamental = cv::findFundamentalMat(cv::Mat(points1),cv::Mat(points2), // matching points CV_FM_RANSAC, // RANSAC method - getEpiTolerance(), // distance to epipolar line - getEpiConfidence(), // confidence probability + v_epiTolerance, // distance to epipolar line + v_epiConfidence, // confidence probability inliers); // match status (inlier or outlier)) } catch ( cv::Exception &e ) { @@ -1150,11 +881,12 @@ cv::Mat RobustMatcher::ransacTest(const std::vector& matches, logger().flush(); } - if ( m_refineF ) { + if ( toBool(m_parameters.get("RefineFundamentalMatrix")) ) { // See if enough points to compute fundamental matrix. Minumum number needed - // for RANSAC is 8 points. - if ( (unsigned int) m_minEpiPoints <= outMatches.size() ) { + // for RANSAC is 8 points. + int v_minEpiPoints = toInt(m_parameters.get("MinimumFundamentalPoints")); + if ( (unsigned int) v_minEpiPoints <= outMatches.size() ) { // Make a copy of the inliers of the first fundamental processing std::vector matches1(outMatches); @@ -1179,8 +911,8 @@ cv::Mat RobustMatcher::ransacTest(const std::vector& matches, try { fundamental2 = cv::findFundamentalMat(cv::Mat(points1), cv::Mat(points2), // matches CV_FM_LMEDS, // Least squares method - getEpiTolerance(), // distance to epipolar line - getEpiConfidence(), // confidence probability + v_epiTolerance, // distance to epipolar line + v_epiConfidence, // confidence probability inliers2); // New set of inliers fundamental = fundamental2; } @@ -1218,7 +950,7 @@ cv::Mat RobustMatcher::ransacTest(const std::vector& matches, else { if ( isDebug() ) { logger() << " Not enough points (" << outMatches.size() - << ", needs " << m_minEpiPoints + << ", needs " << v_minEpiPoints << ") for 2nd Epipolar - returning current state!!\n"; logger().flush(); } @@ -1247,10 +979,11 @@ cv::Mat RobustMatcher::computeHomography(const std::vector& query, const { // Introduce ourselves + double v_hmgTolerance = toDouble(m_parameters.get("HmgTolerance")); if ( isDebug() ) { logger() << "Entered RobustMatcher::computeHomography(keypoints1/2, matches...)...\n"; logger() << " -Running RANSAC Constraints/Homography Matrix...\n"; - logger() << " RobustMatcher::HmgTolerance: " << getHmgTolerance() << "\n"; + logger() << " RobustMatcher::HmgTolerance: " << v_hmgTolerance << "\n"; logger() << " Number Initial Matches: " << matches.size() << "\n"; logger().flush(); } @@ -1271,11 +1004,12 @@ cv::Mat RobustMatcher::computeHomography(const std::vector& query, // Test intial return condition inliers.clear(); - if ( srcPoints.size() < (unsigned int) m_minHomoPoints ) { + int v_minHomoPoints = toInt(m_parameters.get("MinimumHomographyPoints")); + if ( srcPoints.size() < (unsigned int) v_minHomoPoints ) { if ( isDebug() ) { logger() << " Not enough points (" << srcPoints.size() << ") to compute initial homography - need at least " - << m_minHomoPoints << "!\n"; + << v_minHomoPoints << "!\n"; logger().flush(); } return ( homography ); @@ -1293,7 +1027,7 @@ cv::Mat RobustMatcher::computeHomography(const std::vector& query, // Pass only matches with low reprojection error (less than tolerance // value in pixels) - double tolSquared = getHmgTolerance() * getHmgTolerance(); + double tolSquared = v_hmgTolerance * v_hmgTolerance; for (unsigned int i = 0; i < matches.size() ; i++) { cv::Point2f actual = srcPoints[i]; cv::Point2f expected = srcReprojected[i]; @@ -1312,12 +1046,12 @@ cv::Mat RobustMatcher::computeHomography(const std::vector& query, if ( true == refine ) { // Test for bad case - if ( inliers.size() < (unsigned int) m_minHomoPoints ) { + if ( inliers.size() < (unsigned int) v_minHomoPoints ) { inliers.clear(); if ( isDebug() ) { logger() << " Not enough points (" << inliers.size() << ") to compute refined homography - need at least " - << m_minHomoPoints << " - failure!\n"; + << v_minHomoPoints << " - failure!\n"; logger().flush(); } @@ -1378,121 +1112,43 @@ cv::Mat RobustMatcher::computeHomography(const std::vector& query, return ( homography ); } -PvlObject RobustMatcher::info() const { - PvlObject info("FeatureAlgorithm"); - info.addKeyword(PvlKeyword("Name", getDescription())); - info.addKeyword(PvlKeyword("OpenCVVersion", CV_VERSION)); - info.addKeyword(PvlKeyword("Specification", getDescription())); - AlgorithmParameters params; - if ( !m_detector.empty() ) { - // logger() << "FeatureAlgorithm::info(detector): " << m_detector->name() << "\n"; - info.addObject(params.getDescription(m_detector, "Detector")); - } +const PvlFlatMap &RobustMatcher::parameters() const { + return ( m_parameters ); +} - if ( !m_extractor.empty() ) { - // logger() << "FeatureAlgorithm::info(extractor): " << m_extractor->name() << "\n"; - info.addObject(params.getDescription(m_extractor, "Extractor")); - } - if ( !m_matcher.empty() ) { - // logger() << "FeatureAlgorithm::info(matcher): " << m_matcher->name() << "\n"; - info.addObject(params.getDescription(m_matcher, "Matcher")); - } +PvlObject RobustMatcher::info(const QString &p_name) const { + PvlObject description = MatcherAlgorithms::info(p_name); + description.addKeyword(PvlKeyword("OpenCVVersion", CV_VERSION)); + description.addKeyword(PvlKeyword("Name", name())); + // description.addKeyword(PvlKeyword("Specification", name())); - if ( m_parameters.size() > 0 ) { - PvlObject aparms("Parameters"); - BOOST_FOREACH ( const PvlKeyword &key, m_parameters ) { - aparms.addKeyword(key); - } - info.addObject(aparms); + PvlObject aparms("Parameters"); + BOOST_FOREACH ( const PvlKeyword &key, m_parameters ) { + aparms.addKeyword(key); } - return ( info ); -} - + description.addObject(aparms); -void RobustMatcher::init(const QString &name, const PvlFlatMap ¶meters, - const bool &allocateAlgorithms) { - m_name = name; - m_description = m_name; - m_parameters = parameters; - m_matcherSpec = ""; - - m_doRootSift = toBool(getParameter("RootSift", "false")); - m_ratio = toDouble(getParameter("RATIO", "0.65")); - m_epiConfidence = toDouble(getParameter("EPICONFIDENCE", "0.99")); - m_epiTolerance = toDouble(getParameter("EPITOLERANCE", "3.0")); - m_hmgTolerance = toDouble(getParameter("HMGTOLERANCE", "3.0")); - m_maxpoints = toInt(getParameter("MAXPOINTS", "0")); - m_minEpiPoints = toInt(getParameter("MinimumFundamentalPoints", "8")); - m_refineF = toBool(getParameter("RefineFundamentalMatrix", "true")); - m_minHomoPoints = toInt(getParameter("MinimumHomographyPoints", "8")); - - // SURF is the default feature detector and extractor. Use Bruteforce matcher - // with L-2 distance indexing. - if ( allocateAlgorithms ) { - m_detector = new cv::SurfFeatureDetector(); - m_extractor = new cv::SurfDescriptorExtractor(); - m_matcher = allocateMatcher(m_extractor, cv::NORM_L2, false); - } - return; + return ( description ); } -/** - * @brief Allocate a BruteForceMatcher algorithm based upon descriptor extractor - * - * See - * http://docs.opencv.org/modules/features2d/doc/common_interfaces_of_descriptor_matchers.html#bfmatcher-bfmatcher - * for details on this implementation. - * - * @author 2015-08-19 Kris Becker - * - * @param extractor Descriptor extractor algorithm - * @param crossCheck - * - * @return cv::Ptr - */ -cv::Ptr RobustMatcher::allocateMatcher(cv::Ptr &extractor, - const int &normalize, - const bool &crossCheck) { - QString name(QString::fromStdString(extractor->name()).toUpper()); - if ( isDebug() ) { - logger() << "\nDetermining Matcher for " << name << "\n"; - logger().flush(); - } - - int normType(normalize); - if ( name.contains("SURF", Qt::CaseInsensitive) ) { - normType = cv::NORM_L2; - } - else if ( name.contains("SIFT", Qt::CaseInsensitive) ) { - normType = cv::NORM_L2; - } - else if (name.contains("ORB", Qt::CaseInsensitive) ) { - normType = cv::NORM_HAMMING; - try { - if ( extractor->getInt("WTA_K") > 2) { - normType = cv::NORM_HAMMING2; - } - } - catch ( cv::Exception &e ) { - // NOOP - use existing value - } - } - else if ( name.contains("BRISK", Qt::CaseInsensitive) ) { - normType = cv::NORM_HAMMING; - } - else if ( name.contains("BRIEF", Qt::CaseInsensitive) ) { - normType = cv::NORM_HAMMING; - } - - // Update name and return matcher - cv::Ptr matcher(new cv::BFMatcher(normType, crossCheck)); - m_matcherSpec = ("/" + QString::fromStdString(matcher->name()) + - "@normType:" + QString::number(normType) + - "@crossCheck:" + ( (crossCheck) ? "true" : "false" ) ); - return ( matcher ); +void RobustMatcher::init(const PvlFlatMap ¶meters) { + m_parameters.clear(); + m_parameters.add("SaveRenderedImages", "false"); + m_parameters.add("SavePath", "$PWD"); + m_parameters.add("RootSift", "false"); + m_parameters.add("Ratio", "0.65"); + m_parameters.add("EpiConfidence", "0.99"); + m_parameters.add("EpiTolerance", "3.0"); + m_parameters.add("HmgTolerance", "3.0"); + m_parameters.add("MaxPoints", "0"); + m_parameters.add("MinimumFundamentalPoints", "8"); + m_parameters.add("RefineFundamentalMatrix", "true"); + m_parameters.add("MinimumHomographyPoints", "8"); + m_parameters.merge(parameters); + return; } // Compute RootSift descriptors for better matching potential diff --git a/isis/src/control/apps/findfeatures/RobustMatcher.h b/isis/src/control/apps/findfeatures/RobustMatcher.h index a174f2b4e43c9bdd0cf5151fdf6223a5edc290bb..d1b1ffde4eaec7dfad0fb2165dd352817c24d4ec 100644 --- a/isis/src/control/apps/findfeatures/RobustMatcher.h +++ b/isis/src/control/apps/findfeatures/RobustMatcher.h @@ -2,8 +2,8 @@ #define RobustMatcher_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for @@ -29,6 +29,7 @@ #include #include "FeatureMatcherTypes.h" +#include "MatcherAlgorithms.h" #include "MatchImage.h" #include "MatchPair.h" #include "PvlFlatMap.h" @@ -48,63 +49,20 @@ class QDebug; * @history 2015-08-18 Kris Becker - Original Version * @history 2016-10-05 Ian Humphrey & Makayla Shepherd - Changed headers to OpenCV2. */ - class RobustMatcher : public QLogger { + class RobustMatcher : public MatcherAlgorithms, public QLogger { public: - - RobustMatcher(); + RobustMatcher(const QString &name); RobustMatcher(const QString &name, - const PvlFlatMap ¶meters = PvlFlatMap()); - RobustMatcher(const QString &name, cv::Ptr &detector, - cv::Ptr &extractor, + const MatcherAlgorithms &algorithms, const PvlFlatMap ¶meters = PvlFlatMap(), - const int &bfNormType = cv::NORM_L2, - const bool &crossCheck = false); - RobustMatcher(const QString &name, cv::Ptr &detector, - cv::Ptr &extractor, - cv::Ptr &matcher, - const PvlFlatMap ¶meters = PvlFlatMap()); + const QLogger &logger = QLogger()); virtual ~RobustMatcher(); void setName(const QString &name); inline QString name() const { return ( m_name ); } - void setFeatureDetector(cv::Ptr& detector); - - void setDescriptorExtractor(cv::Ptr& extractor); - - void setDescriptorMatcher(cv::Ptr& matcher); - void setDescriptorMatcher(const int &normType, - const bool &crossCheck = false); - QString getMatcherDescription() const; - - void setDescription(const QString &description); - QString getDescription() const; - - void addParameters(const PvlFlatMap ¶meters, - const bool &precedence = false); - bool isParameterNull(const QString &name, const int index = 0) const; - void addParameter(const QString &name, const QString &value); - void addParameter(const PvlKeyword &key, const QString &name = ""); - bool hasParameter(const QString &name) const; - QString getParameter(const QString &name, const QString &defaultValue, - const int &index = 0) const; - QString getParameter(const QString &name, const int &index = 0) const; - int getParameterCount(const QString &name) const; - - void setRatio(const double ratio = 0.65); - void setEpiTolerance(const double tolerance = 3.0); - void setEpiConfidence(const double confidence = 0.99); - void setHmgTolerance(const double tolerance = 3.0); - void setMaxPoints(const int maxpoints = 0); - - double getRatio() const; - double getEpiTolerance() const; - double getEpiConfidence() const; - double getHmgTolerance() const; - int getMaxPoints() const; - // For just images, MatchImage objects are created generically using the // other match interfaces MatchPair match(cv::Mat& query, cv::Mat& trainer) const; @@ -116,15 +74,15 @@ class QDebug; // Robust outlier removal bool removeOutliers(const cv::Mat &queryDescriptors, - const cv::Mat &trainDescriptors, - std::vector& queryKeypoints, - std::vector& trainKeypoints, - std::vector &homography_matches, - std::vector &epipolar_matches, - std::vector &matches, - cv::Mat &homography, cv::Mat &fundamental, - double &mtime, const bool onErrorThrow = true) - const; + const cv::Mat &trainDescriptors, + std::vector& queryKeypoints, + std::vector& trainKeypoints, + std::vector &homography_matches, + std::vector &epipolar_matches, + std::vector &matches, + cv::Mat &homography, cv::Mat &fundamental, + double &mtime, const bool onErrorThrow = true) + const; int ratioTest( std::vector > &matches, double &mtime) const; @@ -149,35 +107,17 @@ class QDebug; const bool refine = true, const bool onErrorThrow = true) const; - - PvlObject info() const; - + + const PvlFlatMap ¶meters() const; + + // This hides the MatcherAlgorithm version which will be augmented + PvlObject info(const QString &p_name = "RobustMatcher") const; private: - QString m_name; // Name of matcher - QString m_description; // Specification string - QString m_matcherSpec; // Derived Matcher spec - - // pointer to the feature detector, extractor, matcher - cv::Ptr m_detector; - cv::Ptr m_extractor; - cv::Ptr m_matcher; - - bool m_doRootSift; // Do a rootsift L1 normalization - double m_ratio; // max ratio between 1st and 2nd NN - bool m_refineF; // if true will refine the fundamental/epipolar matrix - double m_epiTolerance; // min distance to epipolar - double m_epiConfidence; // confidence level (probability) - double m_hmgTolerance; // min distance to homography points - int m_maxpoints; // Restrict maximum returned keypoints - int m_minEpiPoints; // Minimum number of epipolar points - int m_minHomoPoints; // Minimum number homograpy points - PvlFlatMap m_parameters; // Parameters for matcher - void init(const QString &name, const PvlFlatMap ¶meters, - const bool &allocateAlgorithms = false); - cv::Ptr allocateMatcher(cv::Ptr &extractor, - const int &normalize = cv::NORM_L2, - const bool &crossCheck = false); + QString m_name; // Name of matcher + PvlFlatMap m_parameters; // Parameters for matcher + + void init(const PvlFlatMap ¶meters = PvlFlatMap()); void RootSift(cv::Mat &descriptors, const float eps = 1.0E-7) const; double elapsed(const QTime &runtime) const; // returns seconds diff --git a/isis/src/control/apps/findfeatures/SIFTAlgorithm.cpp b/isis/src/control/apps/findfeatures/SIFTAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..5f31cc9ba18f8a57b2c9bc5964d96461583e82b8 --- /dev/null +++ b/isis/src/control/apps/findfeatures/SIFTAlgorithm.cpp @@ -0,0 +1,176 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "SIFTAlgorithm.h" +#include + +namespace Isis { + + /** + * Constructs an empty SiftAlgorithm with default variables. + */ + SIFTAlgorithm::SIFTAlgorithm() : + Feature2DAlgorithm( "SIFT", "Feature2D", + SIFTType::create() ) { + setupParameters(); + } + + + /** + * Constructs a SIFTAlgorithm with input variables. + * + * @param cvars Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + SIFTAlgorithm::SIFTAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("SIFT", "Feature2D", + SIFTType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + const int nfeatures = toInt(variables.get("nfeatures")); + const int nOctaveLayers = toInt(variables.get("nOctaveLayers")); + const double contrastThreshold = toDouble(variables.get("constrastThreshold")); + const double edgeThreshold = toDouble(variables.get("edgeThreshold")); + const double sigma = toDouble(variables.get("sigma")); + + m_algorithm = SIFTType::create(nfeatures, nOctaveLayers, contrastThreshold, + edgeThreshold, sigma); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + SIFTAlgorithm::~SIFTAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap SIFTAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("nfeatures", "0"); + variables.add("nOctaveLayers", "3"); + variables.add("constrastThreshold", "0.04"); + variables.add("edgeThreshold", "10"); + variables.add("sigma", "1.6"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString SIFTAlgorithm::description() const { + QString desc = "The OpenCV SIFT Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d5/d3c/classcv_1_1xfeatures2d_1_1SIFT.html"; + return (desc); + } + + + /** + * Creates and returns an intance of SIFTAlgorithm. + * + * @param vars PvlFlatMap containing algorithm parameters and their values + * @param config A configuration string input by the user + * + * @return @b Feature2DAlgorithm An instance of SIFTAlgorithm + */ + Feature2DAlgorithm *SIFTAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new SIFTAlgorithm(vars, config) ); + } + + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool SIFTAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool SIFTAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool SIFTAlgorithm::hasMatcher() const { + return false; + } + + +/** + * Get and return SIFT's parameters and what they're set to as a PvlFlatMap. + * + * @return @b PvlFlatMap A PvlFlatMap of SIFT's currently set variables and their values. + */ + PvlFlatMap SIFTAlgorithm::getAlgorithmVariables( ) const { + return ( variables() ); + } + + +/** + * @brief Set parameters as provided by the variables, does not work for the + * SIFT algorithm in OpenCV3, so calling this will throw an exception. + * Always returns -1. + * + * @param variables Container of parameters to set + * + * @throws IException::Programmer "SIFT does not have the ability to set algorithm parameters."; + * + * @return @b int -1 Cannot set the Algorithm Variables + */ + int SIFTAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString message = "SIFT does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, message, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis + diff --git a/isis/src/control/apps/findfeatures/SIFTAlgorithm.h b/isis/src/control/apps/findfeatures/SIFTAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..4c3304dba0382c3146cf390699de7ce9bd6fd40c --- /dev/null +++ b/isis/src/control/apps/findfeatures/SIFTAlgorithm.h @@ -0,0 +1,74 @@ +#ifndef SIFTAlgorithm_h +#define SIFTAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/xfeatures2d.hpp" + +#include + +namespace Isis { + +/** + * @brief SIFT Feature matcher algorithm + * + * This class provides the OpenCV3 SIFT Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-11-30 Kris Becker + * + * @internal + * @history 2016-11-30 Kris Becker - Original Version + * @history 2016-12-06 Kristin Berry - Updates for OpenCV3 + */ + +class SIFTAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + SIFTAlgorithm(); + SIFTAlgorithm( const PvlFlatMap &cvars, const QString &config = QString() ); + + virtual ~SIFTAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::SIFT SIFTType; + typedef cv::Ptr SIFTPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/SURFAlgorithm.cpp b/isis/src/control/apps/findfeatures/SURFAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..d9dca5f89713bbd6239ab38888de358b7b283102 --- /dev/null +++ b/isis/src/control/apps/findfeatures/SURFAlgorithm.cpp @@ -0,0 +1,187 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "SURFAlgorithm.h" +#include + +namespace Isis { + + /** + * Constructs a default SURFAlgorithm with default variables. + */ + SURFAlgorithm::SURFAlgorithm() : Feature2DAlgorithm("SURF", "Feature2D", SURFType::create()) { + m_variables.merge( getAlgorithmVariables() ); + } + + +/** + * Constructs a SURFAlgorithm with input variables. + * + * @param cvars Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + SURFAlgorithm::SURFAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("SURF", "Feature2D", + SURFType::create()) { + setConfig(config); + setAlgorithmVariables(cvars); + PvlFlatMap defaults = getAlgorithmVariables(); + defaults.merge(cvars); + m_variables.merge(defaults); + } + + +/** + * Default Destructor + */ + SURFAlgorithm::~SURFAlgorithm() { } + + +/** + * Returns a description of the DaisyAlgorithm. + * + * @return @b QString A description of the algorithm. + */ + QString SURFAlgorithm::description() const { + QString desc = "The OpenCV SURF Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d5/df7/classcv_1_1xfeatures2d_1_1SURF.html"; + return (desc); + } + + +/** + * Creates and returns an instance of SURFAlgorithm. + * + * @param vars PvlFlatMap containing algorithm parameters and their values + * @param config A configuration string input by the user + * + * @return Feature2DAlgorithm + */ + Feature2DAlgorithm *SURFAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + return ( new SURFAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool SURFAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool SURFAlgorithm::hasExtractor() const { + return true; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool SURFAlgorithm::hasMatcher() const { + return false; + } + + + +/** + * @brief Retreive all SURF algorithm variable defaults and populate container + * + * This method will retreive the current values of all the variables as they + * are currently set in the algorithm. + * + * Typically, this is called upon instantiation of the algorithm which provides + * the default state of the variables. However, it is reentrant such that it + * will return the current state of all the variables. + * + * @author 2016-12-07 Kris Becker + * + * @return PvlFlatMap Container with all the SURF variables and values + */ + PvlFlatMap SURFAlgorithm::getAlgorithmVariables( ) const { + PvlFlatMap variables; + SURFPtr v_ref = m_algorithm.dynamicCast(); + variables.add("HessianThreshold", toString(v_ref->getHessianThreshold())); + variables.add("NOctaves", toString(v_ref->getNOctaves())); + variables.add("NOctaveLayers", toString(v_ref->getNOctaveLayers())); + variables.add("Extended", toString(v_ref->getExtended())); + variables.add("Upright", toString(v_ref->getUpright())); + return (variables); + } + +/** + * @brief Set parameters as provided by the variables + * + * @author 2016-12-06 Kris Becker + * + * @param variables Container of parameters to set in the algorithm + * + * @return int Number of variables actually set + */ + int SURFAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + + SURFPtr v_ref = m_algorithm.dynamicCast(); + int nset(0); + if ( variables.exists("HessianThreshold") ) { + v_ref->setHessianThreshold(toDouble(variables.get("HessianThreshold"))); + nset++; + } + + if ( variables.exists("NOctaves") ) { + v_ref->setNOctaves(toInt(variables.get("NOctaves"))); + nset++; + } + + if ( variables.exists("NOctaveLayers") ) { + v_ref->setNOctaveLayers(toInt(variables.get("NOctaveLayers"))); + nset++; + } + + if ( variables.exists("Extended") ) { + v_ref->setExtended(toBool(variables.get("Extended"))); + nset++; + } + + if ( variables.exists("Upright") ) { + v_ref->setUpright(toBool(variables.get("Upright"))); + nset++; + } + + return (nset); + } + +}; + diff --git a/isis/src/control/apps/findfeatures/SURFAlgorithm.h b/isis/src/control/apps/findfeatures/SURFAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..5de47cdbd0ce8798d00cc762c5b43ce319eb7012 --- /dev/null +++ b/isis/src/control/apps/findfeatures/SURFAlgorithm.h @@ -0,0 +1,73 @@ +#ifndef SURFAlgorithm_h +#define SURFAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include "opencv2/xfeatures2d.hpp" + +#include + +namespace Isis { + +/** + * @brief SURF Feature matcher algorithm + * + * This class provides the OpenCV3 SURF Feature2D algortithm. Only the + * necessary methods are implemented here. + * + * The SURF algorithm is in the contrib portion of the OpenCV 3 API. + * + * @author 2016-11-30 Kris Becker + * + * @internal + * @history 2016-11-30 Kris Becker - Original Version + */ + +class SURFAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + SURFAlgorithm(); + SURFAlgorithm(const PvlFlatMap &cvars, const QString &config = QString()); + virtual ~SURFAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, + const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::SURF SURFType; + typedef cv::Ptr SURFPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/ScalingTransform.cpp b/isis/src/control/apps/findfeatures/ScalingTransform.cpp index effdf9a10a0798ba4a1a596a3431ce3d5173f94c..ffdeb210a29ad6d3176e6be1066429e4a32cb1b0 100644 --- a/isis/src/control/apps/findfeatures/ScalingTransform.cpp +++ b/isis/src/control/apps/findfeatures/ScalingTransform.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ - * $Id: ScalingTransform.cpp 6563 2016-02-10 23:56:52Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/control/apps/findfeatures/ScalingTransform.h b/isis/src/control/apps/findfeatures/ScalingTransform.h index ea45386417e5c638549967266b103f1d90246058..19b477d4065c642205586399b7ac28a8b9dd820a 100644 --- a/isis/src/control/apps/findfeatures/ScalingTransform.h +++ b/isis/src/control/apps/findfeatures/ScalingTransform.h @@ -2,8 +2,8 @@ #define ScalingTransform_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/ScharrTransform.h b/isis/src/control/apps/findfeatures/ScharrTransform.h index fdfd89ff10d65f2f0ac8df29c2dfaa9d578dd7b4..c5c184fe01fea56767999732fc376e0c66c1f4b9 100644 --- a/isis/src/control/apps/findfeatures/ScharrTransform.h +++ b/isis/src/control/apps/findfeatures/ScharrTransform.h @@ -2,8 +2,8 @@ #define ScharrTransform_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/SobelTransform.h b/isis/src/control/apps/findfeatures/SobelTransform.h index 33976fe0140e55e16a138b5dea29fea46ab5787e..26b77a5afd3ada63984effec2348ae1e53574f2d 100644 --- a/isis/src/control/apps/findfeatures/SobelTransform.h +++ b/isis/src/control/apps/findfeatures/SobelTransform.h @@ -2,8 +2,8 @@ #define SobelTransform_h /** * @file - * $Revision: 6563 $ - * $Date: 2016-02-10 16:56:52 -0700 (Wed, 10 Feb 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/StarAlgorithm.cpp b/isis/src/control/apps/findfeatures/StarAlgorithm.cpp new file mode 100644 index 0000000000000000000000000000000000000000..1dd0be0267d20f7eac2e3a083bf642061a9fce7d --- /dev/null +++ b/isis/src/control/apps/findfeatures/StarAlgorithm.cpp @@ -0,0 +1,175 @@ +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include +#include "opencv2/opencv.hpp" +#include "opencv2/xfeatures2d.hpp" + +#include "StarAlgorithm.h" +#include + +namespace Isis { + + + /** + * Constructs the algorithm with default variables. + */ + StarAlgorithm::StarAlgorithm() : + Feature2DAlgorithm("Star", "Feature2D", + StarType::create()) { + setupParameters(); + } + + + /** + * Constructs the algorithm with the input variables + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + StarAlgorithm::StarAlgorithm(const PvlFlatMap &cvars, const QString &config) : + Feature2DAlgorithm("Star", "Feature2D", + StarType::create(), cvars) { + setConfig(config); + PvlFlatMap variables = setupParameters(); + variables.merge(cvars); + const int maxSize = toInt(variables.get("MaxSize")); + const int responseThreshold = toInt(variables.get("ResponseThreshold")); + const int lineThresholdProjected = toInt(variables.get("LineThresholdProjected")); + const int lineThresholdBinarized = toInt(variables.get("LineThresholdBinarized")); + const int SuppressNonmaxSize = toInt(variables.get("SuppressNonmaxSize")); + + m_algorithm = StarType::create(maxSize, responseThreshold, lineThresholdProjected, + lineThresholdBinarized, SuppressNonmaxSize); + + m_variables.merge(variables); + } + + + /** + * Destroys the algorithm + */ + StarAlgorithm::~StarAlgorithm() { } + + + /** + * Sets up the algorithm parameters with default values. + * + * @return PvlFlatMap Algorithm parameters and their default values. + */ + PvlFlatMap StarAlgorithm::setupParameters() { + PvlFlatMap variables; + variables.add("MaxSize", "45"); + variables.add("ResponseThreshold", "30"); + variables.add("LineThresholdProjected", "10"); + variables.add("LineThresholdBinarized", "8"); + variables.add("SuppressNonmaxSize", "5"); + m_variables = variables; + return (m_variables); + } + + + /** + * Returns a description of the algorithm. + * + * @return @b QString A description of the algorithm. + */ + QString StarAlgorithm::description() const { + QString desc = "The OpenCV Star Feature2D detector/extractor algorithm." + " See the documentation at " + "http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d_1_1Star.html"; + return (desc); + } + + + /** + * Creates an instance of the algorithm. + * + * @param cvars The variables and values the algorithm will use. + * Variables that are not included will be set to their default. + * @param config The config string used to construct cvars. + */ + Feature2DAlgorithm *StarAlgorithm::create(const PvlFlatMap &vars, const QString &config) { + + return ( new StarAlgorithm(vars, config) ); + } + + + /** + * Returns true if the algorithm has a detector. + * + * @return @b true if the algorithm has a detector. + */ + bool StarAlgorithm::hasDetector() const { + return true; + } + + + /** + * Returns true if the algorithm has an extractor. + * + * @return @b true if the algorithm has an extractor. + */ + bool StarAlgorithm::hasExtractor() const { + return false; + } + + + /** + * Returns true if the algorithm has a matcher. + * + * @return @b true if the algorithm has a matcher. + */ + bool StarAlgorithm::hasMatcher() const { + return false; + } + + + /** + * Returns the variables and their values used by the algorithm. + * + * @return @b PvlFlatMap The variables and their values as keyword, value pairs. + */ + PvlFlatMap StarAlgorithm::getAlgorithmVariables( ) const { + return ( variables() ); + } + + + /** + * @brief Set parameters as provided by the variables + * + * @param variables Container of parameters to set + * + * @return @b int Always -1, variables cannot be set after initialization. + * + * @throws IException::Programmer "StarAlgorithm does not have the ability + * to set algorithm parameters." + */ + int StarAlgorithm::setAlgorithmVariables(const PvlFlatMap &variables) { + QString msg = "StarAlgorithm does not have the ability to set algorithm parameters."; + throw IException(IException::Programmer, msg, _FILEINFO_); + + return (-1); + } + +}; // namespace Isis diff --git a/isis/src/control/apps/findfeatures/StarAlgorithm.h b/isis/src/control/apps/findfeatures/StarAlgorithm.h new file mode 100644 index 0000000000000000000000000000000000000000..bfb91d2e1cd7a8175feafee919338272d1c92087 --- /dev/null +++ b/isis/src/control/apps/findfeatures/StarAlgorithm.h @@ -0,0 +1,70 @@ +#ifndef StarAlgorithm_h +#define StarAlgorithm_h +/** + * @file + * $Revision$ + * $Date$ + * + * Unless noted otherwise, the portions of Isis written by the USGS are public + * domain. See individual third-party library and package descriptions for + * intellectual property information,user agreements, and related information. + * + * Although Isis has been used by the USGS, no warranty, expressed or implied, + * is made by the USGS as to the accuracy and functioning of such software + * and related material nor shall the fact of distribution constitute any such + * warranty, and no responsibility is assumed by the USGS in connection + * therewith. + * + * For additional information, launch + * $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see + * the Privacy & Disclaimers page on the Isis website, + * http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on + * http://www.usgs.gov/privacy.html. + */ + +#include "FeatureAlgorithm.h" +#include + +namespace Isis { + +/** + * @brief StarDetector Feature matcher algorithm + * + * This class provides the OpenCV3 StarDetector Feature2D algortithm. Only the + * necesary methods are implemented here. + * + * @author 2016-12-12 Jesse Mapel + * + * @internal + * @history 2016-12-12 Jesse Mapel - Original Version + */ + +class StarAlgorithm : public Feature2DAlgorithm { // See FeatureAlgorithm.h + // OpenCV 3 API + public: + StarAlgorithm(); + StarAlgorithm(const PvlFlatMap &cvars, const QString &config = QString() ); + + virtual ~StarAlgorithm(); + + QString description() const; + + // Required for all algorithms + static Feature2DAlgorithm *create(const PvlFlatMap &vars, const QString &config = QString()); + + virtual bool hasDetector() const; + virtual bool hasExtractor() const; + virtual bool hasMatcher() const; + + protected: + virtual PvlFlatMap setupParameters(); + virtual PvlFlatMap getAlgorithmVariables() const; + virtual int setAlgorithmVariables(const PvlFlatMap &variables); + + private: + typedef cv::xfeatures2d::StarDetector StarType; + typedef cv::Ptr StarPtr; +}; + +}; // namespace Isis +#endif diff --git a/isis/src/control/apps/findfeatures/Transformer.cpp b/isis/src/control/apps/findfeatures/Transformer.cpp index ae911d9e45d51c3f7086a7b19029c276fd5078ef..973b5aaef808cc438f5da6b19674a55d08d4b1b2 100644 --- a/isis/src/control/apps/findfeatures/Transformer.cpp +++ b/isis/src/control/apps/findfeatures/Transformer.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision: 6598 $ - * $Date: 2016-03-08 11:22:39 -0700 (Tue, 08 Mar 2016) $ - * $Id: Transformer.cpp 6598 2016-03-08 18:22:39Z kbecker@GS.DOI.NET $ + * $Revision$ + * $Date$ + * $Id$ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/control/apps/findfeatures/Transformer.h b/isis/src/control/apps/findfeatures/Transformer.h index b882f59d4f4b28f4e4133d40a053df5b6c17956f..c5e12f72e6d3593cec7da59431c858ddde3c3a8f 100644 --- a/isis/src/control/apps/findfeatures/Transformer.h +++ b/isis/src/control/apps/findfeatures/Transformer.h @@ -2,8 +2,8 @@ #define Transformer_h /** * @file - * $Revision: 6598 $ - * $Date: 2016-03-08 11:22:39 -0700 (Tue, 08 Mar 2016) $ + * $Revision$ + * $Date$ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/control/apps/findfeatures/assets/qnet.png b/isis/src/control/apps/findfeatures/assets/qnet.png index b82bee57f50cd35818a0b3232e7704a7d1debd1b..2a4464ae77301e6990c5683f2cd33e15e5512cd5 100644 Binary files a/isis/src/control/apps/findfeatures/assets/qnet.png and b/isis/src/control/apps/findfeatures/assets/qnet.png differ diff --git a/isis/src/control/apps/findfeatures/findfeatures.cpp b/isis/src/control/apps/findfeatures/findfeatures.cpp index 0e252028c458a923d2381088139986d4a10b56f2..8faf85d143fc89749a2f782dede983ff5d0922db 100644 --- a/isis/src/control/apps/findfeatures/findfeatures.cpp +++ b/isis/src/control/apps/findfeatures/findfeatures.cpp @@ -12,10 +12,7 @@ #include // OpenCV stuff -#include "opencv2/core/core.hpp" -#include "opencv2/nonfree/features2d.hpp" -#include "opencv2/highgui/highgui.hpp" -#include "opencv2/calib3d/calib3d.hpp" +#include "opencv2/core.hpp" // boost library #include @@ -66,16 +63,38 @@ using namespace std; using namespace Isis; +static void writeInfo(const QString &toname, Pvl &data, + UserInterface &ui) { + if ( !toname.isEmpty() ) { + FileName toinfo(toname); + QString fname = toinfo.expanded(); + data.write(fname); + } + else { + if ( !ui.IsInteractive() ) { + std::cout << data << "\n"; + } + else { + Application::GuiLog(data); + } + } + return; +} + void IsisMain() { // Program constants const QString findfeatures_program = "findfeatures"; - const QString findfeatures_version = "0.1"; - const QString findfeatures_revision = "$Revision: 6598 $"; + const QString findfeatures_version = "1.0"; + const QString findfeatures_revision = "$Revision$"; const QString findfeatures_runtime = Application::DateTime(); // Get user interface UserInterface &ui = Application::GetUserInterface(); + QString toinfo; + if ( ui.WasEntered("TOINFO")) { + toinfo = ui.GetAsString("TOINFO"); + } // Set up program debugging and logging QDebugStream logger( QDebugLogger::null() ); @@ -101,25 +120,16 @@ void IsisMain() { logger->flush(); // Set up for info requests - Pvl info; - bool gotInfo(false); FeatureAlgorithmFactory *factory = FeatureAlgorithmFactory::getInstance(); if ( ui.GetBoolean("LISTALL") ) { + Pvl info; QStringList algorithms = factory->getListAll(); // cout << algorithms.join("\n") << "\n"; info.addObject( factory->info(algorithms) ); - gotInfo = true; + writeInfo(toinfo, info, ui); + return; } - if ( ui.GetBoolean("LISTMATCHERS") ) { - QStringList algorithms = factory->getListFeature2D(); - algorithms += factory->getListDetectors(); - algorithms += factory->getListExtractors(); - algorithms += factory->getListMatchers(); - logger->dbugout() << algorithms.join("\n") << "\n"; - info.addObject( factory->info(algorithms)); - gotInfo = true; - } // Get parameters from user PvlFlatMap parameters; @@ -133,13 +143,11 @@ void IsisMain() { // Get individual parameters if provided QStringList parmlist; - parmlist << "RATIO" << "EPITOLERANCE" << "EPICONFIDENCE" << "HMGTOLERANCE" - << "MAXPOINTS" << "FASTGEOM" << "FASTGEOMPOINTS" << "GEOMTYPE" - << "FILTER"; + parmlist << "Ratio" << "EpiTolerance" << "EpiConfidence" << "HmgTolerance" + << "MaxPoints" << "FastGeom" << "FastGeomPoints" << "GeomType" + << "GeomSource" << "Filter"; BOOST_FOREACH (QString p, parmlist ) { - if ( ui.WasEntered(p) ) { - parameters.add(p, ui.GetAsString(p)); - } + parameters.add(p, ui.GetAsString(p)); } // Got all parameters. Add them now and they don't need to be considered @@ -149,7 +157,6 @@ void IsisMain() { // Retrieve the ALGORITHM specification (if requested) QString aspec; - RobustMatcherList algorithms; if ( ui.WasEntered("ALGORITHM") ) { aspec = ui.GetString("ALGORITHM"); } @@ -169,42 +176,21 @@ void IsisMain() { aspec.append( algos.join("|") ); } - // Create the algorithms and list if requested - if ( !aspec.isEmpty() ) { - algorithms = factory->create(aspec); - if ( ui.GetBoolean("LISTSPEC") ) { - info.addObject(factory->info(algorithms)); - gotInfo = true; - } - } - else { - if ( ui.GetBoolean("LISTSPEC") || ( !gotInfo) ) { - QString mess = "Matching ALGORITHM/ALGOSPECFILE must be provided!"; - throw IException(IException::User, mess, _FILEINFO_); - } - } + // Create a list of algorithm specifications from user specs and log it + // if requested + RobustMatcherList algorithms = factory->create(aspec); + if ( ui.GetBoolean("LISTSPEC") ) { + Pvl info; + info.addObject(factory->info(algorithms)); + writeInfo(toinfo, info, ui); - // Write information if requested, write to requested output target and exit - if ( gotInfo ) { - // Check for output options - if ( ui.WasEntered("TOINFO") ) { - FileName toinfo = ui.GetFileName("TOINFO"); - QString fname = toinfo.expanded(); - info.write(fname); - } - else { - if ( !ui.IsInteractive() ) { - std::cout << info << "\n"; - } - else { - Application::GuiLog(info); - } + // If no input files are provided exit here + if ( ! ( ui.WasEntered("FROM") && ui.WasEntered("FROMLIST") ) ) { + return; } - return; } - // First see what we can do about threads if your user is resource conscience int nCPUs = cv::getNumberOfCPUs(); int nthreads = cv::getNumThreads(); @@ -259,12 +245,12 @@ void IsisMain() { // Check for FASTGEOM option if ( ui.GetBoolean("FASTGEOM") ) { - FastGeom geom( factory->getGlobalParameters() ); + FastGeom geom( factory->globalParameters() ); matcher.foreachPair( geom ); } // Check for Sobel/Scharr filtering options for both Train and Images - QString filter = factory->getGlobalParameters().get("FILTER", "").toLower(); + QString filter = factory->globalParameters().get("FILTER", "").toLower(); // Apply the Sobel filter to all image if ( "sobel" == filter ) { matcher.query().addTransform(new SobelTransform("SobelTransform")); @@ -305,11 +291,11 @@ void IsisMain() { } // Got some matches so lets process them - Statistics quality = best->quality(); + Statistics quality = best->qualityStatistics(); PvlGroup bestinfo("MatchSolution"); + bestinfo += PvlKeyword("Matcher", best->matcher()->name()); + bestinfo += PvlKeyword("MatchedPairs", toString(best->size())); bestinfo += PvlKeyword("Efficiency", toString(quality.Average())); - bestinfo += PvlKeyword("MinEfficiency", toString(quality.Minimum())); - bestinfo += PvlKeyword("MaxEfficiency", toString(quality.Maximum())); if ( quality.ValidPixels() > 1 ) { bestinfo += PvlKeyword("StdDevEfficiency", toString(quality.StandardDeviation())); @@ -324,7 +310,7 @@ void IsisMain() { ControlNet cnet; cnet.SetNetworkId(ui.GetString("NETWORKID")); cnet.SetUserName(Application::UserName()); - cnet.SetDescription(best->matcher()->getDescription()); + cnet.SetDescription(best->matcher()->name()); cnet.SetCreatedDate(Application::DateTime()); QString target = ( ui.WasEntered("TARGET") ) ? ui.GetString("TARGET") : best->target(); diff --git a/isis/src/control/apps/findfeatures/findfeatures.xml b/isis/src/control/apps/findfeatures/findfeatures.xml index 61e65e7975c9f8200ff08bb247d63711c392cbd2..e7f785fa3b181c5d543f3bb73cde3a88aee35543 100644 --- a/isis/src/control/apps/findfeatures/findfeatures.xml +++ b/isis/src/control/apps/findfeatures/findfeatures.xml @@ -10,22 +10,24 @@

    Introduction

    findfeatures was developed to provide an alternative approach to - create image-based ISIS control point networks. Traditional ISIS - control networks are typically created using equally spaced grids and - area-based image matching (ABM) techniques. Control points are at the - center of these grids and they are not necessarily associated with any - particular feature or interest point. - findfeatures applies feature-based matching (FBM) algorihms using - the full suite of OpenCV - - feature matching frameworks. The points detected by these - algorithms are associated with special surface features identified by - the type of detector algorithm designed to identify certain - charcteristics. Feature based matching has a - - twenty year history in computer vision and continues to benefit - from improvements and advancements to make development of applications - like this possible. + create image-based ISIS control point networks. Traditional ISIS + control networks are typically created using equally spaced grids and + area-based image matching (ABM) techniques. Control points are at the + center of these grids and they are not necessarily associated with any + particular feature or interest point. + findfeatures applies feature-based matching (FBM) algorihms using + the full suite of OpenCV + + detection and descriptor extraction algorithms and + + descriptor matchers. The points detected by these + algorithms are associated with special surface features identified by + the type of detector algorithm designed to identify certain + charcteristics. Feature based matching has a + + twenty year history in computer vision and continues to benefit + from improvements and advancements to make development of applications + like this possible.

    This application offers alternatives to traditional image matching options @@ -40,223 +42,862 @@

    Overview

    - Feature based algorithms are comprised of three basic processes: - detection of interest points (or keypoints), extraction of interest point - descriptors and finally matching of interest point descriptors from two - image sources. These three operations are performed with individual - algorithms called detectors, extractors and matchers, respectively. - These operations alone do not ensure good, high quality points are - detected as the result set likely contains many outliers. - findfeatures applies a robust outlier detection procedure that - works well for many diverse observing conditions that commonly occur - during the acquisution (e.g., opposing sun angles, wide range of emission - and incidence angeles, etc..). Users can specify unique combinations of - detector, extractor and matcher FBM algorithms using the OpenCV API - through string specifcations. The string specification of the FBM names - the three algorithms and optional parameter values for each using a - custom syntax to provide flexibilty. + findfeatures uses OpenCV 3.1's + FBM algorithms to match a single image, or set of images, called the + trainer image(s) to a different image, called the query image.

    - findfeatures is designed to support many different image - formats. However, ISIS images with camera models provide the greatest - flexibility when using this feature matcher. Level 1 ISIS images with - geometry can be effectively and efficiently matched by applying fast - geometric transforms that project all overlapping candidate images - (referred to as train images in OpenCV terminolgy) to the camera - space of the match (or truth) image (referred to as the - query image in OpenCV terminology). This single feature allows - users to apply virtually all OpenCV detector and extractor, including - algorithms that are not scale and rotation invariant. Other popular - image formats are supported using OpenCV - - imread() image reader API. Images supported here can be provided as - the image input files. However, these images will not have geometric - functionality so support for the fast geometric option is not - available to these images. As a consequence, FBM algorithms that are - not scale and rotation invarant are not recommended for these images - unless they are relatively spatially consistent. Nor can the point - geometries be provided - only line/sample coorelations will be - computed in these cases. + Feature based algorithms are comprised of three basic processes: + detection of features (or keypoints), extraction of feature descriptors + and finally matching of feature descriptors from two image sources. + To improve the quality of matches, findfeatures applies a fourth + process, robust outlier detection. +

    +

    + Feature detection is the search for features of interest (or key + points) in an image. The ultimate goal is to find features that can + also be found in another image of the same subject or location. + Feature detection algorithms are often refered to as detectors. +

    +

    + Detectors describe key points based on their location in a specific + image. Feature descriptors allow features found by a detector to be + described outside of the context of that image. For example, features + could be described by their roundness or how much they contrast the + surrounding area. Feature descriptors provide a way to compare key + points from different images. Algorithms that extract feature + descriptors from keypoints in an image are called extractors. +

    +

    + The third process is to match key points from different images based on + their feature descriptors. The trainer images can be matched to the + query image (called a trainer to query match) or the query image can be + matched to the trainer images (calles a query to trainer match). + findfeatures performs both a trainer to query match and a query + to trainer match. Algorithms for matching feature descriptors are + called matchers. +

    +

    + The final step is to remove outlier matches. This helps improve the + quality and accuracy of matches when conditions make matching + challenging. findfeatures uses a five step outlier removal + process. At each step, matches are rejected and only the surviving + matches are used in the following step. First, a ratio test comparing + the best and second best match for each point removes points that not + sufficiently distinct. Second, the matches are checked for symmetry. If + a match was made in the trainer to query match, but not in the query to + trainer match (or vice versa) then the match is removed. Third, the + homography matrices (projections from one image's perspective into + anothers) from the query image to the trainer images are computed using + the RANSAC algorithm and matches with a high residual are removed. + Fourth, the fundamental matrices between the trainer images and the + query image are computed using the RANSAC algorithm and matches that + are excluded by the RANSAC algorithm are removed. Finally, the + homography matrices from the query image to the trainer images are + computed again and matches with a high residual are removed.

    - The OpenCV FBM algorithms and parameterization of those algoriithms are - selected/provided with a specific string syntax. The string contains a - feature detector, descriptor extractor and descriptor matcher - algorithm specification with optional parameterization of the robust - matcher outlier detection and other processing algorithms. The general - form of the FBM specification string is: + Matches that survive the outlier rejection process are converted into + an output control network. From here, mutliple control networks created + by systematic use of findfeatures can be combined into one + regional or global control network with cnetcombinept. This can + result in extremely larget control networks. cnetthinner can be + used to reduce the size of the network without significantly degrading + its quality. +

    +

    Supported Image Formats

    +

    + findfeatures is designed to support many different image + formats. However, ISIS cubes with camera models provide the greatest + flexibility when using this feature matcher. ISIS cubes with geometry + can be effectively and efficiently matched by applying fast geometric + transforms that project all overlapping candidate images (referred to + as train images in OpenCV terminolgy) to the camera space of the + match (or truth) image (referred to as the query image in OpenCV + terminology). This single feature allows users to apply virtually all + OpenCV detector and extractor, including algorithms that are not scale + and rotation invariant. Other popular image formats are supported using + OpenCV + + imread() image reader API. Images supported here can be provided as + the image input files. However, these images will not have geometric + functionality so support for the fast geometric option is not + available to these images. As a consequence, FBM algorithms that are + not scale and rotation invarant are not recommended for these images + unless they are relatively spatially consistent. Nor can the point + geometries be provided - only line/sample coorelations will be + computed in these cases. +

    +

    Specifying Algorithms and Robust Matcher Parameters

    +

    + Detectors, extractors, matchers, and robust matcher parameters are + specified by a specification string entered as the ALGORITHM + parameter. The basic scheme is shown below (optional portions are + surrounded by [ ]).

    - detector[@param1:value1@...]/extractor[@param1:value@...][/matcher@param1@value1@...][/parameters@param1:value1@...] + detector[@param1:value1@...]/extractor[@param1:value@...][/matcher@param1@value1@...][/parameters@param1:value1@...]

    - where detector - is the name of an OpenCV feature - detector (such as SIFT, SURF, FAST, etc...), - extractor is a name - of a descriptor - - extractor (such as SIFT, SURF, BRISK, BRIEF and FREAK), - matcher is the name of a descriptor - - matcher (such as FlannBased or BruteForce) and - parameters names variables that alter the behavior and - results of image matching processing. Only detectors and - extractors are required (findfeatures will - automatically provide a matcher for the - detector/extractor combination). - The list of parameters for the robust matcher algorithm - currently available are listed in the Robust Matcher Parameters table. + The specification string consists of between two and four components + separated by /. Each component consists of entries + separated by @. The first component of the specification + string, detector[@param1:value1@...], defines the + detector. The first entry is the name of the algorithm. The remaining + entries are separated by @ and define parameters for the + detector. The entries consist of the parameter name followed by + : and then the parameter value. After the detector + component is / and then the extractor component, + extractor[@param1:value@...]. After the extractor + component is / and then the matcher component, + [matcher@param1@value1@...]. The extractor and matcher + components are formatted the same way as the detector component. The + final component of the specification string, + [/parameters@param1:value1@...] defines the robust matcher + parameters. The first entry is the word parameters. The + remaining entries consist of parameter name:value pairs, + just like the parameters in the algorithm components.

    - Outlier detection is implemented as four separate steps and applied - to the results of the FBM detector, extractor and matcher algorithms - have completed. The four main steps are: -

      -
    • - Bi-directional ratio test of two closest matches of each tie point -
      • -
    • - Symmetry test of bi-directional matches -
      • -
    • - - Epipolar (stereo) constraints from fundamental matrix using - random sampling consensus (RANSAC) -
      • -
    • - Projective relationship using - - homography (spatial) matrix -
      • -
    - - This is a significant improvement over existing ABM algorithms - because outlier detection is now performed both in the image matching - phase and jigsaw bundle adjustment! - + An alternative scheme for the specification string allows the + components to be in any order. Each component is formatted the same, + except the first entry in the detector, extractor, and (if specified) + matcher components begin with detector., + extractor., and matcher. respectively. For + example, the specification below would enable root sift in the outlier + detection, define a FAST detector, define a LATCH descriptor extractor, + and define a FlannBased matcher.

    + + extractor.LATCH@Bytes:16@HalfSSDSize:4/parameters@RootSift:true/matcher.FlannBasedMatcher/detector.FAST@Threshold:9@NonmaxSuppression:false +

    - The results of the FBM of all train images to query images will be - written to an ISIS control network. The query image is automatically - selected as the reference image but geometry can come from the train - source for two-pair image matching. It should be noted that the - goodness of fit does not follow the ABM ranges of -1 to 1. Instead it - is computed from the average of the responsivity of the query and - train image keypoints. + Many FBM algorithms are designed to use a specific detector, extractor + pair with shared parameters (SIFT and SURF are good examples of this). + For these cases, the alternative specification scheme allows for the + detector and extractor to be defined in a single component with shared + parameters. To do this, begin the first entry with + feature2d.. For example, the following specification would + define a SIFT algorithm with 4 octave layers for both the detector and + extractor along with a brute force matcher using the L1 norm.

    + matcher.BFMatcher@NormType:Norm_L1/feature2d.SIFT@NOctaveLayers:4.

    - isisminer can be used to determine overlapping image sets for - input into this application for multi-matching FBM processing. - cnetcombinept is designed to take all the resulting control - networks from systematic regional or global processing with - findfeatures. cnetcheck should be used to ensure the - combined network is suitable for bundle adjustment and solving for - radius using jigsaw. The bundle adjusted control network would - now contain adjusted latitude/longitude coordinates and radius values - at each control point, If the control network contains sufficient - density, cnet2dem can be use to produce an interolated DEM from - the control network. And CKs and SPKs can be generated using - ckwriter and spkwriter, respectively, to capture the - control for general distribution and use. + The minimum specification string consists of a detector name and an + extractor name. When no matcher is specified, a brute force matcher + with parameters tailored to the extractor is used. For example + SURF/SURF would result in SURF being used for the + detector, SURF being used for the extractor, and a brute force matcher + used for the matcher. If used with the alternatice specification + scheme, the detector and extractor can be defined in a single + component. So, the specification feature2d.SURF defines + the exact same detector, extractor, and matcher as the previous + specification.

    -

    Parameterization of the Matcher

    - Much of the flexibility in findfeatures is the abilility to - alter parameters for the OpenCV matcher algorithms. Significant - effort has been made to allow the user to change algorithm behaviors. - Not only can users change OpenCV algorithm parameters, but there are - additional parameters available in the robust matcher, particularly - in the outlier detection processing, that can modifed. These - parameters can be very helpful in diagnosing issues with the matching - and outlier aspects of findfeatures. The following table - describes all the parameters available that can be modified through - the /parameters@... option of the matcher algorithm - specification string. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -

    - Robust Matcher Parameters -

    -
    KeywordDefaultDescription
    SaveRenderedImagesFalse - Option to save the images that are matched - after all transforms (e.g., fast geom, filtered, etc...) - have been applied. The query (MATCH) image will have - "_query" will be appended to the base name. All - FROM/FROMLIST images will have "_train" appended to their - names. They are saved as PNG images in the directory - specifed by the SavePath parameter. -
    SavePath$PWD - Specify the directory path to save all transform rendered - images if SaveRenderedImages=TRUE. -
    RootSiftFalse - Apply the - - RootSift algorithm to the descriptors that - normalizes SIFT-type of descriptors. The best description of - the application of this algorithm is described in - - this article. In general, SIFT descriptors histograms are - compared in Euclidean space. RootSift applies a Hellinger - kernel to the descriptor histograms that greatly improve - performance and still allows Euclidean distances in its - evaluation. Be sure to use this for SIFT-type descriptors - only. -
    MinimumFundamentalPoints8 - The Epipolar algorithm in OpenCV requires a minimim of 8 - points in order to properly compute the fundamental matrix. - This parameter allowes the user to specify the minimum number - of points allowed. -
    RefineFundamentalMatrixTrue - A single computation of the fundamental matrix is performed - unless this parameter is set to true. In this case, a new - fundmental matrix is computed after outlier are detected and - removed. This will improve the matrix since outliers are - removed and the matrix is recomputed. -
    MinimumHomographyPoints8 - As in the Epipolar fundamental matrix, a minimum number of 8 - points is required to compute the homography matrix for - outlier detection. This parameter allows the user to specify - a new minimum. -
    -

    + Multiple sets of FBM algorithms and robust matcher parameters can be + entered via the ALGOSPECFILE parameter. It takes a text file + (*.lis) with a specification on each line. For each specification, a + separate set of FBM algorithms and robust matcher parameters will be + created. Each set will be used to match the input images and the set + that produces the best matches will be used to create the output + control network. When the DEBUG and/or DEBUGLOG + parameters are used, the results from each set along with the quality + of the match will be output. +

    +

    + Each algorithm has default parameters that are + suited to most uses. The LISTALL parameter will list every + supported detector, extractor, and matcher algorithm along with its + parameters and default values. The LISTSPEC parameter will + output the results of the parsed specification string(s). A description + of every algorithm supported by findfeatures and if they can be + used as a detector, extractor, and/or matcher can be found in the + Algorithms table. +

    +

    + Descriptions of the robust matcher parameters and their default values + can be found in the Robust Matcher + Parameters table. +

    +

    Choosing Algorithms and Parameters

    +

    + Choosing effective algorithms and parameters is critical to successful + use of findfeatures. If a poor choice of algorithms and/or + parameters is made, findfeatures will usually still complete, + but the computation time and/or outpute control network quality will + suffer. findfeatures supports all of the OpenCV 3.1 + + detectors, extractors, and + + matchers. Some algorithms work well in a wide range of scenarios + (SURF and SIFT are both well tested and very robust), while others are + highly specialized. The following section will help you successfully + determine which algorithms and parameters to use. +

    +

    + findfeatures gives users a wide range of options to adjust how + it works. Such broad power can be daunting when the user is unfamiliar + with FBM. The following are some rules-of-thumb to help make things a + little less daunting. First, when in doubt, trust the defaults. The + defaults in findfeatures are designed to be a good fit for a + wide range of scenarios. They are not a perfect fit for every situation + but a perfect fit ususally is not required. The detector and extractor + do not default to a specific algorithm, but the SIFT algorithm is a + very robust algorithm that will produce a high quality output control + network for most situations. The majority of more modern algorithms are + focused on speed increases. Second, if possible, always use the + FASTGEOM parameter. The majority of problems when using FBM + arise from the trainer and query images not having the same geometry. + The FASTGEOM parameter completely eliminates these challenges. + Combining the FASTGEOM parameter with algorithms that are + designed for speed (the FAST descriptor and BRIEF extractor are good + options) will quickly produce a high quality control network. Finally, + if you are torn between a few options, use the LISTSPEC + parameter to test each of them and then only use the best result. When + the LISTSPEC parameter is used, findfeatures will + automatically determine which specification produced the best matches + and use it to create the output control net. +

    +

    + Different detectors search for different types of features. For + example, the FAST algorithm searchs for corners, while blob detection + algorithms search for regions that contrast their surroundings. + When choosing which detector to use, consider the prominent features + in the image set. The FAST algorithm would work well for finding key + points on a ridgeline, while a blob detection algorithm would work well + for finding key points in nadir images of a heavily cratered area. +

    +

    + When choosing an extractor there are two things to consider: the + invariance of the extractor and the size of the extracted descriptor. + Different extractors are invariant to (not affected by) different + transformations. For example, the SURF algorithm uses descriptors that + are invariant to rotation, while BRIEF feature descriptors are not. + In general, invariance to more transformations comes at a cost, bigger + descriptors. Detectors often find a very large number of key points in + each image. The amount of time it takes to extract and then compare all + of the resultant feature descriptors heavily depends upon the size of + the descriptor. So, more invariance usually means longer computation + times. For example, using the BRIEF extractor (which extracts very + small feature descriptors) instead of the SURF extractor (which has + moderately sized feature descriptors) provides an order of magnitude + speed increases for both extraction and matching. If your images are + from the similar sensors and under similar conditions, then an + extractor that uses smaller descriptors (BRISK, BRIEF, etc.) will be + faster and just as accurate as extractors that use larger, more robust + descriptors (SIFT, SURF, etc.). If your images are from very different + sensors (a spot spectrometer and a highly distorted framing camera, a + low resolution framing camera and a high resolution push broom camera, + etc.) or under very different conditions (very oblique and nadir, + opposing sun angles, etc.) then using an extractor with a more robust + descriptor will take longer but will be significantly more accurate + than using an extractor with a smaller descriptor. +

    +

    + findfeatures has two options for matchers: + brute force matching and a FLANN based matcher. The brute force matcher + attempts to match a key point with every key point in another image and + then pairs it with the closest match. This ensures a good match but can + take a long time for large numbers of images and key points. The FLANN + based matcher trains itself to find the approximate best match. It + does not ensure the same accuracy as the brute force matcher, but is + significantly faster for large numbers of images and key points. By + default findfeatures uses a brute force matcher with parameters + set based upon the extractor used. +

    +

    + Several parameters allow for fine tuning the outlier rejection process. + The RATIO parameter determines how distinct matches must be. A + ratio close to 0 will force findfeatures to consider only + un-ambiguous matches and reject a large number of matches. If many, + indistinct features are detected in each image, a low ratio will result + in a smaller, higher quality control network. If few, indistinct + feates are detected in each image, a high ratio will prevent the + control network from being too sparse. The EPITOLERANCE and + EPICONFIDENCE parameters control how outliers are found when the + fundamental matrices are computed. These parameters will have the + highest impact when the query and trainer images are stereo pairs. The + HMGTOLERANCE parameter controls how outliers are found after the + homography matrices are computed. This parameter will have the highest + impact when the query and trainer images have very different exterior + orientations. +

    +

    + Prior to FBM, findfeatures can apply several transformations to + the images. These transformations can help improve match quality in + specific scenarios. The FASTGEOM, GEOMTYPE, and + FASTGEOMPOINTS parameters allow for reprojection of the trainer + images into the query image's geometry prior to FBM. These parameters + can be used to achieve the speed increases of algorithms that are not + rotation and/or scale invariant (BRIEF, FAST, etc.) without loss of + accuracy. These parameters require that the trainer and query images + are ISIS cubes with geometry. For rotation and scale invariant algorithms + (SIFT, SURF, etc.), these parameters will have little to no + effect. The FILTER parameter allows for the application of + filters to the trainer and query images prior to FBM. The SOBEL + option will emphasize edges in the images. The Sobel filter can + introduce artifacts into some images, so the SCHARR option is + available to apply a more accurate filter. These filters allows for + improved detection when using an edge based detector (FAST, AGAST, + BRISK, etc.). If you are using an edge based detector and not detecting + a sufficient number of key points or your key points are not + sufficienty distinct, these filters may increase the number of + successful matches. +

    +

    + The OpenCV methods used in the outlier rejection process have several + options that can be set along with the algorithms. The available + parameters are listed in the Robust + Matcher Parameters table. +

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    + Robust Matcher Parameters +

    +
    KeywordDefaultDescription
    SaveRenderedImagesFalse + Option to save the images that are matched + after all transforms (e.g., fast geom, filtered, etc...) + have been applied. The query (MATCH) image will have + "_query" will be appended to the base name. All + FROM/FROMLIST images will have "_train" appended to their + names. They are saved as PNG images in the directory + specifed by the SavePath parameter. +
    SavePath$PWD + Specify the directory path to save all transform rendered + images if SaveRenderedImages=TRUE. +
    RootSiftFalse + Apply the + + RootSift algorithm to the descriptors that + normalizes SIFT-type of descriptors. The best description of + the application of this algorithm is described in + + this article. In general, SIFT descriptors histograms are + compared in Euclidean space. RootSift applies a Hellinger + kernel to the descriptor histograms that greatly improve + performance and still allows Euclidean distances in its + evaluation. Be sure to use this for SIFT-type descriptors + only. +
    MinimumFundamentalPoints8 + The Epipolar algorithm in OpenCV requires a minimim of 8 + points in order to properly compute the fundamental matrix. + This parameter allowes the user to specify the minimum number + of points allowed. +
    RefineFundamentalMatrixTrue + A single computation of the fundamental matrix is performed + unless this parameter is set to true. In this case, a new + fundmental matrix is computed after outlier are detected and + removed. This will improve the matrix since outliers are + removed and the matrix is recomputed. +
    MinimumHomographyPoints8 + As in the Epipolar fundamental matrix, a minimum number of 8 + points is required to compute the homography matrix for + outlier detection. This parameter allows the user to specify + a new minimum. +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    + Algorithms +

    +
    NameAlgorithm TypeDescriptionFurther Reading
    AGASTDetector + The AGAST algorithm is a corner detection algorithm that builds on + the FAST algorithm to detect features as quickly as possible. The + main improvements are increased detection speed and less training + time. + + +
    BlobDetector + A simple blob detection algorithm that attempts to identify connected + components of the image based on DN values. The Blob algorithm is + able to filter features after detection based on their + characteristics. + + +
    FASTDetector + The FAST algorithm is a corner detection algorithm that is designed + to detect corners extremely quickly. It uses machine learning to + improve its accuracy. + + +
    GFTTDetector + The GFTT algorithm is based upon the Harris corner detector. The + detection is based upon the idea that a corner varies significantly + from all immediately adjacent regions. + + +
    MSDDetector + MSD stands for Maximal Self-Dissimilarities. It is based upon the + idea that regions that vary significantly from their surroundings are + easy to uniquely identify from different perspectives. The MSD + algorithm detects generic features, so it invariant to many image + transformations and works well with stereo pairs. + + +
    MSERDetector + The MSER algorithm searches for regions which have significantly + higher or lower intensity compared to their immediate surroundings. + It works well for extracting features from images that lack strong + edges. Because it depends upon intensity, MSER is very sensitive to + factors such as solar angle and occlusion. In exchange MSER offers + strong invariance to image geometry factors such, as resolution and + emission angle (as long as features are not occluded). + + +
    StarDetector + The Star algorithm is OpenCV's implementation of the CenSurE + algorithm which is fast and scale-invariant. It is a more robust + version of the SIFT algorithm. + + +
    AKAZEDetector, Extractor + The AKAZE (accelerated KAZE) algorithm is a modified version of the + KAZE algorithm which uses a faster method to compute non-linear + scales. Like the KAZE algorithm, AKAZE works well for situations + where the trainer and query images have different resolutions and + possibly different distortions. AKAZE should be used over KAZE when + strong invariance is needed but the size and/or number of images + presents computation time concerns. The AKAZE algorithm can only + be used as an extractor if either the KAZE or AKAZE algorithm was + used as the detector. + + +
    BRISKDetector, Extractor + The BRISK algorithm uses concentric rings of points around features + to extract a descriptor. It extracts a small, binary descriptor, so + it is very fast. Unlike other binary descriptor extractors, BRISK + offers moderate rotation invariance by use points far from the + feature to determine orientation and then points close to the feature + to determine intensity after accounting for the orientation. + + +
    KAZEDetector, Extractor + The KAZE algorithm is a very robust algorithm that attempts to + provide improved invariance to scale. The method that SIFT and SURF + use to provide scale invariance can result in proliferation of noise. + The KAZE algorithm employs a non-linear scaling method that helps + prevent this. Hence, the KAZE algorithm provides very strong + invariance, but at the cost of large computation time. If very strong + invariance is required but computation time is a concern, use the + AKAZE algorithm instead. The KAZE algorithm can only be used as an + extractor if either the KAZE or AKAZE algorithm was used as the + detector. + + +
    ORBDetector, Extractor + The ORB algorithm extracts a very fast binary descriptor. It provides + improved rotational invariance compared to BRIEF by accounting for + orientation, but at the cost of slower extraction. It also attempts + to learn the best way to extract information from around each + feature. The ORB algorithm is faster than BRISK and FREAK, but + provides less invariance. + + +
    SIFTDetector, Extractor + The SIFT algorithm is one of the oldest and most well tested FMB + algorithms. It is a common benchmark for comparison of new + algorithms. The SIFT algorithm offers good invariance, but can + require large computation times. It is a good choice for both + detector and extractor when a high quality output control network is + needed and computation time is not a major concern. + + +
    SURFDetector, Extractor + The SURF algorithm was created to be a faster version of SIFT. It + provides slightly less invariance, but requires significantly less + computation time. The SURF algorithm is a good choice when a high + quality match is required and there are a large number of images + and/or the image size is very large. + + +
    BRIEFExtractor + The BREIF algorithm extracts an extremely fast binary descriptor. If + the query and trainer images are very similar, then the BRIEF + algorithm offers unmatched speed. This speed comes at a cost, the + BRIEF algorithm behaves very poorly if the query and trainer images + vary significantly. The FASTGEOM parameter can help improve + the quality of the match when using the BRIEF algorithm with varied + query and trainer images. + + +
    DAISYExtractor + The DAISY algorithm is an adaptation of the extractor used by SIFT + and SURF. It was designed for use with stereo imagery. The DAISY + algorithm offers strong invariance similar to SIFT and SURF, but with + significantly faster computation time. + + +
    FREAKExtractor + The FREAK algorithm extracts a fast binary descriptor. Like ORB, it + attempts to learn the best way to extract information from around the + features. The FREAK algorithm replicates how the human retina works + attempting to produce tiered solutions. If the first solution does + not provide uniqueness within a desired threshold, then a second, + more precise solution is computed. The FREAK algorithm provides fast + computation times along with adaptability to the requirements of the + query and trainer images. + + +
    LATCHExtractor + The LATCH algorithm extracts a fast binary descriptor that offers + greater invariance than other binary descriptor extractors. It lies + between the extremely fast binary descriptor extractors (BRIEF and + BRISK) and the very invariant but slow descriptor extractors (SURF + and SIFT). The LATCH algorithm also offers a CUDA implementation + that allows for extremely fast computation times when using multiple + GPUs in parallel. + + +
    LUCIDExtractor + The LUCID algorithm was designed to extract feature descriptors from + color images. It offers invarianve close to SURF and BRIEF with + shorter computation times. + + +
    BFMatcherMatcher + The brute force matcher algorithm attempts to match the query and + train images by brute force. It is guaranteed to find the best match, + because it checks every match. For large numbers of features, this + approach can require considerable computation time. + + +
    FlannBasedMatcherMatcher + The FLANN based matcher algorithm computes matches based on + approximate nearest descriptors. It uses the FLANN library to learn + how to approximate descriptor matches. The FLANN based matcher + algorithm does not guarantee the best match for each feature, but + will match large sets of features and/or images in significantly less + time that the brute force matcher algorithm. When combined with + outleir rejection, the FLANN based matcher algorithm can provide high + quality matches. + + +

    Using Debugging to Diagnose Behavior

    An additional feature of findfeatures is a detaileddebugging @@ -279,22 +920,22 @@ 1 --------------------------------------------------- 2 Program: findfeatures 3 Version 0.1 - 4 Revision: $Revision: 6598 $ - 5 RunTime: 2016-03-15T14:25:18 - 6 OpenCV_Version: 2.4.6.1 + 4 Revision: $Revision: 7311 $ + 5 RunTime: 2017-01-03T16:59:01 + 6 OpenCV_Version: 3.1.0 7 8 System Environment... - 9 Number available CPUs: 8 - 10 Number default threads: 8 - 11 Total threads: 8 + 9 Number available CPUs: 4 + 10 Number default threads: 4 + 11 Total threads: 4 12 13 Total Algorithms to Run: 1 14 - 15 @@ matcher-pair started on 2016-03-15T14:25:19 + 15 @@ matcher-pair started on 2017-01-03T16:59:02 16 17 +++++++++++++++++++++++++++++ 18 Entered RobustMatcher::match(MatchImage &query, MatchImage &trainer)... - 19 Specification: surf@hessianThreshold:100/surf/DescriptorMatcher.BFMatcher@normType:4@crossCheck:false + 19 Specification: surf@hessianThreshold:100/surf/BFMatcher@NormType:NORM_L2@CrossCheck:false 20 ** Query Image: EW0211981114G.lev1.cub 21 FullSize: (1024, 1024) 22 Rendered: (1024, 1024) @@ -304,11 +945,11 @@ 26 --> Feature detection... 27 Total Query keypoints: 11823 [11823] 28 Total Trainer keypoints: 11989 [11989] - 29 Processing Time: 0.476 - 30 Processing Keypoints/Sec: 50025.2 + 29 Processing Time: 0.307 + 30 Processing Keypoints/Sec: 77563.5 31 --> Extracting descriptors... - 32 Processing Time(s): 0.599 - 33 Processing Descriptors/Sec: 39752.9 + 32 Processing Time(s): 0.9 + 33 Processing Descriptors/Sec: 26457.8 34 35 *Removing outliers from image pairs 36 Entered RobustMatcher::removeOutliers(Mat &query, vector<Mat> &trainer)... @@ -316,12 +957,12 @@ 38 Query, Train Descriptors: 11823, 11989 39 Computing query->train Matches... 40 Total Matches Found: 11823 - 41 Processing Time: 0.352 - 42 Matches/second: 33588.1 + 41 Processing Time: 1.906 + 42 Matches/second: 6203.04 43 Computing train->query Matches... 44 Total Matches Found: 11989 - 45 Processing Time: 0.356 <seconds> - 46 Matches/second: 33677 + 45 Processing Time: 2.412 <seconds> + 46 Matches/second: 4970.56 47 -Ratio test on query->train matches... 48 Entered RobustMatcher::ratioTest(matches[2]) for 2 NearestNeighbors (NN)... 49 RobustMatcher::Ratio: 0.65 @@ -329,7 +970,7 @@ 51 Total Passing Ratio Tests: 988 52 Total Matches Removed: 10835 53 Total Failing NN Test: 10835 - 54 Processing Time: 0.001 + 54 Processing Time: 0 55 -Ratio test on train->query matches... 56 Entered RobustMatcher::ratioTest(matches[2]) for 2 NearestNeighbors (NN)... 57 RobustMatcher::Ratio: 0.65 @@ -349,7 +990,7 @@ 71 Number Initial Matches: 669 72 Total 1st Inliers Remaining: 273 73 Total 2nd Inliers Remaining: 266 - 74 Processing Time: 0.05 + 74 Processing Time: 0.041 75 Entered EpiPolar RobustMatcher::ransacTest(matches, keypoints1/2...)... 76 -Running EpiPolar Constraints/Fundamental Matrix... 77 RobustMatcher::EpiTolerance: 1 @@ -358,7 +999,7 @@ 80 Inliers on 1st Epipolar: 219 81 Inliers on 2nd Epipolar: 209 82 Total Passing Epipolar: 209 - 83 Processing Time: 0.011 + 83 Processing Time: 0.01 84 Entered RobustMatcher::computeHomography(keypoints1/2, matches...)... 85 -Running RANSAC Constraints/Homography Matrix... 86 RobustMatcher::HmgTolerance: 1 @@ -366,9 +1007,7 @@ 88 Total 1st Inliers Remaining: 197 89 Total 2nd Inliers Remaining: 197 90 Processing Time: 0.001 - 91 %% match-pair complete in 1.859 seconds! - 92 - 93 + 91 %% match-pair complete in 5.589 seconds!

    In the above example, lines 2-13 provide general information about the @@ -483,9 +1122,9 @@ MatchSolution group. Here is an example: 

     Group = MatchSolution
-  Efficiency    = 0.016662437621585
-  MinEfficiency = 0.016662437621585
-  MaxEfficiency = 0.016662437621585
+  Matcher      = surf@hessianThreshold:100/surf/BFMatcher@NormType:NORM_L2@CrossCheck:false
+  MatchedPairs = 1
+  Efficiency   = 0.016662437621585
 End_Group

    @@ -517,6 +1156,24 @@ End_Group Completed documentation + + Updated to use OpenCV3. Backward Compatibility Issue: The LISTMATCHERS parameter was removed; + Different feature detection, feature extraction, and matching algorithms are available in OpenCV3 + than in version 2, therefore some have been added and some have been removed. References #4556. + + + Corrected a bug in creation of the matcher algorithm if not provided by the user; + updated some additional elements of the documentation to be consistent with OpenCV3; + added additional code to allow for spaces in some areas of the user algorithm string specification; + changed the program version to 1.0 from 0.1. + References #4556. + + + Corrected a bug where keypoints and descriptors were being overwritten + when using multiple algorithm specificiations. Added a new clone() + method to MatchImage and made the MatchImages used by each algorithm + specification independent. Fixes #4765. + @@ -675,46 +1332,31 @@ End_Group *.lis - + boolean - List all OpenCV algorithms irregardles of origin + List result of ALGORITHM specification This parameter will retrieve all the registered OpenCV - algorithms available that can created by name. The ones + algorithms available that can created by name. The ones pertinent to this application are those prepended with - "Feature2D" and "DescriptorMatcher". However, this option lists + "Feature2D" and "DescriptorMatcher". However, this option lists all of the registered OpenCV algorithms. No - - boolean - List OpenCV matcher related algorithms - - This parameter will retrieve all registered OpenCV feature - matcher related algorithms available that can created by name. - These algorithms will have "Feature2D" and "DescriptorMatcher" - prepended to the name of the algorithm. Many of the Detector - and Extractor algorithms are not registered so they will not - appear in this list. This option will create a PVL structure of - individual algorithms and all their parameters. - - No - - - + boolean - List result of ALGORITHM specification + List all OpenCV algorithms irregardles of origin This parameter will retrieve all the registered OpenCV - algorithms available that can created by name. The ones + algorithms available that can created by name. The ones pertinent to this application are those prepended with - "Feature2D" and "DescriptorMatcher". However, this option lists + "Feature2D" and "DescriptorMatcher". However, this option lists all of the registered OpenCV algorithms. No @@ -727,7 +1369,7 @@ End_Group

    - When an information option is requested (LISTALL or LISTSPEC), + When an information option is requested (LISTSPEC), the user can provide the name of an output file here where the information, in the form of a PVL structure, will be written. If those any of those options are selected by the user, and @@ -743,56 +1385,107 @@ End_Group

    findfeatures listspec=true - algorithm=detector.SimpleBlob@minrepeatability:1/orb + algorithm=detector.Blob@minrepeatability:1/orb toinfo=/dev/tty 

     Object = FeatureAlgorithms
-  Object = FeatureAlgorithm
-    Name          = detector.SimpleBlob@minrepeatability:1/orb/DescriptorMatc-
-                    her.BFMatcher@normType:6@crossCheck:false
-    OpenCVVersion = 2.4.6
-    Specification = detector.SimpleBlob@minrepeatability:1/orb/DescriptorMatc-
-                    her.BFMatcher@normType:6@crossCheck:false
-
-    Object = Algorithm
-      Type                = Detector
-      Name                = Feature2D.SimpleBlob
-      blobColor           = 0
-      filterByArea        = Yes
-      filterByCircularity = No
-      filterByColor       = Yes
-      filterByConvexity   = Yes
-      filterByInertia     = Yes
-      maxArea             = 5000.0
-      maxCircularity      = 3.40282346638529e+38
-      maxConvexity        = 3.40282346638529e+38
-      maxInertiaRatio     = 3.40282346638529e+38
-      maxThreshold        = 220.0
-      minDistBetweenBlobs = 10.0
-      minRepeatability    = 1
-      minThreshold        = 50.0
-      thresholdStep       = 10.0
+  Object = RobustMatcher
+    OpenCVVersion = 3.1.0
+    Name          = detector.Blob@minrepeatability:1/orb/BFMatcher@NormType:N-
+                    ORM_HAMMING@CrossCheck:false
+
+    Object = Detector
+      CVVersion    = 3.1.0
+      Name         = Blob
+      Type         = Feature2D
+      Features     = Detector
+      Description  = "The OpenCV simple blob detection algorithm. See the
+                      documentation at
+                      http://docs.opencv.org/3.1.0/d0/d7a/classcv_1_1SimpleBlo-
+                      bDetector.html"
+      CreatedUsing = detector.Blob@minrepeatability:1
+
+      Group = Parameters
+        BlobColor           = 0
+        FilterByArea        = true
+        FilterByCircularity = false
+        FilterByColor       = true
+        FilterByConvexity   = true
+        FilterByInertia     = true
+        MaxArea             = 5000
+        maxCircularity      = inf
+        MaxConvexity        = inf
+        MaxInertiaRatio     = inf
+        MaxThreshold        = 220
+        MinArea             = 25
+        MinCircularity      = 0.8
+        MinConvexity        = 0.95
+        MinDistance         = 10
+        MinInertiaRatio     = 0.1
+        minrepeatability    = 1
+        MinThreshold        = 50
+        ThresholdStep       = 10
+      End_Group
     End_Object
 
-    Object = Algorithm
-      Type          = Extractor
-      Name          = Feature2D.ORB
-      WTA_K         = 2
-      edgeThreshold = 31
-      firstLevel    = 0
-      nFeatures     = 500
-      nLevels       = 8
-      patchSize     = 31
-      scaleFactor   = 1.2000000476837
-      scoreType     = 0
+    Object = Extractor
+      CVVersion    = 3.1.0
+      Name         = ORB
+      Type         = Feature2D
+      Features     = (Detector, Extractor)
+      Description  = "The OpenCV ORB Feature2D detector/extractor algorithm.
+                      See the documentation at
+                      http://docs.opencv.org/3.1.0/db/d95/classcv_1_1ORB.html"
+      CreatedUsing = orb
+
+      Group = Parameters
+        edgeThreshold = 31
+        fastThreshold = 20
+        firstLevel    = 0
+        nfeatures     = 500
+        nlevels       = 8
+        patchSize     = 31
+        scaleFactor   = 1.2000000476837
+        scoreType     = HARRIS_SCORE
+        WTA_K         = 2
+      End_Group
+    End_Object
+
+    Object = Matcher
+      CVVersion    = 3.1.0
+      Name         = BFMatcher
+      Type         = DecriptorMatcher
+      Features     = Matcher
+      Description  = "The OpenCV BFMatcher DescriptorMatcher matcher
+                      algorithm. See the documentation at
+                      http://docs.opencv.org/3.1.0/d3/da1/classcv_1_1BFMatcher-
+                      .html"
+      CreatedUsing = BFMatcher@NormType:NORM_HAMMING@CrossCheck:false
+
+      Group = Parameters
+        CrossCheck = No
+        NormType   = NORM_HAMMING
+      End_Group
     End_Object
 
-    Object = Algorithm
-      Type       = Matcher
-      Name       = DescriptorMatcher.BFMatcher
-      crossCheck = No
-      normType   = 6
+    Object = Parameters
+      EpiConfidence            = 0.99
+      EpiTolerance             = 3.0
+      FastGeom                 = false
+      FastGeomPoints           = 25
+      Filter                   = None
+      GeomSource               = MATCH
+      GeomType                 = CAMERA
+      HmgTolerance             = 3.0
+      MaxPoints                = 0
+      MinimumFundamentalPoints = 8
+      MinimumHomographyPoints  = 8
+      Ratio                    = 0.65
+      RefineFundamentalMatrix  = true
+      RootSift                 = false
+      SavePath                 = $PWD
+      SaveRenderedImages       = false
     End_Object
   End_Object
 End_Object
@@ -861,7 +1554,7 @@ End
                 will cause the matching phase and outlier detection to become 
                 costly and inefficient.
             
-          0
+          0
       
 
     
@@ -889,7 +1582,7 @@ End
                removed by this test. The farther from 1.0, the more matches will 
                be rejected.
            
-           0.65
+           0.65
        
 
           
@@ -902,7 +1595,7 @@ End
                    feature may deviate from the Epipolar lines for each matching 
                    feature.
               
-            3.0
+            3.0
           
 
          
@@ -915,7 +1608,7 @@ End
                    determination ratio. A value of 1.0 requires that all pixels 
                    be valid in the epipolar computation.
               
-            0.99
+            0.99
           
 
           
@@ -944,7 +1637,7 @@ End
                      points.
                 
    
               
-            3.0
+            3.0
               
 
        
@@ -959,7 +1652,7 @@ End
                are used if it exceeds the number of CPUs physically available 
                on the system or no more than MAXTHREADS will be used.
            
-           0
+           0
        
      
 
@@ -989,7 +1682,7 @@ End
            
            
            
-           25
+           25
        
 
       
@@ -1309,38 +2002,84 @@ findfeatures algorithm="surf@hessianThreshold:100/surf" \
         
    
         
     Object = FeatureAlgorithms
-  Object = FeatureAlgorithm
-    Name          = surf@hessianThreshold:100/surf/DescriptorMatcher.BFMatche-
-                    r@normType:4@crossCheck:false
-    OpenCVVersion = 2.4.6.1
-    Specification = surf@hessianThreshold:100/surf/DescriptorMatcher.BFMatche-
-                    r@normType:4@crossCheck:false
-
-    Object = Algorithm
-      Type             = Detector
-      Name             = Feature2D.SURF
-      extended         = No
-      hessianThreshold = 100.0
-      nOctaveLayers    = 3
-      nOctaves         = 4
-      upright          = No
+  Object = RobustMatcher
+    OpenCVVersion = 3.1.0
+    Name          = surf@hessianThreshold:100/surf/BFMatcher
+
+    Object = Detector
+      CVVersion    = 3.1.0
+      Name         = SURF
+      Type         = Feature2D
+      Features     = (Detector, Extractor)
+      Description  = "The OpenCV SURF Feature2D detector/extractor algorithm.
+                      See the documentation at
+                      http://docs.opencv.org/3.1.0/d5/df7/classcv_1_1xfeatures-
+                      2d_1_1SURF.html"
+      CreatedUsing = surf@hessianThreshold:100
+
+      Group = Parameters
+        Extended         = No
+        hessianThreshold = 100
+        NOctaveLayers    = 3
+        NOctaves         = 4
+        Upright          = No
+      End_Group
     End_Object
 
-    Object = Algorithm
-      Type             = Extractor
-      Name             = Feature2D.SURF
-      extended         = No
-      hessianThreshold = 100.0
-      nOctaveLayers    = 3
-      nOctaves         = 4
-      upright          = No
+    Object = Extractor
+      CVVersion    = 3.1.0
+      Name         = SURF
+      Type         = Feature2D
+      Features     = (Detector, Extractor)
+      Description  = "The OpenCV SURF Feature2D detector/extractor algorithm.
+                      See the documentation at
+                      http://docs.opencv.org/3.1.0/d5/df7/classcv_1_1xfeatures-
+                      2d_1_1SURF.html"
+      CreatedUsing = surf
+
+      Group = Parameters
+        Extended         = No
+        HessianThreshold = 100.0
+        NOctaveLayers    = 3
+        NOctaves         = 4
+        Upright          = No
+      End_Group
     End_Object
 
-    Object = Algorithm
-      Type       = Matcher
-      Name       = DescriptorMatcher.BFMatcher
-      crossCheck = No
-      normType   = 4
+    Object = Matcher
+      CVVersion    = 3.1.0
+      Name         = BFMatcher
+      Type         = DecriptorMatcher
+      Features     = Matcher
+      Description  = "The OpenCV BFMatcher DescriptorMatcher matcher
+                      algorithm. See the documentation at
+                      http://docs.opencv.org/3.1.0/d3/da1/classcv_1_1BFMatcher-
+                      .html"
+      CreatedUsing = BFMatcher
+
+      Group = Parameters
+        CrossCheck = No
+        NormType   = NORM_L2
+      End_Group
+    End_Object
+
+    Object = Parameters
+      EpiConfidence            = 0.99
+      EpiTolerance             = 3.0
+      FastGeom                 = false
+      FastGeomPoints           = 25
+      Filter                   = None
+      GeomSource               = MATCH
+      GeomType                 = CAMERA
+      HmgTolerance             = 3.0
+      MaxPoints                = 0
+      MinimumFundamentalPoints = 8
+      MinimumHomographyPoints  = 8
+      Ratio                    = 0.65
+      RefineFundamentalMatrix  = true
+      RootSift                 = false
+      SavePath                 = $PWD
+      SaveRenderedImages       = false
     End_Object
   End_Object
 End_Object
@@ -1354,414 +2093,452 @@ End
         qnet result of first control point
       
     
-
     
       
-           Show all the available algorithms and their default  parameters 
+        Show all the available algorithms and their default parameters
       
       
-           This provides a reference for all the current algorithms and their 
-           default parameters. This list may not include all the available 
-           OpenCV algorithms
-           nor may all algorithms be applicable.  Users should rerun this 
-           command to get the current options available on your system as they 
-           may differ. 
-                

    
-                
-                     findfeatures listall=true
-                
-      
    +This provides a reference for all the current algorithms and their default parameters. This list may not include all the available OpenCV algorithms nor may all algorithms be applicable. Users should rerun this command to get the current options available on your system as they may differ. 
+          
    
+	  
+               findfeatures listall=yes
+          
+	  
    
+        
     Object = Algorithms
-  OpenCVVersion = 2.4.6.1
-
-  Object = Algorithm
-    Name                  = BackgroundSubtractor.GMG
-    backgroundPrior       = 0.8
-    decisionThreshold     = 0.8
-    initializationFrames  = 120
-    learningRate          = 0.025
-    maxFeatures           = 64
-    quantizationLevels    = 16
-    smoothingRadius       = 7
-    updateBackgroundModel = Yes
-  End_Object
-
-  Object = Algorithm
-    Name            = BackgroundSubtractor.MOG
-    backgroundRatio = 0.7
-    history         = 200
-    nmixtures       = 5
-    noiseSigma      = 15.0
-  End_Object
-
-  Object = Algorithm
-    Name             = BackgroundSubtractor.MOG2
-    backgroundRatio  = 0.89999997615814
-    detectShadows    = Yes
-    fCT              = 0.050000000745058
-    fTau             = 0.5
-    fVarInit         = 15.0
-    fVarMax          = 75.0
-    fVarMin          = 4.0
-    history          = 500
-    nShadowDetection = 127
-    nmixtures        = 5
-    varThreshold     = 16.0
-    varThresholdGen  = 9.0
-  End_Object
-
-  Object = Algorithm
-    Name      = CLAHE
-    clipLimit = 40.0
-    tilesX    = 8
-    tilesY    = 8
-  End_Object
-
-  Object = Algorithm
-    Name           = DenseOpticalFlow.DualTVL1
-    epsilon        = 0.01
-    iterations     = 300
-    lambda         = 0.15
-    nscales        = 5
-    tau            = 0.25
-    theta          = 0.3
-    useInitialFlow = No
-    warps          = 5
-  End_Object
-
-  Object = Algorithm
-    Name             = DenseOpticalFlowExt.Brox_GPU
-    alpha            = 0.19699999690056
-    gamma            = 50.0
-    innerIterations  = 10
-    outerIterations  = 77
-    scaleFactor      = 0.80000001192093
-    solverIterations = 10
-  End_Object
-
-  Object = Algorithm
-    Name           = DenseOpticalFlowExt.DualTVL1
-    epsilon        = 0.01
-    iterations     = 300
-    lambda         = 0.15
-    nscales        = 5
-    tau            = 0.25
-    theta          = 0.3
-    useInitialFlow = No
-    warps          = 5
-  End_Object
-
-  Object = Algorithm
-    Name  = DenseOpticalFlowExt.DualTVL1_GPU
-    Error = "/usgs/pkgs/local/v002/src/opencv/opencv-2.4.6.1/release/modules/-
-             gpu/precomp.hpp:137: error: (-216) The library is compiled without
-             GPU support in function throw_nogpu"
-  End_Object
-
-  Object = Algorithm
-    Name      = DenseOpticalFlowExt.Farneback
-    flags     = 0
-    numIters  = 10
-    numLevels = 5
-    polyN     = 5
-    polySigma = 1.1
-    pyrScale  = 0.5
-    winSize   = 13
-  End_Object
-
-  Object = Algorithm
-    Name  = DenseOpticalFlowExt.Farneback_GPU
-    Error = "/usgs/pkgs/local/v002/src/opencv/opencv-2.4.6.1/modules/core/src-
-             /gpumat.cpp:109: error: (-216) The library is compiled without
-             CUDA support in function getDevice"
-  End_Object
-
-  Object = Algorithm
-    Name  = DenseOpticalFlowExt.PyrLK_GPU
-    Error = "/usgs/pkgs/local/v002/src/opencv/opencv-2.4.6.1/release/modules/-
-             gpu/precomp.hpp:137: error: (-216) The library is compiled without
-             GPU support in function throw_nogpu"
-  End_Object
-
-  Object = Algorithm
-    Name                   = DenseOpticalFlowExt.Simple
-    averagingBlockSize     = 2
-    layers                 = 3
-    maxFlow                = 4
-    occThr                 = 0.35
-    postProcessWindow      = 18
-    sigmaColor             = 25.5
-    sigmaColorFix          = 25.5
-    sigmaDist              = 4.1
-    sigmaDistFix           = 55.0
-    speedUpThr             = 10.0
-    upscaleAveragingRadius = 18
-    upscaleSigmaColor      = 25.5
-    upscaleSigmaDist       = 55.0
-  End_Object
-
   Object = Algorithm
-    Name       = DescriptorMatcher.BFMatcher
-    crossCheck = No
-    normType   = 4
+    CVVersion    = 3.1.0
+    Name         = AGAST
+    Type         = Feature2D
+    Features     = Detector
+    Description  = "The OpenCV AGAST Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d7/d19/classcv_1_1AgastFeatur-
+                    eDetector.html"
+    CreatedUsing = agast
+    Aliases      = (agast, detector.agast)
+
+    Group = Parameters
+      NonmaxSuppression = Yes
+      Threshold         = 10
+      Type              = OAST_9_16
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name = DescriptorMatcher.FlannBasedMatcher
+    CVVersion    = 3.1.0
+    Name         = Blob
+    Type         = Feature2D
+    Features     = Detector
+    Description  = "The OpenCV simple blob detection algorithm. See the
+                    documentation at
+                    http://docs.opencv.org/3.1.0/d0/d7a/classcv_1_1SimpleBlobD-
+                    etector.html"
+    CreatedUsing = blob
+    Aliases      = (blob, detector.blob)
+
+    Group = Parameters
+      BlobColor           = 0
+      FilterByArea        = true
+      FilterByCircularity = false
+      FilterByColor       = true
+      FilterByConvexity   = true
+      FilterByInertia     = true
+      MaxArea             = 5000
+      maxCircularity      = inf
+      MaxConvexity        = inf
+      MaxInertiaRatio     = inf
+      MaxThreshold        = 220
+      MinArea             = 25
+      MinCircularity      = 0.8
+      MinConvexity        = 0.95
+      MinDistance         = 10
+      MinInertiaRatio     = 0.1
+      MinRepeatability    = 2
+      MinThreshold        = 50
+      ThresholdStep       = 10
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name         = FaceRecognizer.Eigenfaces
-    eigenvalues  = cv::Mat
-    eigenvectors = cv::Mat
-    labels       = cv::Mat
-    mean         = cv::Mat
-    ncomponents  = 0
-    projections  = cv::Mat_Vector
-    threshold    = 1.79769313486232e+308
+    CVVersion    = 3.1.0
+    Name         = BRISK
+    Type         = Feature2D
+    Features     = (Detector, Extractor)
+    Description  = "The OpenCV BRISK Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/de/dbf/classcv_1_1BRISK.html"
+    CreatedUsing = brisk
+    Aliases      = (brisk, detector.brisk, extractor.brisk, feature2d.brisk)
+
+    Group = Parameters
+      NOctaves     = 3
+      PatternScale = 1.0
+      Threshold    = 30
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name         = FaceRecognizer.Fisherfaces
-    eigenvalues  = cv::Mat
-    eigenvectors = cv::Mat
-    labels       = cv::Mat
-    mean         = cv::Mat
-    ncomponents  = 0
-    projections  = cv::Mat_Vector
-    threshold    = 1.79769313486232e+308
+    CVVersion    = 3.1.0
+    Name         = FAST
+    Type         = Feature2D
+    Features     = Detector
+    Description  = "The OpenCV FAST Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/df/d74/classcv_1_1FASTFeature-
+                    Detector.html"
+    CreatedUsing = fast
+    Aliases      = (detector.fast, fast, fastx)
+
+    Group = Parameters
+      NonmaxSuppression = Yes
+      Threshold         = 10
+      Type              = TYPE_9_16
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name       = FaceRecognizer.LBPH
-    grid_x     = 8
-    grid_y     = 8
-    histograms = cv::Mat_Vector
-    labels     = cv::Mat
-    neighbors  = 8
-    radius     = 1
-    threshold  = 1.79769313486232e+308
+    CVVersion    = 3.1.0
+    Name         = GFTT
+    Type         = Feature2D
+    Features     = Detector
+    Description  = "The OpenCV GFTT Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/df/d21/classcv_1_1GFTTDetecto-
+                    r.html"
+    CreatedUsing = gftt
+    Aliases      = (detector.gftt, gftt)
+
+    Group = Parameters
+      BlockSize      = 3
+      HarrisDetector = No
+      K              = 0.04
+      MaxFeatures    = 1000
+      MinDistance    = 1.0
+      QualityLevel   = 0.01
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name  = Feature2D.BRIEF
-    bytes = 32
+    CVVersion    = 3.1.0
+    Name         = KAZE
+    Type         = Feature2D
+    Features     = (Detector, Extractor)
+    Description  = "The OpenCV KAZE Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d3/d61/classcv_1_1KAZE.html"
+    CreatedUsing = kaze
+    Aliases      = (detector.kaze, extractor.kaze, feature2d.kaze, kaze)
+
+    Group = Parameters
+      Diffusivity   = DIFF_PM_G2
+      Extended      = No
+      NOctaveLayers = 4
+      NOctaves      = 4
+      Threshold     = 0.0010000000474975
+      Upright       = No
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name    = Feature2D.BRISK
-    octaves = 3
-    thres   = 30
+    CVVersion    = 3.1.0
+    Name         = MSD
+    Type         = Feature2D
+    Features     = Detector
+    Description  = "The OpenCV MSD Feature2D detector/extractor algorithm. See
+                    the documentation at
+                    http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d-
+                    _1_1MSD.html"
+    CreatedUsing = msd
+    Aliases      = (detector.msd, msd)
+
+    Group = Parameters
+      ComputeOrientation = false
+      KNN                = 4
+      NMSRadius          = 5
+      NMSScaleRadius     = 0
+      NScales            = -1
+      PatchRadius        = 3
+      ScaleFactor        = 1.25
+      SearchAreaRadius   = 5
+      THSaliency         = 250.0
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name                  = Feature2D.Dense
-    featureScaleLevels    = 1
-    featureScaleMul       = 0.10000000149012
-    initFeatureScale      = 1.0
-    initImgBound          = 0
-    initXyStep            = 6
-    varyImgBoundWithScale = No
-    varyXyStepWithScale   = Yes
+    CVVersion    = 3.1.0
+    Name         = MSERA
+    Type         = Feature2D
+    Features     = Detector
+    Description  = "The OpenCV MSERA Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d3/d28/classcv_1_1MSER.html"
+    CreatedUsing = msera
+    Aliases      = (detector.msera, msera)
+
+    Group = Parameters
+      AreaThreshold = 1.01
+      Delta         = 5
+      EdgeBlurSize  = 5
+      MaxArea       = 14400
+      MaxEvolution  = 200
+      MaxVariation  = 0.25
+      MinArea       = 60
+      MinDiversity  = 0.2
+      MinMargin     = 0.003
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name              = Feature2D.FAST
-    nonmaxSuppression = Yes
-    threshold         = 10
-  End_Object
-
-  Object = Algorithm
-    Name              = Feature2D.FASTX
-    nonmaxSuppression = Yes
-    threshold         = 10
-    type              = 2
-  End_Object
-
-  Object = Algorithm
-    Name                  = Feature2D.FREAK
-    nbOctave              = 4
-    orientationNormalized = Yes
-    patternScale          = 22.0
-    scaleNormalized       = Yes
-  End_Object
-
-  Object = Algorithm
-    Name              = Feature2D.GFTT
-    k                 = 0.04
-    minDistance       = 1.0
-    nfeatures         = 1000
-    qualityLevel      = 0.01
-    useHarrisDetector = No
-  End_Object
-
-  Object = Algorithm
-    Name              = Feature2D.Grid
-    detector          = Null
-    gridCols          = 4
-    gridRows          = 4
-    maxTotalKeypoints = 1000
-  End_Object
-
-  Object = Algorithm
-    Name              = Feature2D.HARRIS
-    k                 = 0.04
-    minDistance       = 1.0
-    nfeatures         = 1000
-    qualityLevel      = 0.01
-    useHarrisDetector = Yes
-  End_Object
-
-  Object = Algorithm
-    Name          = Feature2D.MSER
-    areaThreshold = 1.01
-    delta         = 5
-    edgeBlurSize  = 5
-    maxArea       = 14400
-    maxEvolution  = 200
-    maxVariation  = 0.25
-    minArea       = 60
-    minDiversity  = 0.2
-    minMargin     = 0.003
+    CVVersion    = 3.1.0
+    Name         = ORB
+    Type         = Feature2D
+    Features     = (Detector, Extractor)
+    Description  = "The OpenCV ORB Feature2D detector/extractor algorithm. See
+                    the documentation at
+                    http://docs.opencv.org/3.1.0/db/d95/classcv_1_1ORB.html"
+    CreatedUsing = orb
+    Aliases      = (detector.orb, extractor.orb, feature2d.orb, orb)
+
+    Group = Parameters
+      edgeThreshold = 31
+      fastThreshold = 20
+      firstLevel    = 0
+      nfeatures     = 500
+      nlevels       = 8
+      patchSize     = 31
+      scaleFactor   = 1.2000000476837
+      scoreType     = HARRIS_SCORE
+      WTA_K         = 2
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name          = Feature2D.ORB
-    WTA_K         = 2
-    edgeThreshold = 31
-    firstLevel    = 0
-    nFeatures     = 500
-    nLevels       = 8
-    patchSize     = 31
-    scaleFactor   = 1.2000000476837
-    scoreType     = 0
+    CVVersion    = 3.1.0
+    Name         = SIFT
+    Type         = Feature2D
+    Features     = (Detector, Extractor)
+    Description  = "The OpenCV SIFT Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d5/d3c/classcv_1_1xfeatures2d-
+                    _1_1SIFT.html"
+    CreatedUsing = sift
+    Aliases      = (detector.sift, extractor.sift, feature2d.sift, sift)
+
+    Group = Parameters
+      constrastThreshold = 0.04
+      edgeThreshold      = 10
+      nfeatures          = 0
+      nOctaveLayers      = 3
+      sigma              = 1.6
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name              = Feature2D.SIFT
-    contrastThreshold = 0.04
-    edgeThreshold     = 10.0
-    nFeatures         = 0
-    nOctaveLayers     = 3
-    sigma             = 1.6
+    CVVersion    = 3.1.0
+    Name         = Star
+    Type         = Feature2D
+    Features     = Detector
+    Description  = "The OpenCV Star Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d-
+                    _1_1Star.html"
+    CreatedUsing = star
+    Aliases      = (detector.star, star)
+
+    Group = Parameters
+      LineThresholdBinarized = 8
+      LineThresholdProjected = 10
+      MaxSize                = 45
+      ResponseThreshold      = 30
+      SuppressNonmaxSize     = 5
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name                   = Feature2D.STAR
-    lineThresholdBinarized = 8
-    lineThresholdProjected = 10
-    maxSize                = 45
-    responseThreshold      = 30
-    suppressNonmaxSize     = 5
+    CVVersion    = 3.1.0
+    Name         = SURF
+    Type         = Feature2D
+    Features     = (Detector, Extractor)
+    Description  = "The OpenCV SURF Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d5/df7/classcv_1_1xfeatures2d-
+                    _1_1SURF.html"
+    CreatedUsing = surf
+    Aliases      = (detector.surf, extractor.surf, feature2d.surf, surf)
+
+    Group = Parameters
+      Extended         = No
+      HessianThreshold = 100.0
+      NOctaveLayers    = 3
+      NOctaves         = 4
+      Upright          = No
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name             = Feature2D.SURF
-    extended         = No
-    hessianThreshold = 100.0
-    nOctaveLayers    = 3
-    nOctaves         = 4
-    upright          = No
+    CVVersion    = 3.1.0
+    Name         = AKAZE
+    Type         = Feature2D
+    Features     = Extractor
+    Description  = "The OpenCV AKAZE Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d8/d30/classcv_1_1AKAZE.html"
+    CreatedUsing = akaze
+    Aliases      = (akaze, extractor.akaze)
+
+    Group = Parameters
+      DescriptorChannels = 3
+      DescriptorSize     = 0
+      DescriptorType     = DESCRIPTOR_MLDB
+      Diffusivity        = DIFF_PM_G2
+      NOctaveLayers      = 4
+      NOctaves           = 4
+      Threshold          = 0.0010000000474975
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name                = Feature2D.SimpleBlob
-    blobColor           = 0
-    filterByArea        = Yes
-    filterByCircularity = No
-    filterByColor       = Yes
-    filterByConvexity   = Yes
-    filterByInertia     = Yes
-    maxArea             = 5000.0
-    maxCircularity      = 3.40282346638529e+38
-    maxConvexity        = 3.40282346638529e+38
-    maxInertiaRatio     = 3.40282346638529e+38
-    maxThreshold        = 220.0
-    minDistBetweenBlobs = 10.0
-    minRepeatability    = 2
-    minThreshold        = 50.0
-    thresholdStep       = 10.0
+    CVVersion    = 3.1.0
+    Name         = Brief
+    Type         = Feature2D
+    Features     = Extractor
+    Description  = "The OpenCV simple blob detection algorithm. See the
+                    documentation at
+                    http://docs.opencv.org/3.1.0/d0/d7a/classcv_1_1SimpleBlobD-
+                    etector.html"
+    CreatedUsing = brief
+    Aliases      = (brief, extractor.brief)
+
+    Group = Parameters
+      Bytes          = 32
+      UseOrientation = true
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name           = GeneralizedHough.POSITION
-    dp             = 1.0
-    levels         = 360
-    minDist        = 1.0
-    votesThreshold = 100
+    CVVersion    = 3.1.0
+    Name         = DAISY
+    Type         = Feature2D
+    Features     = Extractor
+    Description  = "The OpenCV DAISY Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d9/d37/classcv_1_1xfeatures2d-
+                    _1_1DAISY.html"
+    CreatedUsing = daisy
+    Aliases      = (daisy, extractor.daisy)
+
+    Group = Parameters
+      H               = "1,0,0,0,1,0,0,0,1"
+      interpolation   = true
+      norm            = NRM_NONE
+      q_hist          = 8
+      q_radius        = 3
+      q_theta         = 8
+      radius          = 15
+      use_orientation = false
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name           = GeneralizedHough.POSITION_ROTATION
-    angleStep      = 1.0
-    dp             = 1.0
-    levels         = 360
-    maxAngle       = 360.0
-    minAngle       = 0.0
-    minDist        = 1.0
-    votesThreshold = 100
+    CVVersion    = 3.1.0
+    Name         = FREAK
+    Type         = Feature2D
+    Features     = Extractor
+    Description  = "The OpenCV FREAK Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/df/db4/classcv_1_1xfeatures2d-
+                    _1_1FREAK.html"
+    CreatedUsing = freak
+    Aliases      = (extractor.freak, freak)
+
+    Group = Parameters
+      NOctaves              = 4
+      OrientationNormalized = true
+      PatternScale          = 22.0
+      ScaleNormalized       = true
+      SelectedPairs         = Null
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name           = GeneralizedHough.POSITION_SCALE
-    dp             = 1.0
-    levels         = 360
-    maxScale       = 2.0
-    minDist        = 1.0
-    minScale       = 0.5
-    scaleStep      = 0.05
-    votesThreshold = 100
+    CVVersion    = 3.1.0
+    Name         = LATCH
+    Type         = Feature2D
+    Features     = Extractor
+    Description  = "The OpenCV LATCH Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d-
+                    _1_1LATCH.html"
+    CreatedUsing = latch
+    Aliases      = (extractor.latch, latch)
+
+    Group = Parameters
+      Bytes              = 32
+      HalfSSDSize        = 3
+      RotationInvariance = true
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name         = GeneralizedHough.POSITION_SCALE_ROTATION
-    angleEpsilon = 1.0
-    angleStep    = 1.0
-    angleThresh  = 15000
-    dp           = 1.0
-    levels       = 360
-    maxAngle     = 360.0
-    maxScale     = 2.0
-    maxSize      = 1000
-    minAngle     = 0.0
-    minDist      = 1.0
-    minScale     = 0.5
-    posThresh    = 100
-    scaleStep    = 0.05
-    scaleThresh  = 1000
-    xi           = 90.0
+    CVVersion    = 3.1.0
+    Name         = LUCID
+    Type         = Feature2D
+    Features     = Extractor
+    Description  = "The OpenCV LUCID Feature2D detector/extractor algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d6/d36/classcv_1_1xfeatures2d-
+                    _1_1LUCID.html"
+    CreatedUsing = lucid
+    Aliases      = (extractor.lucid, lucid)
+
+    Group = Parameters
+      BlurKernel  = 1
+      LucidKernel = 1
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name       = StatModel.EM
-    covMatType = 1
-    covs       = cv::Mat_Vector
-    epsilon    = 1.19209289550781e-07
-    maxIters   = 100
-    means      = cv::Mat
-    nclusters  = 5
-    weights    = cv::Mat
+    CVVersion    = 3.1.0
+    Name         = BFMatcher
+    Type         = DecriptorMatcher
+    Features     = Matcher
+    Description  = "The OpenCV BFMatcher DescriptorMatcher matcher algorithm.
+                    See the documentation at
+                    http://docs.opencv.org/3.1.0/d3/da1/classcv_1_1BFMatcher.h-
+                    tml"
+    CreatedUsing = bfmatcher
+    Aliases      = (bfmatcher, matcher.bfmatcher)
+
+    Group = Parameters
+      CrossCheck = No
+      NormType   = NORM_L2
+    End_Group
   End_Object
 
   Object = Algorithm
-    Name               = SuperResolution.BTVL1
-    alpha              = 0.7
-    blurKernelSize     = 5
-    blurSigma          = 0.0
-    btvKernelSize      = 7
-    iterations         = 180
-    lambda             = 0.03
-    opticalFlow        = DenseOpticalFlowExt.Farneback
-    scale              = 4
-    tau                = 1.3
-    temporalAreaRadius = 4
+    CVVersion    = 3.1.0
+    Name         = FlannBasedMatcher
+    Type         = DecriptorMatcher
+    Features     = Matcher
+    Description  = "The OpenCV FlannBasedMatcher DescriptorMatcher matcher
+                    algorithm. See the documentation at
+                    http://docs.opencv.org/3.1.0/dc/de2/classcv_1_1FlannBasedM-
+                    atcher.html"
+    CreatedUsing = flannbasedmatcher
+    Aliases      = (flannbasedmatcher, matcher.flannbasedmatcher)
+
+    Group = Parameters
+      Checks  = 32
+      Epsilon = 0.0
+      Sorted  = Yes
+    End_Group
   End_Object
 End_Object
 End
-      
    
-
+	
    
           
         
-  
+   
 
 
diff --git a/isis/src/control/apps/findfeatures/tsts/debug/Makefile b/isis/src/control/apps/findfeatures/tsts/debug/Makefile
index 85dd9eddfcf91d0ebdeb6d5ce56e1694a53fda2b..3cf318cdcbd439afc88397961ce230d1d07770cc 100644
--- a/isis/src/control/apps/findfeatures/tsts/debug/Makefile
+++ b/isis/src/control/apps/findfeatures/tsts/debug/Makefile
@@ -31,7 +31,7 @@ commands:
 	       -e 's|\(Image:\).*/\([^/]*\)|\1   \2|' \
 	       -e 's/\(.*second:\).*/\1/' \
 	       -e 's/\(Processing.*:\).*/\1/' \
-	       -e 's/\(.*\)[0-9][0-9]*\.[0-9]* \(seconds*\)/\1\2/' \
+               -e 's/\(.*\) [0-9]*\.[0-9]* \(seconds*\)/\1 \2/' \
 	       $(OUTPUT)/debug_temp.txt > $(OUTPUT)/debug.txt;
 	# Do same to stdoutdebug_temp, and remove total threads and
 	# MatchSolution Group
@@ -45,7 +45,7 @@ commands:
 	       -e 's|\(Image:\).*/\([^/]*\)|\1   \2|' \
 	       -e 's/\(.*second:\).*/\1/' \
 	       -e 's/\(Processing.*:\).*/\1/' \
-	       -e 's/\(.*\)[0-9][0-9]*\.[0-9]* \(seconds*\)/\1\2/' \
+               -e 's/\(.*\) [0-9]*\.[0-9]* \(seconds*\)/\1 \2/' \
 	       -e 's/\(Total threads:\).*/\1/' \
 	       -e '/Group/,/End_Group/d' \
 	       $(OUTPUT)/stdoutdebug_temp.txt > $(OUTPUT)/stdoutdebug.txt;
diff --git a/isis/src/control/apps/findfeatures/tsts/getinfo/Makefile b/isis/src/control/apps/findfeatures/tsts/getinfo/Makefile
index da60e654a15e57ebbdcb5f4e5105b4d9c5a03add..2d11b47f56a30e413aca5c350e29b5ce5d45b84f 100644
--- a/isis/src/control/apps/findfeatures/tsts/getinfo/Makefile
+++ b/isis/src/control/apps/findfeatures/tsts/getinfo/Makefile
@@ -11,9 +11,6 @@ commands:
 	$(APPNAME) listall=yes \
 	           > $(OUTPUT)/listall.pvl
 	           >& /dev/null;
-	$(APPNAME) listmatchers=yes \
-	           toinfo=$(OUTPUT)/listmatchers.pvl \
-	           >& /dev/null;
 	$(APPNAME) algorithm=brisk/brisk \
 	           listspec=yes \
 	           toinfo=$(OUTPUT)/listspec.pvl \
diff --git a/isis/src/control/apps/findfeatures/tsts/multialgo/Makefile b/isis/src/control/apps/findfeatures/tsts/multialgo/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..23744ebe229dfa47102fc632f59cbf852bc6cf9d
--- /dev/null
+++ b/isis/src/control/apps/findfeatures/tsts/multialgo/Makefile
@@ -0,0 +1,18 @@
+APPNAME = findfeatures
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	$(APPNAME) algorithm="brisk/brisk|surf@hessianThreshold:100/surf" \
+	           match=$(INPUT)/EW0211981114G.lev1.cub  \
+	           from=$(INPUT)/EW0242463603G.lev1.cub \
+	           epitolerance=1.0 \
+	           ratio=0.650 \
+	           hmgtolerance=1.0\
+	           networkid="EW0211981114G_EW0242463603G" \
+	           pointid="EW0211981114G_?????" \
+	           onet=$(OUTPUT)/EW0211981114G.net \
+	           description="Test MESSENGER pair" \
+	           debug=false \
+	           >& /dev/null;  
+
diff --git a/isis/src/control/apps/jigsaw/jigsaw.xml b/isis/src/control/apps/jigsaw/jigsaw.xml
index a00e6ce588d0ad4fbd4358e5d2c47a7f93af707e..451a1192bf69551d88d52b73f169c49587111efd 100644
--- a/isis/src/control/apps/jigsaw/jigsaw.xml
+++ b/isis/src/control/apps/jigsaw/jigsaw.xml
@@ -246,6 +246,9 @@
     
       Output control net will be now be written regardless of whether bundle converges. Fixes #4533.
     
+    
+      Updated description and brief for SOLVETARGETBODY and TBPARAMETERS.
+    
   
 
   
@@ -981,12 +984,13 @@
       
         boolean
         false
-        Enter target body parameters and a priori values using a PVL file
+        
+	  Solve for target body parameters. The parameters, their a priori values, and uncertainties are input
+	  using a PVL file specified by TBPARAMETERS below.
         
-          This option indicates that target body parameters are to be input via the PVL file specified
-          by TBPARAMETERS. All of the following values for coefficients must be in the PVL file:
-          body pole RA and DEC; prime meridian; triaxial radii and/or mean radius. An example template
-          PVL file is located at $base/templates/jigsaw/TargetBodyParameters.pvl.
+          Solve for target body parameters. The parameters, their a priori values, and uncertainties are input
+	  using a PVL file specified by TBPARAMETERS below. An example template PVL file is located at
+	  $base/templates/jigsaw/TargetBodyParameters.pvl.
         
         
           TBPARAMETERS
@@ -997,20 +1001,13 @@
         filename
         input
         
-          File containing target body parameters to solve and a priori values
+          File containing target body parameters to solve for, their a priori values and uncertainties.
         
         
-          This file contains target body parameters to use and solve for in the bundle adjustment.
-          File must be in PVL format. It should contain an object called TargetParameters.The
-          SpacecraftName and InstrumentId keywords in the Instrument group
-          of an image file are used to create the name of each group in the PVL file. The
-          group pertaining to each spacecraft/instrument should contain the keyword/value
-          pairs needed to process images taken with that sensor:  CKDEGREE, CKSOLVEDEGREE,
-          CAMSOLVE, TWIST, OVEREXISTING, SPKDEGREE, SPKSOLVEDEGREE, SPSOLVE, OVERHERMITE,
-          SPACECRAFT_POSITION_SIGMA, SPACECRAFT_VELOCITY_SIGMA, SPACECRAFT_ACCELERATION_SIGMA,
-          CAMERA_ANGLES_SIGMA, CAMERA_ANGULAR_VELOCITY_SIGMA, CAMERA_ANGULAR_ACCELERATION_SIGMA.
-          If any of these keywords are missing, then their defaults will be used. An example template
-          PVL file is located at $base/templates/jigsaw/TargetBodyParameters.pvl.
+          This file contains target body parameters to solve for in the bundle adjustment, their
+	  a priori values, and uncertainties. The file must be in PVL format. An example template
+          PVL file is located at $base/templates/jigsaw/TargetBodyParameters.pvl. Instructions for the PVL
+	  structure are given in the template.
         
         
           *.pvl
diff --git a/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-mean-radius/Makefile b/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-mean-radius/Makefile
index 969c1c80cd33b998a52d1e18cc8d5cbea90d65ab..d0d91fcb457ffdd343c9a07e8a722f802383c084 100644
--- a/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-mean-radius/Makefile
+++ b/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-mean-radius/Makefile
@@ -25,15 +25,17 @@ commands:
 	file_prefix=$(OUTPUT)/ > /dev/null;
 	$(CAT) $(OUTPUT)/bundleout.txt  | grep -v "Run Time:" | grep -v "Elapsed Time:" \
 	       | perl -pe 's/(^|,|: )([^,:]+\/)([^,\/:]*\.)(net|cub)/\1\3\4/g' 2>/dev/null \
+	       | $(SED) 's/\([0-9][0-9]*\.[0-9][0-9][0-9]\)\([0-9][0-9]*\)/\1/g' \
 	       | $(SED) s/`date +%Y-%m-%dT`\[0-2\]\[0-9\]:\[0-5\]\[0-9\]:\[0-5\]\[0-9\]/date/ \
 	       > $(OUTPUT)/pole-ra-dec-w0-wDot-mean-radius_bundleout.txt;
 	$(CAT) $(OUTPUT)/bundleout_images.csv \
 	       | perl -pe 's/(^|,|: )([^,:]+\/)([^,\/:]*\.)(net|cub)/\1\3\4/g' 2>/dev/null \
-	       > $(OUTPUT)/bundleout_images.csv;
+	       > $(OUTPUT)/pole-ra-dec-w0-wDot-mean-radius_bundleout_images.csv;
 	$(CAT) $(OUTPUT)/residuals.csv \
 	       | perl -pe 's/(^|,|: )([^,:]+\/)([^,\/:]*\.)(net|cub)/\1\3\4/g' 2>/dev/null \
 	       > $(OUTPUT)/pole-ra-dec-w0-wDot-mean_radius_residuals.csv;
-	$(MV) $(OUTPUT)/bundleout_images.csv $(OUTPUT)/pole-ra-dec-w0-wDot-mean-radius_bundleout_images.csv > /dev/null;
+#$(MV) $(OUTPUT)/bundleout_images1.csv $(OUTPUT)/pole-ra-dec-w0-wDot-mean-radius_bundleout_images.csv > /dev/null;
+	$(RM) $(OUTPUT)/bundleout_images.csv > /dev/null;
 	$(MV) $(OUTPUT)/bundleout_points.csv $(OUTPUT)/pole-ra-dec-w0-wDot-mean-radius_bundleout_points.csv > /dev/null;
 	$(RM) $(OUTPUT)/cubes.lis > /dev/null;
 	$(MV) $(OUTPUT)/mean.net $(OUTPUT)/out-pole-ra-dec-w0-wDot-mean-radiius.net > /dev/null;
diff --git a/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-triaxial-radii/Makefile b/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-triaxial-radii/Makefile
index 1c3c636b1d3535206ad04974f42396eb3e274ff8..b9a3f086beeeb9bcbe433d87f705f77ffb44ee45 100644
--- a/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-triaxial-radii/Makefile
+++ b/isis/src/control/apps/jigsaw/tsts/pole-ra-dec-w0-wDot-triaxial-radii/Makefile
@@ -19,25 +19,29 @@ APPNAME = jigsaw
 #triaxial test
 
 include $(ISISROOT)/make/isismake.tsts
-#jigsaw fromlist=cubes.lis cnet=input/enc_global_fin2-cl14_forken_extract_cl-salih-lon-constrained.net onet=triaxial.net errorpropagation=yes solvetargetbody=yes tb_parameters=input/EnceladusTargetBodyParameters-pole-ra-dec-w0-wDot-triaxial-radii.pvl camera_angles_sigma=2.0
+#jigsaw fromlist=cubes.lis cnet=input/enc_global_fin2-cl14_forken_extract_cl-salih-lon-constrained.net onet=triaxial.net 
+#errorpropagation=yes solvetargetbody=yes 
+#tb_parameters=input/EnceladusTargetBodyParameters-pole-ra-dec-w0-wDot-triaxial-radii.pvl camera_angles_sigma=2.0
 commands:
 	$(LS) -1 $(INPUT)/*.cub > $(OUTPUT)/cubes.lis;
 	$(APPNAME) fromlist=$(OUTPUT)/cubes.lis cnet=$(INPUT)/enc_global_fin2-cl14_forken_extract_cl-salih-lon-constrained.net \
 	onet=$(OUTPUT)/triaxial.net errorpropagation=yes solvetargetbody=yes tbparameters=$(INPUT)/EnceladusTargetBodyParameters-pole-ra-dec-w0-wDot-triaxial-radii.pvl \
-	file_prefix=$(OUTPUT)/ camera_angles_sigma = 2.0 > /dev/null;		
+	file_prefix=$(OUTPUT)/ camera_angles_sigma = 2.0 > /dev/null;           
 	$(CAT) $(OUTPUT)/bundleout.txt  | grep -v "Run Time:" | grep -v "Elapsed Time:" \
 	       | perl -pe 's/(^|,|: )([^,:]+\/)([^,\/:]*\.)(net|cub)/\1\3\4/g' 2>/dev/null \
+	       | $(SED) 's/\([0-9][0-9]*\.[0-9][0-9][0-9]\)\([0-9][0-9]*\)/\1/g' \
 	       | $(SED) s/`date +%Y-%m-%dT`\[0-2\]\[0-9\]:\[0-5\]\[0-9\]:\[0-5\]\[0-9\]/date/ \
 	       > $(OUTPUT)/pole-ra-dec-w0-wDot-triaxial-radii_bundleout.txt;
 	$(CAT) $(OUTPUT)/bundleout_images.csv \
 	       | perl -pe 's/(^|,|: )([^,:]+\/)([^,\/:]*\.)(net|cub)/\1\3\4/g' 2>/dev/null \
-	       > $(OUTPUT)/bundleout_images.csv;
+	       > $(OUTPUT)/pole-ra-dec-w0-wDot-triaxial-radii_bundleout_images.csv;
 	$(CAT) $(OUTPUT)/residuals.csv \
 	       | perl -pe 's/(^|,|: )([^,:]+\/)([^,\/:]*\.)(net|cub)/\1\3\4/g' 2>/dev/null \
 	       > $(OUTPUT)/pole-ra-dec-w0-wDot-triaxial-radii_residuals.csv;
-	$(MV) $(OUTPUT)/bundleout_images.csv $(OUTPUT)/pole-ra-dec-w0-wDot-triaxial-radii_bundleout_images.csv > /dev/null;
 	$(MV) $(OUTPUT)/bundleout_points.csv $(OUTPUT)/pole-ra-dec-w0-wDot-triaxial-radii_bundleout_points.csv > /dev/null;
 	$(RM) $(OUTPUT)/cubes.lis > /dev/null;
 	$(MV) $(OUTPUT)/triaxial.net $(OUTPUT)/out-pole-ra-dec-w0-wDot-triaxial-radii.net > /dev/null;
 	$(RM) $(OUTPUT)/residuals.csv > /dev/null;
 	$(RM) $(OUTPUT)/bundleout.txt > /dev/null;
+	$(RM) $(OUTPUT)/bundleout_images.csv > /dev/null;
+
diff --git a/isis/src/control/apps/sumspice/SumFile.cpp b/isis/src/control/apps/sumspice/SumFile.cpp
index 0de7c0d1f16461ca62e7cfca971856ddc447fd83..7283c33722a7a86f5da010763986d23c4a191d42 100644
--- a/isis/src/control/apps/sumspice/SumFile.cpp
+++ b/isis/src/control/apps/sumspice/SumFile.cpp
@@ -24,6 +24,7 @@
 
 #include "SumFile.h"
 
+#include 
 #include 
 #include 
 #include 
@@ -86,9 +87,9 @@ namespace Isis {
   
 
   /** 
-   *  Returns the time found in the SUMFILE.
+   *  Returns the time found in the SUMFILE in UTC form
    *  
-   *  @return @b QString Start time found in SUMFILE
+   *  @return @b QString Time found in SUMFILE
    */
   QString SumFile::utc() const {
     return (m_obsTime.UTC());
@@ -99,42 +100,35 @@ namespace Isis {
   /** 
    *  Returns the SUMFILE time, in ET.
    *  
-   *  @return @b double Start time converted to ET
+   *  @return @b double Time converted to ET
    */
   double  SumFile::et() const {
     return (m_obsTime.Et());
   }
   
-
-  /** Loads kerneks for the given ISIS cube file from labels
-   *  
-   * @param cube     Cube to load kernels for
-   * @param kernels   Kernel object to use for loading
-   * 
-   * @return @b int  Number of kernels loaded
-   */
-  int SumFile::loadKernels(Cube &cube, Kernels &kernels) const {
-    Kernels mykernels(cube);
-    mykernels.Discover();
-    return ( kernels.Load() );
-  }
-  
-
-  /**  Loads kernels from a given file
-   *  
-   * @param kernfile Name fo file to load kernels from
-   * @param kernels  Kernels object to use for loading kernels
-   * 
-   * @return @b int Number of kernels loaded
-   */
-  int SumFile::loadKernels(const QString &kernfile, Kernels &kernels) const {
-    kernels.Add(kernfile);
-    kernels.Discover();
-    return ( kernels.Load() );
+/**
+ * @brief Returns the Time object found in SUMFILE 
+ * 
+ * @return const iTime& Time in SUMFILE
+ */
+  const iTime &SumFile::time() const {
+    return ( m_obsTime );
   }
-  
 
-  bool SumFile::update(Cube &cube, Camera *camera) const {
+/**
+ * @brief Update SPICE data in ISIS cube 
+ *  
+ * This method will update the SPICE blobs with the contents of the SUMSPICE. 
+ * The contents of the InstrumentPosition will be replaced with SUMSPICE SZ 
+ * vector and InstrumentPointing is replaced by the CX, CY, CZ matrix.
+ * 
+ * @param cube    An intialized ISIS Cube object
+ * @param camera  An option pointer to the camera. If not provided, it is 
+ *                retrieved from the Cube object
+ * 
+ * @return bool   True if succesful, false if the operation fails
+ */
+  bool SumFile::updateSpice(Cube &cube, Camera *camera) const {
     bool good = updatePointing(cube, camera);
     if ( good ) {
      good = updatePosition(cube, camera);
@@ -282,6 +276,7 @@ namespace Isis {
    }
   
 
+
   /**
    * @brief Return the point matrix, in body-fixed format. 
    *  
@@ -325,6 +320,25 @@ namespace Isis {
   }
   
 
+
+  /**
+   * @brief Get Sun postion in body-fixed coordinates
+   *  
+   * This method will return the vector found in the SUMFILE that represents 
+   * the coordinates of the Sun, in body fixed position. 
+   * 
+   * @return std::vector The SUMFILE's Sun position
+   */
+  std::vector SumFile::getSunPosition()  const{
+    std::vector sunPosition;
+    sunPosition.reserve(3);
+    sunPosition.push_back(m_sunPosition[0]);
+    sunPosition.push_back(m_sunPosition[1]);
+    sunPosition.push_back(m_sunPosition[2]);
+    return (sunPosition);
+  }
+  
+
   /**
    * Adds information about the SUMFILE to the output stream: name, start time 
    * (UTC), start time (ET), number of lines, number of samples, DN minimum, DN 
@@ -341,7 +355,7 @@ namespace Isis {
     return (outs); 
   }
   
-  
+
   /**
    * @brief Opens and parses the contents of a SUMFILE.
    *  
@@ -403,7 +417,7 @@ namespace Isis {
   
     // Get sun position
     values = getSumLine(sumin.readLine(), 4, "SZ");
-    for (int i = 0; i < 3; i++) m_sunDirection[i] = cvtDouble(values[i]);
+    for (int i = 0; i < 3; i++) m_sunPosition[i] = cvtDouble(values[i]);
   
     // Get K-matrix
     values = getSumLine(sumin.readLine(), 7, "K-MATRIX");
@@ -549,162 +563,7 @@ namespace Isis {
     return (sum_list);
   }
 
-/** 
- * @brief Find sumfile by name
- *  
- * @param cube         Cube to associate with SUMFILE
- * @param sumFiles     List of SUMFILES
- * @param sumFileName  Name of SUMFILE to find
- * 
- * @return SharedSumFile Pointer to SUMFILE if found, otherwise 0
- */
-  SharedSumFile findSumFile(Cube &cube, 
-                            const SumFileList &sumFiles,
-                            QString sumFileName) {
-
-    for (int i = 0; i < sumFiles.size(); i++) {
-      if (QString::compare(sumFileName, sumFiles[i]->name(), Qt::CaseInsensitive) == 0) {
-        return sumFiles[i];
-      }
-    }
-
-    return SharedSumFile(0);
-  }
-
-
-  /**
-   * @brief Find SUMFILE for the given cube file
-    *  
-   * This method will find the appropriate SUMFILE associated with a Cube object 
-   * given a list of SumFile objects. The time the image was observed is compared 
-   * to the time of a SUMFILE. The SumFile that matches the cube is the one with 
-   * the time closest to the Cube observation time. 
-   * 
-   * @param Cube       Cube object to find a SumFile for.
-   * @param sumFiles   List of SharedSumFile objects to search, sorted in ascending order.
-   * @param deltaTime  Maximum time difference in ISIS cube file time and SumFile time.
-   * 
-   * @return SharedSumFile Pointer to SumFile for ISIS cube
-   */
-  SharedSumFile findSumFile(Cube &cube, 
-                            const SumFileList &sumFiles,
-                            const double &deltaTime) {
-
-    Kernels kernels(cube);
-    kernels.Load();
-
-    SharedSumFile sumFile = sumFiles[0];
-
-    // if a single sum file was given, assume that the user wants to use this sum file 
-    if (sumFiles.size() == 1) {
-      return sumFile;
-    }
-    
-    // Otherwise, find the sum file with start ET closest to the
-    // cube's ET Note that the sum files are already sorted by ET...
-
-    Pvl *cubeLabels = cube.label();
-    PvlGroup &instGrp = cubeLabels->findGroup("Instrument", Pvl::Traverse);
-    PvlKeyword origStartClock = instGrp["SpacecraftClockStartCount"];
-    QString originalClock = origStartClock[0];
-    double cubeStartEt = cube.camera()->getClockTime(originalClock).Et();
-
-    double sumFileEt = sumFile->et();
-
-    double etDiff = fabs(cubeStartEt - sumFileEt);
-
-    int sumIndex = 1;
-    while(fabs(cubeStartEt - sumFiles[sumIndex]->et()) <= etDiff) {
-      sumFile = sumFiles[sumIndex];
-      sumFileEt = sumFile->et();
-      etDiff = fabs(cubeStartEt - sumFileEt);
-      sumIndex++;
-    }
-    
-    if (etDiff <= deltaTime) {
-      return sumFile;
-    }
-
-    // if the tolerance is not met, return a null pointer
-    return SharedSumFile(0);
-  }
-
 }
 // namespace Isis
 
-//  /**
-//   * 
-//   * @param camera 
-//   * 
-//   * @return @b Quaternion 
-//   */
-//  Quaternion SumFile::getBFtoJ2000(Camera *camera) const {
-//    QString target = getFrameName((const int)camera->naifBodyFrameCode());
-//
-//    vector rotation(9);
-//    pxform_c(target.toLatin1().data(), "J2000", camera->time().Et(), 
-//             (SpiceDouble (*)[3]) &rotation[0]);
-//    NaifStatus::CheckErrors();
-//  
-//    QString sep("");//???
-//    BOOST_FOREACH ( double v, rotation ) {
-//      cout << sep << v;
-//      sep = ", "; 
-//    }
-//    cout << "\n";
-//    return (Quaternion(rotation));
-//  }
-
-
-//  /**
-//   * 
-//   * @param fromId 
-//   * @param toId 
-//   * @param timeEt 
-//   * 
-//   * @return @b Quaternion 
-//   */
-//  Quaternion SumFile::getFrameRotation(const int &fromId, const int &toId,
-//                                       const double &timeEt) 
-//                                       const {
-//  
-//    QString fromFrame = getFrameName(fromId);
-//    QString toFrame   = getFrameName(toId);
-//  
-//    vector rotation(9);
-//    pxform_c(fromFrame.toLatin1().data(), toFrame.toAscii().data(), 
-//             timeEt, (SpiceDouble (*)[3]) &rotation[0]);
-//    NaifStatus::CheckErrors();
-//    return (Quaternion(rotation));
-//  }
-  
-  
-//  /**
-//   * @brief Get character representation of the frame identifier
-//   * 
-//   * @param frameid NAIF frame ID to translate to character
-//   * 
-//   * @return QString Character value of the frame id
-//   */
-//  QString SumFile::getFrameName(const int &frameid) const {
-//    SpiceChar frameBuf[81];
-//    (void) frmnam_c ( (SpiceInt) frameid, sizeof(frameBuf), frameBuf);
-//    return (QString(frameBuf));
-//  }
-  
-
-//  /**
-//   * @brief Get character representation of the frame identifier
-//   * 
-//   * @param frameName String frame name to translate to NAIF code
-//   * 
-//   * @return int NAIF frame code
-//   */
-//   int SumFile::getFrameCode(const QString &frameName) const {
-//     int frmcode;
-//     (void) namfrm_c(frameName.toLatin1().data(), &frmcode);
-//     return (frmcode);
-//   }
-  
-  
 
diff --git a/isis/src/control/apps/sumspice/SumFile.h b/isis/src/control/apps/sumspice/SumFile.h
index bf96f1d379e28abfafe4aaf6c570d1bd1a8c7da3..23d3e92f558993cf409f68869836f4a5a77c893a 100644
--- a/isis/src/control/apps/sumspice/SumFile.h
+++ b/isis/src/control/apps/sumspice/SumFile.h
@@ -22,6 +22,8 @@
  *   http://www.usgs.gov/privacy.html.
  */
 #include 
+#include 
+#include 
 
 #include 
 #include 
@@ -33,6 +35,7 @@
 #include "iTime.h"
 #include "Kernels.h"
 #include "Quaternion.h"
+#include "SpecialPixel.h"
 
 namespace Isis {
 
@@ -41,16 +44,23 @@ namespace Isis {
    *  
    * This class will parse the contents of a R. Gaskell SUMFILE used in his 
    * stereo photoclinometry (SPC) system and provide access to the elements that 
-   * are stored therein. 
-   *  
+   * are stored therein.
+   * 
    * @author 2015-02-02 Kris Becker
-   *  
-   * @internal 
-   *   @history 2015-02-02 Kris Becker - Original Version 
+   * 
+   * @internal
+   *   @history 2015-02-02 Kris Becker Original Version 
    *   @history 2016-02-09 Kris Becker - Updated documentation 
+   *   @history 2016-06-07 Kris Becker - Renamed getIlluminationPosition() to 
+   *                           getSunPosition(). updateIlluminationPosition() did
+   *                           not have an implementation so it was removed.
+   *   @history 2016-09-14 Kris Becker - Moved updateTimes() to new SumFinder 
+   *                           class as there is not enough information to do it
+   *                           correctly in SumFile.
    */
   class SumFile {
     public:
+      
       SumFile();
       SumFile(const QString &sumfile);
       virtual ~SumFile() { }
@@ -59,21 +69,18 @@ namespace Isis {
       QString name() const;
       QString utc() const;
       double  et() const;
+      const iTime &time() const;
   
-      int loadKernels(Cube &cube, Kernels &kernels) const;
-      int loadKernels(const QString &kernfile, Kernels &kernels) const;
-  
-      bool update(Cube &cube, Camera *camera = 0) const;
+      bool updateSpice(Cube &cube, Camera *camera = 0) const;
       bool updatePointing(Cube &cube, Camera *camera = 0) const;
       bool updatePosition(Cube &cube, Camera *camera = 0) const;
-      bool updateIlluminatorPosition(Cube &cube, Camera *camera) const;
   
       Quaternion getPointing() const;
       std::vector getPosition() const;
-      std::vector getIlluminatorPosition()  const;
+      std::vector getSunPosition()  const;
   
       std::ostream &brief(std::ostream &outs) const;
-  
+
     private:
       QString m_id;
       iTime   m_obsTime;
@@ -87,14 +94,13 @@ namespace Isis {
   
       double  m_spacecraftPosition[3];
       double  m_pointingMatrix[3][3];
-      double  m_sunDirection[3];
+      double  m_sunPosition[3];
       double  m_kmatrix[6];
       double  m_distortion[4];
       double  m_sigmaSCPos[3];
       double  m_sigmaPntg[3];
       // QList   m_measures;
   
-  
       void parseSumFile(const QString &sumfile);
       QStringList getSumLine(const QString &data, const int &nexpected = 0, 
                              const QString &tag = "") const;
@@ -113,17 +119,11 @@ namespace Isis {
   
   ///!<  Define a resource list
   typedef QList SumFileList;
-  
-  
+
+
   // Global methods
   SumFileList   loadSumFiles(const FileList &sumfiles);
-  SharedSumFile findSumFile(const QString &isisfile, const SumFileList &sumlist,
-                            const double &deltaT = 0.3E-3);
-  SharedSumFile findSumFile(Cube &cube, const SumFileList &sumlist,
-                            const double &deltaT = 1.0);
-  SharedSumFile findSumFile(Cube &cube, 
-                            const SumFileList &sumFiles,
-                            QString sumFileName);
+
 
   /**
    * @brief Ascending order sort functor
@@ -133,9 +133,9 @@ namespace Isis {
    * times of each is compared using the less than operator. 
    * 
    * @author 2015-07-28 Kris Becker
-   *  
-   * @internal 
-   *   @history 2015-07-28 Kris Becker - Original Version 
+   * 
+   * @internal
+   *   @history 2015-07-28 Kris Becker Original Version 
    */
   class SortEtAscending {
     public:
@@ -146,6 +146,5 @@ namespace Isis {
       }
   };
 
-
 };  // namespace Isis
 #endif
diff --git a/isis/src/control/apps/sumspice/SumFinder.cpp b/isis/src/control/apps/sumspice/SumFinder.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..28be3ac67a79553fa88142531b1072123e7d5dcb
--- /dev/null
+++ b/isis/src/control/apps/sumspice/SumFinder.cpp
@@ -0,0 +1,709 @@
+/**                                                                       
+ * @file                                                                  
+ * $Revision: 6565 $
+ * $Date: 2016-02-10 17:15:35 -0700 (Wed, 10 Feb 2016) $
+ * $Id: SumFile.cpp 6565 2016-02-11 00:15:35Z kbecker@GS.DOI.NET $
+ * 
+ *   Unless noted otherwise, the portions of Isis written by the USGS are 
+ *   public domain. See individual third-party library and package descriptions 
+ *   for intellectual property information, user agreements, and related  
+ *   information.                                                         
+ *                                                                        
+ *   Although Isis has been used by the USGS, no warranty, expressed or   
+ *   implied, is made by the USGS as to the accuracy and functioning of such 
+ *   software and related material nor shall the fact of distribution     
+ *   constitute any such warranty, and no responsibility is assumed by the
+ *   USGS in connection therewith.                                        
+ *                                                                        
+ *   For additional information, launch                                   
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html                
+ *   in a browser or see the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.                                    
+ */ 
+
+#include "SumFinder.h"
+
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include 
+#include 
+#include 
+
+// boost library
+#include 
+
+#include "Camera.h"
+#include "IException.h"
+#include "IString.h"
+#include "Kernels.h"
+#include "NaifStatus.h"
+#include "Progress.h"
+
+
+using namespace std;
+
+namespace Isis {
+
+
+  SumFinder::SumFinder() : m_cube(), m_kernels(), m_cubename(),
+                           m_sumfile(), m_timestamp(Center), m_sumtime(), 
+                           m_cubeStartTime(), m_cubeCenterTime(), m_cubeStopTime(),
+                           m_cubeExposureTime(0), m_exposureDelay(0.0), 
+                           m_timeDiff(0.0), m_closest(DBL_MAX) {
+  }
+
+  SumFinder::SumFinder(const QString &cubename, const TimeStamp &tstamp) :
+                       m_cube(), m_kernels(), m_cubename(), 
+                       m_sumfile(), m_timestamp(tstamp), m_sumtime(), 
+                       m_cubeStartTime(), m_cubeCenterTime(), m_cubeStopTime(), 
+                       m_cubeExposureTime(0), m_exposureDelay(0.0), 
+                       m_timeDiff(0.0), m_closest(DBL_MAX) {
+
+    setCube(cubename);
+  }
+
+  SumFinder::SumFinder(const QString &cubename, const SumFileList &sumlist,
+                       const double &tolerance, const TimeStamp &tstamp) : 
+                       m_cube(), m_kernels(), m_cubename(cubename), 
+                       m_sumfile(), m_timestamp(tstamp), m_sumtime(),
+                       m_cubeStartTime(), m_cubeCenterTime(), m_cubeStopTime(),
+                       m_cubeExposureTime(0), m_exposureDelay(0.0), 
+                       m_timeDiff(0.0), m_closest(DBL_MAX) {
+
+    setCube(cubename);
+    seek(sumlist, tolerance);
+  }
+
+  SumFinder::SumFinder(const QString &cubename, const SharedSumFile &sumfile,
+                       const TimeStamp &tstamp) : 
+                       m_cube(), m_kernels(), m_cubename(cubename), 
+                       m_sumfile(sumfile), m_timestamp(tstamp), m_sumtime(), 
+                       m_cubeStartTime(), m_cubeCenterTime(), m_cubeStopTime(),  
+                       m_cubeExposureTime(0), m_exposureDelay(0.0), 
+                       m_timeDiff(0.0), m_closest(DBL_MAX) {
+
+    setCube(cubename);
+    SumFileList sumlist;
+    sumlist.append(sumfile);
+    seek(sumlist, DBL_MAX);  // Should unconditionally succeed
+    if ( !isFound() ) {  // Gut check
+      QString mess = "Failed to unconditionally accept associated SUMFILE!";
+      throw IException(IException::Programmer, mess, _FILEINFO_);
+    }
+  }
+
+  SumFinder::~SumFinder() { }
+
+  bool SumFinder::isValid() const {
+    if ( m_cubename.isEmpty() ) { return ( false ); }
+    return ( isFound() ); 
+  }
+
+  bool SumFinder::isFound() const {
+    return ( !m_sumfile.isNull() );
+  }
+
+  void SumFinder::setTimeStamp(const SumFinder::TimeStamp &tstamp) {
+    m_timestamp = tstamp;
+    return;
+  }
+
+  SumFinder::TimeStamp SumFinder::getTimeStamp() const {
+    return ( m_timestamp );
+  }
+
+  const iTime &SumFinder::cubeStartTime() const {
+    return  ( m_cubeStartTime );
+  }
+
+  const iTime &SumFinder::cubeCenterTime() const {
+    return  ( m_cubeCenterTime );
+  }
+
+
+  const iTime &SumFinder::cubeStopTime() const {
+    return ( m_cubeStopTime );
+  }
+
+  double SumFinder::exposureTime() const {
+    return ( m_cubeExposureTime );
+  }
+
+
+  double SumFinder::sumStartTime() const {
+    if ( Start == getTimeStamp() ) {
+      return ( m_sumtime.Et() );
+    }
+    else if ( Center == getTimeStamp() ) {
+      return ( (m_sumtime.Et() - (exposureTime() / 2.0)) );
+    }
+    else {  // Stop == getTimeStamp()
+      return ( (m_sumtime.Et() - exposureTime()) );
+    }
+  }
+
+
+  double SumFinder::sumCenterTime() const {
+    if ( Start == getTimeStamp() ) {
+      return ( (m_sumtime.Et() + (exposureTime() / 2.0)) );
+    }
+    else if ( Center == getTimeStamp() ) {
+      return ( m_sumtime.Et() );
+    }
+    else {  // Stop == getTimeStamp()
+      return ( (m_sumtime.Et() - (exposureTime() / 2.0)) );
+    }
+  }
+
+
+  double SumFinder::sumStopTime() const {
+    if ( Start == getTimeStamp() ) {
+      return ( (m_sumtime.Et() + exposureTime()) );
+    }
+    else if ( Center == getTimeStamp() ) {
+      return ( (m_sumtime.Et() + (exposureTime() / 2.0)) );
+    }
+    else {  // Stop == getTimeStamp()
+      return ( m_sumtime.Et()  );
+    }
+  }
+
+  double SumFinder::exposureDelay() const {
+    return ( m_exposureDelay );
+  }
+
+  const iTime &SumFinder::timeT() const {
+    if ( Center == m_timestamp ) { return ( m_cubeCenterTime );  }
+    if ( Start  == m_timestamp ) { return ( m_cubeStartTime );  }
+    if ( Stop   == m_timestamp ) { return ( m_cubeStopTime );  }
+    return ( m_cubeCenterTime );
+  }
+ 
+
+  double SumFinder::deltaT() const {
+    return ( m_timeDiff );
+  }
+
+  double SumFinder::closest() const {
+    return ( m_closest );
+  }
+
+  void SumFinder::setCube(const QString &name) {
+
+    // Always close out the kernels and cubes.
+    m_kernels.reset();
+    m_cube.reset(); 
+     
+    // Empty string clears cube from state
+    if ( name.isEmpty() ) {   return;  }
+
+    m_cubename =  name;
+    m_cube.reset( new Cube(name, "rw") );
+
+    // Ensure kernels are loaded for time conversions (mainly)
+    m_kernels.reset( new Kernels(*m_cube) );
+    m_kernels->Load();
+
+    calculateTimes(*m_cube, m_cubeStartTime, m_cubeCenterTime, m_cubeStopTime, 
+                   m_cubeExposureTime, m_exposureDelay);
+    return;
+  }
+
+  const Cube *SumFinder::cube() const {
+    return ( m_cube.data() );
+  }
+
+  const QString &SumFinder::name() const {
+    return ( m_cubename );
+  }
+
+
+  /**
+   * @brief Find SUMFILE for the given cube file
+    *  
+   * This method will find the appropriate SUMFILE associated with a Cube object 
+   * given a list of SumFile objects. The time the image was observed is compared 
+   * to the time of a SUMFILE. The SumFile that matches the cube is the one with 
+   * the time closest to the Cube observation time. 
+   * 
+   * @param Cube       Cube object to find a SumFile for.
+   * @param sumFiles   List of SharedSumFile objects to search, sorted in ascending order.
+   * @param deltaT     Maximum time difference in ISIS cube file time and 
+   *                   SumFile time.
+   * 
+   * @return SharedSumFile Pointer to SumFile for ISIS cube
+   */
+  bool SumFinder::seek(const SumFileList &sumFiles, const double &tolerance ) {
+
+    // Check to see if we got a cube to find
+    confirmValidity(m_cube,"Must set a cube to find an associated SumFile!");
+
+    // Disassociate any previous solution
+    m_sumfile.clear();
+    m_timeDiff = m_closest = DBL_MAX;
+
+    // Just a reset if list is empty
+    if ( !(sumFiles.size() > 0) )  return ( false );
+
+    // Otherwise, find the sum file with start ET closest to the
+    // cube's ET Note that the sum files are already sorted by ET...
+    for ( int index = 0 ; index < sumFiles.size() ; index++) {
+      double tdiff = fabs( sumFiles[index]->et() - timeT().Et() );
+      m_closest = qMin( m_closest, tdiff );  // Only done here
+      if ( tdiff <= tolerance ) {
+        if ( tdiff < fabs(m_timeDiff) ) {
+          setSumFile(sumFiles[index]);
+        }
+      }
+    }
+    
+    // Return results
+    return ( isFound() );
+  }
+
+
+  bool SumFinder::setSumFile(const SharedSumFile &sumfile) {
+    m_sumfile = sumfile;
+    m_sumtime = sumfile->time();
+    m_timeDiff = m_sumtime.Et() - timeT().Et();
+    return ( true );
+  }
+
+
+ const SumFile *SumFinder::sumfile() const {
+   return ( m_sumfile.data() );
+ }
+
+
+/**
+ * @brief Calculate start, end and exposure time from an ISIS Cube file  
+ * 
+ * @author 2016-07-26 Kris Becker
+ * 
+ * @param cube         Cube to extract times from
+ * @param startTime    Start time of observation
+ * @param stopTime     Stop time of observation
+ * @param exposureTime Exposure time of observation
+ * 
+ * @return @b bool True if successful, false if failed
+ */
+  bool SumFinder::calculateTimes(Cube &cube, 
+                                 iTime &startTime, 
+                                 iTime ¢erTime,
+                                 iTime &stopTime, 
+                                 double &exposureTime,
+                                 double &exposureDelay) {
+
+    // Use the mid exposure time and compute endtimes there. Note this assumes
+    // a framing camera
+    exposureDelay    = startExposureDelay(cube);
+    double stopDelay = stopExposureDelay(cube);
+
+    // Exposure and center time is determined. (Assumes its a framing camera!)
+    exposureTime  = getExposureTime(cube);
+    centerTime = cube.camera()->time();
+
+
+    // Get spacecraft clock times for starting/ending elements
+    Pvl *cubeLabels = cube.label();
+    PvlGroup &instGrp = cubeLabels->findGroup("Instrument", Pvl::Traverse);
+
+    // Compute real start time. We are going to trust the SCLK values in the
+    // label 
+    startTime = centerTime - (exposureTime / 2.0 );
+    if ( instGrp.hasKeyword("SpacecraftClockStartCount") ) {
+      PvlKeyword startSClock = instGrp["SpacecraftClockStartCount"];
+      QString originalClock = startSClock[0];
+      startTime = cube.camera()->getClockTime(originalClock) + exposureDelay;
+    }
+
+    // Determine end time where label values take precedence
+    stopTime = centerTime + (exposureTime / 2.0);
+    if ( instGrp.hasKeyword("SpacecraftClockStopCount") ) {
+      PvlKeyword stopSClock = instGrp["SpacecraftClockStopCount"];
+      QString originalClock = stopSClock[0];
+      try {
+        stopTime = cube.camera()->getClockTime(originalClock) - stopDelay;
+      }
+      catch(IException &e) {
+        // The stop time is not required. So, if we cannot access it, move on.
+      }
+    }
+
+    return ( true );
+  }
+
+
+/**
+ * @brief Get the exposure time from the Cube label 
+ * 
+ * @author 2016-08-23 Kris Becker
+ * 
+ * @param cube   Cube to extract expousure time from
+ * 
+ * @return double Provides the expousure time in seconds
+ */
+  double SumFinder::getExposureTime(const Cube &cube) const {
+
+    Pvl *cubeLabels = cube.label();
+    PvlGroup &instGrp = cubeLabels->findGroup("Instrument", Pvl::Traverse);
+    PvlKeyword exptime = instGrp["ExposureDuration"];
+    QString units = exptime.unit(0).toLower();
+    double etime(toDouble(exptime[0]));
+
+    // Convert to seconds if indicated
+    if ( "milliseconds" == units) etime /= 1000.0;
+    if ( "millisecond" == units) etime /= 1000.0;
+    if ( "msecs" == units) etime /= 1000.0;
+    if ( "msec" == units) etime /= 1000.0;
+    if ( "ms" == units) etime /= 1000.0;
+
+    return (etime);
+  }
+
+/**
+ * @brief Update requested items based upon bit mask of options
+ * 
+ * @author 2016-07-26 Kris Becker
+ * 
+ * @param options Bit mask of processing Options
+ * 
+ * @return bool   True if all operations were successful, false 
+ *                if a failure occured
+ */
+  bool SumFinder::update(const unsigned int options)  {
+    confirmValidity(m_cube,"Valid Cube (and SUMFILE) required for updates!");
+
+    bool good(true);
+
+    // Reset timing to original times just needs a cube file.
+    if ( options & Reset) {
+        good = ( good && resetTimes() );
+        return ( good );
+    }
+
+    // All other options require a sumfile to be associated
+    confirmValidity(m_sumfile,"Valid SUMFILE (got a Cube) required for updates!");
+
+    if ( options & Times) {
+        good = ( good && updateTimes() );
+    }
+
+    if ( options & Spice ) {
+        good = ( good && m_sumfile->updateSpice(*m_cube) );
+    }
+    else {
+
+      if ( options & Pointing ) {
+          good = ( good && m_sumfile->updatePointing(*m_cube) );
+      }
+
+      if ( options & Position ) {
+          good = ( good && m_sumfile->updatePosition(*m_cube) );
+      }
+    }
+
+
+    return (good);
+  }
+
+/**
+ * @brief Determine delay at start time to beginning of exposure
+ *  
+ * This method determines the delay from the start time to the begining of the 
+ * exposure if it exists. This is not typically but is usually determined in the 
+ * camera model. 
+ *  
+ * @author 2016-09-13 Kris Becker
+ * 
+ * @param cube  ISIS image cube to determine delay
+ * 
+ * @return double Returns the exposure start time delay in seconds if exists
+ */
+  double SumFinder::startExposureDelay(const Cube &cube) const {
+    
+    Pvl *cubeLabel = cube.label();
+    PvlGroup &instGrp = cubeLabel->findGroup("Instrument", Pvl::Traverse);
+
+    QString scname = instGrp["SpacecraftName"];
+    if ( scname.toLower() != "dawn" ) { return (0.0); }
+
+    QString instname = instGrp["InstrumentId"]; 
+    if ( instname.toLower() == "fc1") { return (0.193); }
+    if ( instname.toLower() == "fc2") { return (0.193); }
+
+    return (0.0);
+  }
+
+
+  double SumFinder::stopExposureDelay(const Cube &cube) const {
+    return (0.0);
+  }
+
+
+
+/**
+ * @brief Update start/end times in the label of an ISIS cube 
+ *  
+ * This method will update the start and end times in the label of an ISIS cube 
+ * file with the contents of the SUMSPICE. The contents of the 
+ * SpacecraftStartClockTime/SpacecraftEndClockTimes with the contents the lines 
+ * of the UTC contained in the SUMFILE 
+ * 
+ * @param cube    An intialized ISIS Cube object
+ * @return bool   True if succesful, false if the operation fails
+ */
+  bool SumFinder::updateTimes() {
+
+    // Check conditions
+    confirmValidity(m_cube,"Must set a cube to update times with SUMFILE times!");
+    confirmValidity(m_sumfile,"Must associated SumFile with a cube to update times!");
+
+    // Acquire keywords
+    Pvl *cubeLabel = m_cube->label();
+    PvlGroup &instGrp = cubeLabel->findGroup("Instrument", Pvl::Traverse);
+    PvlGroup sumtime("SumTimeHistory");
+    PvlGroup *sumtPtr = &sumtime;
+    bool addSumGroup(true);  // Assume the object doesn't exist!
+
+    // Some monkey business for Sumtime history object (see below)
+    PvlObject &isiscube = cubeLabel->findObject("IsisCube");
+    if ( isiscube.hasGroup(sumtime.name()) ) {
+      sumtPtr = &cubeLabel->findGroup(sumtime.name(), Pvl::Traverse);
+      addSumGroup = false;
+    }
+    PvlGroup &sumtGrp = *sumtPtr;
+
+    // Find relevant cube keywords
+    PvlKeyword origStartClock = findKeyword("SpacecraftClockStartCount", instGrp);
+    PvlKeyword origStopClock  = findKeyword("SpacecraftClockStopCount", instGrp);
+    PvlKeyword origStartTime  = findKeyword("StartTime", instGrp);
+    PvlKeyword origStopTime   = findKeyword("StopTime", instGrp);
+
+    // Find relevant archive keywords
+    PvlKeyword sumtStartClock = findKeyword("SpacecraftClockStartCount", sumtGrp);
+    PvlKeyword sumtStopClock  = findKeyword("SpacecraftClockStopCount", sumtGrp); 
+    PvlKeyword sumtStartTime  = findKeyword("StartTime", sumtGrp);
+    PvlKeyword sumtStopTime   = findKeyword("StopTime", sumtGrp);
+
+
+    // Ok, first lets determine if we have any expected keywords in the label.
+    // This will prevent any updates to the label if total failure occurs. This
+    // will also throw an error if this situation is encountered.
+    int nvalid = origStartClock.size() + origStopClock.size() +
+                 origStartTime.size()  + origStopTime.size();
+
+    // Now check to ensure we have at least one valid time that will be
+    // modified and assume that is enough to get it done properly
+    if ( 0 == nvalid ) {
+      QString mess = "No expected timing keywords found on labels - "
+                     "assuming non-standard, time update failed";
+      throw IException(IException::User, mess, _FILEINFO_);
+    }
+
+    // Add the sum file name to the Archive group here. It just looks better to
+    // put this keyword here as it nicely delineates from other keywords.
+    PvlKeyword sumtFileKeyword = findKeyword("SUMFILE", sumtGrp);
+    if (sumtFileKeyword.size() == 0) {
+      sumtFileKeyword.addComment("SUMFILE(s) used to update the SCLK timing "
+                                 "in the instrument group (SPC)."); 
+    }
+    sumtFileKeyword.addValue(m_sumfile->name());
+    setKeyword(sumtFileKeyword, sumtGrp);
+
+    // Compute new values for existing keywords if we got them
+    Camera *camera = m_cube->camera();
+    
+    iTime newStartClock(sumStartTime() - startExposureDelay(*m_cube));
+    iTime newStopClock(sumStopTime()   + stopExposureDelay(*m_cube));
+
+    // Compute start SCLK if present on labels
+    if ( origStartClock.size() > 0 ) {
+      NaifStatus::CheckErrors();
+      char newSCLK[256];
+      sce2s_c(camera->naifSclkCode(), newStartClock.Et(), 
+              sizeof(newSCLK), newSCLK);
+      NaifStatus::CheckErrors();
+
+      sumtStartClock.addValue(origStartClock[0], origStartClock.unit());
+      origStartClock.setValue(QString(newSCLK), origStartClock.unit());
+
+      setKeyword(origStartClock, instGrp);
+      setKeyword(sumtStartClock, sumtGrp);
+    }
+
+
+    // Compute end SCLK if present on labels
+    if ( origStopClock.size() > 0 ) {
+      NaifStatus::CheckErrors();
+      char newSCLK[256];
+      sce2s_c(camera->naifSclkCode(), newStopClock.Et(), 
+              sizeof(newSCLK), newSCLK);
+      NaifStatus::CheckErrors();
+
+      sumtStopClock.addValue(origStopClock[0], origStopClock.unit());
+      origStopClock.setValue(QString(newSCLK), origStopClock.unit());
+
+      setKeyword(origStopClock, instGrp);
+      setKeyword(sumtStopClock, sumtGrp);
+    }
+
+
+    // Now check for StartTime
+    if ( origStartTime.size() > 0 ) {
+      sumtStartTime.addValue(origStartTime[0], origStartTime.unit());
+      origStartTime.setValue(newStartClock.UTC(), origStartTime.unit());
+
+      setKeyword(origStartTime, instGrp);
+      setKeyword(sumtStartTime, sumtGrp);
+    }
+
+    // Now check for StopTime
+    if ( origStopTime.size() > 0 ) {
+      sumtStopTime.addValue(origStopTime[0], origStopTime.unit());
+      origStopTime.setValue(newStopClock.UTC(), origStopTime.unit());
+
+      setKeyword(origStopTime, instGrp);
+      setKeyword(sumtStopTime, sumtGrp);
+    }
+
+    // Now add the SUMFILE time group if needed (first time only)
+    if ( addSumGroup  ) {
+      isiscube.addGroup(sumtGrp);
+    }
+
+    // Disable current SPICE on label
+    (void) disableSpice(*cubeLabel);
+    return ( true );
+  }
+
+  bool SumFinder::resetTimes() {
+
+    // Check conditions
+    confirmValidity(m_cube,"Must set a cube to update times with SUMFILE times!");
+
+    // Acquire keywords
+    Pvl *cubeLabel = m_cube->label();
+    PvlGroup &instGrp = cubeLabel->findGroup("Instrument", Pvl::Traverse);
+    PvlObject &isiscube = cubeLabel->findObject("IsisCube");
+
+    // See if the proper group exists - we're done if doesn't
+    if ( !isiscube.hasGroup("SumTimeHistory") ) {
+      return ( false );
+    }
+
+    // Pull the group from the label
+    PvlGroup sumtGrp = isiscube.findGroup("SumTimeHistory");
+
+    // Find relevant cube keywords
+    PvlKeyword origStartClock = findKeyword("SpacecraftClockStartCount", instGrp);
+    PvlKeyword origStopClock  = findKeyword("SpacecraftClockStopCount", instGrp);
+    PvlKeyword origStartTime  = findKeyword("StartTime", instGrp);
+    PvlKeyword origStopTime   = findKeyword("StopTime", instGrp);
+
+    // Find relevant archive keywords
+    PvlKeyword sumtStartClock = findKeyword("SpacecraftClockStartCount", sumtGrp);
+    PvlKeyword sumtStopClock  = findKeyword("SpacecraftClockStopCount", sumtGrp); 
+    PvlKeyword sumtStartTime  = findKeyword("StartTime", sumtGrp);
+    PvlKeyword sumtStopTime   = findKeyword("StopTime", sumtGrp);
+
+    // Reset start SCLK if present on labels
+    if ( (origStartClock.size() > 0) && (sumtStartClock.size() > 0) ) {
+      origStartClock.setValue(sumtStartClock[0], origStartClock.unit());
+      setKeyword(origStartClock, instGrp);
+    }
+
+    // Reset end SCLK if present on labels
+    if ( (origStopClock.size() > 0) && (sumtStopClock.size() > 0) ) {
+      origStopClock.setValue(sumtStopClock[0], origStopClock.unit());
+      setKeyword(origStopClock, instGrp);
+    }
+
+    // Now check for StartTime
+    if ( (origStartTime.size() > 0) && (sumtStartTime.size() > 0) ) {
+      origStartTime.setValue(sumtStartTime[0], origStartTime.unit());
+      setKeyword(origStartTime, instGrp);
+    }
+
+    // Now check for StopTime
+    if ( (origStopTime.size() > 0) && (sumtStopTime.size() > 0)  ) {
+      origStopTime.setValue(sumtStopTime[0], origStopTime.unit());
+      setKeyword(origStopTime, instGrp);
+    }
+
+    // Now remove the sumtime group from the labels.
+    isiscube.deleteGroup(sumtGrp.name());
+
+    // Disable current SPICE on label
+    (void) disableSpice(*cubeLabel);
+    return ( true );
+  }
+
+
+
+  PvlKeyword SumFinder::findKeyword(const QString &name, 
+                                    const PvlContainer &keys) const {
+    if ( keys.hasKeyword(name) ) {
+      return ( keys.findKeyword(name) );
+    }
+
+    return (PvlKeyword(name));
+  }
+
+
+  void SumFinder::setKeyword(const PvlKeyword &keyword, 
+                             PvlContainer &keys) const {
+    keys.addKeyword(keyword, PvlContainer::Replace);
+    return;
+  }
+
+  bool SumFinder::deleteKeyword(const QString &keyword, 
+                                PvlContainer &keys) const {
+    if ( keys.hasKeyword(keyword) ) {
+      keys.deleteKeyword(keyword);
+      return ( true );
+    }
+
+    return ( false );
+  }
+
+  int SumFinder::disableSpice(Pvl &label) const {
+    int ndeleted(0);
+
+    if ( label.hasObject("IsisCube") ) {
+      PvlObject &iCube = label.findObject("IsisCube");
+      if ( iCube.hasGroup("Kernels") ) {
+        PvlGroup &kernGrp = iCube.findGroup("Kernels", Pvl::Traverse); 
+
+        // Known Kernels group keywords
+        QStringList kernkeys;
+        kernkeys << "LeapSecond" << "TargetAttitudeShape" << "TargetPosition" 
+                 << "InstrumentPointing" << "Instrument" << "SpacecraftClock"
+                 << "InstrumentPosition" << "InstrumentAddendum" << "ShapeModel"
+                 << "Extra" << "InstrumentPositionQuality" 
+                 << "InstrumentPointingQuality" << "SpacecraftPointing"
+                 << "SpacecraftPosition" << "ElevationModel" << "Frame"
+                 << "StartPadding" << "EndPadding" << "CameraVersion";
+
+        // Force user to re-run spiceinit by removing every known keyword in the
+        // Kernels Group that is created by spiceinit (as of 2016-09-15)
+        BOOST_FOREACH ( QString keyword, kernkeys ) {
+          if ( deleteKeyword(keyword, kernGrp) ) {
+            ndeleted++;
+          }
+        }
+      }
+    }
+    return (ndeleted);
+  }
+
+}
+// namespace Isis
+
+
diff --git a/isis/src/control/apps/sumspice/SumFinder.h b/isis/src/control/apps/sumspice/SumFinder.h
new file mode 100644
index 0000000000000000000000000000000000000000..578c19e205539db700c6fe194ee80bfea2ffb3ea
--- /dev/null
+++ b/isis/src/control/apps/sumspice/SumFinder.h
@@ -0,0 +1,185 @@
+#ifndef SumFinder_h
+#define SumFinder_h
+/**
+ * @file
+ * $Revision: 6565 $
+ * $Date: 2016-02-10 17:15:35 -0700 (Wed, 10 Feb 2016) $
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are public
+ *   domain. See individual third-party library and package descriptions for
+ *   intellectual property information,user agreements, and related information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or implied,
+ *   is made by the USGS as to the accuracy and functioning of such software
+ *   and related material nor shall the fact of distribution constitute any such
+ *   warranty, and no responsibility is assumed by the USGS in connection
+ *   therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
+ *   the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include 
+#include 
+
+#include "Cube.h"
+#include "FileList.h"
+#include "iTime.h"
+#include "Kernels.h"
+#include "Quaternion.h"
+#include "SpecialPixel.h"
+#include "SumFile.h"
+
+namespace Isis {
+
+
+
+  /**
+   * Container class for the sums.
+   * 
+   * @author 2016-09-14 Kris Becker
+   * 
+   * @internal 
+   *   @history 2016-09-14 Kris Becker - Original Version
+   *   @history 2017-02-09 Jesse Mapel - Updated to ignore invalid
+   *                           SpacecraftClockStopCount values.
+   */
+  class SumFinder {
+    public:
+      enum Options   { None = 0, Times = 1, Spice = 2, Pointing = 4, 
+                       Position = 8, Reset = 16};
+      enum TimeStamp { Start, Center, Stop };
+
+      SumFinder();
+      SumFinder(const QString &cubename, const TimeStamp &tstamp = Center);
+      SumFinder(const QString &cubename, const SumFileList &sumlist,
+                const double &tolerance = DBL_MAX, 
+                const TimeStamp &tstamp = Center);  
+      SumFinder(const QString &cubename, const SharedSumFile &sumfile,
+                const TimeStamp &tstamp = Center);
+      virtual ~SumFinder();
+
+      bool isValid() const;
+      bool isFound() const;
+
+      void setTimeStamp(const TimeStamp &tstamp);
+      TimeStamp getTimeStamp() const;
+
+      const iTime &cubeStartTime() const;
+      const iTime &cubeCenterTime() const;
+      const iTime &cubeStopTime() const;
+      double exposureTime() const;
+      double exposureDelay() const;
+
+      double sumStartTime() const;
+      double sumCenterTime() const;
+      double sumStopTime() const;
+
+      const iTime &timeT() const;
+      double deltaT() const;
+      double closest() const;
+
+      void setCube(const QString &name = "");
+      const Cube *cube() const;
+      const QString &name() const;
+
+      bool  seek(const SumFileList &sumlist, const double &tolerance = DBL_MAX);
+      bool  setSumFile(const SharedSumFile &sumfile);
+      const SumFile *sumfile() const;
+
+      bool update(const unsigned int options);
+
+   protected:
+      virtual bool calculateTimes(Cube &cube, 
+                                  iTime &startTime, 
+                                  iTime ¢erTime,
+                                  iTime &stopTime, 
+                                  double &exposureTime,
+                                  double &exposureDelay);
+
+      virtual double getExposureTime(const Cube &cube) const;
+      virtual double startExposureDelay(const Cube &cube) const;
+      virtual double stopExposureDelay(const Cube &cube) const;
+
+
+    private:
+      QScopedPointer    m_cube;
+      QScopedPointer m_kernels;
+      QString                 m_cubename; 
+
+      SharedSumFile           m_sumfile;  ///!< Pointer to SumFile if found
+      TimeStamp               m_timestamp;
+      iTime                   m_sumtime;
+
+      iTime                   m_cubeStartTime;
+      iTime                   m_cubeCenterTime;
+      iTime                   m_cubeStopTime;
+      double                  m_cubeExposureTime;
+      double                  m_exposureDelay;
+
+      double                  m_timeDiff;
+      double                  m_closest;
+
+      bool updateTimes();
+      bool resetTimes();
+
+      PvlKeyword findKeyword(const QString &name, const PvlContainer &keys) const;
+      void setKeyword(const PvlKeyword &keyword, PvlContainer &keys) const;
+      bool deleteKeyword(const QString &keyword, PvlContainer &keys) const;
+      int disableSpice(Pvl &label) const;
+
+      template  
+        bool confirmValidity(const T &target, const QString &errmess,
+                             const bool &throwIfInvalid = true) 
+                             const;
+  };
+
+
+/**
+ * @brief Provides a check of a shared pointer and manage error 
+ *        condition
+ *  
+ *  class T must define an isNull() method that returns true when the container
+ *  possesses a valid (pointer) element.
+ *  
+ *  This method is designed to take a QSharedPointer, QScopedPointer and
+ *  QPointer objects and potentially others that have the isNull() method.
+ * 
+ * @param target     Pointer container to check
+ * @param errmess    Error message to throw when null and thow 
+ *                   is enabled
+ * @param throwIfInvalid True if throwing an exception if 
+ *                       non-valid condition.
+ * 
+ * @return bool True if container content is valid, false if 
+ *              error
+ * 
+ * @author 2016-09-14 Kris Becker
+ * 
+ * @internal
+ *   @history 2016-09-14 Kris Becker - Original Version
+ */
+  template  
+     bool SumFinder::confirmValidity(const T &target, const QString &errmess,
+                                     const bool &throwIfInvalid) const {
+
+      if ( !target.isNull() ) {  return (true);  }
+
+      if ( throwIfInvalid ) {
+        throw IException(IException::Programmer, errmess, _FILEINFO_);
+      }
+      return (false);
+    }
+
+
+
+};  // namespace Isis
+#endif
diff --git a/isis/src/control/apps/sumspice/sumspice.cpp b/isis/src/control/apps/sumspice/sumspice.cpp
index 90e1ad2fb485d7eff2de7fc4165e84105cb02f88..46c869f5b607a1e2db541a540fd16c27ec101519 100644
--- a/isis/src/control/apps/sumspice/sumspice.cpp
+++ b/isis/src/control/apps/sumspice/sumspice.cpp
@@ -1,10 +1,10 @@
 // $Id: sumspice.cpp 6565 2016-02-11 00:15:35Z kbecker@GS.DOI.NET $
 #include "Isis.h"
 
-
 #include 
 #include 
 #include 
+#include 
 #include 
 #include 
 
@@ -25,23 +25,39 @@
 #include "Progress.h"
 #include "Pvl.h"
 #include "PvlGroup.h"
+#include "SpecialPixel.h"
 #include "SumFile.h"
+#include "SumFinder.h"
 #include "Target.h"
 
 using namespace std;
 using namespace Isis;
 
+inline QString format(const double &d, const int &precision, 
+                      const QString &defValue = "NULL") {
+  if ( IsSpecial(d) ) {
+    return ( defValue );
+  }
+  return (toString(d, precision));
+}
+
+
 void IsisMain() {
 
+  //  typedef SumFinder::Options Options;
+  typedef SumFinder::TimeStamp TimeStamp;
+
   //  Program constants
   const QString sumspice_program = "sumspice";
-  const QString sumspice_version = "1.0";
+  const QString sumspice_version = "2.0";
   const QString sumspice_revision = "$Revision: 6565 $";
   const QString sumspice_runtime = Application::DateTime();
  
   UserInterface &ui = Application::GetUserInterface();
 
-  // get the list of input cubes to be processed
+
+   
+  //  Get the list of input cubes to be processed
   FileList cubeNameList;
   if ( ui.WasEntered("FROM") ) {
     cubeNameList.append(ui.GetFileName("FROM"));
@@ -67,6 +83,11 @@ void IsisMain() {
     throw IException(IException::User, message, _FILEINFO_);
   }
 
+  // Get the time as represented in the SUMFILE
+  QString sumtime = ui.GetString("SUMTIME").toLower();
+  TimeStamp tstamp = ( "start"  == sumtime ) ? SumFinder::Start : 
+                     ( "center" == sumtime)  ? SumFinder::Center :
+                                               SumFinder::Stop; 
 
   // Load any meta kernels if provided by user
   Kernels meta;
@@ -78,172 +99,140 @@ void IsisMain() {
 
   // Load sumfiles
   SumFileList sumFiles = loadSumFiles(sumFileNameList);
+
   // Sort the sum file list in ascending order by ET
   qSort(sumFiles.begin(), sumFiles.end(), SortEtAscending());
+
   // check for uniqueness of sum files
   PvlGroup duplicates("SumFileWarnings");
   duplicates.addComment("First file will be used to update cube.");
   for (int sumIndex = 1; sumIndex < sumFiles.size(); sumIndex++) {
-    if ( sumFiles[sumIndex]->et() == sumFiles[sumIndex-1]->et()) {
+    double tdiff = fabs(sumFiles[sumIndex]->et() - sumFiles[sumIndex-1]->et());
+    if ( qFuzzyCompare( tdiff+1.0, 0.0+1.0) ) {
       PvlKeyword filePair("SumFilesWithDuplicateTimes", sumFiles[sumIndex-1]->name());
       filePair.addValue(sumFiles[sumIndex]->name());
       duplicates += filePair; 
     }
   }
+
   if (duplicates.keywords() != 0) {
     Application::Log(duplicates);
   }
 
-  if (ui.GetString("MODE") == "UPDATETIMES") {
-    PvlGroup warnings("UpdateStartClockWarnings");
-
-    // loop through the input cubes
-    Progress progress;
-    progress.SetText("Updating Times in Cube List");
-    progress.SetMaximumSteps(cubeNameList.size());
-    double deltaTime = ui.GetDouble("TIMEDIFF");
-    for (int cubeIndex = 0; cubeIndex < cubeNameList.size(); cubeIndex++) {
-      progress.CheckStatus();
-
-      Cube inputCube(cubeNameList[cubeIndex].expanded(), "rw");
-
-      Kernels kernels(inputCube);
-      kernels.Load();
-
-      SharedSumFile sumFile = findSumFile(inputCube, sumFiles, deltaTime);
-      // If findSumFile() returns a Null pointer, 
-      // then no sum file within the given tolerance (deltaTime) was found.
-      // Print a warning. 
-      if ( sumFile.isNull() ) {// create cube file list containing file names that were updated.
-        PvlKeyword file("CubeFileName", cubeNameList[cubeIndex].name());
-        file.addComment("Clocks and times for this cube were NOT updated. "
-                        "No sum file was found whose time was within a tolerance"
-                        " of [" + Isis::toString(deltaTime, 10) + "] of the cube's start time.");
-        warnings += file;
+  // Determine the update mode
+  QString update = ui.GetString("UPDATE").toLower();
+  unsigned int options(0);  // == SumFinder::None
+  if ( "times"    == update ) options |= (unsigned int) SumFinder::Times;
+  if ( "spice"    == update ) options |= (unsigned int) SumFinder::Spice;
+  // These are unnecessary if UPDATE=SPICE!
+  if ( "pointing" == update ) options |= (unsigned int) SumFinder::Pointing;
+  if ( "position" == update ) options |= (unsigned int) SumFinder::Position;
+  if ( "reset"    == update ) options |= (unsigned int) SumFinder::Reset;
+ 
 
-      }
-      else {
+  // Determine observation time tolerances. Default is to find the closest one
+  double tolerance = DBL_MAX;
+  if ( ui.WasEntered("TIMEDIFF") ) {
+    tolerance = ui.GetDouble("TIMEDIFF"); 
+  }
 
-        // If findSumFile() returned a non-null pointer, we will adjust the clock time
-        // since findSumFile() has already verified that the new ET is within the given
-        // tolerance (deltaTime) of the original ET
-        //    1. copy original start/stop clock/time keyword values to Archive group
-        //    2. replace these values in the instrument group with the spaceccraft clock time
-        //       corresponding to the new time from the sum file.
-        //    3. Clean Kernels group because output cube from this run must be re-spiceinited
-        Pvl *cubeLabel = inputCube.label();
-        PvlGroup &instGrp = cubeLabel->findGroup("Instrument", Pvl::Traverse);
-        PvlKeyword origStartClock = instGrp["SpacecraftClockStartCount"];
-        PvlKeyword origStopClock  = instGrp["SpacecraftClockStopCount"];
-        PvlKeyword origStartTime  = instGrp["StartTime"];
-        PvlKeyword origStopTime   = instGrp["StopTime"];
-
-        PvlGroup &archGrp = cubeLabel->findGroup("Archive", Pvl::Traverse);
-        // add the sum file name to the archive group
-        PvlKeyword sumFileKeyword("SumFile", sumFile->name());
-        sumFileKeyword.addComment("The sum file used to update the start count in the instrument group.");
-        archGrp += sumFileKeyword;
-        // add original time it to the archive group
-        origStartClock.addComment("The original times, before sum file was applied.");
-        archGrp += origStartClock;
-        archGrp += origStopClock;
-        archGrp += origStartTime;
-        archGrp += origStopTime;
-
-        // now that we have found the appropriate sum file and new ET, convert back to sclk ticks
-        iTime newStartTime(sumFile->et());
-        instGrp["StartTime"][0] = newStartTime.UTC();
-
-        double exposureDuration = double(instGrp["ExposureDuration"]);
-        QString units = instGrp["ExposureDuration"].unit();
-        if (units.contains("m")) { //milliseconds, ms, millisecond, etc
-          exposureDuration/=1000;
-        }
-        iTime newStopTime = newStartTime + exposureDuration;
-        instGrp["StopTime"][0] = newStopTime.UTC();
-
-        NaifStatus::CheckErrors();
-        char newStartClock[80];
-        sce2s_c(inputCube.camera()->naifSclkCode(), newStartTime.Et() , 80, newStartClock);
-        NaifStatus::CheckErrors();
-        instGrp["SpacecraftClockStartCount"][0] = newStartClock;
-
-        char newStopClock[80];
-        sce2s_c(inputCube.camera()->naifSclkCode(), newStopTime.Et() , 80, newStopClock);
-        NaifStatus::CheckErrors();
-        instGrp["SpacecraftClockStopCount"][0] = newStopClock;
-
-        // force user to re-run spiceinit 
-        // by removing everything from the Kernels Group except NAIF Frame code.
-        PvlGroup kernels("Kernels");
-        kernels += cubeLabel->findObject("IsisCube").findGroup("Kernels")["NaifFrameCode"];
-        cubeLabel->findObject("IsisCube").deleteGroup("Kernels");
-        cubeLabel->findObject("IsisCube") += kernels;
+  // loop through the input cubes
+  Progress progress;
+  progress.SetText("Updating " + update + "...");
+  progress.SetMaximumSteps(cubeNameList.size());
+  progress.CheckStatus();
+
+  // Accumulate the results of the processing...
+  typedef QSharedPointer  SharedFinder;
+  typedef QList        ListOfFinders;
+
+  ListOfFinders resultSet;
+  QStringList warnings;
+
+  for (int cubeIndex = 0; cubeIndex < cubeNameList.size(); cubeIndex++) {
+   
+    // Find the proper SUMFILE for the cube   
+    QString filename(cubeNameList[cubeIndex].expanded());
+    SharedFinder cubesum( new SumFinder(filename, sumFiles, tolerance, tstamp) );
+
+    // Format a warning and save it off for later
+    if ( !cubesum->isFound() ) {
+      QString mess = "No SUMFILE found for " + cubesum->name() +
+                      " - closest time: " + 
+                      Isis::toString(cubesum->closest(), 10) +
+                      " ";
+      warnings <<  mess;
+    }
+    else {
+      if ( !cubesum->update(options) ) {
+        QString msg = "Failed to apply SUMFILE updates on cube " + filename;
+        throw IException(IException::User, msg, _FILEINFO_);
       }
     }
-    if (warnings.keywords() != 0) {
-      Application::Log(warnings);
+
+    // This will close the cube but retain all the pertinent info
+    cubesum->setCube();
+    resultSet.append(cubesum);
+    progress.CheckStatus();
+  }
+
+  if (warnings.size() > 0) {
+    PvlKeyword message("Unmatched");
+    BOOST_FOREACH ( QString mess, warnings ) {
+      message.addValue(mess);
     }
+    PvlGroup loggrp("Warnings");
+    loggrp.addKeyword(message);
+    Application::Log(loggrp);
   }
-  else { // ui.GetString("MODE") == "UPDATESPICETABLES"
-    PvlGroup warnings("UpdateSpiceTablesWarnings");
-
-    // time should already be adjusted, so time in the given sum file (list)
-    // should have the exact time. However, due to rounding errors, we will
-    // allow very small time tolerance.
-    Progress progress;
-    progress.SetText("Updating Tables in Cube List");
-    progress.SetMaximumSteps(cubeNameList.size());
-    for (int cubeIndex = 0; cubeIndex < cubeNameList.size(); cubeIndex++) {
-      progress.CheckStatus();
-
-      Cube inputCube(cubeNameList[cubeIndex].expanded(), "rw");
-
-      PvlGroup &archGrp = inputCube.label()->findGroup("Archive", Pvl::Traverse);
-      if (archGrp.hasKeyword("SumFile")) {
-        PvlKeyword &sumFileKeyword = archGrp.findKeyword("SumFile");
-        QString sumFileName = sumFileKeyword[0];
-        SharedSumFile sumFile = findSumFile(inputCube, sumFiles, sumFileName);
-        
-        // If findSumFile() returns a Null pointer, 
-        // then no sum file was found in the Archive group
-        // Print a warning.
-        if ( sumFile.isNull() ) {
-          PvlKeyword file("CubeFileName", cubeNameList[cubeIndex].name());
-          file.addComment("SPICE tables for this cube were NOT updated. "
-                          "The sum file in the Archive group ["
-                          + sumFileName + "] was not found in the given sum file list.");
-          warnings += file;
-        }
-        else {
-          // If findSumFile() returned a non-null pointer, we will adjust the ck and spk
-          // tables in the cube's label
-          Kernels kernels(inputCube);
-          kernels.Load();
-          QStringList missing = kernels.getMissingList();
-          if (missing.size() != 0) {
-            PvlKeyword file("CubeFileName", cubeNameList[cubeIndex].name());
-            file.addComment("Missing kernel files. Have [" + Isis::toString(kernels.size())
-                            + "] files loaded with " + Isis::toString(kernels.Missing()) 
-                            + " missing (" + missing.join(",") + ").");
-            warnings += file;
-          }
-          // update instrument pointing and position
-          // Delete polygons if found in existing tables
-          sumFile->update(inputCube);
-          sumFileKeyword.addComment("The sum file used to update the SPICE tables.");
-        }
+
+
+  // Log the results of processing
+  if ( ui.WasEntered("TOLOG") ) {
+    FileName filename( ui.GetFileName("TOLOG") );
+    bool exists = filename.fileExists();
+    QFile logfile(filename.expanded());
+    if ( !logfile.open(QIODevice::WriteOnly | QIODevice::Append | 
+                       QIODevice::Text | QIODevice::Unbuffered) ) {
+      QString mess = "Unable to open/create log file " + filename.name();
+      throw IException(IException::User, mess, _FILEINFO_);
+    }
+
+    QTextStream lout(&logfile);
+    if ( !exists) {
+      lout << "Filename,SUMFILE,SumTime,Update,CubeSumDeltaTime, "
+           << "ExposureTime,CubeStartTime,CubeCenterTime,CubeStopTime,"
+           << "SumStartTime,SumCenterTime,SumStopTime\n";
+    }
+
+    BOOST_FOREACH (SharedFinder &cubesum, resultSet ) {
+      lout << cubesum->name()<< ",";
+
+      if ( !cubesum->isFound() ) {
+        lout << "NULL," << sumtime << "," << update << "," 
+             << format(cubesum->closest(), 7) << ","
+             << format(cubesum->exposureTime(), 7) << ","
+             << cubesum->cubeStartTime().UTC() << "," 
+             << cubesum->cubeCenterTime().UTC() << "," 
+             << cubesum->cubeStopTime().UTC() << ","
+             << "NULL,NULL,NULL";
       }
       else {
-        PvlKeyword file("CubeFileName", cubeNameList[cubeIndex].name());
-        file.addComment("SPICE tables for this cube were NOT updated. "
-                        "No sum file was found in the Archive group.");
-        warnings += file;
+        lout << cubesum->sumfile()->name() << "," 
+             << sumtime << "," << update << ","
+             << format(cubesum->deltaT(), 7) << ","
+             << format(cubesum->exposureTime(), 7) << ","
+             << cubesum->cubeStartTime().UTC() << "," 
+             << cubesum->cubeCenterTime().UTC() << "," 
+             << cubesum->cubeStopTime().UTC() << ","
+             << iTime(cubesum->sumStartTime()).UTC() << "," 
+             << iTime(cubesum->sumCenterTime()).UTC() << "," 
+             << iTime(cubesum->sumStopTime()).UTC();
       }
+
+      lout << "\n";
     }
-    if (warnings.keywords() != 0) {
-      Application::Log(warnings);
-    }
+
   }
 
   // Unload meta kernels - automatic, but done for completeness
diff --git a/isis/src/control/apps/sumspice/sumspice.xml b/isis/src/control/apps/sumspice/sumspice.xml
index acd543677d6f72fe682e465b6871793da7222125..7743e47e016bc42445e8d222be863d180f9501b4 100644
--- a/isis/src/control/apps/sumspice/sumspice.xml
+++ b/isis/src/control/apps/sumspice/sumspice.xml
@@ -3,40 +3,89 @@
 
 
   
-    Update ISIS start times, pointing and spacecraft position with Gaskell 
-  SUMFILEs 
+    Update ISIS start times, pointing and spacecraft position with Gaskell SPC
+  SUMFILEs
   
 
   
    
    Overview
    
     
    
-      This program allows the user to update a cube's labels, spaceraft attitude 
-      (pointing) and position with more accurate information found in the 
-      appropriate Gaskell SUMFILE. There are multiple options for the how the 
-      labels should be updated. See the MODE parameter documentation for a 
-      description of these options.
+      This program allows the user to update a cube's labels, spaceraft attitude
+      (pointing) and position with the information found in a corresponding
+      Gaskell SUMFILE. SUMFILEs are a product of  Gaskell's stereo
+      photoclinometry (SPC) digital elevation model (DEM) generation process.
+      SUMFILEs are generated for each file included in the processing to
+      generate the DEM.
     
    
     
    
-      The Gaskell SUMFILEs provided are expected to have a format
-      described below:
+       Part of the SPC DEM processing flow is to control all the images. The
+       SUMFILE is a direct product from the SPIC control process that
+       (typically) corresponds to a single file. The SUMFILE contains updates to
+       pointing attitude and spacecraft position, among other things. The
+       contents of the SUMFILE and their purpose are described below.
+    
    
+    
    
+       The objective of this program is to (optionally) apply timing changes (as
+       seen in Hayabusa 1 images), pointing and spacecraft updates directly to
+       ISIS cubes. This provides ISIS users the ability to apply consistent
+       control to ISIS images that have corresponding SUMFILEs and use the DEM
+       generated from the SPC process for orthorectiifed cartographic
+       mapping processes in ISIS. This includes creating CK and SPK kernels from
+       the result of this application for more widely distributed use of SPC
+       results.
+    
    
+    
    
+      Here is an example of the contents of a Gaskell SPC SUMFILE (NOTE: 
+      Line numbers are not part of the SUMFILE but are annotated here for
+      documentation purposes which follows):
+      
    +  1   W46908480918
+  2   2014 NOV 12 17:20:03.128
+  3     2048  2048   500 65535                                       NPX, NLN, THRSH
+  4       0.1356800000D+03    0.1044000000D+04    0.9380000000D+03   MMFL, CTR
+  5      -0.9665063720D+01    0.1326644487D+02   -0.6673084308D+01   SCOBJ
+  6      -0.6442479111D+00   -0.1829032409D-01    0.7645979944D+00   CX
+  7       0.5935707119D+00    0.6184779444D+00    0.5149357652D+00   CY
+  8      -0.4823053379D+00    0.7855892670D+00   -0.3875965231D+00   CZ
+  9       0.7254908676D+00   -0.3292717307D+00    0.6043534796D+00   SZ
+ 10     74.07410   0.00000   0.00000   0.00000  74.07410   0.00000   K-MATRIX
+ 11     0.00000D+00    0.00000D+00    0.00000D+00    0.00000D+00   DISTORTION
+ 12     0.1007758363D-02    0.1482813397D-02    0.8902614968D-03   SIGMA_VSO
+ 13     0.3071768580D-04    0.3093941486D-04    0.1565302183D-04   SIGMA_PTG
+ 14 LANDMARKS
+ 15 AO0001   2049.39    668.15
+ 16 AO0002   2020.70    644.81
+ 17 AO0003   2035.17    708.66
+ 18 BD0009   1902.39    884.05
+ 19 BD0010   1891.13    909.86
+ 20    ...
+ 21 EK0022    675.73   1371.97
+ 22 EQ0088    721.76    738.13
+ 23 FI0002    727.77    220.40
+ 24 LIMB FITS
+ 25 END FILE
+    
    
+      The lines of a Gaskell SUMFILEs are described as:
       
      
         
    • 
-          Line 1: An ID for the SUMFILE (usually the image name).
+          Line 1: An ID for the SUMFILE (occasionally, but not always, the image
+          name).
         
      • 
         
    • 
-          Line 2: The correct start UTC for the image.
+          Line 2: The potentially corrected start, center or stop time in UTC
+          for the image.
         
      • 
         
    • 
-          Line 3: The number of pixels, the number of lines, the lower DN 
+          Line 3: The number of pixels, the number of lines, the lower DN
           threshold, and the upper DN threshold.
         
      • 
         
    • 
-          Line 4: The focal length (in mm), followed by the pixel center and the 
+          Line 4: The focal length (in mm), followed by the pixel center and the
           line center (i.e. boresight/optical axis).
         
      • 
         
    • 
-          Line 5: The vector from the spacecraft to the object center (i.e. the 
-        spacecraft position in body fixed coordinates). 
+          Line 5: The vector from the spacecraft to the object center (i.e. the
+        spacecraft position in body fixed coordinates).
         
      • 
         
    • 
           Line 6: The pixel (x) unit vector, in body fixed coordinates.
@@ -63,71 +112,173 @@
           Line 13: The formal spacecraft orientation uncertainty , ie. the sigma PTG.
         
      • 
         
    • 
-          A list of landmarks containing the ID, pixel center, and line center.
+          Line 14-23: A list of landmarks containing the ID, pixel sample
+          center, and pixel line center.
         
      • 
         
    • 
-          A list of limb fits containing the landmark-on-limb centers.
+          Line 24+: A list of limb fits containing the landmark-on-limb centers.
+        
      • 
+        
    • 
+          Line 25: Last line of a Gaskell SUMFILE ends with the END FILE
+          statement.
         
      • 
       
    
-
-      Here is an example:
-      
    -  W46908480918
-  2014 NOV 12 17:20:03.128
-    2048  2048   500 65535                                       NPX, NLN, THRSH
-      0.1356800000D+03    0.1044000000D+04    0.9380000000D+03   MMFL, CTR
-     -0.9665063720D+01    0.1326644487D+02   -0.6673084308D+01   SCOBJ    
-     -0.6442479111D+00   -0.1829032409D-01    0.7645979944D+00   CX       
-      0.5935707119D+00    0.6184779444D+00    0.5149357652D+00   CY       
-     -0.4823053379D+00    0.7855892670D+00   -0.3875965231D+00   CZ       
-      0.7254908676D+00   -0.3292717307D+00    0.6043534796D+00   SZ       
-    74.07410   0.00000   0.00000   0.00000  74.07410   0.00000   K-MATRIX 
-    0.00000D+00    0.00000D+00    0.00000D+00    0.00000D+00   DISTORTION 
-    0.1007758363D-02    0.1482813397D-02    0.8902614968D-03   SIGMA_VSO  
-    0.3071768580D-04    0.3093941486D-04    0.1565302183D-04   SIGMA_PTG  
-LANDMARKS                                                                       
-AO0001   2049.39    668.15                                                      
-AO0002   2020.70    644.81                                                      
-AO0003   2035.17    708.66
-BD0009   1902.39    884.05                                                      
-BD0010   1891.13    909.86                                                      
-   ...
-EK0022    675.73   1371.97                                                      
-EQ0088    721.76    738.13                                                      
-FI0002    727.77    220.40                                                      
-LIMB FITS
-END FILE                                                                        
-    
    
     
    
    
    Usage
    
     
    
-      sumspice has been used to apply Gaskell control to Hayabusa Itokawa 
-      AMICA images. There is up to 12 seconds of uncertainty in the start times 
-      of these images. The Hayabusa team improved the start time with brute 
-      force comparisons of the position of Itokawa in the AMICA field of view. 
-      The SUMFILEs contained the correction of the start time. This was the 
-      motivation behind adding support for the start time adjustment.
+      sumspice has been used to apply Gaskell SPC control to Hayabusa
+      Itokawa AMICA images. There is up to 12 seconds of uncertainty in the
+      start times of these images. The Hayabusa team improved the start time
+      with brute force comparisons of the position of Itokawa in the AMICA field
+      of view. The SUMFILEs contained the correction of the start time.
+      Unfortunately, the PDS archive of the AMICA data has not been updated with
+      the new start times. This was the motivation behind adding support for the
+      start time adjustment.
     
    
     
    
-      To apply the complete functionality of sumspice, the start time 
-      must be updated first if required. Note that it is rather uncommon the 
-      start time will need to be updated. If it is, this option will recompute 
-      the SpacecraftClockStartTIme which is used primarily by most camera models 
-      for best accuracy of image acquisition times. This mode will require a 
-      rerun of  spiceinit mainly to reestablish the body orientation for 
-      the new start time. 
+      The basic processing options are to update the start times (UPDATE=TIMES)
+      and pointing (CK) (UPDATE=POINTING) and spacecraft position (SPK)
+      (UPDATE=POSITION) data in the ISIS label/file with that contained in the
+      SUMFILE. Both the pointing and spacecraft position can be updated in the
+      same run (UPDATE=SPICE). And, finally, it may be useful to start over by
+      resetting the times to their original values - UPDATE=RESET provides this
+      option (and removes the SumTimeHistory and disables SPICE requiring a
+      rerun of
+               spiceinit.
     
    
     
    
-      The update of pointing attitude and spacecraft position requires 
-      spiceinit to be applied to the image. This operation will update 
-      the InstrumentPointing and InstrumentPosition Tables in the label of the 
-      ISIS cube with the contents of the Gaskell SUMFILE. Note that SUMFILEs 
-      contain vectors in body-fixed format, so you must ensure the proper PCK is 
-      used with the image. NAIF routines are used to apply any required 
-      transformations to retain the integrity of the data. Once the fidelity of 
-      the updates are confirmed, new CK and SPK kernels can be created using the 
+      To apply the complete functionality of sumspice, the start time
+      must be updated first if required. Note that it is rather uncommon the
+      start time will need to be updated. If it needed/desired,
+      the UPDATE=TIMES option will recompute the SpacecraftClockStartTime, which
+      is used primarily by most camera models for best accuracy of image
+      acquisition times. This option will force a rerun of spiceinit
+      after observation times are updated mainly to reestablish the body
+      orientation and solar illumination angles for the new start time. This
+      option will reassign computed values, relative to the SUMFILE reference
+      time (see SUMTIMES) to  SpacecraftClockStartCount,
+      SpacecraftClockStopCount, StartTime and StopTime label keywords. Most
+      camera models use at least one of these values to establish observation
+      times. These times are used to associate the correct ephemeris data from
+      SPICE kernels.
+    
    
+    
    
+      The update of pointing attitude and spacecraft position requires
+      spiceinit to be applied to the image. This operation will update
+      the InstrumentPointing and InstrumentPosition Tables in the label of the
+      ISIS cube with the contents of the Gaskell SUMFILE. Note that SUMFILEs
+      contain vectors in body-fixed format, so you must ensure the proper PCK is
+      used with the image. NAIF routines are used to apply any required
+      transformations to retain the integrity of the data. Once the fidelity of
+      the updates are confirmed, new CK and SPK kernels can be created using the
       ISIS ckwriter and spkwriter applications, respectively.
     
    
+    
    Activity Tracking
    
+    
    
+      sumspice does supply some aid in tracking its activity in the ISIS
+      label. When timing is updated, there is a group called
+      SumTimeHistory that is created upon the first operation pertaining
+      to  changes that were made to the timing keywords (typically) in the
+      Instrument group in the ISIS label. Four keywords are affected by
+      timing operations in sumspice. These are SpacecraftClockStartCount,
+      SpacecraftClockStopCount, StartTime, and StopTime. The first two keywords,
+      SpacecraftClockStartCount and pacecraftClockStopCount, are in the form of
+      spacecraft clock, or SCLK, format. Manipulation of these two keywords
+      requires the existance of an ISIS camera model to determine the
+      appropriate SCLK NAIF id for conversion from UTC (as stored in the
+      SUMFILE, line 2) to SCLK. The later two keywords, StartTime, and StopTime,
+      are conversions of the times to UTC. These keywords are only updated if
+      they exist in the Instrument group in the ISIS label.
+    
    
+    
    
+      When any of these keywords are updated in the ISIS label, previous values
+      are recorded in the SumTimeHistory group created upon the first run
+      of sumspice that modifies these keywords. Any subsequent run of
+      sumspice that modifies times have previous values appended to the
+      corresponding keywords, thus creating an running history of timing
+      operations and enabling the UPDATE=RESET option to retain original timing
+      values if needed. Using the reset option removes the
+      SumTimeHistory group. Here is an example of the
+      SumTimeHistory group after an update.
+    
    
+    
    +  Group = SumTimeHistory
+    # SUMFILE(s) used to update the SCLK timing in the instrument group (SPC).
+    SUMFILE                   = N2395699394
+    SpacecraftClockStartCount = 2395694888 <1/32sec>
+    SpacecraftClockStopCount  = 2395695365 <1/32sec>
+    StartTime                 = 2005-09-21T10:44:07
+    StopTime                  = 2005-09-21T10:44:07
+  End_Group
+    
    
+    
    
+      Note that the TOLOG file, if specified, will also contain a record of the
+      activities that were applied, including the timing values resulting from
+      these operations.
+    
    
+    
    
+       When updating pointing or spacecraft position, a keyword named SUMFILE is
+      added to the  InstrumentPointing and InstrumentPosition
+      tables, respectively that records the name of the SUMFILE used to update
+      the ephemeris data in those objects. When spiceinit is run, this
+      table is replaced, thus removing the keyword, indicating original SPICE
+      data is contained in those objects.
+    
    
+    
    SUMTIME Considerations
    
+    
    
+       Regarding the SUMFILE reference time, the SUMTIME parameter is provided
+       for the user to specify that the UTC time in the SUMFILE represents the
+       start, mid or end time of the image exposure time. The following table
+       provides known reference times contained in SUMFILEs for
+       spacecraft/instruments. Knowing the correct reference contained in the
+       SUMFILE is critical to determine the correct SUMFILE for a given ISIS
+       cube and updating the ISIS labels with the time and ephemeris data
+       contained therein.
+    
    
+    
+        
+        
+          
+          
+          
+        
+        
+          
+          
+          
+        
+        
+          
+          
+          
+        
+       
+         
+          
+          
+        
+        
+          
+          
+          
+        
+    
    SUMFILE SUMTIME References
    SpacecraftInstrumentReference
    Hayabusa 1AMICAStart
    DawnFCCenter (Note: Dawn FC has a 193 ms delay from start time)
    OSIRIS-RExOCAMS (MapCam, SamCam, PolyCam)Center
    MESSENGERMDISCenter
    
+   
    Processing Sequences
    
+    
    
+       Here is an example that shows the commonly used command sequence for the
+       Hayabusa AMICA instrument. This process will update times and ephemeris
+       data, which includes pointing and spacecraft position.
+      
    +# First transfer the SUMFILE timing to the ISIS cube labels
+sumspice from=st_2395699394_v.lev0.cub sumfile=N2395699394.SUM  update=times sumtime=start  tolog=haya_amica.log
+
+# Now rerun spiceinit as a timing update forces this
+spiceinit   from=st_2395699394_v.lev0.cub shape=user model='$hayabusa/kernels/dsk/hay_a_amica_5_itokawashape_v1_0_512q.bds'
+
+# Finally, apply the pointing and spacecraft position update in a single run
+sumspice from=st_2395699394_v.lev0.cub sumfile=N2395699394.SUM  update=spice sumtime=start  tolog=haya_amica.log
+      
    
+    
    
       
 
   
@@ -135,13 +286,33 @@ END FILE
       Original Version
     
     
-      Generalized to program work with Dawn and Hayabusa data. Clock times are 
-      now updated in the instrument group and the original times are saved in 
+      Generalized to program work with Dawn and Hayabusa data. Clock times are
+      now updated in the instrument group and the original times are saved in
       the Archive group of the cube labels.
     
     
-      Added implementation to support NAIF META kernel files. Updated 
-      documentation. 
+      Added implementation to support NAIF META kernel files. Updated
+      documentation.
+    
+    
+      Refactored code to: 1) accomdate for different time references in
+      SUMFILEs (start, center, stop - see SUMTIME parameter), 2) modified
+      update options to be more flexible (see UPDATE parameter), 3) added more
+      robust determination of observation times, 4) added start time delay
+      options, particularly for Dawn FC, which has a 193 ms start time delay,
+      5) added a log option that reports operations and timing operations for
+      confirmation and analysis, 6) improved logging of timing activities to
+      labels, 7) timing updates are no longer required before applying SPICE
+      update options (not required for all instruments), 8) modified how
+      SPICE/camera model is disabled (in Kernels group) after a timing update,
+      9) added SUMTIME, UPDATE, TOLOG parameters and removed the MODE
+      parameter, 10) changed the default for TIMEDIFF to INFINITY from 0 so
+      success is guaranteed, and 11) added UPDATE=RESET option to restore
+      original times. Some of these changes breaks backwards compatibility.
+    
+    
+      Changed pvl.DIFF of input for hayabusa app test to ignore file names. Allows test to pass when
+      not using default data area. Fixes #4738.
     
   
 
@@ -157,10 +328,10 @@ END FILE
         input
         
           A single cube to process.
-         
+        
         
-          The name of a single input cube whose labels will be updated using a 
-          Gaskell SUMFILE.  Note: Use the FROMLIST parameter instead of 
+          The name of a single input cube whose labels will be updated using a
+          Gaskell SUMFILE.  Note: Use the FROMLIST parameter instead of
           this one if there are multiple cubes to process.
         
         None
@@ -174,10 +345,10 @@ END FILE
         input
         
           A list of cubes to process.
-         
+        
         
-          A text file containing a list of input cubes whose labels will be 
-          updated using Gaskell SUMFILEs. Note: Use the FROM parameter 
+          A text file containing a list of input cubes whose labels will be
+          updated using Gaskell SUMFILEs. Note: Use the FROM parameter
           instead of this one if there is only one cube to process.
         
         None
@@ -194,16 +365,15 @@ END FILE
           The name of the SUMFILE to be used to update the input cube(s).
         
         
-          The name of a single Gaskell SUMFILE containing an updated start time 
-          and SPICE information. Note: Use the SUMFILELIST parameter 
-          instead of this one if the exact SUMFILE that should be used 
-          to update the cube(s) is unknown or if there are more than one.
+          The name of a single Gaskell SUMFILE containing time and SPICE
+          information. Note: Use the SUMFILELIST parameter instead of
+          this one if the exact SUMFILE that should be used to update the
+          cube(s) is unknown or if there are more than one.
         
         *.SUM
         None
         
           SUMFILELIST
-          TIMEDIFF
         
           
 
@@ -211,14 +381,14 @@ END FILE
         filename
         input
         
-          A list of SUMFILEs to search for the best match to update the given 
-        cube(s). 
+          A list of SUMFILEs to search for the best match to update the given
+        cube(s).
         
         
-          A text file containing a list of Gaskell SUMFILEs that each contain an 
-          updated start time and SPICE information.  Note: Use the 
-          SUMFILE parameter instead of this one if the exact SUMFILE is known 
-          for the given cube(s). 
+          A text file containing a list of Gaskell SUMFILEs that each contain
+          time and SPICE information.  Note: Use the SUMFILE parameter
+          instead of this one if the desired SUMFILE is known for the given
+          cube(s).
         
         *.lis
         None
@@ -227,80 +397,229 @@ END FILE
         
       
 
-      
+      
+         filename output
+         
+           Optional output log file of results
+         
+         
+           If a name is provided, the results of each cube
+           file is written to the specified file.
+         
+         *.log
+         None
+       
+
+      
+        string
+        
+          Specify what the time in the SUMFILE represents: start, center or
+          end time
+        
+        
+          
    
+            This parameter is provided to explicity specify what the time in the
+            SUMFILE represents. Typically, this is the start time (default) but
+            not always. The user must make this determination.
+          
    
+          
    
+            This may be important when searching for the SUMFILE associated with
+            the ISIS cube when using the times from each source. sumspice
+            will make adjustments based upon this value and the exposure
+            duration as found in the ISIS cube file label.
+          
    
+            
+        
+
+          
+
+          
+
+          
+        
+        CENTER
+          
+
+      
         string
         
-          Determines how the program will use the appropriate SUMFILE to update 
-          the labels. 
+          Determines update operation to apply to ISIS file from SUMFILE data
         
         
-          Determines how the program will use the appropriate SUMFILE to update 
-          the labels. Note that there are input requirements for each option.
+          Determines which elements of the ISIS cube to update with the
+          appropriate SUMFILE contents. Note that there are input
+          requirements for each option. if a SUMFILELIST was provided, the
+          program will search for the file in the given list whose time is
+          within the specified TIMEDIFF tolerance and is the closest to the
+          SpacecraftClockStartCount in the cube. If multiple files in the
+          SUMFILELIST have the same time, this program will choose to use the
+          first one in the list with the closest time. If no SUMFILE is found
+          within this tolerance, a warning will be printed to the output log and
+          the program will exit without updating the input cube.
         
         
-          
-          
+
+          
+
+          
+
+          
+
+          
+
         
-        UPDATETIMES
+        SPICE
       
 
       
           double
         
-          The maximum allowed time difference between the cube's current start 
+          The maximum allowed time difference between the cube
           time and the time found in the SUMFILE.
         
         
-          This value is used when the UPDATETIME option is selected and a 
-          SUMFILELIST is provided. The file in the SUMFILELIST with the time 
-          that is closest to the cube's start clock must be within this 
-          tolerance for the cube to be updated.
+          
    
+            This value is always considered to specify the time differential when
+            looking for matching SUMFILES. This tolerance is used when both the
+            SUMFILE and  SUMFILELIST are given to constrain the difference in
+            observation times contained in the cube label and the SUMFILE. If no
+            value is provided, then the default behavior is to choose the SUMFILE
+            that has the closest time as specified in  SUMTIME to the
+            corresponding time contained in cube label, assertained in conjunction
+            with the camera model.
+          
    
+          
    
+              Note that it is critical to provided a tolerance value here if
+              known (e.g., ~12 seconds for Hayabusa/AMICA) so that the correct
+              SUMFILE is determined.
+          
    
             
-        0.0
+        INFINITY
           
 
       
@@ -308,15 +627,16 @@ END FILE
         input
         List of SPICE kernels to support conversions
         
-            In some cases, additional kernels may be required in order to 
-            compute some of the data acquired from the NAIF toolkit. If the ISIS 
-            labels do not contain sufficient kernels, this parameter can specify 
-            a NAIF meta kernel, or a single kernel of any supported NAIF type 
-            that will be loaded prior to any computations. These kernels remain 
-            loaded for all files and for the entirety of the runtime of this 
-            application. See 
-            SPICE Kernel Required Reading for additional information about 
-            NAIF meta kernels.
+            In some cases, additional kernels may be required in order to
+            compute some of the data acquired from the NAIF toolkit. If
+            the ISIS labels do not contain sufficient kernels, this
+            parameter can specify a NAIF meta kernel, or a single kernel
+            of any supported NAIF type that will be loaded prior to any
+            computations. These kernels remain loaded for all files and
+            for the entirety of the runtime of this application. See 
+            SPICE Kernel Required Reading for additional information
+            about NAIF meta kernels.
         
         *.meta *.tm
         None
diff --git a/isis/src/control/apps/sumspice/tsts/dawn/Makefile b/isis/src/control/apps/sumspice/tsts/dawn/Makefile
index f258a5c00201c34831d33647c7189e3c4d198ebc..f08f5ed61352c2df73d4868f6334ddba895d0e42 100644
--- a/isis/src/control/apps/sumspice/tsts/dawn/Makefile
+++ b/isis/src/control/apps/sumspice/tsts/dawn/Makefile
@@ -1,4 +1,5 @@
 # this tests sumspice using cubelist and sumfilelist inputs on DAWN images
+# updated for addition of UPDATE, SUMTIME, and TOLOG 2016-12-06 Kristin Berry
 APPNAME = sumspice
 
 include $(ISISROOT)/make/isismake.tsts
@@ -15,8 +16,10 @@ commands:
 	# first run of sumspice updates the time
 	$(APPNAME) fromlist=$(OUTPUT)/cubelist.txt \
 	sumfilelist=$(OUTPUT)/sumfilelist.txt \
-	mode=updatetime \
+	sumtime=start\
+	update=times \
 	timediff=1.0 \
+	tolog=$(OUTPUT)/sumspiceUpdateClocksToLog.txt \
 	-log=$(OUTPUT)/sumspiceUpdateClocksLog.pvl \
 	> /dev/null;
 
@@ -66,7 +69,8 @@ commands:
 	# second run of sumspice updates the tables
 	$(APPNAME) fromlist=$(OUTPUT)/cubelist.txt \
 	sumfilelist=$(OUTPUT)/sumfilelist.txt \
-	mode=updatespice \
+	sumtime=start \
+	update=spice \
 	-log=$(OUTPUT)/sumspiceUpdateSpiceLog.pvl \
 	> /dev/null;
 
diff --git a/isis/src/control/apps/sumspice/tsts/hayabusa/Makefile b/isis/src/control/apps/sumspice/tsts/hayabusa/Makefile
index 6096cc8808a49da21e7bddf645d6de5c6f000407..3a9d2e3ad9c6b32c166bd6a7c0d269495b19a0af 100644
--- a/isis/src/control/apps/sumspice/tsts/hayabusa/Makefile
+++ b/isis/src/control/apps/sumspice/tsts/hayabusa/Makefile
@@ -1,4 +1,5 @@
 # this tests sumspice using a single cube and sumfile as inputs on a Hayabusa image
+# updated for addition of UPDATE, SUMTIME, and TOLOG 2016-12-06 Kristin Berry
 APPNAME = sumspice
 
 include $(ISISROOT)/make/isismake.tsts
@@ -10,7 +11,9 @@ commands:
 	# first run of sumspice updates the time
 	$(APPNAME) from=$(OUTPUT)/st_2395699394_v.lev0.cub \
 	sumfile=$(INPUT)/N2395699394.SUM \
-	mode=updatetime \
+	sumtime=start \
+	update=times \
+	tolog=$(OUTPUT)/sumspiceUpdateClocksToLog.txt \
 	-log=$(OUTPUT)/sumspiceUpdateClocksLog.pvl \
 	> /dev/null;
 
@@ -53,7 +56,8 @@ commands:
 	# second run of sumspice updates the tables
 	$(APPNAME) from=$(OUTPUT)/st_2395699394_v.lev0.cub \
 	sumfile=$(INPUT)/N2395699394.SUM \
-	mode=updatespice \
+	sumtime=start \
+	update=spice \
 	-log=$(OUTPUT)/sumspiceUpdateSpiceLog.pvl \
 	> /dev/null;
 
diff --git a/isis/src/control/objs/BundleAdjust/BundleAdjust.cpp b/isis/src/control/objs/BundleAdjust/BundleAdjust.cpp
index 72ba7402d76e22cbed0c8f93c70390713be1e493..fb6b5f3752c67a27600ac5a4aafdd5e7877f7c33 100644
--- a/isis/src/control/objs/BundleAdjust/BundleAdjust.cpp
+++ b/isis/src/control/objs/BundleAdjust/BundleAdjust.cpp
@@ -53,14 +53,14 @@ namespace Isis {
   /**
    * Custom error handler for CHOLMOD.
    * If CHOLMOD encounters an error then this will be called.
-   * 
+   *
    * @param status The CHOLMOD error status.
    * @param file The name of the source code file where the error occured.
    * @param lineNumber The line number in file where the error occured.
    * @param message The error message.
    */
-  static void cholmodErrorHandler(int nStatus, 
-                                  const char* file, 
+  static void cholmodErrorHandler(int nStatus,
+                                  const char* file,
                                   int nLineNo,
                                   const char* message) {
     QString errlog;
@@ -85,7 +85,7 @@ namespace Isis {
   /**
    * Construct a BundleAdjust object from the given settings, control network file,
    * and cube list.
-   * 
+   *
    * @param bundleSettings A shared pointer to the BundleSettings to be used.
    * @param cnetFile The filename of the control network to be used.
    * @param cubeList The list of filenames of the cubes to be adjusted.
@@ -115,7 +115,7 @@ namespace Isis {
 
   /**
    * Construct a BundleAdjust object with held cubes.
-   * 
+   *
    * @param bundleSettings A shared pointer to the BundleSettings to be used.
    * @param cnetFile The filename of the control network to be used.
    * @param cubeList The list of filenames of the cubes to be adjusted.
@@ -148,7 +148,7 @@ namespace Isis {
   /**
    * Constructs a BundleAdjust object using a Control object.
    * A new control network object will be created as a copy of the Control's control network.
-   * 
+   *
    * @param bundleSettings A shared pointer to the BundleSettings to be used.
    * @param cnet The Control object whose control network will be copied.
    *             The Control will not be modified by the BundleAdjust.
@@ -180,7 +180,7 @@ namespace Isis {
   /**
    * Constructs a BundleAdjust object using a ControlNet object.
    * A copy of the ControlNet will be used.
-   * 
+   *
    * @param bundleSettings A shared pointer to the BundleSettings to be used.
    * @param cnet The ControlNet that will be copied.  The original ControlNet
    *             will not be modified.
@@ -210,7 +210,7 @@ namespace Isis {
 
   /**
    * Constructs a BundleAdjust from an already created ControlNet within a shared pointer.
-   * 
+   *
    * @param bundleSettings QSharedPointer to the bundle settings to use.
    * @param cnet QSharedPointer to the control net to adjust.
    * @param cubeList QString name of list of cubes to create serial numbers for.
@@ -229,14 +229,14 @@ namespace Isis {
     m_serialNumberList = new SerialNumberList(cubeList);
     m_bundleSettings = bundleSettings;
     m_bundleTargetBody = bundleSettings->bundleTargetBody();
-    
+
     init();
   }
 
 
   /**
    * Thread safe constructor.
-   * 
+   *
    * @param bundleSettings A shared pointer to the BundleSettings to be used.
    * @param control The Control object whose control network will be copied.
    *                The Control will not be modified by the BundleAdjust.
@@ -254,10 +254,13 @@ namespace Isis {
     m_controlNet = ControlNetQsp( new ControlNet(control.fileName(), &progress) );
     m_bundleResults.setOutputControlNet(m_controlNet);
 
+    m_imageLists = imgLists;
+
     // this is too slow and we need to get rid of the serial number list anyway
     // should be unnecessary as Image class has serial number
     // could hang on to image list until creating BundleObservations?
     m_serialNumberList = new SerialNumberList;
+
     foreach (ImageList *imgList, imgLists) {
       foreach (Image *image, *imgList) {
         m_serialNumberList->add(image->fileName());
@@ -271,15 +274,15 @@ namespace Isis {
 
     m_cleanUp = false;
     m_cnetFileName = control.fileName();
-    
+
     init();
   }
 
 
-  /** 
-   * Destroys BundleAdjust object, deallocates pointers (if we have ownership), 
+  /**
+   * Destroys BundleAdjust object, deallocates pointers (if we have ownership),
    * and frees variables from cholmod library.
-   * 
+   *
    * @internal
    *   @history 2016-10-13 Ian Humphrey - Removed deallocation of m_pHeldSnList, since this
    *                           member was removed. References #4293.
@@ -296,8 +299,8 @@ namespace Isis {
 
 
   /**
-   * Initialize all solution parameters. This method is called 
-   * by constructors to 
+   * Initialize all solution parameters. This method is called
+   * by constructors to
    * 
      
    *   
    •  initialize member variables                            
      • 
    *   
    •  set up the control net                                 
      • 
@@ -310,9 +313,9 @@ namespace Isis {
    *   
    •  set up matrix initializations                          
      • 
    *   
    •  initialize cholomod library variables                  
      • 
    * 
    
-   * 
+   *
    * @param progress A pointer to the progress of creating the cameras.
-   * 
+   *
    * @throws IException::Programmer "In BundleAdjust::init(): image is null."
    * @throws IException::Programmer "In BundleAdjust::init(): observation is null."
    *
@@ -322,11 +325,14 @@ namespace Isis {
    *                           a single measure on a point
    *   @history 2016-10-13 Ian Humphrey - Removed verification of held images in the from list
    *                           and counting of the number of held images. References #4293.
-   *  
+   *
    *   @todo remove printf statements
    *   @todo answer comments with questions, TODO, ???, and !!!
    */
   void BundleAdjust::init(Progress *progress) {
+
+    m_previousNumberImagePartials = 0;
+
     // initialize
     //
     // JWB
@@ -402,7 +408,7 @@ namespace Isis {
             m_bundleObservations.addNew(image, observationNumber, instrumentId, m_bundleSettings);
 
         if (!observation) {
-          QString msg = "In BundleAdjust::init(): observation " 
+          QString msg = "In BundleAdjust::init(): observation "
                         + observationNumber + "is null." + "\n";
           throw IException(IException::Programmer, msg, _FILEINFO_);
         }
@@ -490,6 +496,8 @@ namespace Isis {
     // initializations for cholmod
     initializeCHOLMODLibraryVariables();
 
+    // initialize normal equations matrix
+    initializeNormalEquationsMatrix();
   }
 
 
@@ -499,11 +507,11 @@ namespace Isis {
    *
    * checks implemented for ...
    *  (1) images with 0 or 1 measures
-   * 
+   *
    * @return @b bool If the control network is valid.
-   * 
+   *
    * @throws IException::User "Images with one or less measures:"
-   * 
+   *
    * @internal
    *   @history  2011-08-04 Debbie A. Cook - Changed error message to
    *                            indicate it fails with one measure as
@@ -546,45 +554,80 @@ namespace Isis {
 
   /**
    * Initializations for CHOLMOD sparse matrix package.
-   * Calls cholmod_start, sets m_cholmodCommon options, and resizes m_sparseNormals.
-   * 
+   * Calls cholmod_start, sets m_cholmodCommon options.
+   *
    * @return @b bool If the CHOLMOD library variables were successfully initialized.
    */
   bool BundleAdjust::initializeCHOLMODLibraryVariables() {
+    if ( m_rank <= 0 ) {
+      return false;
+    }
 
-      if ( m_rank <= 0 ) {
-          return false;
-      }
+    m_cholmodTriplet = NULL;
 
-      m_cholmodTriplet = NULL;
+    cholmod_start(&m_cholmodCommon);
 
-      cholmod_start(&m_cholmodCommon);
+    // set user-defined cholmod error handler
+    m_cholmodCommon.error_handler = cholmodErrorHandler;
 
-      // set user-defined cholmod error handler
-      m_cholmodCommon.error_handler = cholmodErrorHandler;
+    // testing not using metis
+    m_cholmodCommon.nmethods = 1;
+    m_cholmodCommon.method[0].ordering = CHOLMOD_AMD;
 
-      // testing not using metis
-      m_cholmodCommon.nmethods = 1;
-      m_cholmodCommon.method[0].ordering = CHOLMOD_AMD;
+    return true;
+  }
 
-      // set size of sparse block normal equations matrix
-      if (m_bundleSettings->solveTargetBody()) {
-        m_sparseNormals.setNumberOfColumns(m_bundleObservations.size()+1);
+
+  /**
+   * Initialize Normal Equations matrix (m_sparseNormals).
+   *
+   * Ken NOTE: Currently we are explicitly setting the start column for each block in the normal
+   *           equations matrix below. I think it should be possible (and relatively easy) to make
+   *           the m_sparseNormals smart enough to set the start column of a column block
+   *           automatically when it is added to the matrix.
+   *
+   * @return @b bool.
+   */
+  bool BundleAdjust::initializeNormalEquationsMatrix() {
+
+    int nBlockColumns = m_bundleObservations.size();
+
+    if (m_bundleSettings->solveTargetBody())
+      nBlockColumns += 1;
+
+    m_sparseNormals.setNumberOfColumns(nBlockColumns);
+
+    m_sparseNormals.at(0)->setStartColumn(0);
+
+    int nParameters = 0;
+    if (m_bundleSettings->solveTargetBody()) {
+      nParameters += m_bundleSettings->numberTargetBodyParameters();
+      m_sparseNormals.at(1)->setStartColumn(nParameters);
+
+      int observation = 0;
+      for (int i = 2; i < nBlockColumns; i++) {
+        nParameters += m_bundleObservations.at(observation)->numberParameters();
+        m_sparseNormals.at(i)->setStartColumn(nParameters);
+        observation++;
       }
-      else {
-        m_sparseNormals.setNumberOfColumns(m_bundleObservations.size());
+    }
+    else {     
+      for (int i = 0; i < nBlockColumns; i++) {
+        m_sparseNormals.at(i)->setStartColumn(nParameters);
+        nParameters += m_bundleObservations.at(i)->numberParameters();
       }
+    }
 
-      return true;
+    return true;
   }
 
 
   /**
    * @brief Free CHOLMOD library variables.
-   * 
+   *
    * Frees m_cholmodTriplet, m_cholmodNormal, and m_L.
    * Calls cholmod_finish when complete.
-   * 
+   *
    * @return @b bool If the CHOLMOD library successfully cleaned up.
    */
   bool BundleAdjust::freeCHOLMODLibraryVariables() {
@@ -601,11 +644,11 @@ namespace Isis {
 
   /**
    * Compute the least squares bundle adjustment solution using Cholesky decomposition.
-   * 
+   *
    * @return @b BundleSolutionInfo A container with settings and results from the adjustment.
-   * 
+   *
    * @see BundleAdjust::solveCholesky
-   * 
+   *
    * @TODO make solveCholesky return a BundleSolutionInfo object and delete this placeholder ???
    */
   BundleSolutionInfo BundleAdjust::solveCholeskyBR() {
@@ -625,7 +668,7 @@ namespace Isis {
 
   /**
    * Compute the least squares bundle adjustment solution using Cholesky decomposition.
-   * 
+   *
    * @return @b bool If the solution was successfully computed.
    *
    * @internal
@@ -770,7 +813,7 @@ namespace Isis {
         if (m_abort) {
           m_bundleResults.setConverged(false);
           emit statusUpdate("\n aborting...");
-          emit finished(); 
+          emit finished();
           return false;
         }
         // testing
@@ -828,7 +871,7 @@ namespace Isis {
             }
           }
         }
-        else { 
+        else {
           // bundleSettings.convergenceCriteria() == BundleSettings::ParameterCorrections
           int numConvergedParams = 0;
           int numImgParams = m_imageSolution.size();
@@ -919,17 +962,18 @@ namespace Isis {
       throw IException(e, e.errorType(), msg, _FILEINFO_);
     }
 
+    emit finished();
     return true;
   }
 
 
   /**
    * Create a BundleSolutionInfo containing the settings and results from the bundle adjustment.
-   * 
+   *
    * @return @b BundleSolutionInfo A container with solve information from the adjustment.
    */
   BundleSolutionInfo BundleAdjust::bundleSolveInformation() {
-    BundleSolutionInfo results(m_bundleSettings, FileName(m_cnetFileName), m_bundleResults);
+    BundleSolutionInfo results(m_bundleSettings, FileName(m_cnetFileName), m_bundleResults, imageLists());
     results.setRunTime("");
     return results;
   }
@@ -939,9 +983,9 @@ namespace Isis {
    * Form the least-squares normal equations matrix via cholmod.
    * Each BundleControlPoint will stores its Q matrix and NIC vector once finished.
    * The covariance matrix for each point will be stored in its adjusted surface point.
-   * 
-   * @return @b bool 
-   * 
+   *
+   * @return @b bool
+   *
    * @see BundleAdjust::formMeasureNormals
    * @see BundleAdjust::formPointNormals
    * @see BundleAdjust::formWeightedNormals
@@ -1031,8 +1075,10 @@ namespace Isis {
         // update number of observations
         int numObs = m_bundleResults.numberObservations();
         m_bundleResults.setNumberObservations(numObs + 2);
+
         formMeasureNormals(N22, N12, n1, n2, coeffTarget, coeffImage, coeffPoint3D, coeffRHS,
                              measure->observationIndex());
+
       } // end loop over this points measures
 
       formPointNormals(N22, N12, n2, m_RHS, point);
@@ -1044,7 +1090,6 @@ namespace Isis {
   } // end loop over 3D points
 
   // finally, form the reduced normal equations
-
   formWeightedNormals(n1, m_RHS);
 
   // update number of unknown parameters
@@ -1057,7 +1102,7 @@ namespace Isis {
   /**
    * Form the auxilary normal equation matrices for a measure.
    * N22, N12, n1, and n2 will contain the auxilary matrices when completed.
-   * 
+   *
    * @param N22 The normal equation matrix for the point on the body.
    * @param N12 The normal equation matrix for the camera and the target body.
    * @param n1 The right hand side vector for the camera and the target body.
@@ -1068,9 +1113,9 @@ namespace Isis {
    * @param coeffRHS The vector containing weighted x,y residuals.
    * @param observationIndex The index of the observation containing the measure that
    *                         the partial derivative matrices are for.
-   * 
+   *
    * @return @b bool If the matrices were successfully formed.
-   * 
+   *
    * @see BundleAdjust::formNormalEquations
    */
   bool BundleAdjust::formMeasureNormals(symmetric_matrix&N22,
@@ -1113,9 +1158,9 @@ namespace Isis {
       N11TargetImage.clear();
       N11TargetImage = prod(trans(coeffTarget),coeffImage);
 
-      m_sparseNormals.insertMatrixBlock(observationIndex+1, 0,
+      m_sparseNormals.insertMatrixBlock(blockIndex, 0,
                                         numTargetPartials, coeffImage.size2());
-      (*(*m_sparseNormals[observationIndex+1])[0]) += N11TargetImage;
+      (*(*m_sparseNormals[blockIndex])[0]) += N11TargetImage;
 
       // form N12 target portion
       static matrix N12Target(numTargetPartials, 3);
@@ -1153,14 +1198,7 @@ namespace Isis {
 
     N11 = prod(trans(coeffImage), coeffImage);
 
-    int t = 0;
-    //testing
-    for (int a = 0; a < observationIndex; a++) {
-      BundleObservationQsp observation = m_bundleObservations.at(a);
-      t += observation->numberParameters();
-    }
-    // account for target parameters
-    t += numTargetPartials;
+    int t = m_sparseNormals.at(blockIndex)->startColumn();
 
     // insert submatrix at column, row
     m_sparseNormals.insertMatrixBlock(blockIndex, blockIndex,
@@ -1204,16 +1242,16 @@ namespace Isis {
    * come from calling formMeasureNormals() with the control point's measures.
    * The Q matrix and NIC vector are stored in the BundleControlPoint.
    * R = N12 x Q is accumulated into m_sparseNormals.
-   * 
+   *
    * @param N22 The normal equation matrix for the point on the body.
    * @param N12 The normal equation matrix for the camera and the target body.
    * @param n2 The right hand side vector for the point on the body.
    * @param nj The output right hand side vector.
    * @param bundleControlPoint The control point that the Q matrixs are NIC vector
    *                           are being formed for.
-   * 
+   *
    * @return @b bool If the matrices were successfully formed.
-   * 
+   *
    * @see BundleAdjust::formNormalEquations
    */
   bool BundleAdjust::formPointNormals(symmetric_matrix&N22,
@@ -1261,7 +1299,6 @@ namespace Isis {
     bundleControlPoint->setAdjustedSurfacePoint(SurfacePoint);
 
     // form Q (this is N22{-1} * N12{T})
-    // Q = prod(N22, trans(N12));
     productATransB(N22, N12, Q);
 
     // form product of N22(inverse) and n2; store in NIC
@@ -1271,7 +1308,6 @@ namespace Isis {
     productAB(N12, Q);
 
     // accumulate -nj
-    // nj -= prod(trans(Q),n2);
     accumProductAlphaAB(-1.0, Q, n2, nj);
 
     return true;
@@ -1281,12 +1317,12 @@ namespace Isis {
   /**
    * Apply weighting for spacecraft position, velocity, acceleration and camera angles, angular
    * velocities, angular accelerations if so stipulated (legalese).
-   * 
+   *
    * @param n1 The right hand side vector for the camera and the target body.
    * @param nj The right hand side vector
-   * 
+   *
    * @return @b bool If the weights were successfully applied.
-   * 
+   *
    * @see BundleAdjust::formNormalEquations
    */
   bool BundleAdjust::formWeightedNormals(compressed_vector &n1,
@@ -1353,7 +1389,7 @@ namespace Isis {
 
   /**
    * Perform the matrix multiplication v2 = alpha ( Q x v1 ).
-   * 
+   *
    * @param alpha A constant multiplier.
    * @param v2 The output vector.
    * @param Q A sparse block matrix.
@@ -1366,15 +1402,15 @@ namespace Isis {
     QMapIterator< int, LinearAlgebra::Matrix * > Qit(Q);
 
     int subrangeStart, subrangeEnd;
-
+    
     while ( Qit.hasNext() ) {
       Qit.next();
 
       int columnIndex = Qit.key();
 
-      subrangeStart = m_sparseNormals.getLeadingColumnsForBlock(columnIndex);
+      subrangeStart = m_sparseNormals.at(columnIndex)->startColumn();
       subrangeEnd = subrangeStart + Qit.value()->size2();
-
+      
       v2 += alpha * prod(*(Qit.value()),subrange(v1,subrangeStart,subrangeEnd));
     }
   }
@@ -1382,11 +1418,11 @@ namespace Isis {
 
   /**
    * Perform the matrix multiplication Q = N22 x N12(transpose)
-   * 
+   *
    * @param N22 A symmetric matrix
    * @param N12 A sparse block matrix
    * @param Q The output sparse block matrix
-   * 
+   *
    * @see BundleAdjust::formPointNormals
    */
   bool BundleAdjust::productATransB(symmetric_matrix  &N22,
@@ -1413,10 +1449,10 @@ namespace Isis {
   /**
    * Perform the matrix multiplication C = N12 x Q.
    * The result, C, is stored in m_sparseNormals.
-   * 
+   *
    * @param N12 A sparse block matrix.
    * @param Q A sparse block matrix
-   * 
+   *
    * @see BundleAdjust::formPointNormals
    */
   void BundleAdjust::productAB(SparseBlockColumnMatrix &N12,
@@ -1456,12 +1492,12 @@ namespace Isis {
 
   /**
    * Performs the matrix multiplication nj = nj + alpha (Q x n2).
-   * 
+   *
    * @param alpha A constant multiplier.
    * @param Q A sparse block matrix.
    * @param n2 A vector.
    * @param nj The output accumulation vector.
-   * 
+   *
    * @see BundleAdjust::formPointNormals
    */
   void BundleAdjust::accumProductAlphaAB(double alpha,
@@ -1473,7 +1509,7 @@ namespace Isis {
       return;
     }
 
-    int numTargetParameters = m_bundleSettings->numberTargetBodyParameters();
+    int numParams;
 
     QMapIterator Qit(Q);
 
@@ -1485,22 +1521,7 @@ namespace Isis {
 
       LinearAlgebra::Vector blockProduct = prod(trans(*Qblock),n2);
 
-      int numParams = 0;
-      for (int observationIndex = 0; observationIndex < columnIndex; observationIndex++) {
-        if (numTargetParameters > 0 && observationIndex == 0) {
-          numParams += numTargetParameters;
-        }
-        else {
-          if (numTargetParameters > 0 ) {
-            BundleObservationQsp observation = m_bundleObservations.at(observationIndex-1);
-            numParams += observation->numberParameters();
-          }
-          else {
-            BundleObservationQsp observation = m_bundleObservations.at(observationIndex);
-            numParams += observation->numberParameters();
-          }
-        }
-      }
+      numParams = m_sparseNormals.at(columnIndex)->startColumn();
 
       for (unsigned i = 0; i < blockProduct.size(); i++) {
         nj(numParams+i) += alpha*blockProduct(i);
@@ -1513,9 +1534,9 @@ namespace Isis {
    * Compute the solution to the normal equations using the CHOLMOD library.
    *
    * @return @b bool If the solution was successfully computed.
-   * 
+   *
    * @throws IException::Programmer "CHOLMOD: Failed to load Triplet matrix"
-   * 
+   *
    * @see BundleAdjust::solveCholesky
    */
   bool BundleAdjust::solveSystem() {
@@ -1580,13 +1601,13 @@ namespace Isis {
 
   /**
    * @brief Load sparse normal equations matrix into CHOLMOD triplet.
-   * 
+   *
    * Blocks from the sparse block normal matrix are loaded into a CHOLMOD triplet.
    * Before the triplet can be used with CHOLMOD, it must be converted to a
    * CHOLMOD sparse matrix via cholmod_triplet_to_sparse.
-   * 
+   *
    * @return @b bool If the triplet was successfully formed.
-   * 
+   *
    * @see BundleAdjust::solveSystem
    */
   bool BundleAdjust::loadCholmodTriplet() {
@@ -1622,7 +1643,7 @@ namespace Isis {
         return false;
       }
 
-      int numLeadingColumns = m_sparseNormals.getLeadingColumnsForBlock(columnIndex);
+      int numLeadingColumns = normalsColumn->startColumn();
 
       QMapIterator< int, LinearAlgebra::Matrix * > it(*normalsColumn);
 
@@ -1631,7 +1652,9 @@ namespace Isis {
 
         int rowIndex = it.key();
 
-        int numLeadingRows = m_sparseNormals.getLeadingRowsForBlock(rowIndex);
+        // note: as the normal equations matrix is symmetric, the # of leading rows for a block is
+        //       equal to the # of leading columns for a block column at the "rowIndex" position
+        int numLeadingRows = m_sparseNormals.at(rowIndex)->startColumn();
 
         LinearAlgebra::Matrix *normalsBlock = it.value();
         if ( !normalsBlock ) {
@@ -1689,9 +1712,9 @@ namespace Isis {
   /**
    * Compute inverse of normal equations matrix for CHOLMOD.
    * The inverse is stored in m_normalInverse.
-   * 
+   *
    * @return @b bool If the inverse was successfully computed.
-   * 
+   *
    * @TODO This seems to be unused. JAM
    */
   bool BundleAdjust::cholmodInverse() {
@@ -1733,12 +1756,12 @@ namespace Isis {
 
   /**
    * Dedicated quick inverse of 3x3 matrix
-   * 
+   *
    * @param m The 3x3 matrix to invert.  Overwritten with the inverse.
-   * 
+   *
    * @return @b bool If the matrix was inverted.
    *                 False usually means the matrix is not invertible.
-   * 
+   *
    * @see BundleAdjust::formPointNormals
    *
    * @TODO Move to LinearAlgebra
@@ -1775,7 +1798,7 @@ namespace Isis {
    * Compute partial derivatives and weighted residuals for a measure.
    * coeffTarget, coeffImage, coeffPoint3D, and coeffRHS will be filled
    * with the different partial derivatives.
-   * 
+   *
    * @param coeffTarget A matrix that will contain target body
    *                    pertial derivatives.
    * @param coeffImage A matrix that will contain camera position and orientation
@@ -1785,12 +1808,12 @@ namespace Isis {
    * @param coeffRHS A vector that will contain weighted x,y residuals.
    * @param measure The measure that partials are being computed for.
    * @param point The point containing measure.
-   * 
+   *
    * @return @b bool If the partials were successfully computed.
-   * 
+   *
    * @throws IException::User "Unable to map apriori surface point for measure"
    */
-  bool BundleAdjust::computePartials(matrix &coeffTarget, 
+  bool BundleAdjust::computePartials(matrix &coeffTarget,
                                      matrix &coeffImage,
                                      matrix &coeffPoint3D,
                                      vector &coeffRHS,
@@ -1816,7 +1839,14 @@ namespace Isis {
     BundleObservationQsp observation = measure.parentBundleObservation();
 
     int numImagePartials = observation->numberParameters();
-    coeffImage.resize(2,numImagePartials);
+
+    // we're saving the number of image partials in m_previousNumberImagePartials
+    // to compare to the previous computePartials call to avoid unnecessary resizing of the
+    // coeffImage matrix
+    if (numImagePartials != m_previousNumberImagePartials) {
+      coeffImage.resize(2,numImagePartials);
+      m_previousNumberImagePartials = numImagePartials;
+    }
 
     // clear partial derivative matrices and vectors
     if (m_bundleSettings->solveTargetBody()) {
@@ -1897,7 +1927,7 @@ namespace Isis {
                                                       &coeffTarget(1, index));
       index++;
     }
-      
+
     if (m_bundleSettings->solveTargetBody() && m_bundleTargetBody->solveMeanRadius()) {
       std::vector lookBWRTMeanRadius =
           measureCamera->GroundMap()->MeanRadiusPartial(surfacePoint,
@@ -2040,7 +2070,7 @@ namespace Isis {
       double residualR2ZScore
                  = sqrt(deltaX * deltaX + deltaY * deltaY) / observationSigma / sqrt(2.0);
       //dynamically build the cumulative probability distribution of the R^2 residual Z Scores
-      m_bundleResults.addProbabilityDistributionObservation(residualR2ZScore);  
+      m_bundleResults.addProbabilityDistributionObservation(residualR2ZScore);
       int currentModelIndex = m_bundleResults.maximumLikelihoodModelIndex();
       observationWeight *= m_bundleResults.maximumLikelihoodModelWFunc(currentModelIndex)
                             .sqrtWeightScaler(residualR2ZScore);
@@ -2076,7 +2106,7 @@ namespace Isis {
 
       t += numTargetBodyParameters;
     }
-
+       
     // Update spice for each BundleObservation
     int numObservations = m_bundleObservations.size();
     for (int i = 0; i < numObservations; i++) {
@@ -2092,12 +2122,10 @@ namespace Isis {
 
       t += numParameters;
     }
-
-    // TODO: CHECK - do we need point index in case of rejected points????
-
+        
     // TODO: Below code should move into BundleControlPoint->updateParameterCorrections
     //       except, what about the productAlphaAV method?
-
+    
     // Update lat/lon for each control point
     double latCorrection, lonCorrection, radCorrection;
     int pointIndex = 0;
@@ -2114,9 +2142,8 @@ namespace Isis {
       boost::numeric::ublas::bounded_vector< double, 3 > &NIC = point->nicVector();
       SparseBlockRowMatrix &Q = point->cholmodQMatrix();
       boost::numeric::ublas::bounded_vector< double, 3 > &corrections = point->corrections();
-
+      
       // subtract product of Q and nj from NIC
-      // NIC -= prod(Q, m_imageSolution);
       productAlphaAV(-1.0, NIC, Q, m_imageSolution);
 
       // get point parameter corrections
@@ -2156,7 +2183,7 @@ namespace Isis {
       corrections(0) += latCorrection;
       corrections(1) += lonCorrection;
       corrections(2) += radCorrection;
-
+           
       // ken testing - if solving for target body mean radius, set radius to current
       // mean radius value
       if (m_bundleTargetBody && (m_bundleTargetBody->solveMeanRadius()
@@ -2191,7 +2218,7 @@ namespace Isis {
 
   /**
    * This method computes the focal plane residuals for the measures.
-   * 
+   *
    * @return @b double Weighted sum of the squares of the residuals, vtpv.
    *
    * @internal
@@ -2253,7 +2280,7 @@ namespace Isis {
 
       // get weight and correction vector for this point
       boost::numeric::ublas::bounded_vector weights = bundleControlPoint->weights();
-      boost::numeric::ublas::bounded_vector corrections = 
+      boost::numeric::ublas::bounded_vector corrections =
                                                              bundleControlPoint->corrections();
 
       if ( weights(0) > 0.0 ) {
@@ -2327,9 +2354,9 @@ namespace Isis {
    *
    * Computes the median and the median absolute deviation (M.A.D.) of the residuals.
    * Then, sets the rejection limit in m_bundleResults to median + RejectionMultiplier * M.A.D.
-   * 
+   *
    * @return @b bool If the rejection limit was successfully computed and set.
-   * 
+   *
    * @TODO should this be in BundleResults?
    *
    * @internal
@@ -2421,9 +2448,9 @@ namespace Isis {
 
   /**
    * Flags outlier measures and control points.
-   * 
+   *
    * @return @b bool If the flagging was successful.
-   * 
+   *
    * @TODO How should we handle points with few measures.
    */
   bool BundleAdjust::flagOutliers() {
@@ -2533,14 +2560,49 @@ namespace Isis {
   }
 
 
+  /**
+  * This method returns the image list used in the bundle adjust. If a QList was passed
+  * into the constructor then it uses that list, otherwise it constructs the QList using the
+  * m_serialNumberList
+  *
+  * @return QList The ImageLists used for the bundle adjust
+  */
+  QList BundleAdjust::imageLists() {
+
+    if (m_imageLists.count() > 0) {
+      return m_imageLists;
+    }
+    else if (m_serialNumberList->size() > 0) {
+      ImageList *imgList = new ImageList;
+      try {
+        for (int i = 0; i < m_serialNumberList->size(); i++) {
+          Image *image = new Image(m_serialNumberList->fileName(i));
+          imgList->append(image);
+        }
+        m_imageLists.append(imgList);
+      }
+      catch (IException &e) {
+        QString msg = "Invalid image in serial number list\n";
+        throw IException(IException::Programmer, msg, _FILEINFO_);
+      }
+    }
+    else {
+      QString msg = "No images used in bundle adjust\n";
+      throw IException(IException::Programmer, msg, _FILEINFO_);
+    }
+
+    return m_imageLists;
+  }
+
+
   /**
    * Error propagation for solution.
-   * 
+   *
    * @return @b bool If the error propagation was successful.
-   * 
+   *
    * @throws IException::User "Input data and settings are not sufficiently stable
    *                           for error propagation."
-   * 
+   *
    * @internal
    *   @history 2016-10-05 Ian Humphrey - Updated to check to see if bundle settings is allowing
    *                           us to create the inverse matrix correlation file. References #4315.
@@ -2599,20 +2661,19 @@ namespace Isis {
     int columnIndex = 0;
     int numColumns = 0;
     int numBlockColumns = m_sparseNormals.size();
-
     for (i = 0; i < numBlockColumns; i++) {
 
       // columns in this column block
       SparseBlockColumnMatrix *normalsColumn = m_sparseNormals.at(i);
       if (i == 0) {
         numColumns = normalsColumn->numberOfColumns();
-        int numRows = m_sparseNormals.at(i)->numberOfRows();
+        int numRows = normalsColumn->numberOfRows();
         inverseMatrix.insertMatrixBlock(i, numRows, numColumns);
         inverseMatrix.zeroBlocks();
       }
       else {
         if (normalsColumn->numberOfColumns() == numColumns) {
-          int numRows = m_sparseNormals.at(i)->numberOfRows();
+          int numRows = normalsColumn->numberOfRows();
           inverseMatrix.insertMatrixBlock(i, numRows, numColumns);
           inverseMatrix.zeroBlocks();
         }
@@ -2637,7 +2698,7 @@ namespace Isis {
       // solve for inverse for nCols
       for (j = 0; j < numColumns; j++) {
         if ( columnIndex > 0 ) {
-          pb[columnIndex- 1] = 0.0;
+          pb[columnIndex - 1] = 0.0;
         }
         pb[columnIndex] = 1.0;
 
@@ -2710,7 +2771,9 @@ namespace Isis {
         }
 
         // get corresponding Q matrix
-        SparseBlockRowMatrix Q = point->cholmodQMatrix();
+        // NOTE: we are getting a reference to the Q matrix stored
+        //       in the BundleControlPoint for speed (without the & it is dirt slow)
+        SparseBlockRowMatrix &Q = point->cholmodQMatrix();
 
         T.clear();
 
@@ -2840,7 +2903,7 @@ namespace Isis {
 
   /**
    * Returns a pointer to the output control network.
-   * 
+   *
    * @return @b ControlNetQsp A shared pointer to the output control network.
    */
   ControlNetQsp BundleAdjust::controlNet() {
@@ -2850,7 +2913,7 @@ namespace Isis {
 
   /**
    * Returns a pointer to the serial number list.
-   * 
+   *
    * @return @b SerialNumberList* A pointer to the serial number list.
    */
   SerialNumberList *BundleAdjust::serialNumberList() {
@@ -2860,7 +2923,7 @@ namespace Isis {
 
   /**
    * Returns the number of images.
-   * 
+   *
    * @return @b int The number of images.
    */
   int BundleAdjust::numberOfImages() const {
@@ -2872,7 +2935,7 @@ namespace Isis {
    * Return the ith filename in the cube list file given to constructor.
    *
    * @param i The index of the cube.
-   * 
+   *
    * @return @b QString The filename of the cube.
    */
   // TODO: probably don't need this, can get from BundleObservation
@@ -2883,7 +2946,7 @@ namespace Isis {
 
   /**
    * Returns what iteration the BundleAdjust is currently on.
-   * 
+   *
    * @return @b double The current iteration number.
    */
   double BundleAdjust::iteration() const {
@@ -2895,7 +2958,7 @@ namespace Isis {
    * Return a table cmatrix for the ith cube in the cube list given to the constructor.
    *
    * @param i The index of the cube
-   * 
+   *
    * @return @b Table The InstrumentPointing table for the cube.
    */
   Table BundleAdjust::cMatrix(int i) {
@@ -2905,9 +2968,9 @@ namespace Isis {
   /**
    * Return a table spacecraft vector for the ith cube in the cube list given to the
    * constructor.
-   * 
+   *
    * @param i The index of the cube
-   * 
+   *
    * @return @b Table The InstrumentPosition table for the cube.
    */
   Table BundleAdjust::spVector(int i) {
@@ -2985,7 +3048,7 @@ namespace Isis {
 
   /**
    * Returns if the BundleAdjust converged.
-   * 
+   *
    * @return @b bool If the BundleAdjust converged.
    */
   bool BundleAdjust::isConverged() {
@@ -2995,9 +3058,9 @@ namespace Isis {
 
   /**
    * Returns the iteration summary string.
-   * 
+   *
    * @return @b QString the iteration summary string.
-   * 
+   *
    * @see iterationSummary()
    */
   QString BundleAdjust::iterationSummaryGroup() const {
@@ -3007,49 +3070,53 @@ namespace Isis {
 
   /**
    * Slot for deltack and jigsaw to output the bundle status.
-   * 
+   *
    * @param status The bundle status string to output.
+   *
+   * @internal
+   *   @history 2016-12-01 Ian Humphrey - Added %s as first paramter to prevent a
+   *                           -Wformat-security warning during the build.
    */
   void BundleAdjust::outputBundleStatus(QString status) {
     status += "\n";
-    printf(status.toStdString().c_str());
+    printf("%s", status.toStdString().c_str());
   }
 
 
 
   /**
    * @brief Compute Bundle statistics and store them in m_bundleResults.
-   *  
-   * Sets: 
-   * m_rmsImageSampleResiduals 
-   * m_rmsImageLineResiduals 
-   * m_rmsImageResiduals 
-   * 
+   *
+   * Sets:
+   * m_rmsImageSampleResiduals
+   * m_rmsImageLineResiduals
+   * m_rmsImageResiduals
+   *
    * m_rmsImageXSigmas
    * m_rmsImageYSigmas
    * m_rmsImageZSigmas
    * m_rmsImageRASigmas
    * m_rmsImageDECSigmas
    * m_rmsImageTWISTSigmas
-   *  
-   * m_maxSigmaLatitude 
-   * m_maxSigmaLatitudePointId 
-   * m_maxSigmaLongitude 
-   * m_maxSigmaLongitudePointId 
-   * m_maxSigmaRadius 
+   *
+   * m_maxSigmaLatitude
+   * m_maxSigmaLatitudePointId
+   * m_maxSigmaLongitude
+   * m_maxSigmaLongitudePointId
+   * m_maxSigmaRadius
    * m_maxSigmaRadiusPointId
-   *                       
-   * m_minSigmaLatitude   
-   * m_minSigmaLatitudePointId  
-   * m_minSigmaLongitude  
-   * m_minSigmaLongitudePointId 
-   * m_minSigmaRadius     
-   * m_minSigmaRadiusPointId    
-   *  
+   *
+   * m_minSigmaLatitude
+   * m_minSigmaLatitudePointId
+   * m_minSigmaLongitude
+   * m_minSigmaLongitudePointId
+   * m_minSigmaRadius
+   * m_minSigmaRadiusPointId
+   *
    * m_rmsSigmaLat
    * m_rmsSigmaLon
    * m_rmsSigmaRad
-   * 
+   *
    * @return @b bool If the statistics were successfully computed and stored.
    */
   bool BundleAdjust::computeBundleStatistics() {
@@ -3100,22 +3167,22 @@ namespace Isis {
       // initialize lat/lon/rad boundaries
       Distance minSigmaLatDist;
       QString  minSigmaLatPointId = "";
-      
+
       Distance maxSigmaLatDist;
       QString  maxSigmaLatPointId = "";
-      
+
       Distance minSigmaLonDist;
       QString  minSigmaLonPointId = "";
-      
+
       Distance maxSigmaLonDist;
       QString  maxSigmaLonPointId = "";
-      
+
       Distance minSigmaRadDist;
       QString  minSigmaRadPointId = "";
-      
+
       Distance maxSigmaRadDist;
       QString  maxSigmaRadPointId = "";
-      
+
       // compute stats for point sigmas
       Statistics sigmaLatStats;
       Statistics sigmaLonStats;
@@ -3192,7 +3259,7 @@ namespace Isis {
         }
       }
 
-      // update bundle results 
+      // update bundle results
       m_bundleResults.resizeSigmaStatisticsVectors(numberImages);
 
       m_bundleResults.setSigmaLatitudeRange(minSigmaLatDist, maxSigmaLatDist,
diff --git a/isis/src/control/objs/BundleAdjust/BundleAdjust.h b/isis/src/control/objs/BundleAdjust/BundleAdjust.h
index e7e9e90ba2c96e592c308b9eee329efff22a6d6b..90a8c18f2480cd34929ac4ce135643074938b62c 100644
--- a/isis/src/control/objs/BundleAdjust/BundleAdjust.h
+++ b/isis/src/control/objs/BundleAdjust/BundleAdjust.h
@@ -62,11 +62,11 @@ namespace Isis {
 
   /**
    * @brief An image bundle adjustment object.
-   * 
+   *
    * BundleAdjust is used to perform a bundle adjustment on overlapping ISIS 3 cubes.
    * Using the collineariy condition, BundleAdjust can construct a system of normal equations
    * and then using the CHOLMOD library, solve that system.
-   * 
+   *
    * @author 2006-05-30 Jeff Anderson, Debbie A. Cook, and Tracie Sucharski
    *
    * @internal
@@ -83,7 +83,7 @@ namespace Isis {
    *   @history 2007-11-17 Debbie A. Cook - Added method SetSolution Method.
    *   @history 2007-12-21 Debbie A. Cook - Added member p_Degree and methods m_nsolveCamDegree and
    *                           ckDegree.
-   *   @history 2008-01-11 Debbie A. Cook - Added observation mode functionality for spacecraft 
+   *   @history 2008-01-11 Debbie A. Cook - Added observation mode functionality for spacecraft
    *                           position and upgraded ObservationNumber methods for compatability.
    *   @history 2008-01-14 Debbie A. Cook - Added code to solve for local radii.
    *   @history 2008-04-18 Debbie A. Cook - Added progress for ControlNet.
@@ -149,11 +149,11 @@ namespace Isis {
    *                           single ControlPoint and ControlMeasure.
    *   @history 2011-08-08 Tracie Sucharski - Added method to return the iteration summary to be
    *                           used in qtie which does not have a log file. In SetImages, clear the
-   *                           cameraMavtpv_targetBodyp and cameraList.  Added this back in (was 
+   *                           cameraMavtpv_targetBodyp and cameraList.  Added this back in (was
    *                           originally added on 2011-01-19), was deleted somewhere along the
    *                           line.
    *   @history 2011-09-28 Debbie A. Cook - Renamed SPARSE solve method to OLDSPARSE and CHOLMOD to
-   *                           SPARSE. 
+   *                           SPARSE.
    *   @history 2011-10-14 Ken Edmundson - Added call to m_pCnet->ClearJigsawRejected() to the
    *                           init() method to set all measure/point JigsawRejected flags to false
    *                           prior to bundle.
@@ -165,7 +165,7 @@ namespace Isis {
    *                           m_bSolvePolyOverHermite and m_positionType.
    *   @history 2012-03-26 Orrin Thomas - Added maximum likelihood capabilities.
    *   @history 2012-05-21 Debbie A. Cook - Added initialization of m_dRejectionMultiplier.
-   *   @history 2012-07-06 Debbie A. Cook - Updated Spice members to be more compliant with Isis 
+   *   @history 2012-07-06 Debbie A. Cook - Updated Spice members to be more compliant with Isis
    *                           coding standards. References #972.
    *   @history 2012-09-28 Ken Edmundson - Initialized variables for bundle statistic computations.
    *                           The bundleout.txt file was modifed to show N/A for RMS, Min, Max of
@@ -190,7 +190,7 @@ namespace Isis {
    *   @history 2014-07-14 Kimberly Oyama - Added support for correlation matrix. Covariance matrix
    *                           is now written to a file and the location is saved as part of the
    *                           CorrelationMatrix object.
-   *   @history 2014-07-23 Jeannie Backer - Modified to print "N/A" for rejection multiplier if 
+   *   @history 2014-07-23 Jeannie Backer - Modified to print "N/A" for rejection multiplier if
    *                           outlier rejection is turned off.
    *   @history 2014-09-18 Kimberly Oyama - Added a constructor for running the bunlde in a
    *                           separate thread.
@@ -237,7 +237,7 @@ namespace Isis {
    *   @history 2016-08-24 Jesse Mapel - Updated documentation and member variable names.  Brought
    *                           closer to ISIS 3 coding standards.  Fixes #4183, #4188, #4235.
    *   @history 2016-08-28 Kelvin Rodriguez - Remvoed useless register keywords to squash warnigns
-   *                         in clang. Part of porting to OS X 10.11. 
+   *                         in clang. Part of porting to OS X 10.11.
    *   @history 2016-09-22 Ian Humphrey - Modified validateNetwork() so that validation status
    *                           messages are logged to stdout. Fixes #4313.
    *   @history 2016-10-05 Ian Humphrey - Modified errorPropagation_CHOLMOD() to check bundle
@@ -265,25 +265,40 @@ namespace Isis {
    *                           References #4463.
    *   @history 2016-11-16 Ian Humphrey - Modified solveCholesky() to throw caught exceptions that
    *                           occur. Removed bundleException(QString) signal. Fixes #4483.
+   *   @history 2016-12-01 Ian Humphrey - Modified outputBundleStatus()'s printf() call so that
+   *                           there is no longer a -Wformat-security warning.
+   *   @history 2017-05-01 Makayla Shepherd - Added imageLists() to track and return the images
+   *                           bundled. Fixes #4818.
+   *   @history 2017-05-09 Tracie Sucharski - Fixed an empty pointer in ::imgeLists method. 
+   *   @history 2017-05-09 Ken Edmundson - Speed improvements and error propagation bug fix.
+   *                           Separated initializations for Normal Equations matrix out of
+   *                           ::initializeCholmodLibraryVariables() into
+   *                           ::initializeNormalEquationsMatrix(). Added
+   *                           m_previousNumberImagePartials to avoid unnecessary resizing of the
+   *                           "coeffImage" matrix in ::computePartials. New m_startColumn member in
+   *                           SparseBlockColumnMatrix eliminates costly computation of leading
+   *                           colums and rows. In ::errorPropagation method, call to get Q matrix
+   *                           from BundleControlPoint was creating a copy instead of getting a
+   *                           reference. References #4664.
    */
   class BundleAdjust : public QObject {
       Q_OBJECT
     public:
       BundleAdjust(BundleSettingsQsp bundleSettings,
-                   const QString &cnetFile, 
+                   const QString &cnetFile,
                    const QString &cubeList,
                    bool printSummary = true);
       BundleAdjust(BundleSettingsQsp bundleSettings,
-                   QString &cnet, 
-                   SerialNumberList &snlist, 
+                   QString &cnet,
+                   SerialNumberList &snlist,
                    bool printSummary = true);
       BundleAdjust(BundleSettingsQsp bundleSettings,
                    Control &cnet,
                    SerialNumberList &snlist,
                    bool bPrintSummary);
       BundleAdjust(BundleSettingsQsp bundleSettings,
-                   ControlNet &cnet, 
-                   SerialNumberList &snlist, 
+                   ControlNet &cnet,
+                   SerialNumberList &snlist,
                    bool printSummary = true);
       BundleAdjust(BundleSettingsQsp bundleSettings,
                    ControlNetQsp cnet,
@@ -296,6 +311,8 @@ namespace Isis {
       ~BundleAdjust();
       BundleSolutionInfo    solveCholeskyBR();
 
+      QList imageLists();
+
     public slots:
       bool solveCholesky();
       void abortBundle();
@@ -324,6 +341,7 @@ namespace Isis {
       //TODO Should there be a resetBundle(BundleSettings bundleSettings) method
       //     that allows for rerunning with new settings? JWB
       void init(Progress *progress = 0);
+      bool initializeNormalEquationsMatrix();
       bool validateNetwork();
       bool solveSystem();
       void iterationSummary();
@@ -364,22 +382,22 @@ namespace Isis {
                                LinearAlgebra::Vector                               &nj);
 
       // dedicated matrix functions
-      
+
       void productAB(SparseBlockColumnMatrix &A,
                      SparseBlockRowMatrix    &B);
       void accumProductAlphaAB(double                alpha,
                                SparseBlockRowMatrix  &A,
                                LinearAlgebra::Vector &B,
                                LinearAlgebra::Vector &C);
-      bool invert3x3(boost::numeric::ublas::symmetric_matrix< 
+      bool invert3x3(boost::numeric::ublas::symmetric_matrix<
                           double, boost::numeric::ublas::upper >  &m);
-      bool productATransB(boost::numeric::ublas::symmetric_matrix< 
+      bool productATransB(boost::numeric::ublas::symmetric_matrix<
                               double, boost::numeric::ublas::upper >  &N22,
                           SparseBlockColumnMatrix                     &N12,
                           SparseBlockRowMatrix                        &Q);
-      void productAlphaAV(double alpha, 
+      void productAlphaAV(double alpha,
                           boost::numeric::ublas::bounded_vector< double, 3 >  &v2,
-                          SparseBlockRowMatrix                                &Q, 
+                          SparseBlockRowMatrix                                &Q,
                           LinearAlgebra::Vector                               &v1);
 
       // CHOLMOD library methods
@@ -427,6 +445,8 @@ namespace Isis {
                                                                    meters conversion factor.*/
       double m_metersToRadians;                              /**!< The body specific meters to
                                                                    radians conversion factor.*/
+      QList m_imageLists;                        /**!< The lists of images used in the
+                                                                   bundle.*/
 
       // ==========================================================================================
       // === BEYOND THIS PLACE (THERE BE DRAGONS) all refers to the folded bundle solution.     ===
@@ -435,7 +455,7 @@ namespace Isis {
       // ==========================================================================================
 
       //! Inverse of the normal equations matrix.  Set by cholmodInverse.
-      boost::numeric::ublas::symmetric_matrix< 
+      boost::numeric::ublas::symmetric_matrix<
           double,
           boost::numeric::ublas::upper,
           boost::numeric::ublas::column_major > m_normalInverse;
@@ -465,8 +485,11 @@ namespace Isis {
                                                                    cholmod_factorize.*/
       LinearAlgebra::Vector m_imageSolution;                 /**!< The image parameter solution
                                                                    vector.*/
+                                                                   
+      int m_previousNumberImagePartials;                     /**!< used in ::computePartials method
+                                                                   to avoid unnecessary resizing
+                                                                   of the coeffImage matrix.*/
   };
 }
 
 #endif
-
diff --git a/isis/src/control/objs/BundleAdjust/unitTest.cpp b/isis/src/control/objs/BundleAdjust/unitTest.cpp
index bfbdc2e81c6018130f5c4641cd2896d497c06558..7b797b55549c854026e2cb74c1c7f1d6fac36c40 100644
--- a/isis/src/control/objs/BundleAdjust/unitTest.cpp
+++ b/isis/src/control/objs/BundleAdjust/unitTest.cpp
@@ -38,9 +38,6 @@ These have partial coverage
     (m_bundleSettings.validateNetwork()==false) -- this is never the case for jigsaw, need to test elsewhere
 
 
- bool BundleAdjust::initializeCHOLMODLibraryVariables() {
-    ( m_rank <= 0 )
-
 Errors:
  void BundleAdjust::init(Progress *progress) {
     (image==false) for BundleImage* image = new BundleImage(camera, serialNumber, fileName);
diff --git a/isis/src/control/objs/BundleResults/BundleResults.cpp b/isis/src/control/objs/BundleResults/BundleResults.cpp
index c5fdb89f9cf53492b35e51dd0022e883303fcf1a..7ee446184d13d8875c14d4b6b634ef08cbd44823 100644
--- a/isis/src/control/objs/BundleResults/BundleResults.cpp
+++ b/isis/src/control/objs/BundleResults/BundleResults.cpp
@@ -12,10 +12,6 @@
 #include 
 #include 
 
-#include 
-#include 
-#include 
-
 #include "Camera.h"
 #include "ControlMeasure.h"
 #include "ControlPoint.h"
@@ -38,14 +34,13 @@ namespace Isis {
 
   /**
    * Constructs a BundleSettings object.
-   * 
+   *
    * @param parent The Qt-relationship parent.
    */
   BundleResults::BundleResults(QObject *parent) : QObject(parent) {
 
     initialize();
 
-    m_id = new QUuid(QUuid::createUuid());
     m_correlationMatrix = new CorrelationMatrix;
     m_cumPro = new StatCumProbDistDynCalc;
     m_cumProRes = new StatCumProbDistDynCalc;
@@ -66,7 +61,7 @@ namespace Isis {
    * @param parent The Qt-relationship parent.
    */
   BundleResults::BundleResults(Project *project, XmlStackedHandlerReader *xmlReader,
-                               QObject *parent) : QObject(parent) {   
+                               QObject *parent) : QObject(parent) {
                                // TODO: does xml stuff need project???
 
     initialize();
@@ -77,28 +72,14 @@ namespace Isis {
   }
 
 
-  /**
-   * Constructs this BundleSettings object from Hdf5.
-   * 
-   * @param locationObject The Hdf5 project file to be used.
-   * @param locationName The name of the project file containing the BundleResults.
-   * 
-   * @see openH5Group
-   */
-  BundleResults::BundleResults(H5::CommonFG &locationObject, QString locationName) {
-    openH5Group(locationObject, locationName);
-  }
-
-
   /**
    * Copy constructor for BundleResults.  Creates this BundleSettings object as a copy
    * of another BundleResults object.
-   * 
+   *
    * @param src The other BundleResults object to be copied.
    */
   BundleResults::BundleResults(const BundleResults &src)
-      : m_id(new QUuid(src.m_id->toString())),
-        m_correlationMatrix(new CorrelationMatrix(*src.m_correlationMatrix)),
+      : m_correlationMatrix(new CorrelationMatrix(*src.m_correlationMatrix)),
         m_numberFixedPoints(src.m_numberFixedPoints),
         m_numberIgnoredPoints(src.m_numberIgnoredPoints),
         m_numberHeldImages(src.m_numberHeldImages),
@@ -126,11 +107,11 @@ namespace Isis {
         m_rmsImageSampleResiduals(src.m_rmsImageSampleResiduals),
         m_rmsImageLineResiduals(src.m_rmsImageLineResiduals),
         m_rmsImageResiduals(src.m_rmsImageResiduals),
-        m_rmsImageXSigmas(src.m_rmsImageXSigmas),    
-        m_rmsImageYSigmas(src.m_rmsImageYSigmas),    
-        m_rmsImageZSigmas(src.m_rmsImageZSigmas),    
-        m_rmsImageRASigmas(src.m_rmsImageRASigmas),   
-        m_rmsImageDECSigmas(src.m_rmsImageDECSigmas),  
+        m_rmsImageXSigmas(src.m_rmsImageXSigmas),
+        m_rmsImageYSigmas(src.m_rmsImageYSigmas),
+        m_rmsImageZSigmas(src.m_rmsImageZSigmas),
+        m_rmsImageRASigmas(src.m_rmsImageRASigmas),
+        m_rmsImageDECSigmas(src.m_rmsImageDECSigmas),
         m_rmsImageTWISTSigmas(src.m_rmsImageTWISTSigmas),
         m_minSigmaLatitudeDistance(src.m_minSigmaLatitudeDistance),
         m_maxSigmaLatitudeDistance(src.m_maxSigmaLatitudeDistance),
@@ -150,9 +131,8 @@ namespace Isis {
         m_maximumLikelihoodFunctions(src.m_maximumLikelihoodFunctions),
         m_maximumLikelihoodIndex(src.m_maximumLikelihoodIndex),
         m_cumPro(new StatCumProbDistDynCalc(*src.m_cumPro)),
-        m_cumProRes(new StatCumProbDistDynCalc(*src.m_cumProRes)), 
+        m_cumProRes(new StatCumProbDistDynCalc(*src.m_cumProRes)),
         m_maximumLikelihoodMedianR2Residuals(src.m_maximumLikelihoodMedianR2Residuals) {
-
   }
 
 
@@ -160,9 +140,6 @@ namespace Isis {
    * Destroys this BundleResults object.
    */
   BundleResults::~BundleResults() {
-    
-    delete m_id;
-    m_id = NULL;
 
     delete m_correlationMatrix;
     m_correlationMatrix = NULL;
@@ -179,16 +156,12 @@ namespace Isis {
   /**
    * Assignment operator for BundleResults. Overwrites this BundleResults object with
    * another BundleResults object.
-   * 
+   *
    * @param src The other BundleResults object to be copied from.
    */
   BundleResults &BundleResults::operator=(const BundleResults &src) {
 
     if (&src != this) {
-      delete m_id;
-      m_id = NULL;
-      m_id = new QUuid(src.m_id->toString());
-
       delete m_correlationMatrix;
       m_correlationMatrix = NULL;
       m_correlationMatrix = new CorrelationMatrix(*src.m_correlationMatrix);
@@ -264,7 +237,6 @@ namespace Isis {
    * QLists are cleared, and all other members are set to NULL.
    */
   void BundleResults::initialize() {
-    m_id = NULL;
     m_correlationMatrix = NULL;
 
     m_numberFixedPoints = 0; // set in BA constructor->init->fillPointIndexMap
@@ -311,13 +283,13 @@ namespace Isis {
 
     // set by compute rejection limit
     m_rejectionLimit = 0.0;
-    
-    // set by flag outliers    
+
+    // set by flag outliers
     m_numberRejectedObservations = 0;
 
     // set by formNormalEquations_CHOLMOD, formNormalEquations_SPECIALK, or solve
     m_numberObservations = 0;
-    m_numberImageParameters = 0; 
+    m_numberImageParameters = 0;
 
 // ??? unused variable ???    m_numberHeldPoints = 0;
 
@@ -343,7 +315,7 @@ namespace Isis {
     m_maximumLikelihoodMedianR2Residuals = 0.0;
     m_maximumLikelihoodFunctions.clear();
     m_cumProRes = NULL;
-    
+
     m_radiansToMeters = 0;
     m_observations.clear();
     m_outNet.clear();
@@ -353,7 +325,7 @@ namespace Isis {
 
   /**
    * Resizes all image sigma vectors.
-   * 
+   *
    * @param numberImages The new size for the image sigma vectors.
    */
   void BundleResults::resizeSigmaStatisticsVectors(int numberImages) {
@@ -380,7 +352,7 @@ namespace Isis {
 
   /**
    * Sets the root mean square image residual Statistics lists.
-   * 
+   *
    * @param rmsImageLineResiduals The new image line residuals list.
    * @param rmsImageSampleResiduals The new image sample residuals list.
    * @param rmsImageResiduals The new image residuals list.
@@ -396,7 +368,7 @@ namespace Isis {
 
   /**
    * Sets the min and max sigma latitude distances and point ids.
-   * 
+   *
    * @param minLatDist The new minimum sigma latitude distance.
    * @param maxLatDist The new maximum sigma latitude distance.
    * @param minLatPointId The new minimum sigma latitude point id.
@@ -413,7 +385,7 @@ namespace Isis {
 
   /**
    * Sets the min and max sigma longitude distances and point ids.
-   * 
+   *
    * @param minLonDist The new minimum sigma longitude distance.
    * @param maxLonDist The new maximum sigma longitude distance.
    * @param minLonPointId The new minimum sigma longitude point id.
@@ -430,7 +402,7 @@ namespace Isis {
 
   /**
    * Sets the min and max sigma radius distances and point ids.
-   * 
+   *
    * @param minRadDist The new minimum sigma radius distance.
    * @param maxRadDist The new maximum sigma radius distance.
    * @param minRadPointId The new minimum sigma radius point id.
@@ -448,7 +420,7 @@ namespace Isis {
   /**
    * Sets the root mean square values of the adjusted latitiude sigmas, adjusted longitude sigmas,
    * and adjusted radius sigmas.
-   * 
+   *
    * @param rmsFromSigmaLatStats The new RMS value of the adjusted latitude sigmas.
    * @param rmsFromSigmaLonStats The new RMS value of the adjusted longitude sigmas.
    * @param rmsFromSigmaRadStats The new RMS value of the adjusted radius sigmas.
@@ -462,10 +434,10 @@ namespace Isis {
   }
 
 
-  /** 
+  /**
   * This method steps up the maximum likelihood estimation solution.  Up to three successive
   * solutions models are available.
-  * 
+  *
   * @param modelsWithQuantiles The maixmum likelihood models and their quantiles.  If empty,
   *                            then maximum likelihood estimation will not be used.
   */
@@ -496,11 +468,11 @@ namespace Isis {
 
       // set up the w functions for the maximum likelihood estimation
       m_maximumLikelihoodFunctions.append(
-          qMakePair(MaximumLikelihoodWFunctions(modelsWithQuantiles[i].first), 
+          qMakePair(MaximumLikelihoodWFunctions(modelsWithQuantiles[i].first),
                     modelsWithQuantiles[i].second));
 
     }
-    
+
 
     //maximum likelihood estimation tiered solutions requiring multiple convergeances are supported,
     // this index keeps track of which tier the solution is in
@@ -512,7 +484,7 @@ namespace Isis {
    * Prints out information about which tier the solution is in and the status of the residuals.
    */
   void BundleResults::printMaximumLikelihoodTierInformation() {
-    printf("Maximum Likelihood Tier: %d\n", m_maximumLikelihoodIndex);
+//  printf("Maximum Likelihood Tier: %d\n", m_maximumLikelihoodIndex);
     if (numberMaximumLikelihoodModels() > m_maximumLikelihoodIndex) {
       // if maximum likelihood estimation is being used
       // at the end of every iteration
@@ -522,7 +494,7 @@ namespace Isis {
       m_maximumLikelihoodFunctions[m_maximumLikelihoodIndex].first.setTweakingConstant(tc);
       //  print meadians of residuals
       m_maximumLikelihoodMedianR2Residuals = m_cumPro->value(0.5);
-      printf("Median of R^2 residuals:  %lf\n", m_maximumLikelihoodMedianR2Residuals);
+//    printf("Median of R^2 residuals:  %lf\n", m_maximumLikelihoodMedianR2Residuals);
 
       //restart the dynamic calculation of the cumulative probility distribution of |R^2 residuals|
       // so it will be up to date for the next iteration
@@ -533,7 +505,7 @@ namespace Isis {
 
   /**
    * Initializes or resets the cumulative probability distribution of |R^2 residuals|.
-   * 
+   *
    * @param nodes The number of quantiles in the cumulative probability distribution.
    */
   void BundleResults::initializeProbabilityDistribution(unsigned int nodes) {
@@ -543,7 +515,7 @@ namespace Isis {
 
   /**
    * Initializes or resets the cumulative probability distribution of residuals used for reporting.
-   * 
+   *
    * @param nodes The number of quantiles in the cumulative probability distribution.
    */
   void BundleResults::initializeResidualsProbabilityDistribution(unsigned int nodes) {
@@ -554,7 +526,7 @@ namespace Isis {
   /**
    * Adds an observation to the cumulative probability distribution
    * of |R^2 residuals|.
-   * 
+   *
    * @param observationValue The value of the added observation.
    */
   void BundleResults::addProbabilityDistributionObservation(double observationValue) {
@@ -565,7 +537,7 @@ namespace Isis {
   /**
    * Adds an observation to the cumulative probability distribution
    * of residuals used for reporting.
-   * 
+   *
    * @param observationValue The value of the added observation.
    */
   void BundleResults::addResidualsProbabilityDistributionObservation(double observationValue) {
@@ -592,7 +564,7 @@ namespace Isis {
 
   /**
    * Returns the number of 'fixed' (ground) points.
-   * 
+   *
    * @return @b int The number of fixed points.
    */
   int BundleResults::numberFixedPoints() const {
@@ -610,7 +582,7 @@ namespace Isis {
 
   /**
    * Returns the number of 'held' images.
-   * 
+   *
    * @return @b int The number of held images.
    */
   int BundleResults::numberHeldImages() const {
@@ -628,7 +600,7 @@ namespace Isis {
 
   /**
    * Returns the number of ignored points.
-   * 
+   *
    * @return @b int The number of ignored points.
    */
   int BundleResults::numberIgnoredPoints() const {
@@ -638,7 +610,7 @@ namespace Isis {
 
   /**
    * Sets the root mean square of the x and y residuals.
-   * 
+   *
    * @param rx The RMS value of the x residuals.
    * @param ry The RMS value of the y residuals.
    * @param rxy The RMS value of both the x and y residuals.
@@ -652,7 +624,7 @@ namespace Isis {
 
   /**
    * Sets the rejection limit.
-   * 
+   *
    * @param rejectionLimit The rejection limit.
    */
   void BundleResults::setRejectionLimit(double rejectionLimit) {
@@ -662,7 +634,7 @@ namespace Isis {
 
   /**
    * Sets the number of rejected observations.
-   * 
+   *
    * @param numberRejectedObservations The number of rejected observations.
    */
   void BundleResults::setNumberRejectedObservations(int numberRejectedObservations) {
@@ -672,7 +644,7 @@ namespace Isis {
 
   /**
    * Sets the number of observations.
-   * 
+   *
    * @param numberObservations The number of observations.
    */
   void BundleResults::setNumberObservations(int numberObservations) {
@@ -682,7 +654,7 @@ namespace Isis {
 
   /**
    * Sets the number of image parameters.
-   * 
+   *
    * @param numberParameters The number of image parameters.
    */
   void BundleResults::setNumberImageParameters(int numberParameters) {
@@ -700,7 +672,7 @@ namespace Isis {
 
   /**
    * Increase the number of contrained point parameters.
-   * 
+   *
    * @param incrementAmount The amount to increase by.
    */
   void BundleResults::incrementNumberConstrainedPointParameters(int incrementAmount) {
@@ -718,7 +690,7 @@ namespace Isis {
 
   /**
    * Increase the number of constrained image parameters.
-   * 
+   *
    * @param incrementAmount The amount to increase by.
    */
   void BundleResults::incrementNumberConstrainedImageParameters(int incrementAmount) {
@@ -736,7 +708,7 @@ namespace Isis {
 
   /**
    * Increases the number of constrained target parameters.
-   * 
+   *
    * @param incrementAmount The amount to increase by.
    */
   void BundleResults::incrementNumberConstrainedTargetParameters(int incrementAmount) {
@@ -746,7 +718,7 @@ namespace Isis {
 
   /**
    * Sets the total number of parameters to solve for.
-   * 
+   *
    * @param numberParameters The number of parameters to solve for.
    */
   void BundleResults::setNumberUnknownParameters(int numberParameters) {
@@ -768,13 +740,13 @@ namespace Isis {
 
   /**
    * Computes the sigma0 and stores it internally.
-   * 
+   *
    * @param dvtpv The weighted sum of the squares of the residuals.  Computed by
    *              V transpose * P * V, where
    *              V is the vector of residuals and
    *              P is the weight matrix.
    * @param criteria The convergence criteria for the bundle adjustment.
-   * 
+   *
    * @throws IException::Io "Computed degrees of freedom is invalid."
    */
   void BundleResults::computeSigma0(double dvtpv, BundleSettings::ConvergenceCriteria criteria) {
@@ -798,7 +770,7 @@ namespace Isis {
 
   /**
    * Sets the degrees of freedom.
-   * 
+   *
    * @param degreesOfFreedom The degrees of freedom.
    */
   void BundleResults::setDegreesOfFreedom(double degreesOfFreedom) { // old sparse
@@ -808,7 +780,7 @@ namespace Isis {
 
   /**
    * Sets the sigma0.
-   * 
+   *
    * @param sigma0 The sigma0.
    */
   void BundleResults::setSigma0(double sigma0) { // old sparse
@@ -818,7 +790,7 @@ namespace Isis {
 
   /**
    * Sets the elapsed time for the bundle adjustment.
-   * 
+   *
    * @param time The elapsed time.
    */
   void BundleResults::setElapsedTime(double time) {
@@ -828,7 +800,7 @@ namespace Isis {
 
   /**
    * Sets the elapsed time for error propegation.
-   * 
+   *
    * @param time The elapsed time.
    */
   void BundleResults::setElapsedTimeErrorProp(double time) {
@@ -838,7 +810,7 @@ namespace Isis {
 
   /**
    * Sets the radians to meters conversion constant for the target body.
-   * 
+   *
    * @param rtm The (double) conversion factor.
    */
   void BundleResults::setRadiansToMeters(double rtm) {
@@ -848,7 +820,7 @@ namespace Isis {
 
   /**
    * Sets if the bundle adjustment converged.
-   * 
+   *
    * @param converged If the bundle adjustment converged.
    */
   void BundleResults::setConverged(bool converged) {
@@ -858,7 +830,7 @@ namespace Isis {
 
   /**
    * Sets the bundle control point vector.
-   * 
+   *
    * @param controlPoints The vector of BundleControlPointQsps.
    */
   void BundleResults::setBundleControlPoints(QVector controlPoints) {
@@ -868,7 +840,7 @@ namespace Isis {
 
   /**
    * Sets the output ControlNet.
-   * 
+   *
    * @param outNet A QSharedPointer to the output ControlNet.
    */
   void BundleResults::setOutputControlNet(ControlNetQsp outNet) {
@@ -878,7 +850,7 @@ namespace Isis {
 
   /**
    * Sets the number of iterations taken by the BundleAdjust.
-   * 
+   *
    * @param iterations The number of iterations.
    */
   void BundleResults::setIterations(int iterations) {
@@ -888,7 +860,7 @@ namespace Isis {
 
   /**
    * Sets the vector of BundleObservations.
-   * 
+   *
    * @param observations The vector of BundleObservations.
    */
   void BundleResults::setObservations(BundleObservationVector observations) {
@@ -898,10 +870,10 @@ namespace Isis {
 
 
   //************************* Accessors **********************************************************//
-  
+
   /**
    * Returns the list of RMS image sample residuals statistics.
-   * 
+   *
    * @return @b QList The RMS image sample residual statistics.
    */
   QList BundleResults::rmsImageSampleResiduals() const {
@@ -911,7 +883,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image line residuals statistics.
-   * 
+   *
    * @return @b QList The RMS image line residual statistics.
    */
   QList BundleResults::rmsImageLineResiduals() const {
@@ -921,7 +893,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image residuals statistics.
-   * 
+   *
    * @return @b QList The RMS image residual statistics.
    */
   QList BundleResults::rmsImageResiduals() const {
@@ -931,7 +903,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image x sigma statistics.
-   * 
+   *
    * @return @b QList The RMS image x sigma statistics.
    */
   QVector BundleResults::rmsImageXSigmas() const {
@@ -941,7 +913,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image y sigma statistics.
-   * 
+   *
    * @return @b QList The RMS image y sigma statistics.
    */
   QVector BundleResults::rmsImageYSigmas() const {
@@ -951,7 +923,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image z sigma statistics.
-   * 
+   *
    * @return @b QList The RMS image z sigma statistics.
    */
   QVector BundleResults::rmsImageZSigmas() const {
@@ -961,7 +933,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image right ascension sigma statistics.
-   * 
+   *
    * @return @b QList The RMS image right ascension sigma statistics.
    */
   QVector BundleResults::rmsImageRASigmas() const {
@@ -971,7 +943,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image declination sigma statistics.
-   * 
+   *
    * @return @b QList The RMS image declination sigma statistics.
    */
   QVector BundleResults::rmsImageDECSigmas() const {
@@ -981,7 +953,7 @@ namespace Isis {
 
   /**
    * Returns the list of RMS image twist sigma statistics.
-   * 
+   *
    * @return @b QList The RMS image twist sigma statistics.
    */
   QVector BundleResults::rmsImageTWISTSigmas() const {
@@ -991,7 +963,7 @@ namespace Isis {
 
   /**
    * Returns the minimum sigma latitude distance.
-   * 
+   *
    * @return @b Distance The minimum sigma latitude.
    */
   Distance BundleResults::minSigmaLatitudeDistance() const {
@@ -1001,7 +973,7 @@ namespace Isis {
 
   /**
    * Returns the maximum sigma latitude distance.
-   * 
+   *
    * @return @b Distance The maximum sigma latitude.
    */
   Distance BundleResults::maxSigmaLatitudeDistance() const {
@@ -1011,7 +983,7 @@ namespace Isis {
 
   /**
    * Returns the minimum sigma longitude distance.
-   * 
+   *
    * @return @b Distance The minimum sigma longitude.
    */
   Distance BundleResults::minSigmaLongitudeDistance() const {
@@ -1021,7 +993,7 @@ namespace Isis {
 
   /**
    * Returns the maximum sigma longitude distance.
-   * 
+   *
    * @return @b Distance The maximum sigma longitude.
    */
   Distance BundleResults::maxSigmaLongitudeDistance() const {
@@ -1031,7 +1003,7 @@ namespace Isis {
 
   /**
    * Returns the minimum sigma redius distance.
-   * 
+   *
    * @return @b Distance The minimum sigma redius.
    */
   Distance BundleResults::minSigmaRadiusDistance() const {
@@ -1041,7 +1013,7 @@ namespace Isis {
 
   /**
    * Returns the maximum sigma redius distance.
-   * 
+   *
    * @return @b Distance The maximum sigma radius.
    */
   Distance BundleResults::maxSigmaRadiusDistance() const {
@@ -1051,7 +1023,7 @@ namespace Isis {
 
   /**
    * Returns the minimum sigma latitude point id.
-   * 
+   *
    * @return @b @QString The minimum sigma latitude point id.
    */
   QString BundleResults::minSigmaLatitudePointId() const {
@@ -1061,7 +1033,7 @@ namespace Isis {
 
   /**
    * Returns the maximum sigma latitude point id.
-   * 
+   *
    * @return @b @QString The maximum sigma latitude point id.
    */
   QString BundleResults::maxSigmaLatitudePointId() const {
@@ -1071,7 +1043,7 @@ namespace Isis {
 
   /**
    * Returns the minimum sigma longitude point id.
-   * 
+   *
    * @return @b @QString The minimum sigma longitude point id.
    */
   QString BundleResults::minSigmaLongitudePointId() const {
@@ -1081,7 +1053,7 @@ namespace Isis {
 
   /**
    * Returns the maximum sigma longitude point id.
-   * 
+   *
    * @return @b @QString The maximum sigma longitude point id.
    */
   QString BundleResults::maxSigmaLongitudePointId() const {
@@ -1091,7 +1063,7 @@ namespace Isis {
 
   /**
    * Returns the minimum sigma radius point id.
-   * 
+   *
    * @return @b @QString The minimum sigma radius point id.
    */
   QString BundleResults::minSigmaRadiusPointId() const {
@@ -1101,7 +1073,7 @@ namespace Isis {
 
   /**
    * Returns the maximum sigma radius point id.
-   * 
+   *
    * @return @b @QString The maximum sigma radius point id.
    */
   QString BundleResults::maxSigmaRadiusPointId() const {
@@ -1111,7 +1083,7 @@ namespace Isis {
 
   /**
    * Returns the RMS of the adjusted latitude sigmas.
-   * 
+   *
    * @return @b double The RMS of the adjusted latitude sigmas.
    */
   double BundleResults::sigmaLatitudeStatisticsRms() const {
@@ -1121,7 +1093,7 @@ namespace Isis {
 
   /**
    * Returns the RMS of the adjusted longitude sigmas.
-   * 
+   *
    * @return @b double The RMS of the adjusted longitude sigmas.
    */
   double BundleResults::sigmaLongitudeStatisticsRms() const {
@@ -1131,7 +1103,7 @@ namespace Isis {
 
   /**
    * Returns the RMS of the adjusted raidus sigmas.
-   * 
+   *
    * @return @b double The RMS of the adjusted radius sigmas.
    */
   double BundleResults::sigmaRadiusStatisticsRms() const {
@@ -1141,7 +1113,7 @@ namespace Isis {
 
   /**
    * Returns the RMS of the x residuals.
-   * 
+   *
    * @return @b double The RMS of the x residuals.
    */
   double BundleResults::rmsRx() const {
@@ -1151,7 +1123,7 @@ namespace Isis {
 
   /**
    * Returns the RMS of the y residuals.
-   * 
+   *
    * @return @b double The RMS of the y residuals.
    */
   double BundleResults::rmsRy() const {
@@ -1161,7 +1133,7 @@ namespace Isis {
 
   /**
    * Returns the RMS of the x and y residuals.
-   * 
+   *
    * @return @b double The RMS of the x and y residuals.
    */
   double BundleResults::rmsRxy() const {
@@ -1171,7 +1143,7 @@ namespace Isis {
 
   /**
    * Returns the rejection limit.
-   * 
+   *
    * @return @b double The rejection limit.
    */
   double BundleResults::rejectionLimit() const {
@@ -1181,7 +1153,7 @@ namespace Isis {
 
   /**
    * Returns the radians to meters conversion factor for the target body.
-   * 
+   *
    * @return @b double The conversion factor.
    */
   double BundleResults::radiansToMeters() const {
@@ -1191,7 +1163,7 @@ namespace Isis {
 
   /**
    * Returns the number of observation that were rejected.
-   * 
+   *
    * @return @b int The number of rejected observations.
    */
   int BundleResults::numberRejectedObservations() const {
@@ -1201,7 +1173,7 @@ namespace Isis {
 
   /**
    * Returns the number of observations.
-   * 
+   *
    * @return @b int The number of observations.
    */
   int BundleResults::numberObservations() const {
@@ -1211,7 +1183,7 @@ namespace Isis {
 
   /**
    * Returns the total number of image parameters.
-   * 
+   *
    * @return @b int The total number of image parameters.
    */
   int BundleResults::numberImageParameters() const {
@@ -1221,7 +1193,7 @@ namespace Isis {
 
   /**
    * Returns the number of constrained point parameters.
-   * 
+   *
    * @return @b int The number of constrained point parameters.
    */
   int BundleResults::numberConstrainedPointParameters() const {
@@ -1231,7 +1203,7 @@ namespace Isis {
 
   /**
    * Returns the number of constrained image parameters.
-   * 
+   *
    * @return @b int The number of constrained image parameters.
    */
   int BundleResults::numberConstrainedImageParameters() const {
@@ -1241,7 +1213,7 @@ namespace Isis {
 
   /**
    * Return the number of constrained target parameters.
-   * 
+   *
    * @return @b int The number of constrained target parameters.
    */
   int BundleResults::numberConstrainedTargetParameters() const {
@@ -1251,7 +1223,7 @@ namespace Isis {
 
   /**
    * Returns the number of unknown parameters.
-   * 
+   *
    * @return @b int The number of unknown parameters.
    */
   int BundleResults::numberUnknownParameters() const {
@@ -1261,7 +1233,7 @@ namespace Isis {
 
   /**
    * Returns the degrees of freedom.
-   * 
+   *
    * @return @b int the degrees of freedom.
    */
   int BundleResults::degreesOfFreedom() const {
@@ -1271,7 +1243,7 @@ namespace Isis {
 
   /**
    * Returns the Sigma0 of the bundle adjustment.
-   * 
+   *
    * @return @b double The Sigma0.
    */
   double BundleResults::sigma0() const {
@@ -1281,7 +1253,7 @@ namespace Isis {
 
   /**
    * Returns the elapsed time for the bundle adjustment.
-   * 
+   *
    * @return @b double The elapsed time for the bundle adjustment.
    */
   double BundleResults::elapsedTime() const {
@@ -1291,7 +1263,7 @@ namespace Isis {
 
   /**
    * Returns the elapsed time for error propagation.
-   * 
+   *
    * @return @b double The elapsed time for error propagation.
    */
   double BundleResults::elapsedTimeErrorProp() const {
@@ -1301,8 +1273,8 @@ namespace Isis {
 
   /**
    * Returns whether or not the bundle adjustment converged.
-   * 
-   * @return @b bool If the bundle adjustment converged. 
+   *
+   * @return @b bool If the bundle adjustment converged.
    */
   bool BundleResults::converged() const {
     return m_converged;
@@ -1311,7 +1283,7 @@ namespace Isis {
 
   /**
    * Returns a reference to the BundleControlPoint vector.
-   * 
+   *
    * @return @b QVector& The BundleControlPoint vector.
    */
   QVector &BundleResults::bundleControlPoints() {
@@ -1321,14 +1293,14 @@ namespace Isis {
 
   /**
    * Returns a shared pointer to the output control network.
-   * 
+   *
    * @return @b ControlNetQsp A shared pointer to the output control network.
-   * 
+   *
    * @throws IException::Programmer "Output Control Network has not been set."
    */
   ControlNetQsp BundleResults::outputControlNet() const {
     if (!m_outNet) {
-      throw IException(IException::Programmer, 
+      throw IException(IException::Programmer,
                        "Output Control Network has not been set.",
                        _FILEINFO_);
     }
@@ -1338,7 +1310,7 @@ namespace Isis {
 
   /**
    * Returns the number of iterations taken by the BundleAdjust.
-   * 
+   *
    * @return @b int The number of iterations.
    */
   int BundleResults::iterations() const {
@@ -1348,7 +1320,7 @@ namespace Isis {
 
   /**
    * Returns a reference to the observations used by the BundleAdjust.
-   * 
+   *
    * @return @b BundleObservationVector& A reference to the observation vector.
    */
   const BundleObservationVector &BundleResults::observations() const {
@@ -1358,7 +1330,7 @@ namespace Isis {
 
   /**
    * Returns how many maximum likelihood models were used in the bundle adjustment.
-   * 
+   *
    * @return @b int The number fo maximum likelihood models.
    */
   int BundleResults::numberMaximumLikelihoodModels() const {
@@ -1368,7 +1340,7 @@ namespace Isis {
 
   /**
    * Returns which step the bundle adjustment is on.
-   * 
+   *
    * @return @b int The maximum likelihood model that the bundle adjustment is currently using.
    */
   int BundleResults::maximumLikelihoodModelIndex() const {
@@ -1378,7 +1350,7 @@ namespace Isis {
 
   /**
    * Returns the cumulative probability distribution of the |R^2 residuals|.
-   * 
+   *
    * @return @b StatCumProbDistDynCalc The cumulative probability distribution of the
    *                                   |R^2 residuals|.
    */
@@ -1389,7 +1361,7 @@ namespace Isis {
 
   /**
    * Returns the cumulative probability distribution of the residuals used for reporting.
-   * 
+   *
    * @return @b StatCumProbDistDynCalc the cumulative probability distribution of the residuals.
    */
   StatCumProbDistDynCalc BundleResults::residualsCumulativeProbabilityDistribution() const {
@@ -1399,7 +1371,7 @@ namespace Isis {
 
   /**
    * Returns the median of the |R^2 residuals|.
-   * 
+   *
    * @return @b double The median of the |R^2 residuals|.
    */
   double BundleResults::maximumLikelihoodMedianR2Residuals() const {
@@ -1409,9 +1381,9 @@ namespace Isis {
 
   /**
    * Returns the maximum likelihood model at the given index.
-   * 
+   *
    * @param modelIndex The index of the maximum likelihood model to be returned.
-   * 
+   *
    * @return @b MaximumLikelihoodWFunctions The maximum likelihood model at the input index.
    */
   MaximumLikelihoodWFunctions BundleResults::maximumLikelihoodModelWFunc(int modelIndex) const {
@@ -1421,9 +1393,9 @@ namespace Isis {
 
   /**
    * Returns the quantile of the maximum likelihood model at the given index.
-   * 
+   *
    * @param modelIndex The index of the maximum likelihood model whose quantile will be returned.
-   * 
+   *
    * @return @b double The quantile of the desired maximum likelihood model.
    */
   double BundleResults::maximumLikelihoodModelQuantile(int modelIndex) const {
@@ -1437,101 +1409,11 @@ namespace Isis {
 //  }
 
 
-  /**
-   * Saves the BundleResults object as a PvlObject.
-   * 
-   * @param name The name of the PvlObject to save to.
-   * 
-   * @return @b PvlObject A PvlObject containing the BundleResults object's information.
-   */
-  PvlObject BundleResults::pvlObject(QString name) const {
-
-    PvlObject pvl(name);
-
-    pvl += PvlKeyword("NumberFixedPoints", toString(numberFixedPoints()));
-    pvl += PvlKeyword("NumberIgnoredPoints", toString(numberIgnoredPoints()));
-    pvl += PvlKeyword("NumberHeldImages", toString(numberHeldImages()));
-    pvl += PvlKeyword("RMSResidualX", toString(rmsRx()));
-    pvl += PvlKeyword("RMSResidualY", toString(rmsRy()));
-    pvl += PvlKeyword("RMSResidualXY", toString(rmsRxy()));
-    pvl += PvlKeyword("RejectionLimit", toString(rejectionLimit()));
-    pvl += PvlKeyword("RadiansToMeters", toString(radiansToMeters()));
-    pvl += PvlKeyword("NumberRejectedObservations", toString(numberRejectedObservations()));
-    pvl += PvlKeyword("NumberObservations", toString(numberObservations()));
-    pvl += PvlKeyword("NumberImageParameters", toString(numberImageParameters()));
-    pvl += PvlKeyword("NumberConstrainedPointParameters",
-                      toString(numberConstrainedPointParameters()));
-    pvl += PvlKeyword("NumberConstrainedImageParameters",
-                      toString(numberConstrainedImageParameters()));
-    pvl += PvlKeyword("NumberConstrainedTargetParameters",
-                      toString(numberConstrainedTargetParameters()));
-    pvl += PvlKeyword("NumberUnknownParameters", toString(numberUnknownParameters()));
-    pvl += PvlKeyword("DegreesOfFreedom", toString(degreesOfFreedom()));
-    pvl += PvlKeyword("Sigma0", toString(sigma0()));
-    pvl += PvlKeyword("ElapsedTime", toString(elapsedTime()));
-    pvl += PvlKeyword("ElapsedTimeErrorProp", toString(elapsedTimeErrorProp()));
-    pvl += PvlKeyword("Iterations", toString(iterations()));
-    pvl += PvlKeyword("Converged", toString(converged()));
-#if 0
-    // loop through these ??? what value to store???
-    pvl += PvlKeyword("RmsImageSampleResidualsSize", toString(m_rmsImageSampleResiduals.size());
-    pvl += PvlKeyword("RmsImageLineResidualsSize",   toString(m_rmsImageLineResiduals.size());
-    pvl += PvlKeyword("RmsImageResidualsSize",       toString(m_rmsImageResiduals.size());
-    pvl += PvlKeyword("RmsImageXSigmasSize",         toString(m_rmsImageXSigmas.size());
-    pvl += PvlKeyword("RmsImageYSigmasSize",         toString(m_rmsImageYSigmas.size());
-    pvl += PvlKeyword("RmsImageZSigmasSize",         toString(m_rmsImageZSigmas.size());
-    pvl += PvlKeyword("RmsImageRASigmasSize",        toString(m_rmsImageRASigmas.size());
-    pvl += PvlKeyword("RmsImageDECSigmasSize",       toString(m_rmsImageDECSigmas.size());
-    pvl += PvlKeyword("RmsImageTWISTSigmasSize",     toString(m_rmsImageTWISTSigmas.size());
-#endif 
-    pvl += PvlKeyword("MinSigmaLatitude", toString(minSigmaLatitudeDistance().meters()));
-    pvl += PvlKeyword("MinSigmaLatitudePointId", minSigmaLatitudePointId());
-    pvl += PvlKeyword("MaxSigmaLatitude", toString(maxSigmaLatitudeDistance().meters()));
-    pvl += PvlKeyword("MaxSigmaLatitudePointId", maxSigmaLatitudePointId());
-    pvl += PvlKeyword("MinSigmaLongitude", toString(minSigmaLongitudeDistance().meters()));
-    pvl += PvlKeyword("MinSigmaLongitudePointId", minSigmaLongitudePointId());
-    pvl += PvlKeyword("MaxSigmaLongitude", toString(maxSigmaLongitudeDistance().meters()));
-    pvl += PvlKeyword("MaxSigmaLongitudePointId", maxSigmaLongitudePointId());
-    pvl += PvlKeyword("MinSigmaRadius", toString(minSigmaRadiusDistance().meters()));
-    pvl += PvlKeyword("MinSigmaRadiusPointId", minSigmaRadiusPointId());
-    pvl += PvlKeyword("MaxSigmaRadius", toString(maxSigmaRadiusDistance().meters()));
-    pvl += PvlKeyword("MaxSigmaRadiusPointId", maxSigmaRadiusPointId());
-    pvl += PvlKeyword("RmsSigmaLat", toString(sigmaLatitudeStatisticsRms()));
-    pvl += PvlKeyword("RmsSigmaLon", toString(sigmaLongitudeStatisticsRms()));
-    pvl += PvlKeyword("RmsSigmaRad", toString(sigmaRadiusStatisticsRms()));
-    pvl += PvlKeyword("NumberMaximumLikelihoodModels", toString(numberMaximumLikelihoodModels()));
-    if (numberMaximumLikelihoodModels() > 0) {
-
-      PvlKeyword models("MaximumLikelihoodModels");
-      PvlKeyword quantiles("MaximumLikelihoodQuantiles"); 
-      
-      for (int i = 0; i < m_maximumLikelihoodFunctions.size(); i++) {
-        models.addValue(MaximumLikelihoodWFunctions::modelToString(
-                            m_maximumLikelihoodFunctions[i].first.model()));
-        quantiles.addValue(toString(m_maximumLikelihoodFunctions[i].second));
-      }
-      pvl += models;
-      pvl += quantiles;
-      pvl += PvlKeyword("MaximumLikelihoodMedianR2Residuals", 
-                          toString(m_maximumLikelihoodMedianR2Residuals));
-    }
-
-    if (m_correlationMatrix) {
-      pvl += correlationMatrix().pvlObject();
-    }
-    else {
-      pvl += PvlKeyword("CorrelationMatrix", "None");
-    }
-
-    return pvl;
-  }
-
-
   /**
    * Returns the Correlation Matrix.
    *
    * @return @b CorrelationMatrix The correlation matrix.
-   * 
+   *
    * @throws IException::Unknown "Correlation matrix for this bundle is NULL."
    */
   CorrelationMatrix BundleResults::correlationMatrix() const {
@@ -1539,7 +1421,7 @@ namespace Isis {
       return *m_correlationMatrix;
     }
     else {
-      throw IException(IException::Unknown, 
+      throw IException(IException::Unknown,
                        "Correlation matrix for this bundle is NULL.",
                        _FILEINFO_);
     }
@@ -1570,39 +1452,33 @@ namespace Isis {
 
   /**
    * Saves the BundleResults object to an XML file.
-   * 
+   *
    * @param stream The QXMLStreamWriter that will be used to write out the XML file.
    * @param project The project that the BundleResults object belongs to.
    */
   void BundleResults::save(QXmlStreamWriter &stream, const Project *project) const {
-    // TODO: does xml stuff need project???
-
     stream.writeStartElement("bundleResults");
-    stream.writeTextElement("id", m_id->toString());
- 
-//    stream.writeTextElement("instrumentId", m_instrumentId);
-
     stream.writeStartElement("correlationMatrix");
     stream.writeAttribute("correlationFileName",
-                          correlationMatrix().correlationFileName().expanded()); 
+                          correlationMatrix().correlationFileName().expanded());
     stream.writeAttribute("covarianceFileName",
-                          correlationMatrix().covarianceFileName().expanded()); 
+                          correlationMatrix().covarianceFileName().expanded());
     stream.writeStartElement("imagesAndParameters");
     QMapIterator imgParamIt(*correlationMatrix().imagesAndParameters());
     while (imgParamIt.hasNext()) {
       imgParamIt.next();
-      stream.writeStartElement("image"); 
+      stream.writeStartElement("image");
       stream.writeAttribute("id", imgParamIt.key());
       QStringList parameters = imgParamIt.value();
       for (int i = 0; i < parameters.size(); i++) {
         stream.writeTextElement("parameter", parameters[i]);
       }
       stream.writeEndElement(); // end image
-      
+
     }
     stream.writeEndElement(); // end images and parameters
     stream.writeEndElement(); // end correlationMatrix
-    
+
     stream.writeStartElement("generalStatisticsValues");
     stream.writeTextElement("numberFixedPoints", toString(numberFixedPoints()));
     stream.writeTextElement("numberIgnoredPoints", toString(numberIgnoredPoints()));
@@ -1625,19 +1501,19 @@ namespace Isis {
 
     stream.writeStartElement("rms");
     stream.writeStartElement("residuals");
-    stream.writeAttribute("x", toString(rmsRx())); 
-    stream.writeAttribute("y", toString(rmsRy())); 
-    stream.writeAttribute("xy", toString(rmsRxy())); 
+    stream.writeAttribute("x", toString(rmsRx()));
+    stream.writeAttribute("y", toString(rmsRy()));
+    stream.writeAttribute("xy", toString(rmsRxy()));
     stream.writeEndElement(); // end residuals element
     stream.writeStartElement("sigmas");
-    stream.writeAttribute("lat", toString(sigmaLatitudeStatisticsRms())); 
-    stream.writeAttribute("lon", toString(sigmaLongitudeStatisticsRms())); 
-    stream.writeAttribute("rad", toString(sigmaRadiusStatisticsRms())); 
+    stream.writeAttribute("lat", toString(sigmaLatitudeStatisticsRms()));
+    stream.writeAttribute("lon", toString(sigmaLongitudeStatisticsRms()));
+    stream.writeAttribute("rad", toString(sigmaRadiusStatisticsRms()));
     stream.writeEndElement(); // end sigmas element
 
     stream.writeStartElement("imageResidualsLists");
     stream.writeStartElement("residualsList");
-    stream.writeAttribute("listSize", toString(rmsImageResiduals().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageResiduals().size()));
     for (int i = 0; i < m_rmsImageResiduals.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageResiduals[i].save(stream, project);
@@ -1645,7 +1521,7 @@ namespace Isis {
     }
     stream.writeEndElement(); // end residuals list
     stream.writeStartElement("sampleList");
-    stream.writeAttribute("listSize", toString(rmsImageSampleResiduals().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageSampleResiduals().size()));
     for (int i = 0; i < m_rmsImageSampleResiduals.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageSampleResiduals[i].save(stream, project);
@@ -1654,7 +1530,7 @@ namespace Isis {
     stream.writeEndElement(); // end sample residuals list
 
     stream.writeStartElement("lineList");
-    stream.writeAttribute("listSize", toString(rmsImageLineResiduals().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageLineResiduals().size()));
     for (int i = 0; i < m_rmsImageLineResiduals.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageLineResiduals[i].save(stream, project);
@@ -1665,17 +1541,17 @@ namespace Isis {
 
     stream.writeStartElement("imageSigmasLists");
     stream.writeStartElement("xSigmas");
-    stream.writeAttribute("listSize", toString(rmsImageXSigmas().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageXSigmas().size()));
     for (int i = 0; i < m_rmsImageXSigmas.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageXSigmas[i].save(stream, project);
       stream.writeEndElement(); // end statistics item
     }
-    
+
     stream.writeEndElement(); // end x sigma list
 
     stream.writeStartElement("ySigmas");
-    stream.writeAttribute("listSize", toString(rmsImageYSigmas().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageYSigmas().size()));
     for (int i = 0; i < m_rmsImageYSigmas.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageYSigmas[i].save(stream, project);
@@ -1684,7 +1560,7 @@ namespace Isis {
     stream.writeEndElement(); // end y sigma list
 
     stream.writeStartElement("zSigmas");
-    stream.writeAttribute("listSize", toString(rmsImageZSigmas().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageZSigmas().size()));
     for (int i = 0; i < m_rmsImageZSigmas.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageZSigmas[i].save(stream, project);
@@ -1693,7 +1569,7 @@ namespace Isis {
     stream.writeEndElement(); // end z sigma list
 
     stream.writeStartElement("raSigmas");
-    stream.writeAttribute("listSize", toString(rmsImageRASigmas().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageRASigmas().size()));
     for (int i = 0; i < m_rmsImageRASigmas.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageRASigmas[i].save(stream, project);
@@ -1702,7 +1578,7 @@ namespace Isis {
     stream.writeEndElement(); // end ra sigma list
 
     stream.writeStartElement("decSigmas");
-    stream.writeAttribute("listSize", toString(rmsImageDECSigmas().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageDECSigmas().size()));
     for (int i = 0; i < m_rmsImageDECSigmas.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageDECSigmas[i].save(stream, project);
@@ -1711,7 +1587,7 @@ namespace Isis {
     stream.writeEndElement(); // end dec sigma list
 
     stream.writeStartElement("twistSigmas");
-    stream.writeAttribute("listSize", toString(rmsImageTWISTSigmas().size())); 
+    stream.writeAttribute("listSize", toString(rmsImageTWISTSigmas().size()));
     for (int i = 0; i < m_rmsImageTWISTSigmas.size(); i++) {
       stream.writeStartElement("statisticsItem");
       m_rmsImageTWISTSigmas[i].save(stream, project);
@@ -1722,59 +1598,59 @@ namespace Isis {
     stream.writeEndElement(); // end rms
 
     stream.writeStartElement("elapsedTime");
-    stream.writeAttribute("time", toString(elapsedTime())); 
-    stream.writeAttribute("errorProp", toString(elapsedTimeErrorProp())); 
+    stream.writeAttribute("time", toString(elapsedTime()));
+    stream.writeAttribute("errorProp", toString(elapsedTimeErrorProp()));
     stream.writeEndElement(); // end elapsed time
 
     stream.writeStartElement("minMaxSigmas");
     stream.writeStartElement("minLat");
-    stream.writeAttribute("value", toString(minSigmaLatitudeDistance().meters())); 
-    stream.writeAttribute("pointId", minSigmaLatitudePointId()); 
+    stream.writeAttribute("value", toString(minSigmaLatitudeDistance().meters()));
+    stream.writeAttribute("pointId", minSigmaLatitudePointId());
     stream.writeEndElement();
     stream.writeStartElement("maxLat");
-    stream.writeAttribute("value", toString(maxSigmaLatitudeDistance().meters())); 
-    stream.writeAttribute("pointId", maxSigmaLatitudePointId()); 
+    stream.writeAttribute("value", toString(maxSigmaLatitudeDistance().meters()));
+    stream.writeAttribute("pointId", maxSigmaLatitudePointId());
     stream.writeEndElement();
     stream.writeStartElement("minLon");
-    stream.writeAttribute("value", toString(minSigmaLongitudeDistance().meters())); 
-    stream.writeAttribute("pointId", minSigmaLongitudePointId()); 
+    stream.writeAttribute("value", toString(minSigmaLongitudeDistance().meters()));
+    stream.writeAttribute("pointId", minSigmaLongitudePointId());
     stream.writeEndElement();
     stream.writeStartElement("maxLon");
-    stream.writeAttribute("value", toString(maxSigmaLongitudeDistance().meters())); 
-    stream.writeAttribute("pointId", maxSigmaLongitudePointId()); 
+    stream.writeAttribute("value", toString(maxSigmaLongitudeDistance().meters()));
+    stream.writeAttribute("pointId", maxSigmaLongitudePointId());
     stream.writeEndElement();
     stream.writeStartElement("minRad");
-    stream.writeAttribute("value", toString(minSigmaRadiusDistance().meters())); 
-    stream.writeAttribute("pointId", minSigmaRadiusPointId()); 
+    stream.writeAttribute("value", toString(minSigmaRadiusDistance().meters()));
+    stream.writeAttribute("pointId", minSigmaRadiusPointId());
     stream.writeEndElement();
     stream.writeStartElement("maxRad");
-    stream.writeAttribute("value", toString(maxSigmaRadiusDistance().meters())); 
-    stream.writeAttribute("pointId", maxSigmaRadiusPointId()); 
+    stream.writeAttribute("value", toString(maxSigmaRadiusDistance().meters()));
+    stream.writeAttribute("pointId", maxSigmaRadiusPointId());
     stream.writeEndElement();
     stream.writeEndElement(); // end minMaxSigmas
 
-    // call max likelihood setup from startElement to fill the rest of these values... 
+    // call max likelihood setup from startElement to fill the rest of these values...
     stream.writeStartElement("maximumLikelihoodEstimation");
-    stream.writeAttribute("numberModels", toString(numberMaximumLikelihoodModels())); 
-    stream.writeAttribute("maximumLikelihoodIndex", toString(maximumLikelihoodModelIndex())); 
+    stream.writeAttribute("numberModels", toString(numberMaximumLikelihoodModels()));
+    stream.writeAttribute("maximumLikelihoodIndex", toString(maximumLikelihoodModelIndex()));
     stream.writeAttribute("maximumLikelihoodMedianR2Residuals",
                           toString(maximumLikelihoodMedianR2Residuals()));
 
     stream.writeStartElement("cumulativeProbabilityCalculator");
-    cumulativeProbabilityDistribution().save(stream, project);
+    // cumulativeProbabilityDistribution().save(stream, project);
     stream.writeEndElement(); // end cumulativeProbabilityCalculator
 
     stream.writeStartElement("residualsCumulativeProbabilityCalculator");
-    residualsCumulativeProbabilityDistribution().save(stream, project);
+    // residualsCumulativeProbabilityDistribution().save(stream, project);
     stream.writeEndElement(); // end residualsCumulativeProbabilityCalculator
 
     for (int i = 0; i < numberMaximumLikelihoodModels(); i++) {
       stream.writeStartElement("model");
-      stream.writeAttribute("modelNumber", toString(i+1)); 
-      stream.writeAttribute("modelSelection", 
+      stream.writeAttribute("modelNumber", toString(i+1));
+      stream.writeAttribute("modelSelection",
         MaximumLikelihoodWFunctions::modelToString(m_maximumLikelihoodFunctions[i].first.model()));
       stream.writeAttribute("tweakingConstant",
-                            toString(m_maximumLikelihoodFunctions[i].first.tweakingConstant())); 
+                            toString(m_maximumLikelihoodFunctions[i].first.tweakingConstant()));
       stream.writeAttribute("quantile", toString(m_maximumLikelihoodFunctions[i].second));
       stream.writeEndElement(); // end this model
     }
@@ -1785,12 +1661,13 @@ namespace Isis {
 
   /**
    * Constructs an XmlHandler used to save a BundleResults object.
-   * 
+   *
    * @param statistics The BundleResults that the XmlHandler will save.
    * @param project The project that the BundleResults object belongs to.
    */
   BundleResults::XmlHandler::XmlHandler(BundleResults *statistics, Project *project) {
     // TODO: does xml stuff need project???
+    m_xmlHandlerCumProCalc = NULL;
     m_xmlHandlerBundleResults = NULL;
     m_xmlHandlerProject = NULL;
 
@@ -1820,33 +1697,33 @@ namespace Isis {
     // passed into StatCumProbDistDynCalc constructor as pointer
     // delete m_xmlHandlerProject;    // TODO: does xml stuff need project???
     m_xmlHandlerProject = NULL;
-    
+
     // delete m_xmlHandlerBundleResults;
     // m_xmlHandlerBundleResults = NULL;
-    
+
   }
-  
+
 
   /**
-   * Writes a starting XML element
-   * 
-   * @param namespaceURI ???
-   * @param localName ???
-   * @param qName The name of the element.
-   * @param atts The attributes of the element.
-   * 
-   * @return @b bool If the XmlHandler should continue to be used, usually true.
+   * Handle an XML start element. This method is called when the reader finds an open tag.
+   * handle the read when the startElement with the name localName has been found.
+   *
+   * @param qName SAX namespace for this tag
+   * @param localName SAX local name
+   * @param qName SAX qualified name of the tag.
+   * @param attributes The list of attributes for the tag.
+   *
+   * @return @b bool Indicates whether to continue reading the XML (usually true).
    */
-  bool BundleResults::XmlHandler::startElement(const QString &namespaceURI, 
+  bool BundleResults::XmlHandler::startElement(const QString &namespaceURI,
                                                const QString &localName,
                                                const QString &qName,
                                                const QXmlAttributes &atts) {
     m_xmlHandlerCharacters = "";
 
     if (XmlStackedHandler::startElement(namespaceURI, localName, qName, atts)) {
-        
-      if (qName == "correlationMatrix") {
 
+      if (qName == "correlationMatrix") {
         m_xmlHandlerBundleResults->m_correlationMatrix = NULL;
         m_xmlHandlerBundleResults->m_correlationMatrix = new CorrelationMatrix();
 
@@ -1861,7 +1738,6 @@ namespace Isis {
           FileName covarianceFile(covarianceFileName);
           m_xmlHandlerBundleResults->m_correlationMatrix->setCovarianceFileName(covarianceFile);
         }
-
       }
       else if (qName == "image") {
         QString correlationMatrixImageId = atts.value("id");
@@ -1870,7 +1746,6 @@ namespace Isis {
         }
       }
       else if (qName == "residuals") {
-        
         QString rx = atts.value("x");
         if (!rx.isEmpty()) {
           m_xmlHandlerBundleResults->m_rmsXResiduals = toDouble(rx);
@@ -1885,10 +1760,8 @@ namespace Isis {
         if (!rxy.isEmpty()) {
           m_xmlHandlerBundleResults->m_rmsXYResiduals = toDouble(rxy);
         }
-
       }
       else if (qName == "sigmas") {
-
         QString lat = atts.value("lat");
         if (!lat.isEmpty()) {
           m_xmlHandlerBundleResults->m_rmsSigmaLatitudeStats = toDouble(lat);
@@ -1903,58 +1776,44 @@ namespace Isis {
         if (!rad.isEmpty()) {
           m_xmlHandlerBundleResults->m_rmsSigmaRadiusStats = toDouble(rad);
         }
-
       }
       else if (qName == "residualsList") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerResidualsListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "sampleList") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerSampleResidualsListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "lineList") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerLineResidualsListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "xSigmas") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerXSigmasListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "ySigmas") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerYSigmasListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "zSigmas") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerZSigmasListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "raSigmas") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerRASigmasListSize = toInt(listSizeStr);
@@ -1962,20 +1821,16 @@ namespace Isis {
 
       }
       else if (qName == "decSigmas") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerDECSigmasListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "twistSigmas") {
-
         QString listSizeStr = atts.value("listSize");
         if (!listSizeStr.isEmpty()) {
           m_xmlHandlerTWISTSigmasListSize = toInt(listSizeStr);
         }
-
       }
       else if (qName == "statisticsItem") {
         // add statistics object to the xml handler's current statistics list.
@@ -1983,7 +1838,6 @@ namespace Isis {
             new Statistics(m_xmlHandlerProject, reader()));
       }
       else if (qName == "elapsedTime") {
-
         QString time = atts.value("time");
         if (!time.isEmpty()) {
           m_xmlHandlerBundleResults->m_elapsedTime = toDouble(time);
@@ -2004,7 +1858,6 @@ namespace Isis {
 // ???        }
 // ???      }
       else if (qName == "minLat") {
-
         QString minLat = atts.value("value");
         if (!minLat.isEmpty()) {
           m_xmlHandlerBundleResults->m_minSigmaLatitudeDistance.setMeters(toDouble(minLat));
@@ -2014,10 +1867,8 @@ namespace Isis {
         if (!minLatPointId.isEmpty()) {
           m_xmlHandlerBundleResults->m_minSigmaLatitudePointId = minLatPointId;
         }
-
       }
       else if (qName == "maxLat") {
-
         QString maxLat = atts.value("value");
         if (!maxLat.isEmpty()) {
           m_xmlHandlerBundleResults->m_maxSigmaLatitudeDistance.setMeters(toDouble(maxLat));
@@ -2027,10 +1878,8 @@ namespace Isis {
         if (!maxLatPointId.isEmpty()) {
           m_xmlHandlerBundleResults->m_maxSigmaLatitudePointId = maxLatPointId;
         }
-
       }
       else if (qName == "minLon") {
-
         QString minLon = atts.value("value");
         if (!minLon.isEmpty()) {
           m_xmlHandlerBundleResults->m_minSigmaLongitudeDistance.setMeters(toDouble(minLon));
@@ -2040,10 +1889,8 @@ namespace Isis {
         if (!minLonPointId.isEmpty()) {
           m_xmlHandlerBundleResults->m_minSigmaLongitudePointId = minLonPointId;
         }
-
       }
       else if (qName == "maxLon") {
-
         QString maxLon = atts.value("value");
         if (!maxLon.isEmpty()) {
           m_xmlHandlerBundleResults->m_maxSigmaLongitudeDistance.setMeters(toDouble(maxLon));
@@ -2053,10 +1900,8 @@ namespace Isis {
         if (!maxLonPointId.isEmpty()) {
           m_xmlHandlerBundleResults->m_maxSigmaLongitudePointId = maxLonPointId;
         }
-
       }
       else if (qName == "minRad") {
-
         QString minRad = atts.value("value");
         if (!minRad.isEmpty()) {
           m_xmlHandlerBundleResults->m_minSigmaRadiusDistance.setMeters(toDouble(minRad));
@@ -2066,10 +1911,8 @@ namespace Isis {
         if (!minRadPointId.isEmpty()) {
           m_xmlHandlerBundleResults->m_minSigmaRadiusPointId = minRadPointId;
         }
-
       }
       else if (qName == "maxRad") {
-
         QString maxRad = atts.value("value");
         if (!maxRad.isEmpty()) {
           m_xmlHandlerBundleResults->m_maxSigmaRadiusDistance.setMeters(toDouble(maxRad));
@@ -2079,10 +1922,8 @@ namespace Isis {
         if (!maxRadPointId.isEmpty()) {
           m_xmlHandlerBundleResults->m_maxSigmaRadiusPointId = maxRadPointId;
         }
-
       }
       else if (qName == "maximumLikelihoodEstimation") {
-
         QString maximumLikelihoodIndex = atts.value("maximumLikelihoodIndex");
         if (!maximumLikelihoodIndex.isEmpty()) {
           m_xmlHandlerBundleResults->m_maximumLikelihoodIndex = toInt(maximumLikelihoodIndex);
@@ -2094,7 +1935,6 @@ namespace Isis {
           m_xmlHandlerBundleResults->m_maximumLikelihoodMedianR2Residuals =
             toDouble(maximumLikelihoodMedianR2Residuals);
         }
-
       }
       else if (qName == "model") {
         QString model = atts.value("modelSelection");
@@ -2129,10 +1969,10 @@ namespace Isis {
 
   /**
    * Adds a QString to the XmlHandler's internal character data.
-   * 
+   *
    * @param ch The data to be added.
-   * 
-   * @return @b bool If false, then the data was not successfully added.
+   *
+   * @return @b bool true
    */
   bool BundleResults::XmlHandler::characters(const QString &ch) {
     m_xmlHandlerCharacters += ch;
@@ -2141,25 +1981,18 @@ namespace Isis {
 
 
   /**
-   * Writes an ending XML element.
-   * 
-   * @param namespaceURI ???
-   * @param localName ???
-   * @param qName The name of the element.
-   * 
-   * @return @b bool If the XmlHandler should continue to be used.
+   * @brief Handle end tags for the BundleResults serialized XML.
+   *
+   * @param namespaceURI URI of the specified tags namespce
+   * @param localName SAX localName
+   * @param qName SAX qualified name
+   *
+   * @return true
    */
   bool BundleResults::XmlHandler::endElement(const QString &namespaceURI, const QString &localName,
                                              const QString &qName) {
 
     if (!m_xmlHandlerCharacters.isEmpty()) {
-      if (qName == "id") {
-        m_xmlHandlerBundleResults->m_id = NULL;
-        m_xmlHandlerBundleResults->m_id = new QUuid(m_xmlHandlerCharacters);
-      }
-//      else if (qName == "instrumentId") {
-//        m_xmlHandlerBundleResults->m_instrumentId = m_xmlHandlerCharacters;
-//      }
       if (qName == "parameter") {
         // add the parameter to the current list
         m_xmlHandlerCorrelationParameterList.append(m_xmlHandlerCharacters);
@@ -2167,7 +2000,7 @@ namespace Isis {
       if (qName == "image") {
         // add this image and its parameters to the map
         if (m_xmlHandlerCorrelationImageId != "") {
-          m_xmlHandlerCorrelationMap.insert(m_xmlHandlerCorrelationImageId, 
+          m_xmlHandlerCorrelationMap.insert(m_xmlHandlerCorrelationImageId,
                                             m_xmlHandlerCorrelationParameterList);
         }
         m_xmlHandlerCorrelationImageId = "";
@@ -2227,21 +2060,20 @@ namespace Isis {
       }
       // copy the xml handler's statistics list to the appropriate bundle statistics list
       else if (qName == "residualsList") {
-        // do this check or assume the xml is valid???
-        // ??? if (m_xmlHandlerResidualsListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid residualsList", _FILEINFO_);
-        // ??? }
+        if (m_xmlHandlerResidualsListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid residualsList", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageResiduals.append(m_xmlHandlerStatisticsList[i]);
         }
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "sampleList") {
-        // ??? if (m_xmlHandlerSampleResidualsListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid sampleList", _FILEINFO_);
-        // ??? }
+        if (m_xmlHandlerSampleResidualsListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid sampleList", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageSampleResiduals.append(
                                                                    m_xmlHandlerStatisticsList[i]);
@@ -2249,70 +2081,70 @@ namespace Isis {
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "lineList") {
-        // ??? if (m_xmlHandlerLineResidualsListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid lineList", _FILEINFO_);
-        // ??? }
+        if (m_xmlHandlerLineResidualsListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid lineList", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageLineResiduals.append(m_xmlHandlerStatisticsList[i]);
         }
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "xSigmas") {
-        // ??? if (m_xmlHandlerXSigmasListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid xSigmas", _FILEINFO_); ???
-        // }
+        if (m_xmlHandlerXSigmasListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid xSigmas", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageXSigmas.append(m_xmlHandlerStatisticsList[i]);
         }
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "ySigmas") {
-        // ??? if (m_xmlHandlerYSigmasListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid ySigmas", _FILEINFO_);
-        // ??? }
+        if (m_xmlHandlerYSigmasListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid ySigmas", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageYSigmas.append(m_xmlHandlerStatisticsList[i]);
         }
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "zSigmas") {
-        // ??? if (m_xmlHandlerZSigmasListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid zSigmas", _FILEINFO_);
-        // ??? }
+        if (m_xmlHandlerZSigmasListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid zSigmas", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageZSigmas.append(m_xmlHandlerStatisticsList[i]);
         }
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "raSigmas") {
-        // ??? if (m_xmlHandlerRASigmasListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid raSigmas", _FILEINFO_);
-        // ??? }
+        if (m_xmlHandlerRASigmasListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid raSigmas", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageRASigmas.append(m_xmlHandlerStatisticsList[i]);
         }
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "decSigmas") {
-        // ??? if (m_xmlHandlerDECSigmasListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid decSigmas", _FILEINFO_);
-        // ??? }
+        if (m_xmlHandlerDECSigmasListSize != m_xmlHandlerStatisticsList.size()) {
+          throw IException(IException::Unknown,
+                           "Unable to read xml file. Invalid decSigmas", _FILEINFO_);
+        }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageDECSigmas.append(m_xmlHandlerStatisticsList[i]);
         }
         m_xmlHandlerStatisticsList.clear();
       }
       else if (qName == "twistSigmas") {
-        // ??? if (m_xmlHandlerTWISTSigmasListSize != m_xmlHandlerStatisticsList.size()) {
-        // ???   throw IException(IException::Unknown, 
-        // ???                    "Unable to read xml file. Invalid twistSigmas", _FILEINFO_);
-        // ??? }
+          if (m_xmlHandlerTWISTSigmasListSize != m_xmlHandlerStatisticsList.size()) {
+            throw IException(IException::Unknown,
+                             "Unable to read xml file. Invalid twistSigmas", _FILEINFO_);
+          }
         for (int i = 0; i < m_xmlHandlerStatisticsList.size(); i++) {
           m_xmlHandlerBundleResults->m_rmsImageTWISTSigmas.append(m_xmlHandlerStatisticsList[i]);
         }
@@ -2322,772 +2154,4 @@ namespace Isis {
     m_xmlHandlerCharacters = "";
     return XmlStackedHandler::endElement(namespaceURI, localName, qName);
   }
-
-
-  /**
-   * Writes the BundleResults object to a QDataStream.
-   * 
-   * @param stream The QDataStream that the BundleResults will be written to.
-   * 
-   * @return @b QDataStream& A reference to the QDataStream that
-   *                         the BundleResults where written to.
-   */
-  QDataStream &BundleResults::write(QDataStream &stream) const {
-    stream << m_id->toString()
-           << *m_correlationMatrix
-           << (qint32)m_numberFixedPoints
-           << (qint32)m_numberIgnoredPoints
-           << (qint32)m_numberHeldImages
-           << m_rmsXResiduals << m_rmsYResiduals << m_rmsXYResiduals
-           << m_rejectionLimit
-           << (qint32)m_numberObservations
-           << (qint32)m_numberRejectedObservations
-           << (qint32)m_numberUnknownParameters
-           << (qint32)m_numberImageParameters
-           << (qint32)m_numberConstrainedImageParameters
-           << (qint32)m_numberConstrainedPointParameters
-           << (qint32)m_numberConstrainedTargetParameters
-           << (qint32)m_degreesOfFreedom
-           << m_sigma0
-           << m_elapsedTime << m_elapsedTimeErrorProp
-           << m_converged
-           << m_rmsImageSampleResiduals << m_rmsImageLineResiduals
-           << m_rmsImageResiduals
-           << m_rmsImageXSigmas << m_rmsImageYSigmas << m_rmsImageZSigmas
-           << m_rmsImageRASigmas << m_rmsImageDECSigmas << m_rmsImageTWISTSigmas
-           << m_minSigmaLatitudeDistance.meters()
-           << m_maxSigmaLatitudeDistance.meters()
-           << m_minSigmaLongitudeDistance.meters()
-           << m_maxSigmaLongitudeDistance.meters()
-           << m_minSigmaRadiusDistance.meters()
-           << m_maxSigmaRadiusDistance.meters()
-           << m_minSigmaLatitudePointId        
-           << m_maxSigmaLatitudePointId        
-           << m_minSigmaLongitudePointId       
-           << m_maxSigmaLongitudePointId       
-           << m_minSigmaRadiusPointId          
-           << m_maxSigmaRadiusPointId          
-           << m_rmsSigmaLatitudeStats << m_rmsSigmaLongitudeStats << m_rmsSigmaRadiusStats
-           << m_maximumLikelihoodFunctions
-           << (qint32)m_maximumLikelihoodIndex << *m_cumPro << *m_cumProRes
-           << m_maximumLikelihoodMedianR2Residuals;
-    return stream;
-  }
-
-
-  /**
-   * Reads the data from a QDataStream into the BundleResults object.
-   * 
-   * @param stream The QDataStream to read from.
-   * 
-   * @return @b QDataStream& A reference to the stream after reading from it.
-   */
-  QDataStream &BundleResults::read(QDataStream &stream) {
-    QString id;
-    CorrelationMatrix correlationMatrix;
-    qint32 numberFixedPoints, numberIgnoredPoints, numberHeldImages, numberRejectedObservations,
-           numberObservations, numberImageParameters, numberConstrainedPointParameters,
-           numberConstrainedImageParameters, numberConstrainedTargetParameters,
-           numberUnknownParameters, degreesOfFreedom, maximumLikelihoodIndex;
-    double minSigmaLatitudeDistance, maxSigmaLatitudeDistance, minSigmaLongitudeDistance,
-           maxSigmaLongitudeDistance, minSigmaRadiusDistance, maxSigmaRadiusDistance;   
-    StatCumProbDistDynCalc cumPro;
-    StatCumProbDistDynCalc cumProRes;
-
-    stream >> id;
-    stream >> correlationMatrix;
-    stream >> numberFixedPoints;
-    stream >> numberIgnoredPoints;
-    stream >> numberHeldImages;
-    stream >> m_rmsXResiduals >> m_rmsYResiduals >> m_rmsXYResiduals;
-    stream >> m_rejectionLimit;
-    stream >> numberObservations;
-    stream >> numberRejectedObservations;
-    stream >> numberUnknownParameters;
-    stream >> numberImageParameters;
-    stream >> numberConstrainedImageParameters;
-    stream >> numberConstrainedPointParameters;
-    stream >> numberConstrainedTargetParameters;
-    stream >> degreesOfFreedom;
-    stream >> m_sigma0;
-    stream >> m_elapsedTime >> m_elapsedTimeErrorProp;
-    stream >> m_converged;
-    stream >> m_rmsImageSampleResiduals >> m_rmsImageLineResiduals;
-    stream >> m_rmsImageResiduals;
-    stream >> m_rmsImageXSigmas >> m_rmsImageYSigmas >> m_rmsImageZSigmas;
-    stream >> m_rmsImageRASigmas >> m_rmsImageDECSigmas >> m_rmsImageTWISTSigmas;
-    stream >> minSigmaLatitudeDistance;
-    stream >> maxSigmaLatitudeDistance;
-    stream >> minSigmaLongitudeDistance;
-    stream >> maxSigmaLongitudeDistance;
-    stream >> minSigmaRadiusDistance;
-    stream >> maxSigmaRadiusDistance;
-    stream >> m_minSigmaLatitudePointId;   
-    stream >> m_maxSigmaLatitudePointId;   
-    stream >> m_minSigmaLongitudePointId;  
-    stream >> m_maxSigmaLongitudePointId;  
-    stream >> m_minSigmaRadiusPointId;     
-    stream >> m_maxSigmaRadiusPointId;     
-    stream >> m_rmsSigmaLatitudeStats >> m_rmsSigmaLongitudeStats >> m_rmsSigmaRadiusStats;
-    stream >> m_maximumLikelihoodFunctions;
-    stream >> maximumLikelihoodIndex;
-    stream >> cumPro >> cumProRes;
-    stream >> m_maximumLikelihoodMedianR2Residuals;
-
-    m_id = NULL;
-    m_id = new QUuid(id);
-
-    m_correlationMatrix = NULL;
-    m_correlationMatrix = new CorrelationMatrix(correlationMatrix);
-
-    m_numberFixedPoints                 = (int)numberFixedPoints;
-    m_numberIgnoredPoints               = (int)numberIgnoredPoints;
-    m_numberHeldImages                  = (int)numberHeldImages;
-    m_numberRejectedObservations        = (int)numberRejectedObservations;
-    m_numberObservations                = (int)numberObservations;
-    m_numberImageParameters             = (int)numberImageParameters;
-    m_numberConstrainedPointParameters  = (int)numberConstrainedPointParameters;
-    m_numberConstrainedImageParameters  = (int)numberConstrainedImageParameters;
-    m_numberConstrainedTargetParameters = (int)numberConstrainedTargetParameters;
-    m_numberUnknownParameters           = (int)numberUnknownParameters;
-    m_degreesOfFreedom                  = (int)degreesOfFreedom;
-    m_maximumLikelihoodIndex            = (int)maximumLikelihoodIndex;
-
-    m_minSigmaLatitudeDistance.setMeters(minSigmaLatitudeDistance); 
-    m_maxSigmaLatitudeDistance.setMeters(maxSigmaLatitudeDistance); 
-    m_minSigmaLongitudeDistance.setMeters(minSigmaLongitudeDistance);
-    m_maxSigmaLongitudeDistance.setMeters(maxSigmaLongitudeDistance);
-    m_minSigmaRadiusDistance.setMeters(minSigmaRadiusDistance);   
-    m_maxSigmaRadiusDistance.setMeters(maxSigmaRadiusDistance);   
-
-    m_cumPro = NULL;
-    m_cumPro = new StatCumProbDistDynCalc(cumPro);
-
-    m_cumProRes = NULL;
-    m_cumProRes = new StatCumProbDistDynCalc(cumProRes);
-    
-    return stream;
-  }
-
-
-  /**
-   * Insertion operator to save the BundleResults object to a QDataStream.
-   * 
-   * @param stream The QDataStream to write to.
-   * @param bundleResults The BundleResults object to save.
-   * 
-   * @return @b QDataStream& A reference to the QDataStream after saving.
-   *
-   * @see write
-   */
-  QDataStream &operator<<(QDataStream &stream, const BundleResults &bundleResults) {
-    return bundleResults.write(stream);
-  }
-
-
-  /**
-   * Extraction operator to read the BundleResults object from a QDataStream.
-   *
-   * @param stream The QDataStream to read from.
-   * @param bundleResults The BundleResults objec to read to.
-   *
-   * @return @b QDataStream& A reference to the QDataStream after reading.
-   * 
-   * @see read
-   */
-  QDataStream &operator>>(QDataStream &stream, BundleResults &bundleResults) {
-    return bundleResults.read(stream);
-  } 
-  
-  
-  /**
-   * Saves an hdf5 group
-   * 
-   * @param locationObject The hdf5 group.
-   * @param localName The filename for the hdf5 group.
-   * 
-   * @throws IException::Unknown "H5 ATTRIBUTE exception handler has detected an error 
-   *                              when invoking the function"
-   * @throws IException::Unknown "Unable to save bundle results information to an HDF5 group."
-   */  
-  void BundleResults::createH5Group(H5::CommonFG &locationObject, QString locationName) const {
-    try {
-      // Try block to detect exceptions raised by any of the calls inside it
-      try {
-        /*
-         * Turn off the auto-printing when failure occurs so that we can
-         * handle the errors appropriately
-         */
-  //      H5::Exception::dontPrint();
-
-        // create a results group to add to the given H5 object
-        QString resultsGroupName = locationName + "/BundleResults"; 
-        H5::Group resultsGroup = locationObject.createGroup(resultsGroupName.toLatin1());
-
-        // use H5S_SCALAR data space type for single valued spaces
-        H5::DataSpace spc(H5S_SCALAR);
-        Attribute att;
-
-        /* 
-         * Add string attributes as predefined data type H5::PredType::C_S1 (string)
-         */ 
-        H5::StrType strDataType;
-        int stringSize = 0; 
-
-        //TODO: finish Correlation Matrix
-        //Create a dataset with compression
-  //    m_correlationMatrix->createH5Group(resultsGroup, resultsGroupName);
-        QString correlationFileName = correlationMatrix().correlationFileName().expanded();
-        stringSize = qMax(correlationFileName.length(), 1);
-        strDataType = H5::StrType(H5::PredType::C_S1, stringSize); 
-        att = resultsGroup.createAttribute("correlationFileName", strDataType, spc);
-        att.write(strDataType, correlationFileName.toStdString());
-
-        QString covarianceFileName = correlationMatrix().covarianceFileName().expanded();
-        stringSize = qMax(covarianceFileName.length(), 1);
-        strDataType = H5::StrType(H5::PredType::C_S1, stringSize); 
-        att = resultsGroup.createAttribute("covarianceFileName", strDataType, spc);
-        att.write(strDataType, covarianceFileName.toStdString());
-        // TODO: table???
-        // correlationMatrix().imagesAndParameters()???
-        // QMapIterator a list of images with their
-        // corresponding parameters...
-
-
-        /* 
-         * Add integer attributes as predefined data type H5::PredType::NATIVE_INT
-         */ 
-        att = resultsGroup.createAttribute("numberFixedPoints", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberFixedPoints);
-
-        att = resultsGroup.createAttribute("numberIgnoredPoints", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberIgnoredPoints);
-
-        att = resultsGroup.createAttribute("numberHeldImages", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberHeldImages);
-
-        att = resultsGroup.createAttribute("numberObservations", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberObservations);
-
-
-        att = resultsGroup.createAttribute("numberRejectedObservations", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberRejectedObservations);
-
-        att = resultsGroup.createAttribute("numberImageParameters", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberImageParameters);
-
-        att = resultsGroup.createAttribute("numberConstrainedPointParameters", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberConstrainedPointParameters);
-
-        att = resultsGroup.createAttribute("numberConstrainedImageParameters", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberConstrainedImageParameters);
-
-        att = resultsGroup.createAttribute("numberUnknownParameters", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_numberUnknownParameters);
-
-        att = resultsGroup.createAttribute("degreesOfFreedom", 
-                                            H5::PredType::NATIVE_INT,
-                                            spc);
-        att.write(H5::PredType::NATIVE_INT, &m_degreesOfFreedom);
-
-        /* 
-         * Add double attributes as predefined data type H5::PredType::NATIVE_DOUBLE
-         */ 
-        att = resultsGroup.createAttribute("rejectionLimit", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_rejectionLimit);
-
-        att = resultsGroup.createAttribute("sigma0", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_sigma0);
-
-        att = resultsGroup.createAttribute("elapsedTime", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_elapsedTime);
-
-        att = resultsGroup.createAttribute("elapsedTimeErrorProp", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_elapsedTimeErrorProp);
-
-        // todo: put rms in their own table/dataset/group???
-        att = resultsGroup.createAttribute("rmsXResiduals", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_rmsXResiduals);
-
-        att = resultsGroup.createAttribute("rmsYResiduals", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_rmsYResiduals);
-
-        att = resultsGroup.createAttribute("rmsXYResiduals", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_rmsXYResiduals);
-
-        att = resultsGroup.createAttribute("rmsSigmaLatitudeStats", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_rmsSigmaLatitudeStats);
-
-        att = resultsGroup.createAttribute("rmsSigmaLongitudeStats", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_rmsSigmaLongitudeStats);
-
-        att = resultsGroup.createAttribute("rmsSigmaRadiusStats", 
-                                            H5::PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(H5::PredType::NATIVE_DOUBLE, &m_rmsSigmaRadiusStats);
-
-        /*
-         * Add bool attributes as predefined data type H5::PredType::NATIVE_HBOOL
-         */ 
-        att = resultsGroup.createAttribute("converged", 
-                                            H5::PredType::NATIVE_HBOOL,
-                                            spc);
-        int converged = (int)m_converged;
-        att.write(H5::PredType::NATIVE_HBOOL, &converged);
-        /*
-         * Add Statistics lists as data sets
-         */ 
-        QString dataSetName;
-        H5::DataSet dataSet;
-        hsize_t dims[1];
-        H5::CompType compoundDataType = Statistics::compoundH5DataType();
-
-
-        // IMAGE LINE RESIDUALS LIST
-        {
-          int listLength = 1;
-          if (!m_rmsImageLineResiduals.isEmpty()) {
-            listLength = m_rmsImageLineResiduals.size();
-          }
-
-          // Set the data space dimension to be the number of Statistics elements in this data set
-          dims[0] = (hsize_t)listLength;
-          H5::DataSpace dataSetSpace(1, dims);
-
-          dataSetName = resultsGroupName + "/RmsImageLineResidualsStatistics"; 
-          dataSet = resultsGroup.createDataSet(dataSetName.toLatin1(),
-                                               compoundDataType,
-                                               dataSetSpace);
-
-          QByteArray byteArray;
-          QDataStream stream(&byteArray, QIODevice::WriteOnly);
-          stream.setByteOrder(QDataStream::LittleEndian);
-          for (int i = 0; i < listLength; i++) {
-            stream << m_rmsImageLineResiduals[i];
-          }
-          char *buf = byteArray.data();
-          dataSet.write(buf, compoundDataType);
-          dataSet.close();
-        }
-
-        // IMAGE SAMPLE RESIDUALS LIST
-        {
-          int listLength = 1;
-          if (!m_rmsImageSampleResiduals.isEmpty()) {
-            listLength = m_rmsImageSampleResiduals.size();
-          }
-
-          // Set the data space dimension to be the number of Statistics elements in this data set
-          dims[0] = (hsize_t)listLength;
-          H5::DataSpace dataSetSpace(1, dims);
-
-          dataSetName = resultsGroupName + "/RmsImageSampleResidualsStatistics"; 
-          dataSet = resultsGroup.createDataSet(dataSetName.toLatin1(),
-                                               compoundDataType,
-                                               dataSetSpace);
-
-          QByteArray byteArray;
-          QDataStream stream(&byteArray, QIODevice::WriteOnly);
-          stream.setByteOrder(QDataStream::LittleEndian);
-          for (int i = 0; i < listLength; i++) {
-            stream << m_rmsImageSampleResiduals[i];
-          }
-          char *buf = byteArray.data();
-          dataSet.write(buf, compoundDataType);
-          dataSet.close();
-        }
-
-        // IMAGE RESIDUALS LIST
-        {
-          int listLength = 1;
-          if (!m_rmsImageResiduals.isEmpty()) {
-            listLength = m_rmsImageResiduals.size();
-          }
-
-          // Set the data space dimension to be the number of Statistics elements in this data set
-          dims[0] = (hsize_t)listLength;
-          H5::DataSpace dataSetSpace(1, dims);
-
-          dataSetName = resultsGroupName + "/RmsImageResidualsStatistics"; 
-          dataSet = resultsGroup.createDataSet(dataSetName.toLatin1(),
-                                               compoundDataType,
-                                               dataSetSpace);
-
-          QByteArray byteArray;
-          QDataStream stream(&byteArray, QIODevice::WriteOnly);
-          stream.setByteOrder(QDataStream::LittleEndian);
-          for (int i = 0; i < listLength; i++) {
-            stream << m_rmsImageResiduals[i];
-          }
-          char *buf = byteArray.data();
-          dataSet.write(buf, compoundDataType);
-          dataSet.close();
-        }
-
-      }  // end of try block
-      // catch failure caused by the Attribute operations
-      catch ( H5::AttributeIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 ATTRIBUTE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataSet operations
-      catch ( H5::DataSetIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA SET exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataSpace operations
-      catch ( H5::DataSpaceIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA SPACE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataType operations
-      catch ( H5::DataTypeIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA TYPE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the H5File operations
-      catch ( H5::FileIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 FILE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the Group operations
-      catch ( H5::GroupIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 GROUP exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      //??? how to improve printed msg using major/minor error codes?
-      catch ( H5::Exception error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 GENERAL exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-    }
-    catch (IException &e) {
-      throw IException(e,
-                       IException::Unknown, 
-                       "Unable to save bundle results information to an HDF5 group.",
-                       _FILEINFO_);
-    }
-      
-  }
-
-  
-  /**
-   * Reads from an hdf5 group.
-   * 
-   * @param locationObject The hdf5 group.
-   * @param locationName The filename of the hdf5 group.
-   * 
-   * @throws IException::Unknown "H5 GENERAL exception handler has detected an error
-   *                              when invoking the function"
-   * @throws IException::Unknown "Unable to read bundle results information to an HDF5 group."
-   */
-  void BundleResults::openH5Group(H5::CommonFG &locationObject, QString locationName) {
-    try {
-      // Try block to detect exceptions raised by any of the calls inside it
-      try {
-        /*
-         * Turn off the auto-printing when failure occurs so that we can
-         * handle the errors appropriately
-         */
-  //      H5::Exception::dontPrint();
-
-        // create a results group to add to the given H5 object
-        QString resultsGroupName = locationName + "/BundleResults"; 
-        H5::Group resultsGroup = locationObject.openGroup(resultsGroupName.toLatin1());
-
-        Attribute att;
-
-        //TODO: finish Correlation Matrix
-        //Create a dataset with compression
-  //    m_correlationMatrix->openH5Group(resultsGroup, resultsGroupName);
-
-        /* 
-         * read string atts as predefined data type H5::PredType::C_S1 (string)
-         */ 
-        H5::StrType strDataType;
-        H5std_string strAttValue;
-
-        att = resultsGroup.openAttribute("correlationFileName");
-        strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());
-        att.read(strDataType, strAttValue);
-        m_correlationMatrix->setCorrelationFileName(QString::fromStdString(strAttValue));
-
-        att = resultsGroup.openAttribute("covarianceFileName");
-        strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());
-        att.read(strDataType, strAttValue);
-        m_correlationMatrix->setCovarianceFileName(QString::fromStdString(strAttValue));
-
-        // TODO: table??? data set???
-        // correlationMatrix().imagesAndParameters()???
-        // QMapIterator a list of images with their
-        // corresponding parameters...
-
-
-        /* 
-         * read int attributes as predefined data type H5::PredType::NATIVE_INT
-         */ 
-        att = resultsGroup.openAttribute("numberFixedPoints");
-        att.read(H5::PredType::NATIVE_INT, &m_numberFixedPoints);
-
-        att = resultsGroup.openAttribute("numberIgnoredPoints");
-        att.read(H5::PredType::NATIVE_INT, &m_numberIgnoredPoints);
-
-        att = resultsGroup.openAttribute("numberHeldImages");
-        att.read(H5::PredType::NATIVE_INT, &m_numberHeldImages);
-
-        att = resultsGroup.openAttribute("numberObservations");
-        att.read(H5::PredType::NATIVE_INT, &m_numberObservations);
-
-        att = resultsGroup.openAttribute("numberRejectedObservations");
-        att.read(H5::PredType::NATIVE_INT, &m_numberRejectedObservations);
-
-        att = resultsGroup.openAttribute("numberImageParameters");
-        att.read(H5::PredType::NATIVE_INT, &m_numberImageParameters);
-
-        att = resultsGroup.openAttribute("numberConstrainedImageParameters");
-        att.read(H5::PredType::NATIVE_INT, &m_numberConstrainedImageParameters);
-
-        att = resultsGroup.openAttribute("numberConstrainedPointParameters");
-        att.read(H5::PredType::NATIVE_INT, &m_numberConstrainedPointParameters);
-
-        att = resultsGroup.openAttribute("numberUnknownParameters");
-        att.read(H5::PredType::NATIVE_INT, &m_numberUnknownParameters);
-
-        att = resultsGroup.openAttribute("degreesOfFreedom");
-        att.read(H5::PredType::NATIVE_INT, &m_degreesOfFreedom);
-
-        /* 
-         * read double attributes as predefined data type H5::PredType::NATIVE_DOUBLE
-         */ 
-        att = resultsGroup.openAttribute("rejectionLimit");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_rejectionLimit);
-
-        att = resultsGroup.openAttribute("sigma0");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_sigma0);
-
-        att = resultsGroup.openAttribute("elapsedTime");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_elapsedTime);
-
-        att = resultsGroup.openAttribute("elapsedTimeErrorProp");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_elapsedTimeErrorProp);
-
-        // todo: put rms in their own table/dataset/group???
-        att = resultsGroup.openAttribute("rmsXResiduals");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_rmsXResiduals);
-
-        att = resultsGroup.openAttribute("rmsYResiduals");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_rmsYResiduals);
-
-        att = resultsGroup.openAttribute("rmsXYResiduals");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_rmsXYResiduals);
-
-        att = resultsGroup.openAttribute("rmsSigmaLatitudeStats");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_rmsSigmaLatitudeStats);
-
-        att = resultsGroup.openAttribute("rmsSigmaLongitudeStats");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_rmsSigmaLongitudeStats);
-
-        att = resultsGroup.openAttribute("rmsSigmaRadiusStats");
-        att.read(H5::PredType::NATIVE_DOUBLE, &m_rmsSigmaRadiusStats);
-
-        /* 
-         * read bool attributes as predefined data type H5::PredType::NATIVE_HBOOL
-         */ 
-        int boolAttValue = 0;
-        att = resultsGroup.openAttribute("converged");
-        att.read(H5::PredType::NATIVE_HBOOL, &boolAttValue);
-        m_converged = (bool)boolAttValue;
-
-        /*
-         * read data sets of Statistics objects
-         */ 
-        QString dataSetName = "";
-        H5::DataSet dataSet;
-        H5::CompType compoundDataType = Statistics::compoundH5DataType();
-
-        // IMAGE LINE RESIDUALS LIST
-        {
-          dataSetName = resultsGroupName + "/RmsImageLineResidualsStatistics";
-          herr_t status = H5Gget_objinfo(resultsGroup.getId(), dataSetName.toLatin1(), 0, NULL);
-          if (status != 0) {
-            // group DNE...
-            qDebug() << "didn't find or couldn't read stats list.";//???
-          }
-          try {
-
-            // if this doesn't throw an error, then the group exists???
-            H5G_stat_t info;
-            resultsGroup.getObjinfo(dataSetName.toLatin1(), info);
-
-            dataSet = resultsGroup.openDataSet(dataSetName.toLatin1());
-            H5::DataSpace dataSetSpace = dataSet.getSpace();
-
-            char statsList[dataSet.getStorageSize()];
-            dataSet.read(statsList, compoundDataType);
-    
-            int listLength = dataSetSpace.getSimpleExtentNpoints();
-            int statsSize = compoundDataType.getSize();
-            for (int i = 0; i < listLength; i++) {
-              QByteArray byteArray(&(statsList[i*statsSize]), statsSize);
-              QDataStream stream(&byteArray, QIODevice::ReadOnly);
-              stream.setByteOrder(QDataStream::LittleEndian);
-      
-              Statistics tempStats;
-              stream >> tempStats;
-              m_rmsImageLineResiduals.append(tempStats);
-            }
-    
-          } 
-          catch (H5::GroupIException groupError) {
-            // don't do anything???
-          }
-        }
-          
-        // IMAGE SAMPLE RESIDUALS LIST
-        {
-          dataSetName = resultsGroupName + "/RmsImageSampleResidualsStatistics"; 
-          herr_t status = H5Gget_objinfo(resultsGroup.getId(), dataSetName.toLatin1(), 0, NULL);
-          if (status != 0) {
-            // group DNE...
-            qDebug() << "didn't find or couldn't read stats list.";
-          }
-          try {
-
-            // if this doesn't throw an error, then the group exists???
-            H5G_stat_t info;
-            resultsGroup.getObjinfo(dataSetName.toLatin1(), info);
-
-            dataSet = resultsGroup.openDataSet(dataSetName.toLatin1());
-            H5::DataSpace dataSetSpace = dataSet.getSpace();
-
-            char statsList[dataSet.getStorageSize()];
-            dataSet.read(statsList, compoundDataType);
-    
-            int listLength = dataSetSpace.getSimpleExtentNpoints();
-            int statsSize = compoundDataType.getSize();
-            for (int i = 0; i < listLength; i++) {
-              QByteArray byteArray(&(statsList[i*statsSize]), statsSize);
-              QDataStream stream(&byteArray, QIODevice::ReadOnly);
-              stream.setByteOrder(QDataStream::LittleEndian);
-      
-              Statistics tempStats;
-              stream >> tempStats;
-              m_rmsImageLineResiduals.append(tempStats);
-            }
-    
-          } 
-          catch (H5::GroupIException groupError) {
-            // don't do anything???
-          }
-        }
-        // IMAGE RESIDUALS LIST
-        {
-          dataSetName = resultsGroupName + "/RmsImageResidualsStatistics"; 
-          herr_t status = H5Gget_objinfo(resultsGroup.getId(), dataSetName.toLatin1(), 0, NULL);
-          if (status != 0) {
-            // group DNE...
-            qDebug() << "didn't find or couldn't read stats list.";//???
-          }
-          try {
-
-            // if this doesn't throw an error, then the group exists???
-            H5G_stat_t info;
-            resultsGroup.getObjinfo(dataSetName.toLatin1(), info);
-
-            dataSet = resultsGroup.openDataSet(dataSetName.toLatin1());
-            H5::DataSpace dataSetSpace = dataSet.getSpace();
-
-            char statsList[dataSet.getStorageSize()];
-            dataSet.read(statsList, compoundDataType);
-    
-            int listLength = dataSetSpace.getSimpleExtentNpoints();
-            int statsSize = compoundDataType.getSize();
-            for (int i = 0; i < listLength; i++) {
-              QByteArray byteArray(&(statsList[i*statsSize]), statsSize);
-              QDataStream stream(&byteArray, QIODevice::ReadOnly);
-              stream.setByteOrder(QDataStream::LittleEndian);
-      
-              Statistics tempStats;
-              stream >> tempStats;
-              m_rmsImageLineResiduals.append(tempStats);
-            }
-    
-          } 
-          catch (H5::GroupIException groupError) {
-            // don't do anything???
-          }
-        }
-      }
-      catch (H5::Exception error) {  //??? how to improve printed msg using major/minor error codes?
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 GENERAL exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-    }
-    catch (IException &e) {
-      throw IException(e,
-                       IException::Unknown, 
-                       "Unable to read bundle results information to an HDF5 group.",
-                       _FILEINFO_);
-    }
-  }
 }
diff --git a/isis/src/control/objs/BundleResults/BundleResults.h b/isis/src/control/objs/BundleResults/BundleResults.h
index 2304414a779a5e4916cc405417364e878fa23b4e..69a5bbce99fcb19f7f8b578c2db7b3cf227e5888 100644
--- a/isis/src/control/objs/BundleResults/BundleResults.h
+++ b/isis/src/control/objs/BundleResults/BundleResults.h
@@ -30,11 +30,6 @@
 #include 
 #include 
 
-// hdf5 Library
-#include 
-#include 
-#include 
-
 // Isis Library
 #include "BundleControlPoint.h"
 #include "BundleObservationVector.h"
@@ -63,8 +58,8 @@ namespace Isis {
   class XmlStackedHandlerReader;
 
   /**
-   * A container class for statistical results from a BundleAdjust solution. 
-   *  
+   * A container class for statistical results from a BundleAdjust solution.
+   *
    * @author 2014-07-01 Jeannie Backer
    *
    * @internal
@@ -86,6 +81,9 @@ namespace Isis {
    *   @history 2016-08-15 Jesse Mapel - Added iteration count, radians to meters conversion,
    *                           observation vector, bundle control point vector, and output control
    *                           network for write methods in BundleSolutionInfo.  Fixes #4159.
+   *   @history 2017-04-24 Ian Humphrey - Removed pvlObject() method. Commented out m_id serialization
+   *                           for save() (causes segfault in unit test for empty xml). Fixes #4797.
+   *   @history 2017-04-27 J Bonn - Updated serialization code and tests.
    */
   class BundleResults : public QObject {
     Q_OBJECT
@@ -173,7 +171,7 @@ namespace Isis {
       void setOutputControlNet(ControlNetQsp outNet);
       void setIterations(int iterations);
       void setObservations(BundleObservationVector observations);
-      
+
       // Accessors...
       QList rmsImageSampleResiduals() const;
       QList rmsImageLineResiduals() const;
@@ -221,7 +219,7 @@ namespace Isis {
       ControlNetQsp outputControlNet() const;
       int iterations() const;
       const BundleObservationVector &observations() const;
-      
+
       int numberMaximumLikelihoodModels() const;
       int maximumLikelihoodModelIndex() const;
       StatCumProbDistDynCalc cumulativeProbabilityDistribution() const;
@@ -235,8 +233,6 @@ namespace Isis {
       bool setNumberHeldImages(SerialNumberList pHeldSnList,
                                SerialNumberList *pSnList);
 
-      PvlObject pvlObject(QString name = "BundleResults") const;
-
       // Correlation Matrix accessors for cnetsuite and mutators for bundle adjust.
       CorrelationMatrix correlationMatrix() const;
       void setCorrMatCovFileName(FileName name);
@@ -244,23 +240,14 @@ namespace Isis {
 
       // TODO: does xml stuff need project???
       void save(QXmlStreamWriter &stream, const Project *project) const;
-      
-      QDataStream &write(QDataStream &stream) const;
-      QDataStream &read(QDataStream &stream);
 
-      void createH5Group(hid_t locationId, QString locationName) const;// delete these
-      void parseH5Group(hid_t locationId, QString locationName);       // delete these
-
-      void createH5Group(H5::CommonFG &locationObject, QString locationName) const;
-      void openH5Group(H5::CommonFG &locationObject, QString locationName);
-      BundleResults(H5::CommonFG &locationObject, QString locationName);
 
     private:
       /**
        * This class is an XmlHandler used to read and write BundleResults objects
        * from and to XML files.  Documentation will be updated when it is decided
        * if XML support will remain.
-       * 
+       *
        * @author 2014-07-28 Jeannie Backer
        *
        * @internal
@@ -270,16 +257,16 @@ namespace Isis {
           // TODO: does xml stuff need project???
           XmlHandler(BundleResults *statistics, Project *project);
           ~XmlHandler();
-   
+
           virtual bool startElement(const QString &namespaceURI, const QString &localName,
                                     const QString &qName, const QXmlAttributes &atts);
           virtual bool characters(const QString &ch);
           virtual bool endElement(const QString &namespaceURI, const QString &localName,
                                   const QString &qName);
-   
+
         private:
           Q_DISABLE_COPY(XmlHandler);
-   
+
           BundleResults *m_xmlHandlerBundleResults;
           Project *m_xmlHandlerProject;   // TODO: does xml stuff need project???
           QString m_xmlHandlerCharacters;
@@ -300,32 +287,21 @@ namespace Isis {
           QMap m_xmlHandlerCorrelationMap;
       };
 
-      /**
-       * A unique ID for this object (useful for others to reference this object
-       *   when saving to disk).
-       */
-      QUuid *m_id;
-//???      QString m_instrumentId;               //!< The spacecraft instrument id for this observation.
       CorrelationMatrix *m_correlationMatrix; //!< The correlation matrix from the BundleAdjust.
 
-// ???       Statistics m_statsx;                       //!<  x errors
-// ???       Statistics m_statsy;                       //!<  y errors
-// ???       Statistics m_statsrx;                      //!<  x residuals
-// ???       Statistics m_statsry;                      //!<  y residuals
-// ???       Statistics m_statsrxy;                     //!< xy residuals
 
       int m_numberFixedPoints;                //!< number of 'fixed' (ground) points (define)
       // Currently set but unused
       int m_numberIgnoredPoints;              //!< number of ignored points
-      int m_numberHeldImages;                 //!< number of 'held' images (define)          
+      int m_numberHeldImages;                 //!< number of 'held' images (define)
 
       // The following three members are set but unused.
       double m_rmsXResiduals;                 //!< rms of x residuals
       double m_rmsYResiduals;                 //!< rms of y residuals
       double m_rmsXYResiduals;                //!< rms of all x and y residuals
-      
+
       double m_rejectionLimit;                //!< current rejection limit
-      // TODO:??? reorder read/write data stream, init, copy constructor, operator= 
+      // TODO:??? reorder read/write data stream, init, copy constructor, operator=
       int m_numberObservations;                //!< number of image coordinate observations
       int m_numberRejectedObservations;        //!< number of rejected image coordinate observations
       int m_numberUnknownParameters;           //!< total number of parameters to solve for
@@ -341,7 +317,7 @@ namespace Isis {
       bool m_converged;
 
       // Variables for output methods in BundleSolutionInfo
-      
+
       QVector m_bundleControlPoints; /**< The vector of BundleControlPoints
                                                                  from BundleAdjust.  Equivalent to
                                                                  the output control net minus
@@ -360,13 +336,13 @@ namespace Isis {
 
       //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       // variables set in computeBundleResults()
-      //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 
-      // QList??? jigsaw apptest gives - ASSERT failure in QList::operator[]: "index out of range", 
+      //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+      // QList??? jigsaw apptest gives - ASSERT failure in QList::operator[]: "index out of range",
       QList m_rmsImageSampleResiduals;/**< List of RMS image sample residual statistics
                                                        for each image in the bundle  */
       QList m_rmsImageLineResiduals;  /**< List of RMS image line residual statistics
                                                        for each image in the bundle  */
-      QList m_rmsImageResiduals;      /**< RMS image sample and line residual statistics 
+      QList m_rmsImageResiduals;      /**< RMS image sample and line residual statistics
                                                        for each image in the bundle  */
 
       //!< The root mean square image x sigmas.
@@ -403,20 +379,20 @@ namespace Isis {
       //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       // variables for maximum likelihood estimation
       //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-      
+
       //!< The maximum likelihood models and their quantiles.
       QList< QPair< MaximumLikelihoodWFunctions, double > > m_maximumLikelihoodFunctions;
 
-      /**< The number of maximum likelihood estimation 
+      /**< The number of maximum likelihood estimation
       models. Up to three different models can be used
       in succession.*/
-      /**< This class is used to reweight observations in 
-           order to achieve more robust parameter 
-           estimation, up to three different maximum 
+      /**< This class is used to reweight observations in
+           order to achieve more robust parameter
+           estimation, up to three different maximum
            likelihood estimation models can be used in
            succession.*/
       /**< Quantiles of the |residual| distribution to be
-           used for tweaking constants of the maximum 
+           used for tweaking constants of the maximum
            probability models.*/
       int m_maximumLikelihoodIndex;            /**< This count keeps track of which stage of the
                                                     maximum likelihood adjustment the bundle is
@@ -426,16 +402,14 @@ namespace Isis {
                                                     |R^2 residuals|, quantiles of this distribution
                                                     are used to adjust the maximum likelihood
                                                     functions dynamically iteration by iteration.*/
-      StatCumProbDistDynCalc *m_cumProRes;     /**< This class keeps track of the cumulative 
+      StatCumProbDistDynCalc *m_cumProRes;     /**< This class keeps track of the cumulative
                                                     probability distribution of residuals
-                                                    (in unweighted pixels), this is used for 
+                                                    (in unweighted pixels), this is used for
                                                     reporting, and not for computation.*/
-      double m_maximumLikelihoodMedianR2Residuals; /**< Median of R^2 residuals.*/ 
-       
+      double m_maximumLikelihoodMedianR2Residuals; /**< Median of R^2 residuals.*/
+
   };
-  // operators to read/write BundleResults to/from binary disk file
-  QDataStream &operator<<(QDataStream &stream, const BundleResults &bundleResults);
-  QDataStream &operator>>(QDataStream &stream, BundleResults &bundleResults);
+
 };
 
 Q_DECLARE_METATYPE(Isis::BundleResults);
diff --git a/isis/src/control/objs/BundleResults/BundleResults.truth b/isis/src/control/objs/BundleResults/BundleResults.truth
old mode 100755
new mode 100644
index 4f9286df54d8efeb7964f15fc69cbba2067ede11..bd039dce5fadf9d7efb56ba710de65c385db6c5b
--- a/isis/src/control/objs/BundleResults/BundleResults.truth
+++ b/isis/src/control/objs/BundleResults/BundleResults.truth
@@ -1,266 +1,282 @@
 Unit test for BundleResults...
-Printing PVL group with results from the default constructor...
-Object = DefaultResultsObject
-  NumberFixedPoints                 = 0
-  NumberIgnoredPoints               = 0
-  NumberHeldImages                  = 0
-  RMSResidualX                      = 0.0
-  RMSResidualY                      = 0.0
-  RMSResidualXY                     = 0.0
-  RejectionLimit                    = 0.0
-  RadiansToMeters                   = 0.0
-  NumberRejectedObservations        = 0
-  NumberObservations                = 0
-  NumberImageParameters             = 0
-  NumberConstrainedPointParameters  = 0
-  NumberConstrainedImageParameters  = 0
-  NumberConstrainedTargetParameters = 0
-  NumberUnknownParameters           = 0
-  DegreesOfFreedom                  = -1
-  Sigma0                            = 0.0
-  ElapsedTime                       = 0.0
-  ElapsedTimeErrorProp              = 0.0
-  Iterations                        = 0
-  Converged                         = No
-  MinSigmaLatitude                  = 1000000000000.0
-  MinSigmaLatitudePointId           = Null
-  MaxSigmaLatitude                  = 0.0
-  MaxSigmaLatitudePointId           = Null
-  MinSigmaLongitude                 = 1000000000000.0
-  MinSigmaLongitudePointId          = Null
-  MaxSigmaLongitude                 = 0.0
-  MaxSigmaLongitudePointId          = Null
-  MinSigmaRadius                    = 1000000000000.0
-  MinSigmaRadiusPointId             = Null
-  MaxSigmaRadius                    = 0.0
-  MaxSigmaRadiusPointId             = Null
-  RmsSigmaLat                       = 0.0
-  RmsSigmaLon                       = 0.0
-  RmsSigmaRad                       = 0.0
-  NumberMaximumLikelihoodModels     = 0
+XML from the default constructor...
+
+
+    
+        
+    
+    
+        0
+        0
+        0
+        0.0
+        0
+        0
+        0
+        0
+        0
+        0
+        0
+        -1
+        0.0
+        No
+    
+    
+        
+        
+        
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+            
+        
+    
+    
+    
+        
+        
+        
+        
+        
+        
+    
+    
+        
+        
+    
+ 
 
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = Null
-    CorrelationMatrixFileName = Null
-
-    Group = ImagesAndParameters
-    End_Group
-  End_Object
-End_Object
 
 Testing copy constructor...
-Object = CopyResultsObject
-  NumberFixedPoints                 = 0
-  NumberIgnoredPoints               = 0
-  NumberHeldImages                  = 0
-  RMSResidualX                      = 0.0
-  RMSResidualY                      = 0.0
-  RMSResidualXY                     = 0.0
-  RejectionLimit                    = 0.0
-  RadiansToMeters                   = 0.0
-  NumberRejectedObservations        = 0
-  NumberObservations                = 0
-  NumberImageParameters             = 0
-  NumberConstrainedPointParameters  = 0
-  NumberConstrainedImageParameters  = 0
-  NumberConstrainedTargetParameters = 0
-  NumberUnknownParameters           = 0
-  DegreesOfFreedom                  = -1
-  Sigma0                            = 0.0
-  ElapsedTime                       = 0.0
-  ElapsedTimeErrorProp              = 0.0
-  Iterations                        = 0
-  Converged                         = No
-  MinSigmaLatitude                  = 1000000000000.0
-  MinSigmaLatitudePointId           = Null
-  MaxSigmaLatitude                  = 0.0
-  MaxSigmaLatitudePointId           = Null
-  MinSigmaLongitude                 = 1000000000000.0
-  MinSigmaLongitudePointId          = Null
-  MaxSigmaLongitude                 = 0.0
-  MaxSigmaLongitudePointId          = Null
-  MinSigmaRadius                    = 1000000000000.0
-  MinSigmaRadiusPointId             = Null
-  MaxSigmaRadius                    = 0.0
-  MaxSigmaRadiusPointId             = Null
-  RmsSigmaLat                       = 0.0
-  RmsSigmaLon                       = 0.0
-  RmsSigmaRad                       = 0.0
-  NumberMaximumLikelihoodModels     = 0
 
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = Null
-    CorrelationMatrixFileName = Null
+
+    
+        
+    
+    
+        0
+        0
+        0
+        0.0
+        0
+        0
+        0
+        0
+        0
+        0
+        0
+        -1
+        0.0
+        No
+    
+    
+        
+        
+        
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+            
+        
+    
+    
+    
+        
+        
+        
+        
+        
+        
+    
+    
+        
+        
+    
+ 
 
-    Group = ImagesAndParameters
-    End_Group
-  End_Object
-End_Object
 
 Add maximum likelihood models, then test the assignment operator...
 
 Testing assignment operator=...
-Maximum Likelihood Tier: 0
-Median of R^2 residuals:  0.495050
-Maximum Likelihood Tier: 1
-Median of R^2 residuals:  0.495050
-Maximum Likelihood Tier: 2
-Median of R^2 residuals:  0.495050
-Maximum Likelihood Tier: 3
-
-Object = SelfAssignedResultsObject
-  NumberFixedPoints                  = 0
-  NumberIgnoredPoints                = 0
-  NumberHeldImages                   = 0
-  RMSResidualX                       = 0.0
-  RMSResidualY                       = 0.0
-  RMSResidualXY                      = 0.0
-  RejectionLimit                     = 0.0
-  RadiansToMeters                    = 0.0
-  NumberRejectedObservations         = 0
-  NumberObservations                 = 0
-  NumberImageParameters              = 0
-  NumberConstrainedPointParameters   = 0
-  NumberConstrainedImageParameters   = 0
-  NumberConstrainedTargetParameters  = 0
-  NumberUnknownParameters            = 0
-  DegreesOfFreedom                   = -1
-  Sigma0                             = 0.0
-  ElapsedTime                        = 0.0
-  ElapsedTimeErrorProp               = 0.0
-  Iterations                         = 0
-  Converged                          = No
-  MinSigmaLatitude                   = 1000000000000.0
-  MinSigmaLatitudePointId            = Null
-  MaxSigmaLatitude                   = 0.0
-  MaxSigmaLatitudePointId            = Null
-  MinSigmaLongitude                  = 1000000000000.0
-  MinSigmaLongitudePointId           = Null
-  MaxSigmaLongitude                  = 0.0
-  MaxSigmaLongitudePointId           = Null
-  MinSigmaRadius                     = 1000000000000.0
-  MinSigmaRadiusPointId              = Null
-  MaxSigmaRadius                     = 0.0
-  MaxSigmaRadiusPointId              = Null
-  RmsSigmaLat                        = 0.0
-  RmsSigmaLon                        = 0.0
-  RmsSigmaRad                        = 0.0
-  NumberMaximumLikelihoodModels      = 3
-  MaximumLikelihoodModels            = (Huber, Welsch, Chen)
-  MaximumLikelihoodQuantiles         = (0.1, 0.2, 0.3)
-  MaximumLikelihoodMedianR2Residuals = 0.49504950495049
-
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = Null
-    CorrelationMatrixFileName = Null
 
-    Group = ImagesAndParameters
-    End_Group
-  End_Object
-End_Object
+
+    
+        
+    
+    
+        0
+        0
+        0
+        0.0
+        0
+        0
+        0
+        0
+        0
+        0
+        0
+        -1
+        0.0
+        No
+    
+    
+        
+        
+        
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+            
+        
+    
+    
+    
+        
+        
+        
+        
+        
+        
+    
+    
+        
+        
+        
+        
+        
+    
+ 
+
+
+
+
+    
+        
+    
+    
+        0
+        0
+        0
+        0.0
+        0
+        0
+        0
+        0
+        0
+        0
+        0
+        -1
+        0.0
+        No
+    
+    
+        
+        
+        
+            
+            
+            
+        
+        
+            
+            
+            
+            
+            
+            
+        
+    
+    
+    
+        
+        
+        
+        
+        
+        
+    
+    
+        
+        
+        
+        
+        
+    
+ 
 
-Object = AssignedNewResultsObject
-  NumberFixedPoints                  = 0
-  NumberIgnoredPoints                = 0
-  NumberHeldImages                   = 0
-  RMSResidualX                       = 0.0
-  RMSResidualY                       = 0.0
-  RMSResidualXY                      = 0.0
-  RejectionLimit                     = 0.0
-  RadiansToMeters                    = 0.0
-  NumberRejectedObservations         = 0
-  NumberObservations                 = 0
-  NumberImageParameters              = 0
-  NumberConstrainedPointParameters   = 0
-  NumberConstrainedImageParameters   = 0
-  NumberConstrainedTargetParameters  = 0
-  NumberUnknownParameters            = 0
-  DegreesOfFreedom                   = -1
-  Sigma0                             = 0.0
-  ElapsedTime                        = 0.0
-  ElapsedTimeErrorProp               = 0.0
-  Iterations                         = 0
-  Converged                          = No
-  MinSigmaLatitude                   = 1000000000000.0
-  MinSigmaLatitudePointId            = Null
-  MaxSigmaLatitude                   = 0.0
-  MaxSigmaLatitudePointId            = Null
-  MinSigmaLongitude                  = 1000000000000.0
-  MinSigmaLongitudePointId           = Null
-  MaxSigmaLongitude                  = 0.0
-  MaxSigmaLongitudePointId           = Null
-  MinSigmaRadius                     = 1000000000000.0
-  MinSigmaRadiusPointId              = Null
-  MaxSigmaRadius                     = 0.0
-  MaxSigmaRadiusPointId              = Null
-  RmsSigmaLat                        = 0.0
-  RmsSigmaLon                        = 0.0
-  RmsSigmaRad                        = 0.0
-  NumberMaximumLikelihoodModels      = 3
-  MaximumLikelihoodModels            = (Huber, Welsch, Chen)
-  MaximumLikelihoodQuantiles         = (0.1, 0.2, 0.3)
-  MaximumLikelihoodMedianR2Residuals = 0.49504950495049
-
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = Null
-    CorrelationMatrixFileName = Null
-
-    Group = ImagesAndParameters
-    End_Group
-  End_Object
-End_Object
 
 Testing mutator methods...
-Object = MutatedResultsObject
-  NumberFixedPoints                  = 1
-  NumberIgnoredPoints                = 1
-  NumberHeldImages                   = 1
-  RMSResidualX                       = 4.0
-  RMSResidualY                       = 5.0
-  RMSResidualXY                      = 6.0
-  RejectionLimit                     = 7.0
-  RadiansToMeters                    = 23.68
-  NumberRejectedObservations         = 8
-  NumberObservations                 = 9
-  NumberImageParameters              = 10
-  NumberConstrainedPointParameters   = 11
-  NumberConstrainedImageParameters   = 10
-  NumberConstrainedTargetParameters  = 2
-  NumberUnknownParameters            = 13
-  DegreesOfFreedom                   = 14
-  Sigma0                             = 15.0
-  ElapsedTime                        = 16.0
-  ElapsedTimeErrorProp               = 17.0
-  Iterations                         = 6
-  Converged                          = Yes
-  MinSigmaLatitude                   = 0.5
-  MinSigmaLatitudePointId            = MinLatId
-  MaxSigmaLatitude                   = 89.6
-  MaxSigmaLatitudePointId            = MaxLatId
-  MinSigmaLongitude                  = 0.7
-  MinSigmaLongitudePointId           = MinLonId
-  MaxSigmaLongitude                  = 179.2
-  MaxSigmaLongitudePointId           = MaxLonId
-  MinSigmaRadius                     = 0.9
-  MinSigmaRadiusPointId              = MinRadId
-  MaxSigmaRadius                     = 354.4
-  MaxSigmaRadiusPointId              = MaxRadId
-  RmsSigmaLat                        = 0.123
-  RmsSigmaLon                        = 0.456
-  RmsSigmaRad                        = 0.789
-  NumberMaximumLikelihoodModels      = 3
-  MaximumLikelihoodModels            = (Huber, Welsch, Chen)
-  MaximumLikelihoodQuantiles         = (0.1, 0.2, 0.3)
-  MaximumLikelihoodMedianR2Residuals = 0.49504950495049
 
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = Null
-    CorrelationMatrixFileName = Null
+
+    
+        
+    
+    
+        1
+        1
+        1
+        7.0
+        8
+        9
+        10
+        11
+        10
+        2
+        13
+        14
+        15.0
+        Yes
+    
+    
+        
+        
+        
+            
+                
+                    
+                
+            
+        
+    
+    
+    
+        
+        
+        
+        
+        
+        
+    
+    
+        
+        
+        
+        
+        
+    
+ 
 
-    Group = ImagesAndParameters
-    End_Group
-  End_Object
-End_Object
 
 
 Testing more computation methods...
@@ -287,161 +303,131 @@ bundle observations
 "InstrumentId1"
 ("TestImageFileName")
 
-Testing serialization...
-Object = BundleResults
-  NumberFixedPoints                  = 1
-  NumberIgnoredPoints                = 1
-  NumberHeldImages                   = 1
-  RMSResidualX                       = 4.0
-  RMSResidualY                       = 5.0
-  RMSResidualXY                      = 6.0
-  RejectionLimit                     = 7.0
-  RadiansToMeters                    = 0.0
-  NumberRejectedObservations         = 8
-  NumberObservations                 = 9
-  NumberImageParameters              = 10
-  NumberConstrainedPointParameters   = 11
-  NumberConstrainedImageParameters   = 10
-  NumberConstrainedTargetParameters  = 2
-  NumberUnknownParameters            = 32
-  DegreesOfFreedom                   = 0
-  Sigma0                             = 0.0
-  ElapsedTime                        = 16.0
-  ElapsedTimeErrorProp               = 17.0
-  Iterations                         = 0
-  Converged                          = Yes
-  MinSigmaLatitude                   = 0.5
-  MinSigmaLatitudePointId            = MinLatId
-  MaxSigmaLatitude                   = 89.6
-  MaxSigmaLatitudePointId            = MaxLatId
-  MinSigmaLongitude                  = 0.7
-  MinSigmaLongitudePointId           = MinLonId
-  MaxSigmaLongitude                  = 179.2
-  MaxSigmaLongitudePointId           = MaxLonId
-  MinSigmaRadius                     = 0.9
-  MinSigmaRadiusPointId              = MinRadId
-  MaxSigmaRadius                     = 354.4
-  MaxSigmaRadiusPointId              = MaxRadId
-  RmsSigmaLat                        = 0.123
-  RmsSigmaLon                        = 0.456
-  RmsSigmaRad                        = 0.789
-  NumberMaximumLikelihoodModels      = 3
-  MaximumLikelihoodModels            = (Huber, Welsch, Chen)
-  MaximumLikelihoodQuantiles         = (0.1, 0.2, 0.3)
-  MaximumLikelihoodMedianR2Residuals = 0.49504950495049
-
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = covariance.dat
-    CorrelationMatrixFileName = covariance.dat
-
-    Group = ImagesAndParameters
-      img1 = "param1,param2"
-      img2 = "param3,param4,param5"
-    End_Group
-  End_Object
-End_Object
-
-Testing XML write/read...
-Object = BundleResultsFromXml
-  NumberFixedPoints                  = 1
-  NumberIgnoredPoints                = 1
-  NumberHeldImages                   = 1
-  RMSResidualX                       = 4.0
-  RMSResidualY                       = 5.0
-  RMSResidualXY                      = 6.0
-  RejectionLimit                     = 7.0
-  RadiansToMeters                    = 0.0
-  NumberRejectedObservations         = 8
-  NumberObservations                 = 9
-  NumberImageParameters              = 10
-  NumberConstrainedPointParameters   = 11
-  NumberConstrainedImageParameters   = 10
-  NumberConstrainedTargetParameters  = 2
-  NumberUnknownParameters            = 32
-  DegreesOfFreedom                   = 0
-  Sigma0                             = 0.0
-  ElapsedTime                        = 16.0
-  ElapsedTimeErrorProp               = 17.0
-  Iterations                         = 0
-  Converged                          = Yes
-  MinSigmaLatitude                   = 0.5
-  MinSigmaLatitudePointId            = MinLatId
-  MaxSigmaLatitude                   = 89.6
-  MaxSigmaLatitudePointId            = MaxLatId
-  MinSigmaLongitude                  = 0.7
-  MinSigmaLongitudePointId           = MinLonId
-  MaxSigmaLongitude                  = 179.2
-  MaxSigmaLongitudePointId           = MaxLonId
-  MinSigmaRadius                     = 0.9
-  MinSigmaRadiusPointId              = MinRadId
-  MaxSigmaRadius                     = 354.4
-  MaxSigmaRadiusPointId              = MaxRadId
-  RmsSigmaLat                        = 0.123
-  RmsSigmaLon                        = 0.456
-  RmsSigmaRad                        = 0.789
-  NumberMaximumLikelihoodModels      = 3
-  MaximumLikelihoodModels            = (Huber, Welsch, Chen)
-  MaximumLikelihoodQuantiles         = (0.1, 0.2, 0.3)
-  MaximumLikelihoodMedianR2Residuals = 0.49504950495049
-
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = covariance.dat
-    CorrelationMatrixFileName = covariance.dat
-
-    Group = ImagesAndParameters
-      img1 = "param1,param2"
-      img2 = "param3,param4,param5"
-    End_Group
-  End_Object
-End_Object
-
-Object = BundleResultsFromEmptyXml
-  NumberFixedPoints                 = 0
-  NumberIgnoredPoints               = 0
-  NumberHeldImages                  = 0
-  RMSResidualX                      = 0.0
-  RMSResidualY                      = 0.0
-  RMSResidualXY                     = 0.0
-  RejectionLimit                    = 0.0
-  RadiansToMeters                   = 0.0
-  NumberRejectedObservations        = 0
-  NumberObservations                = 0
-  NumberImageParameters             = 0
-  NumberConstrainedPointParameters  = 0
-  NumberConstrainedImageParameters  = 0
-  NumberConstrainedTargetParameters = 0
-  NumberUnknownParameters           = 0
-  DegreesOfFreedom                  = -1
-  Sigma0                            = 0.0
-  ElapsedTime                       = 0.0
-  ElapsedTimeErrorProp              = 0.0
-  Iterations                        = 0
-  Converged                         = No
-  MinSigmaLatitude                  = 1000000000000.0
-  MinSigmaLatitudePointId           = Null
-  MaxSigmaLatitude                  = 0.0
-  MaxSigmaLatitudePointId           = Null
-  MinSigmaLongitude                 = 1000000000000.0
-  MinSigmaLongitudePointId          = Null
-  MaxSigmaLongitude                 = 0.0
-  MaxSigmaLongitudePointId          = Null
-  MinSigmaRadius                    = 1000000000000.0
-  MinSigmaRadiusPointId             = Null
-  MaxSigmaRadius                    = 0.0
-  MaxSigmaRadiusPointId             = Null
-  RmsSigmaLat                       = 0.0
-  RmsSigmaLon                       = 0.0
-  RmsSigmaRad                       = 0.0
-  NumberMaximumLikelihoodModels     = 0
-
-  Object = CorrelationMatrixData
-    CovarianceMatrixFileName  = Null
-    CorrelationMatrixFileName = Null
+Testing XML serialization 1: round trip serialization of fully populated BundleSettings object...
+Serializing test XML object to file...
+
+
+    
+        
+            
+                param1
+                param2
+            
+            
+                param3
+                param4
+                param5
+            
+        
+    
+    
+        1
+        1
+        1
+        7.0
+        8
+        9
+        10
+        11
+        10
+        2
+        32
+        0
+        0.0
+        Yes
+    
+    
+        
+        
+        
+            
+                
+                    
+                
+            
+        
+    
+    
+    
+        
+        
+        
+        
+        
+        
+    
+    
+        
+        
+        
+        
+        
+    
+ 
+
+
+Testing XML: reading serialized BundleResults back in...
+Testing XML: Object deserialized as (should match object above):
+
+
+    
+        
+            
+                param1
+                param2
+            
+            
+                param3
+                param4
+                param5
+            
+        
+    
+    
+        1
+        1
+        1
+        7.0
+        8
+        9
+        10
+        11
+        10
+        2
+        32
+        0
+        0.0
+        Yes
+    
+    
+        
+        
+        
+            
+                
+                    
+                
+            
+        
+    
+    
+    
+        
+        
+        
+        
+        
+        
+    
+    
+        
+        
+        
+        
+        
+    
+ 
 
-    Group = ImagesAndParameters
-    End_Group
-  End_Object
-End_Object
 
 Testing error throws...
 **I/O ERROR** Computed degrees of freedom [-1] is invalid.
diff --git a/isis/src/control/objs/BundleResults/unitTest.cpp b/isis/src/control/objs/BundleResults/unitTest.cpp
index e8a9c62faffe5dbd4474045fc7d2e089284c7d50..79a99c157511a6bbfb5dc13e060bfc1df897f423 100755
--- a/isis/src/control/objs/BundleResults/unitTest.cpp
+++ b/isis/src/control/objs/BundleResults/unitTest.cpp
@@ -27,12 +27,14 @@
 using namespace std;
 using namespace Isis;
 
+void printXml(const BundleResults &);
+
 namespace Isis {
   /**
    * This class is used to test BundleResults' XmlHandler class.
-   * 
+   *
    * @author 2014-07-28 Jeannie Backer
-   * 
+   *
    * @internal
    *   @history 2014-07-28 Jeannie Backer - Original version.
    */
@@ -45,7 +47,7 @@ namespace Isis {
        * @param reader The XmlStackedHandlerReader that reads the xml file.
        * @param xmlFile The xml file to construct the tester from.
        */
-      BundleResultsXmlHandlerTester(Project *project, XmlStackedHandlerReader *reader, 
+      BundleResultsXmlHandlerTester(Project *project, XmlStackedHandlerReader *reader,
                                      FileName xmlFile) : BundleResults(project, reader) {
 
         QString xmlPath(xmlFile.expanded());
@@ -60,7 +62,7 @@ namespace Isis {
         QXmlInputSource xmlInputSource(&file);
         bool success = reader->parse(xmlInputSource);
         if (!success) {
-          throw IException(IException::Unknown, 
+          throw IException(IException::Unknown,
                            QString("Failed to parse xml file, [%1]").arg(xmlPath),
                             _FILEINFO_);
         }
@@ -77,13 +79,15 @@ namespace Isis {
 }
 
 
-
 /**
  * Unit test for BundleResults.
  *
  * @internal
  *   @history 2016-07-01 Jesse Mapel - Added TargetBody tests.
  *   @history 2016-10-13 Ian Humphrey - Changed call from addnew to addNew(). References #4293.
+ *   @history 2017-04-24 Ian Humphrey - Removed pvlObject serialization, replaced with XML
+ *                           serialization for checking the state of the bundle results during the
+ *                           unit test. Fixes #4797.
  */
 int main(int argc, char *argv[]) {
   try {
@@ -92,16 +96,15 @@ int main(int argc, char *argv[]) {
     cout.precision(6);
 
     qDebug() << "Unit test for BundleResults...";
-    qDebug() << "Printing PVL group with results from the default constructor...";
+    qDebug() << "XML from the default constructor...";
     QObject *parent = NULL;
     BundleResults results(parent);
-    PvlObject pvl = results.pvlObject("DefaultResultsObject");
-    cout << pvl << endl << endl;
+
+    printXml(results);
 
     qDebug() << "Testing copy constructor...";
     BundleResults copyResults(results);
-    pvl = copyResults.pvlObject("CopyResultsObject");
-    cout << pvl << endl << endl;
+    printXml(copyResults);
 
     qDebug() << "Add maximum likelihood models, then test the assignment operator...";
     QList< QPair< MaximumLikelihoodWFunctions::Model, double > > modelsWithQuantiles;
@@ -125,13 +128,11 @@ int main(int argc, char *argv[]) {
 
     qDebug() << "Testing assignment operator=...";
     results = results;
-    pvl = results.pvlObject("SelfAssignedResultsObject");
-    cout << endl << pvl << endl << endl;
+    printXml(results);
 
     BundleResults assignmentOpResults;
     assignmentOpResults = results;
-    pvl = assignmentOpResults.pvlObject("AssignedNewResultsObject");
-    cout << pvl << endl << endl;
+    printXml(assignmentOpResults);
 
     qDebug() << "Testing mutator methods...";
     results.resizeSigmaStatisticsVectors(1);
@@ -156,13 +157,13 @@ int main(int argc, char *argv[]) {
     results.setRmsImageResidualLists(rmsImageLineResiduals,
                                      rmsImageSampleResiduals,
                                      rmsImageResiduals);
-    results.setSigmaLatitudeRange(Distance(0.5, Distance::Meters), 
+    results.setSigmaLatitudeRange(Distance(0.5, Distance::Meters),
                                   Distance(89.6, Distance::Meters),
                                   "MinLatId", "MaxLatId");
-    results.setSigmaLongitudeRange(Distance(0.7, Distance::Meters), 
+    results.setSigmaLongitudeRange(Distance(0.7, Distance::Meters),
                                   Distance(179.2, Distance::Meters),
                                   "MinLonId", "MaxLonId");
-    results.setSigmaRadiusRange(Distance(0.9, Distance::Meters), 
+    results.setSigmaRadiusRange(Distance(0.9, Distance::Meters),
                                 Distance(354.4, Distance::Meters),
                                 "MinRadId", "MaxRadId");
     results.setRmsFromSigmaStatistics(0.123, 0.456, 0.789);
@@ -188,8 +189,7 @@ int main(int argc, char *argv[]) {
     results.incrementIgnoredPoints();
     results.setRadiansToMeters(23.68);
     results.setIterations(6);
-    pvl = results.pvlObject("MutatedResultsObject");
-    cout << pvl << endl << endl;
+    printXml(results);
     qDebug() << "";
 
     qDebug() << "Testing more computation methods...";
@@ -208,7 +208,7 @@ int main(int argc, char *argv[]) {
     imgsAndParams.insert("img2", list2);
     results.setCorrMatImgsAndParams(imgsAndParams);
     qDebug() << "";
-    
+
     qDebug() << "Testing storage for output methods...";
     ControlPoint *freePoint = new ControlPoint("FreePoint");
     ControlMeasure *freeMeasure1 = new ControlMeasure;
@@ -223,8 +223,8 @@ int main(int argc, char *argv[]) {
     freePoint->Add(freeMeasure2);
     ControlPoint *fixedPoint = new ControlPoint("FixedPoint");
     fixedPoint->SetType(ControlPoint::Fixed);
-    SurfacePoint fixedSurfacePoint(Latitude(90.0, Angle::Degrees), 
-                                   Longitude(180.0, Angle::Degrees), 
+    SurfacePoint fixedSurfacePoint(Latitude(90.0, Angle::Degrees),
+                                   Longitude(180.0, Angle::Degrees),
                                    Distance(10.0, Distance::Meters));
     fixedPoint->SetAdjustedSurfacePoint(fixedSurfacePoint);
     ControlNet outNet;
@@ -283,21 +283,10 @@ int main(int argc, char *argv[]) {
     }
 
     qDebug() << "";
- 
-  
-    qDebug() << "Testing serialization...";
-    QByteArray byteArray;
-    QDataStream outputData(&byteArray, QIODevice::WriteOnly);
-    outputData << results;
-    QDataStream inputData(byteArray);
-    BundleResults newResults;
-    inputData >> newResults;
-    pvl = newResults.pvlObject();
-    cout << pvl << endl;
-    qDebug() << "";
- 
-    qDebug() << "Testing XML write/read...";
-    // write xml 
+
+    qDebug() << "Testing XML serialization 1: round trip serialization of fully populated BundleSettings object...";
+    qDebug() << "Serializing test XML object to file...";
+    printXml(results);
     FileName xmlFile("./BundleResults.xml");
     QString xmlPath = xmlFile.expanded();
     QFile qXmlFile(xmlPath);
@@ -313,18 +302,14 @@ int main(int argc, char *argv[]) {
     results.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
+
+    qDebug() << "Testing XML: reading serialized BundleResults back in...";
     XmlStackedHandlerReader reader;
     BundleResultsXmlHandlerTester bsFromXml(project, &reader, xmlFile);
-    pvl = bsFromXml.pvlObject("BundleResultsFromXml");
-    cout << pvl << endl << endl;
-
-    // read xml with no attributes or values
-    FileName emptyXmlFile("./unitTest_NoElementValues.xml");
-    BundleResultsXmlHandlerTester bsFromEmptyXml(project, &reader, emptyXmlFile);
-    pvl = bsFromEmptyXml.pvlObject("BundleResultsFromEmptyXml");
-    cout << pvl << endl << endl;
- 
+    qDebug() << "Testing XML: Object deserialized as (should match object above):";
+    printXml(bsFromXml);
+
+
     qDebug() << "Testing error throws...";
     try {
       results.setNumberObservations(0);
@@ -333,7 +318,7 @@ int main(int argc, char *argv[]) {
       results.resetNumberConstrainedTargetParameters();
       results.setNumberUnknownParameters(1);
       results.computeSigma0(1.0, BundleSettings::Sigma0);
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
@@ -344,7 +329,7 @@ int main(int argc, char *argv[]) {
       results.resetNumberConstrainedTargetParameters();
       results.setNumberUnknownParameters(1);
       results.computeSigma0(1.0, BundleSettings::Sigma0);
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
@@ -366,3 +351,20 @@ int main(int argc, char *argv[]) {
     e.print();
   }
 }
+
+
+/**
+ * Prints the serialized BundleResults as XML.
+ *
+ * @param const BundleResults &printable The bundle results to print.
+ */
+void printXml(const BundleResults &printable) {
+  QString output;
+  QXmlStreamWriter writer(&output);
+  writer.setAutoFormatting(true);
+  printable.save(writer, NULL);
+  output.remove(QRegExp("[^<]*"));
+  // Note Statistics class does not serialize/restore properly as of 2017-04-27
+  output.remove(QRegExp(".*"));
+  qDebug().noquote() << output << endl << endl;
+}
diff --git a/isis/src/control/objs/BundleSettings/BundleSettings.cpp b/isis/src/control/objs/BundleSettings/BundleSettings.cpp
index e47c4c6576bbb8c245548d60d84a50fc75a31760..d66a2e92e23c1966720dd24175c9936bfad9e0e3 100644
--- a/isis/src/control/objs/BundleSettings/BundleSettings.cpp
+++ b/isis/src/control/objs/BundleSettings/BundleSettings.cpp
@@ -27,17 +27,25 @@
 namespace Isis {
 
   /**
-   * Constructs a BundleSettings object. 
+   * @brief Constructs a BundleSettings object.
    * Default values are set for all member variables. By default, BundleSettings allows creation
    * of the inverse correlation matrix file.
-   * 
+   *
    * @see createInverseMatrix()
    * @see setCreateInverseMatrix()
    */
   BundleSettings::BundleSettings() {
-    m_id = NULL;
-    m_id = new QUuid(QUuid::createUuid());
+    init();
+    BundleObservationSolveSettings defaultSolveSettings;
+    m_observationSolveSettings.append(defaultSolveSettings);
+  }
 
+  /**
+   * @brief Set Default vales for a BundleSettings object.
+   * Note we call the default constructor to initialize the TargetBody information
+   * that is not currently in the XML.
+   */
+  void BundleSettings::init() {
     m_validateNetwork = true;
 
     m_solveObservationMode = false;
@@ -54,9 +62,6 @@ namespace Isis {
     m_globalLongitudeAprioriSigma = Isis::Null;
     m_globalRadiusAprioriSigma    = Isis::Null;
 
-    BundleObservationSolveSettings defaultSolveSettings;
-    m_observationSolveSettings.append(defaultSolveSettings);
-
     // Convergence Criteria
     m_convergenceCriteria = BundleSettings::Sigma0;
     m_convergenceCriteriaThreshold = 1.0e-10;
@@ -80,11 +85,11 @@ namespace Isis {
 
 
   /**
-   * Construct a BundleSettings object from member data read from an XML file. 
-   *  
-   * @code 
+   * Construct a BundleSettings object from member data read from an XML file.
+   *
+   * @code
    *   FileName xmlFile("bundleSettingsFileName.xml");
-   *  
+   *
    *   QString xmlPath = xmlFile.expanded();
    *   QFile file(xmlPath);
    *   file.open(QFile::ReadOnly);
@@ -93,86 +98,24 @@ namespace Isis {
    * @endcode
    *
    * @param project A pointer to the project where the Settings will be saved.
-   * @param xmlReader An XML reader that's up to an  tag.
+   * @param xmlReader The Content handler to parse the BundleSettings XML
    */
-  BundleSettings::BundleSettings(Project *project, 
+  BundleSettings::BundleSettings(Project *project,
                                  XmlStackedHandlerReader *xmlReader) {
-    m_id = NULL;
-    // what about the rest of the member data ??? should we set defaults ??? CREATE INITIALIZE METHOD
-
-    xmlReader->pushContentHandler(new XmlHandler(this, project));
+    init();
     xmlReader->setErrorHandler(new XmlHandler(this, project));
-
-  }
-
-
-#if 0
-  /**
-   * Construct this BundleSettings object from XML.
-   *
-   * @param bundleSettingsFolder Where this settings XML resides - /work/.../projectRoot/images/import1
-   * @param xmlReader An XML reader that's up to an  tag.
-   * 
-   * @throw
-   * @throw
-   */
-  BundleSettings::BundleSettings(FileName xmlFile,
-                                 Project *project, 
-                                 XmlStackedHandlerReader *xmlReader) {
-
-
-    m_id = NULL;
-    // what about the rest of the member data ??? should we set defaults ???
-
-    QString xmlPath = xmlFile.expanded();
-    QFile qXmlFile(xmlPath);
-    if (!qXmlFile.open(QFile::ReadOnly) ) {
-      throw IException(IException::Io,
-                       QString("Unable to open xml file, [%1],  with read access").arg(xmlPath),
-                       _FILEINFO_);
-    }
-
-    QXmlInputSource xmlInputSource(&qXmlFile);
-
     xmlReader->pushContentHandler(new XmlHandler(this, project));
-    xmlReader->setErrorHandler(new XmlHandler(this, project));
-    bool success = xmlReader->parse(xmlInputSource);
-    if (!success) {
-      throw IException(IException::Unknown, 
-                       QString("Failed to parse xml file, [%1]").arg(xmlPath),
-                        _FILEINFO_);
-    }
-  }
-
-
-  /** 
-   * TODO
-   * @param xmlReader An XML reader that's up to an  tag.
-   */
-  BundleSettings::BundleSettings(XmlStackedHandlerReader *xmlReader) {
-    m_id = NULL;
-    xmlReader->pushContentHandler(new XmlHandler(this));
-    xmlReader->setErrorHandler(new XmlHandler(this));
-  }
-
-  /** 
-   * TODO
-   */
-  BundleSettings::BundleSettings(H5::CommonFG &locationObject, QString locationName) {
-    openH5Group(locationObject, locationName);
   }
-#endif
 
 
   /**
-   * This copy constructor sets this BundleSettings' member data to match 
-   * that of the 'other' given BundleSettings. 
-   *  
-   * @param other The BundleSettings object to be copied. 
+   * This copy constructor sets this BundleSettings' member data to match
+   * that of the 'other' given BundleSettings.
+   *
+   * @param other The BundleSettings object to be copied.
    */
   BundleSettings::BundleSettings(const BundleSettings &other)
-      : m_id(new QUuid(other.m_id->toString())),
-        m_validateNetwork(other.m_validateNetwork),
+      : m_validateNetwork(other.m_validateNetwork),
         m_solveObservationMode(other.m_solveObservationMode),
         m_solveRadius(other.m_solveRadius),
         m_updateCubeLabel(other.m_updateCubeLabel),
@@ -195,28 +138,22 @@ namespace Isis {
 
 
   /**
-   * Destroys the BundleSettings object. 
+   * Destroys the BundleSettings object.
    */
-  BundleSettings::~BundleSettings() {    
-    delete m_id;
-    m_id = NULL;
+  BundleSettings::~BundleSettings() {
   }
 
 
-  /** 
-   * Assignment operator to allow proper copying of the 'other' BundleSettings 
-   * object to this one. 
-   *  
+  /**
+   * Assignment operator to allow proper copying of the 'other' BundleSettings
+   * object to this one.
+   *
    * @param other The BundleSettings object to be copied.
-   * 
+   *
    * @return @b BundleSettings& A reference to the copied BundleSettings object.
    */
   BundleSettings &BundleSettings::operator=(const BundleSettings &other) {
     if (&other != this) {
-      delete m_id;
-      m_id = NULL;
-      m_id = new QUuid(other.m_id->toString());
-
       m_validateNetwork = other.m_validateNetwork;
       m_solveObservationMode = other.m_solveObservationMode;
       m_solveRadius = other.m_solveRadius;
@@ -242,14 +179,14 @@ namespace Isis {
 
 
   /**
-   * Sets the internal flag to indicate whether to validate the network before 
-   * the bundle adjustment. 
-   *  
-   * @see BundleAdjust::validateNetwork() 
-   *  
-   * @param validate Indicates whether the network should be validated by 
+   * Sets the internal flag to indicate whether to validate the network before
+   * the bundle adjustment.
+   *
+   * @see BundleAdjust::validateNetwork()
+   *
+   * @param validate Indicates whether the network should be validated by
    *                 BundleAdjust.
-   *  
+   *
    */
   void BundleSettings::setValidateNetwork(bool validate) {
     m_validateNetwork = validate;
@@ -257,14 +194,14 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether to validate the network before 
-   * the bundle adjustment. 
-   *  
-   * @see BundleAdjust::validateNetwork() 
-   *  
-   * @return @b bool Indicates whether the network should be validated by 
+   * This method is used to determine whether to validate the network before
+   * the bundle adjustment.
+   *
+   * @see BundleAdjust::validateNetwork()
+   *
+   * @return @b bool Indicates whether the network should be validated by
    *                 BundleAdjust.
-   *  
+   *
    */
   bool BundleSettings::validateNetwork() const {
     return m_validateNetwork;
@@ -277,13 +214,13 @@ namespace Isis {
 
   /**
    * Set the solve options for the bundle adjustment.
-   * 
+   *
    * @param solveObservationMode A boolean value indicating whether to solve for
    *                             observation mode.
-   * @param updateCubeLabel A boolean value indicating whether to update the 
+   * @param updateCubeLabel A boolean value indicating whether to update the
    *                        cube labels after the bundle adjustment is
    *                        completed.
-   * @param errorPropagation A boolean value indicating whether to use the 
+   * @param errorPropagation A boolean value indicating whether to use the
    *                         cholmod library's error propagation.
    * @param solveRadius A boolean value indicating whether to solve for radius.
    * @param globalLatitudeAprioriSigma The global a priori sigma for latitude.
@@ -291,11 +228,11 @@ namespace Isis {
    * @param globalRadiusAprioriSigma The global a priori sigma for radius.
    */
   void BundleSettings::setSolveOptions(bool solveObservationMode,
-                                       bool updateCubeLabel, 
-                                       bool errorPropagation, 
-                                       bool solveRadius, 
-                                       double globalLatitudeAprioriSigma, 
-                                       double globalLongitudeAprioriSigma, 
+                                       bool updateCubeLabel,
+                                       bool errorPropagation,
+                                       bool solveRadius,
+                                       double globalLatitudeAprioriSigma,
+                                       double globalLongitudeAprioriSigma,
                                        double globalRadiusAprioriSigma) {
     m_solveObservationMode = solveObservationMode;
     m_solveRadius = solveRadius;
@@ -326,9 +263,9 @@ namespace Isis {
 
 
   /**
-   * Set the outlier rejection options for the bundle adjustment. 
-   * 
-   * @param outlierRejection Indicates whether to perform automatic outlier 
+   * Set the outlier rejection options for the bundle adjustment.
+   *
+   * @param outlierRejection Indicates whether to perform automatic outlier
    *                         rejection during the bundle adjustment.
    * @param mutliplier The outlier rejection multiplier.
    */
@@ -345,8 +282,8 @@ namespace Isis {
 
   /**
    * Add the list of solve options for each observation.
-   * 
-   * @param observationSolveSettings A list of BundleObservationSolveSettings objects 
+   *
+   * @param observationSolveSettings A list of BundleObservationSolveSettings objects
    *                                 to indicate the settings for each observation of
    *                                 the bundle adjustment.
    */
@@ -358,13 +295,13 @@ namespace Isis {
 
   /**
    * Indicates if the settings will allow the inverse correlation matrix to be created.
-   * 
+   *
    * This method is used to determine if the inverse correlation matrix file will be created when
    * creating error propagation information in the bundle adjust. If error propagation is not
    * turned on, then the inverse correlation matrix file will not be created.
-   * 
+   *
    * @return @b bool Returns whether or now the inverse correlation matrix is allowed to be created.
-   * 
+   *
    * @see BundleAdjust::errorPropagation()
    */
   bool BundleSettings::createInverseMatrix() const {
@@ -373,10 +310,10 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether outlier rejection will be 
-   * performed on this bundle adjustment. 
-   * 
-   * @return @b bool Indicates whether to perform automatic outlier 
+   * This method is used to determine whether outlier rejection will be
+   * performed on this bundle adjustment.
+   *
+   * @return @b bool Indicates whether to perform automatic outlier
    *                 rejection during the bundle adjustment.
    */
   bool BundleSettings::outlierRejection() const {
@@ -385,9 +322,9 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether this bundle adjustment will solve 
-   * for observation mode. 
-   * 
+   * This method is used to determine whether this bundle adjustment will solve
+   * for observation mode.
+   *
    * @return @b bool Indicates whether to solve for observation mode.
    */
   bool BundleSettings::solveObservationMode() const {
@@ -396,9 +333,9 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether this bundle adjustment will solve 
-   * for radius. 
-   * 
+   * This method is used to determine whether this bundle adjustment will solve
+   * for radius.
+   *
    * @return @b bool Indicates whether to solve for radius.
    */
   bool BundleSettings::solveRadius() const {
@@ -407,9 +344,9 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether this bundle 
-   * adjustment will update the cube labels. 
-   * 
+   * This method is used to determine whether this bundle
+   * adjustment will update the cube labels.
+   *
    * @return @b bool Indicates whether to update the cube labels after the bundle adjustment
    *                 is completed.
    */
@@ -419,27 +356,27 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether this bundle adjustment will 
-   * perform error propagation. 
-   * 
+   * This method is used to determine whether this bundle adjustment will
+   * perform error propagation.
+   *
    * @return @b bool Indicates whether to perform error propagation.
    */
   bool BundleSettings::errorPropagation() const {
     return m_errorPropagation;
   }
 
- 
+
   /**
    * Turn the creation of the inverse correlation matrix file on or off.
-   * 
+   *
    * Note that the inverse correlation matrix is created in BundleAdjust, and will only be created
    * if error propagation is turned on. By default, BundleSettings allows the inverse matrix to
    * be created. This requires stand-alone applications (e.g. jigsaw) to call this method
-   * to turn of the correlation matrix creation. 
-   * 
+   * to turn of the correlation matrix creation.
+   *
    * @param createMatrixFile Boolean indicating whether or not to allow the inverse matrix file to
    *                         be created.
-   * 
+   *
    * @see BundleAdjust::errorPropagation()
    */
   void BundleSettings::setCreateInverseMatrix(bool createMatrixFile) {
@@ -448,8 +385,8 @@ namespace Isis {
 
 
   /**
-   * Retrieves the outlier rejection multiplier for the bundle adjustment. 
-   * 
+   * Retrieves the outlier rejection multiplier for the bundle adjustment.
+   *
    * @return @b double The outlier rejection multiplier.
    */
   double BundleSettings::outlierRejectionMultiplier() const {
@@ -458,9 +395,9 @@ namespace Isis {
 
 
   /**
-   * Retrieves the global a priori sigma latitude value for this bundle 
-   * adjustment. 
-   * 
+   * Retrieves the global a priori sigma latitude value for this bundle
+   * adjustment.
+   *
    * @return @b double The global a priori sigma for latitude.
    */
   double BundleSettings::globalLatitudeAprioriSigma() const {
@@ -469,9 +406,9 @@ namespace Isis {
 
 
   /**
-   * Retrieves the global a priori sigma longitude value for this bundle 
-   * adjustment. 
-   * 
+   * Retrieves the global a priori sigma longitude value for this bundle
+   * adjustment.
+   *
    * @return @b double The global a priori sigma for longitude.
    */
   double BundleSettings::globalLongitudeAprioriSigma() const {
@@ -480,9 +417,9 @@ namespace Isis {
 
 
   /**
-   * Retrieves the global a priori sigma radius value for this bundle 
-   * adjustment. 
-   * 
+   * Retrieves the global a priori sigma radius value for this bundle
+   * adjustment.
+   *
    * @return @b double The global a priori sigma for radius.
    */
   double BundleSettings::globalRadiusAprioriSigma() const {
@@ -490,10 +427,10 @@ namespace Isis {
   }
 
 
-  /** 
-   * Retrieves the number of observation solve settings. 
-   *  
-   * @return @b int The number of solve settings object for this run of the 
+  /**
+   * Retrieves the number of observation solve settings.
+   *
+   * @return @b int The number of solve settings object for this run of the
    *                bundle adjustment.
    */
   int BundleSettings::numberSolveSettings() const {
@@ -501,20 +438,20 @@ namespace Isis {
   }
 
 
-  /** 
-   * Retrieves solve settings for the observation corresponding to the given 
+  /**
+   * Retrieves solve settings for the observation corresponding to the given
    * observation number.
-   *  
-   * @param observationNumber The observation number associated with the 
+   *
+   * @param observationNumber The observation number associated with the
    *                          BundleObservationSolveSettings object to be accessed.
-   *  
+   *
    * @return @b BundleObservationSolveSettings The observation settings object that contains
    *                                           the observation number passed.
-   *  
-   * @throw IException::Unknown "Unable to find BundleObservationSolveSettings 
+   *
+   * @throw IException::Unknown "Unable to find BundleObservationSolveSettings
    *                             for given observation number"
    */
-  BundleObservationSolveSettings 
+  BundleObservationSolveSettings
       BundleSettings::observationSolveSettings(QString observationNumber) const {
 
     for (int i = 0; i < numberSolveSettings(); i++) {
@@ -529,21 +466,21 @@ namespace Isis {
 
 
   /**
-   * Retrieves solve settings for the observation corresponding to the given 
-   * index. 
-   *  
-   * @param n The index of the BundleObservationSolveSettings object to be 
+   * Retrieves solve settings for the observation corresponding to the given
+   * index.
+   *
+   * @param n The index of the BundleObservationSolveSettings object to be
    *          accessed.
    * @return @b BundleObservationSolveSettings The observation settings object corresponding
    *                                           to the given index.
-   * @throw IException::Unknown "Unable to find BundleObservationSolveSettings 
+   * @throw IException::Unknown "Unable to find BundleObservationSolveSettings
    *                             with given index"
    */
-  BundleObservationSolveSettings 
-      BundleSettings::observationSolveSettings(int n) const { 
+  BundleObservationSolveSettings
+      BundleSettings::observationSolveSettings(int n) const {
 
     if (n >= 0 && n < numberSolveSettings()) {
-      return m_observationSolveSettings[n]; 
+      return m_observationSolveSettings[n];
     }
     QString msg = "Unable to find BundleObservationSolveSettings with index = ["
                   + toString(n) + "].";
@@ -556,21 +493,21 @@ namespace Isis {
   // =============================================================================================//
 
   /**
-   * Converts the given string value to a BundleSettings::ConvergenceCriteria 
-   * enumeration. Currently accepted inputs are listed below. This method is 
-   * case insensitive. 
-   * 
       
+   * Converts the given string value to a BundleSettings::ConvergenceCriteria
+   * enumeration. Currently accepted inputs are listed below. This method is
+   * case insensitive.
+   * 
        
    *   
      • Sigma0
        • 
    *   
      • ParameterCorrections
        • 
    * 
      
-   *  
+   *
    * @param criteria Convergence criteria name to be converted.
-   * 
+   *
    * @return @b ConvergenceCriteria The enumeration corresponding to the given name.
-   * 
+   *
    * @throw Isis::Exception::Programmer "Unknown bundle convergence criteria."
    */
-  BundleSettings::ConvergenceCriteria 
+  BundleSettings::ConvergenceCriteria
       BundleSettings::stringToConvergenceCriteria(QString criteria) {
     if (criteria.compare("SIGMA0", Qt::CaseInsensitive) == 0) {
       return BundleSettings::Sigma0;
@@ -585,14 +522,14 @@ namespace Isis {
 
 
   /**
-   * Converts the given BundleSettings::ConvergenceCriteria enumeration to a string. 
-   * This method is used to print the type of convergence criteria used in 
-   * the bundle adjustment. 
-   * 
+   * Converts the given BundleSettings::ConvergenceCriteria enumeration to a string.
+   * This method is used to print the type of convergence criteria used in
+   * the bundle adjustment.
+   *
    * @param criteria The ConvergenceCriteria enumeration to be converted.
-   * 
+   *
    * @return @b QString The name associated with the given convergence criteria.
-   * 
+   *
    * @throw Isis::Exception::Programmer "Unknown bundle convergence criteria enum."
    */
   QString BundleSettings::convergenceCriteriaToString(
@@ -606,8 +543,8 @@ namespace Isis {
 
 
   /**
-   * Set the convergence criteria options for the bundle adjustment. 
-   * 
+   * Set the convergence criteria options for the bundle adjustment.
+   *
    * @param criteria An enumeration for the convergence criteria to be
    *                 used for this bundle adjustment.
    * @param threshold The convergence threshold for this bundle adjustment.
@@ -615,8 +552,8 @@ namespace Isis {
    *                          before the bundle adjustment determines
    *                          that the data is not converging.
    */
-  void BundleSettings::setConvergenceCriteria(BundleSettings::ConvergenceCriteria criteria, 
-                                              double threshold, 
+  void BundleSettings::setConvergenceCriteria(BundleSettings::ConvergenceCriteria criteria,
+                                              double threshold,
                                               int maximumIterations) {
     m_convergenceCriteria = criteria;
     m_convergenceCriteriaThreshold = threshold;
@@ -625,9 +562,9 @@ namespace Isis {
 
 
   /**
-   * Retrieves the convergence criteria to be used to solve the bundle 
-   * adjustment. 
-   * 
+   * Retrieves the convergence criteria to be used to solve the bundle
+   * adjustment.
+   *
    * @return @b ConvergenceCriteria The enumeration of the convergence criteria.
    */
   BundleSettings::ConvergenceCriteria BundleSettings::convergenceCriteria() const {
@@ -636,9 +573,9 @@ namespace Isis {
 
 
   /**
-   * Retrieves the convergence threshold to be used to solve the bundle 
-   * adjustment. 
-   * 
+   * Retrieves the convergence threshold to be used to solve the bundle
+   * adjustment.
+   *
    * @return @b double The threshold that determines convergence.
    */
   double BundleSettings::convergenceCriteriaThreshold() const {
@@ -647,9 +584,9 @@ namespace Isis {
 
 
   /**
-   * Retrieves the maximum number of iterations allowed to solve the 
-   * bundle adjustment. 
-   * 
+   * Retrieves the maximum number of iterations allowed to solve the
+   * bundle adjustment.
+   *
    * @param maximumIterations The maximum number of iterations allowed
    *                          before the bundle adjustment determines
    *                          that the data is not converging.
@@ -659,22 +596,22 @@ namespace Isis {
   }
 
 
-  
+
   // =============================================================================================//
   // ======================== Parameter Uncertainties (Weighting) ================================//
   // =============================================================================================//
 //   void BundleSettings::setGlobalLatitudeAprioriSigma(double sigma) {
 //     m_globalLatitudeAprioriSigma = sigma;
 //   }
-// 
-// 
-// 
+//
+//
+//
 //   void BundleSettings::setGlobalLongitudeAprioriSigma(double sigma) {
 //     m_globalLongitudeAprioriSigma = sigma;
 //   }
-// 
-// 
-// 
+//
+//
+//
 //   void BundleSettings::setGlobalRadiiAprioriSigma(double sigma) {
 //     m_globalRadiusAprioriSigma = sigma;
 //   }
@@ -687,17 +624,17 @@ namespace Isis {
 
   /**
    * Add a maximum likelihood estimator (MLE) model to the bundle adjustment.
-   * 
+   *
    * @param model The enumeration for the model to be used.
-   * @param maxModelCQuantile The C-Quantile of the residual to be used to 
+   * @param maxModelCQuantile The C-Quantile of the residual to be used to
    *                          compute the tweaking constant.
-   * 
-   * 
-   * @throw Isis::Exception::Programmer "For bundle adjustments with multiple maximum 
+   *
+   *
+   * @throw Isis::Exception::Programmer "For bundle adjustments with multiple maximum
    *                                     likelihood estimators, the first model must be of
    *                                     type HUBER or HUBER_MODIFIED."
    */
-  void BundleSettings::addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Model model, 
+  void BundleSettings::addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Model model,
                                                           double maxModelCQuantile) {
 
     if (m_maximumLikelihood.size() == 0 && model > MaximumLikelihoodWFunctions::HuberModified) {
@@ -711,14 +648,14 @@ namespace Isis {
 
 
   /**
-   * Retrieves the list of maximum likelihood estimator (MLE) models with their 
-   * corresponding C-Quantiles. 
-   * 
-   * @return QList< QPair< MaximumLikelihoodWFunctions::Model, double > > 
+   * Retrieves the list of maximum likelihood estimator (MLE) models with their
+   * corresponding C-Quantiles.
+   *
+   * @return QList< QPair< MaximumLikelihoodWFunctions::Model, double > >
    *             The list of tuples of the form (model, quantile) to be used for the
    *             bundle adjustment.
    */
-  QList< QPair< MaximumLikelihoodWFunctions::Model, double > >  
+  QList< QPair< MaximumLikelihoodWFunctions::Model, double > >
       BundleSettings::maximumLikelihoodEstimatorModels() const {
     return m_maximumLikelihood;
   }
@@ -727,15 +664,15 @@ namespace Isis {
   // =============================================================================================//
   // ======================== Self Calibration ??? (from cnetsuite only) =========================//
   // =============================================================================================//
-  
+
   // =============================================================================================//
   // ======================== Target Body ??? (from cnetsuite only) ==============================//
   // =============================================================================================//
 
   /**
    * Sets the target body for the bundle adjustment.
-   *  
-   * @param bundleTargetBody A pointer to the BundleTargetBody object for the 
+   *
+   * @param bundleTargetBody A pointer to the BundleTargetBody object for the
    *                         bundle adjustment to be run.
    */
   void BundleSettings::setBundleTargetBody(BundleTargetBodyQsp bundleTargetBody) {
@@ -745,7 +682,7 @@ namespace Isis {
 
   /**
    * Retrieves a pointer to target body information for the bundle adjustment.
-   *  
+   *
    * @return @b BundleTargetBodyQsp A pointer to the BundleTargetBody object for
    *                                the bundle adjustment to be run.
    */
@@ -755,9 +692,9 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment 
-   * will solve for target body pole position. 
-   *  
+   * This method is used to determine whether the bundle adjustment
+   * will solve for target body pole position.
+   *
    * @return @b bool Indicates whether to solve for target pole position.
    */
 //  bool BundleSettings::solveTargetBodyPolePosition() const {
@@ -766,9 +703,9 @@ namespace Isis {
 
 
   /**
-   * Retrieves the number of target body parameters. If the BundleTargetBody 
+   * Retrieves the number of target body parameters. If the BundleTargetBody
    * associated with this bundle adjustment is NULL, this method returns 0.
-   *  
+   *
    * @return @b int The number of target body parameters.
    */
   int BundleSettings::numberTargetBodyParameters() const {
@@ -780,9 +717,9 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment will solve 
-   * for target body. 
-   *  
+   * This method is used to determine whether the bundle adjustment will solve
+   * for target body.
+   *
    * @return @b bool Indicates whether to solve for target body.
    */
   bool BundleSettings::solveTargetBody() const {
@@ -796,12 +733,12 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment will 
-   * solve for target body pole right ascension. 
-   * 
+   * This method is used to determine whether the bundle adjustment will
+   * solve for target body pole right ascension.
+   *
    * @see BundleTargetBody::solvePoleRA()
-   * 
-   * @return @b bool Indicates whether to solve for target pole RA. 
+   *
+   * @return @b bool Indicates whether to solve for target pole RA.
    */
   bool BundleSettings::solvePoleRA() const {
     if (!m_bundleTargetBody) {
@@ -812,11 +749,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment will 
-   * solve for target body pole right ascension velocity. 
-   * 
+   * This method is used to determine whether the bundle adjustment will
+   * solve for target body pole right ascension velocity.
+   *
    * @see BundleTargetBody::solvePoleRAVelocity()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target pole RA velocity.
    */
   bool BundleSettings::solvePoleRAVelocity() const {
@@ -828,11 +765,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment will 
-   * solve for target body pole declination. 
-   * 
+   * This method is used to determine whether the bundle adjustment will
+   * solve for target body pole declination.
+   *
    * @see BundleTargetBody::solvePoleDeclination()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target pole declination.
    */
   bool BundleSettings::solvePoleDec() const {
@@ -844,11 +781,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment will 
-   * solve for target body pole declination velocity. 
-   * 
+   * This method is used to determine whether the bundle adjustment will
+   * solve for target body pole declination velocity.
+   *
    * @see BundleTargetBody::solvePoleDeclinationVelocity()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target pole declination velocity.
    */
   bool BundleSettings::solvePoleDecVelocity() const {
@@ -860,11 +797,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment 
-   * will solve for target body prime meridian. 
-   * 
+   * This method is used to determine whether the bundle adjustment
+   * will solve for target body prime meridian.
+   *
    * @see BundleTargetBody::solvePM()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target PM.
    */
   bool BundleSettings::solvePM() const {
@@ -876,11 +813,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment 
-   * will solve for target body prime meridian velocity. 
-   * 
+   * This method is used to determine whether the bundle adjustment
+   * will solve for target body prime meridian velocity.
+   *
    * @see BundleTargetBody::solvePMVelocity()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target PM velocity.
    */
   bool BundleSettings::solvePMVelocity() const {
@@ -892,11 +829,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment 
-   * will solve for target body prime meridian acceleration. 
-   * 
+   * This method is used to determine whether the bundle adjustment
+   * will solve for target body prime meridian acceleration.
+   *
    * @see BundleTargetBody::solvePMAcceleration()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target PM acceleration.
    */
   bool BundleSettings::solvePMAcceleration() const {
@@ -908,11 +845,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment 
-   * will solve for target body triaxial radii. 
-   * 
+   * This method is used to determine whether the bundle adjustment
+   * will solve for target body triaxial radii.
+   *
    * @see BundleTargetBody::solveTriaxialRadii()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target triaxial radii.
    */
   bool BundleSettings::solveTriaxialRadii() const {
@@ -924,11 +861,11 @@ namespace Isis {
 
 
   /**
-   * This method is used to determine whether the bundle adjustment 
-   * will solve for target body mean radius. 
-   * 
+   * This method is used to determine whether the bundle adjustment
+   * will solve for target body mean radius.
+   *
    * @see BundleTargetBody::solveMeanRadius()
-   * 
+   *
    * @return @b bool Indicates whether to solve for target mean radius.
    */
   bool BundleSettings::solveMeanRadius() const {
@@ -982,15 +919,15 @@ namespace Isis {
 //                                         sigmaRadiusA, aprioriRadiusB, sigmaRadiusB, aprioriRadiusC,
 //                                         sigmaRadiusC, aprioriMeanRadius, sigmaMeanRadius);
 //  }
-  
+
 
   // =============================================================================================//
   // ========================= Output Options (from Jigsaw only) ================================//
   // =============================================================================================//
   /**
-   * Set the output file prefix for the bundle adjustment. 
-   * 
-   * @param outputFilePrefix A string containing a prefix and/or directory path 
+   * Set the output file prefix for the bundle adjustment.
+   *
+   * @param outputFilePrefix A string containing a prefix and/or directory path
    */
   void BundleSettings::setOutputFilePrefix(QString outputFilePrefix) {
     m_outputFilePrefix = outputFilePrefix;
@@ -998,11 +935,11 @@ namespace Isis {
 
 
   /**
-   * Retrieve the output file prefix. This string will be 
-   * appended to all of the output files created by the bundle 
-   * adjustment. 
-   * 
-   * @return @b QString A string containing a prefix and/or 
+   * Retrieve the output file prefix. This string will be
+   * appended to all of the output files created by the bundle
+   * adjustment.
+   *
+   * @return @b QString A string containing a prefix and/or
    *                    directory path to be appended to all
    *                    output files.
    */
@@ -1012,121 +949,18 @@ namespace Isis {
 
 
   /**
-   * Create PvlObject with the given name containing the BundleSettings 
-   * information. 
-   * 
-   * @param name The name of the output PvlObject. Defaults to "BundleSettings".
-   * 
-   * @return @b PvlObject A PVL containing all of the BundleSettings 
-   *                      information for this bundle adjustment.
-   */
-  PvlObject BundleSettings::pvlObject(QString name) const {
-
-    PvlObject pvl(name);
-
-    // General Solve Options
-    pvl += PvlKeyword("NetworkValidated", toString(validateNetwork()));
-    pvl += PvlKeyword("SolveObservationMode", toString(solveObservationMode()));
-    pvl += PvlKeyword("SolveRadius", toString(solveRadius()));
-    pvl += PvlKeyword("UpdateCubeLabel", toString(updateCubeLabel()));
-    pvl += PvlKeyword("ErrorPropagation", toString(errorPropagation()));
-    pvl += PvlKeyword("CreateInverseMatrix", toString(createInverseMatrix()));
-    pvl += PvlKeyword("OutlierRejection", toString(outlierRejection()));
-    if (m_outlierRejection) {
-      pvl += PvlKeyword("OutlierMultiplier", toString(outlierRejectionMultiplier()));
-    }
-    if ( !IsSpecial(globalLatitudeAprioriSigma()) ) {
-      pvl += PvlKeyword("GlobalLatitudeAprioriSigma", toString(globalLatitudeAprioriSigma()));
-    }
-    else {
-      pvl += PvlKeyword("GlobalLatitudeAprioriSigma", "None");
-    }
-    if (!IsSpecial(globalLongitudeAprioriSigma())) {
-      pvl += PvlKeyword("GlobalLongitudeAprioriSigma", toString(globalLongitudeAprioriSigma()));
-    }
-    else {
-      pvl += PvlKeyword("GlobalLongitudeAprioriSigma", "None");
-    }
-    if (m_solveRadius) {
-      if ( !IsSpecial(globalLongitudeAprioriSigma()) ) {
-      pvl += PvlKeyword("GlobalRadiiAprioriSigma", toString(globalRadiusAprioriSigma()));
-      }
-      else {
-        pvl += PvlKeyword("GlobalRadiiAprioriSigma", "None");
-      }
-    }
-
-    // Convergence Criteria
-    pvl += PvlKeyword("ConvergenceCriteria", convergenceCriteriaToString(convergenceCriteria()));
-    pvl += PvlKeyword("ConvergenceCriteriaThreshold", toString(convergenceCriteriaThreshold()));
-    pvl += PvlKeyword("ConvergenceCriteriaMaximumIterations",
-                        toString(convergenceCriteriaMaximumIterations()));
-
-    // Target body
-    pvl += PvlKeyword("SolveTargetBody", toString(solveTargetBody()));
-    pvl += PvlKeyword("NumberTargetBodyParameters", toString(numberTargetBodyParameters()));
-    pvl += PvlKeyword("SolvePoleRightAscension", toString(solvePoleRA()));
-    pvl += PvlKeyword("SolvePoleRightAscensionVelocity", toString(solvePoleRAVelocity()));
-    pvl += PvlKeyword("SolvePoleDeclination", toString(solvePoleDec()));
-    pvl += PvlKeyword("SolvePoleDeclinationVelocity", toString(solvePoleDecVelocity()));
-    pvl += PvlKeyword("SolvePolePrimeMeridian", toString(solvePM()));
-    pvl += PvlKeyword("SolvePolePrimeMeridianVelocity", toString(solvePMVelocity()));
-    pvl += PvlKeyword("SolvePolePrimeMeridianAcceleration", toString(solvePMAcceleration()));
-    pvl += PvlKeyword("solveTriaxialRadii", toString(solveTriaxialRadii()));
-    pvl += PvlKeyword("solveMeanRadius", toString(solveMeanRadius()));
-
-    // Output Options
-    pvl += PvlKeyword("FilePrefix", outputFilePrefix());
-
-    // Maximum Likelihood Options
-    PvlKeyword models("MaximumLikelihoodModels"); 
-    if (m_maximumLikelihood.size() > 0) {
-
-      models.addValue(MaximumLikelihoodWFunctions::modelToString(m_maximumLikelihood[0].first));
-
-      PvlKeyword quantiles("MaximumLikelihoodQuantiles", 
-                           toString(m_maximumLikelihood[0].second));
-
-      for (int i = 1; i < m_maximumLikelihood.size(); i++) {
-        models.addValue(MaximumLikelihoodWFunctions::modelToString(m_maximumLikelihood[i].first));
-        quantiles.addValue(toString(m_maximumLikelihood[i].second));
-      }
-      pvl += models;
-      pvl += quantiles;
-    }
-    else {
-      models.addValue("None");
-    }
-
-    pvl += PvlKeyword("NumberObservationSolveSettings", toString(numberSolveSettings()));
-
-    for (int i = 0; i < numberSolveSettings(); i++) {
-      BundleObservationSolveSettings boss = observationSolveSettings(i);
-      PvlObject bundleObsSolveSettingsPvl = boss.pvlObject();
-      pvl += bundleObsSolveSettingsPvl;
-    }
-
-    return pvl;
-  }
-
-
-  /**
-   * This method is used to write a BundleSettings object to an XML format 
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
+   * @brief This method is used to write a BundleSettings object in an XML format
+   *
+   * @param stream The stream to write serialized XML output
+   * @param project The project that contains the settings
    */
   void BundleSettings::save(QXmlStreamWriter &stream, const Project *project) const {
-//#if 0
-    // option 2
     stream.writeStartElement("bundleSettings");
 
     stream.writeStartElement("globalSettings");
 
-    stream.writeTextElement("id", m_id->toString());
     stream.writeTextElement("validateNetwork", toString(validateNetwork()));
-    
+
     stream.writeStartElement("solveOptions");
     stream.writeAttribute("solveObservationMode", toString(solveObservationMode()));
     stream.writeAttribute("solveRadius", toString(solveRadius()));
@@ -1155,7 +989,7 @@ namespace Isis {
       stream.writeAttribute("radius", toString(globalRadiusAprioriSigma()));
     }
     stream.writeEndElement();
-    
+
     stream.writeStartElement("outlierRejectionOptions");
     stream.writeAttribute("rejection", toString(outlierRejection()));
     if (outlierRejection()) {
@@ -1165,7 +999,7 @@ namespace Isis {
       stream.writeAttribute("multiplier", "N/A");
     }
     stream.writeEndElement();
-    
+
     stream.writeStartElement("convergenceCriteriaOptions");
     stream.writeAttribute("convergenceCriteria",
                           convergenceCriteriaToString(convergenceCriteria()));
@@ -1174,21 +1008,21 @@ namespace Isis {
     stream.writeAttribute("maximumIterations",
                           toString(convergenceCriteriaMaximumIterations()));
     stream.writeEndElement();
-    
+
     stream.writeStartElement("maximumLikelihoodEstimation");
     for (int i = 0; i < m_maximumLikelihood.size(); i++) {
       stream.writeStartElement("model");
-      stream.writeAttribute("type", 
+      stream.writeAttribute("type",
                           MaximumLikelihoodWFunctions::modelToString(m_maximumLikelihood[i].first));
       stream.writeAttribute("quantile", toString(m_maximumLikelihood[i].second));
       stream.writeEndElement();
     }
     stream.writeEndElement();
-    
+
     stream.writeStartElement("outputFileOptions");
     stream.writeAttribute("fileNamePrefix", outputFilePrefix());
     stream.writeEndElement();
-    
+
     stream.writeEndElement(); // end global settings
 
     if (!m_observationSolveSettings.isEmpty()) {
@@ -1199,88 +1033,16 @@ namespace Isis {
       stream.writeEndElement();
     }
     else {
-      // throw error??? should not write if no observation settings... 
-    }
-//#endif
-
-
-
-#if 0
-    // option 3
-    stream.writeStartDocument("1.0");
-    //stream.writeStartDocument("BundleSettingsOption3");
-    stream.writeStartElement("globalSettings");
-
-    stream.writeTextElement("id", m_id->toString());
-    stream.writeTextElement("validateNetwork", toString(validateNetwork()));
-    
-    stream.writeStartElement("solveOptions");
-    stream.writeTextElement("solveObservationMode", toString(solveObservationMode()));
-    stream.writeTextElement("solveRadius", toString(solveRadius()));
-    stream.writeTextElement("updateCubeLabel", toString(updateCubeLabel()));
-    stream.writeTextElement("errorPropagation", toString(errorPropagation()));
-    stream.writeEndElement();
-
-    stream.writeStartElement("aprioriSigmas");
-    stream.writeTextElement("latitude", toString(globalLatitudeAprioriSigma()));
-    stream.writeTextElement("longitude", toString(globalLongitudeAprioriSigma()));
-    if (solveRadius()) {
-      stream.writeTextElement("radius", toString(globalRadiusAprioriSigma()));
-    }
-    else {
-      stream.writeTextElement("radius", "N/A");
-    }
-    stream.writeEndElement();
-    
-    stream.writeStartElement("outlierRejectionOptions");
-    stream.writeTextElement("rejection", toString(outlierRejection()));
-    if (outlierRejection()) {
-      stream.writeTextElement("multiplier", toString(outlierRejectionMultiplier()));
-    }
-    else {
-      stream.writeTextElement("multiplier", "N/A");
+      // throw error??? should not write if no observation settings...
     }
     stream.writeEndElement();
-    
-    stream.writeStartElement("convergenceCriteriaOptions");
-    stream.writeTextElement("convergenceCriteria", convergenceCriteriaToString(convergenceCriteria()));
-    stream.writeTextElement("threshold", toString(convergenceCriteriaThreshold()));
-    stream.writeTextElement("maximumIterations", toString(convergenceCriteriaMaximumIterations()));
-    stream.writeEndElement();
-    
-    stream.writeStartElement("maximumLikelihoodEstimation");
-    for (int i = 0; i < m_maximumLikelihood.size(); i++) {
-      stream.writeStartElement("model");
-      stream.writeAttribute("type", 
-                          MaximumLikelihoodWFunctions::modelToString(m_maximumLikelihood[i].first));
-      stream.writeAttribute("quantile", toString(m_maximumLikelihood[i].second));
-      stream.writeEndElement();
-    }
-    stream.writeEndElement();
-    
-    stream.writeStartElement("outputFileOptions");
-    stream.writeTextElement("fileNamePrefix", outputFilePrefix());
-    stream.writeEndElement();
-    
-    stream.writeEndElement(); // end global settings
-
-    stream.writeStartElement("observationSolveSettingsList");
-    stream.writeAttribute("listSize", toString(numberSolveSettings()));
-    for (int i = 0; i < m_observationSolveSettings.size(); i++) {
-      stream.writeStartElement("observationSolveSettings");
-      m_observationSolveSettings[i].save(stream, project);
-      stream.writeEndElement();
-    }
-    stream.writeEndElement();
-#endif
-    stream.writeEndElement();
   }
 
 
   /**
-   * Create an XML Handler (reader) that can populate the BundleSettings class data. See
-   * BundleSettings::save() for the expected format. This contructor is called inside the
-   * BundleSettings constructor that takes an XmlStackedHandlerReader. 
+   * @brief Create an XML Handler (reader) that can populate the BundleSettings class data.
+   * See BundleSettings::save() for the expected format. This contructor is called
+   * inside the BundleSettings constructor that takes an XmlStackedHandlerReader.
    *
    * @param bundleSettings The BundleSettings we're going to be initializing
    * @param project The project that contains the settings
@@ -1293,49 +1055,27 @@ namespace Isis {
   }
 
 
-
-//  /**
-//   * Create an XML Handler (reader) that can populate the BundleSettings class data. See
-//   *   BundleSettings::save() for the expected format.
-//   *
-//   * @param bundleSettings The BundleSettings we're going to be initializing
-//   * @param imageFolder The folder that contains the Cube
-//   */
-//  BundleSettings::XmlHandler::XmlHandler(BundleSettings *bundleSettings) {
-//    m_xmlHandlerBundleSettings = bundleSettings;
-//    m_xmlHandlerProject = NULL;
-//    m_xmlHandlerCharacters = "";
-//    m_xmlHandlerObservationSettings.clear();
-//  }
-
-
   /**
-   * Destroys BundleSettings::XmlHandler object.
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
+   * @brief Destroys BundleSettings::XmlHandler object.
    */
   BundleSettings::XmlHandler::~XmlHandler() {
-    // do not delete these pointers...
-    // we don't own them, do we??? project passed into StatCumProbDistDynCalc constructor as pointer and bundleSettings = this
-    // delete m_xmlHandlerProject;
-    m_xmlHandlerProject = NULL;
   }
 
 
   /**
    * Handle an XML start element. This method is called when the reader finds an open tag.
    * handle the read when the startElement with the name localName has been found.
-   * 
-   * @param qName The qualified name of the tag.
-   * @param attributes The list of attributes for the tag. 
-   *  
+   *
+   * @param qName SAX namespace for this tag
+   * @param localName SAX local name
+   * @param qName SAX qualified name of the tag.
+   * @param attributes The list of attributes for the tag.
+   *
    * @return @b bool Indicates whether to continue reading the XML (usually true).
    */
-  bool BundleSettings::XmlHandler::startElement(const QString &namespaceURI, 
+  bool BundleSettings::XmlHandler::startElement(const QString &namespaceURI,
                                                 const QString &localName,
-                                                const QString &qName, 
+                                                const QString &qName,
                                                 const QXmlAttributes &attributes) {
     m_xmlHandlerCharacters = "";
 
@@ -1414,7 +1154,7 @@ namespace Isis {
         QString outlierRejectionMultiplierStr = attributes.value("multiplier");
         if (!outlierRejectionMultiplierStr.isEmpty()) {
           if (outlierRejectionMultiplierStr != "N/A") {
-            m_xmlHandlerBundleSettings->m_outlierRejectionMultiplier 
+            m_xmlHandlerBundleSettings->m_outlierRejectionMultiplier
                 = toDouble(outlierRejectionMultiplierStr);
           }
           else {
@@ -1426,19 +1166,19 @@ namespace Isis {
 
         QString convergenceCriteriaStr = attributes.value("convergenceCriteria");
         if (!convergenceCriteriaStr.isEmpty()) {
-          m_xmlHandlerBundleSettings->m_convergenceCriteria 
+          m_xmlHandlerBundleSettings->m_convergenceCriteria
               = stringToConvergenceCriteria(convergenceCriteriaStr);
         }
 
         QString convergenceCriteriaThresholdStr = attributes.value("threshold");
         if (!convergenceCriteriaThresholdStr.isEmpty()) {
-          m_xmlHandlerBundleSettings->m_convergenceCriteriaThreshold 
+          m_xmlHandlerBundleSettings->m_convergenceCriteriaThreshold
               = toDouble(convergenceCriteriaThresholdStr);
         }
 
         QString convergenceCriteriaMaximumIterationsStr = attributes.value("maximumIterations");
         if (!convergenceCriteriaMaximumIterationsStr.isEmpty()) {
-          m_xmlHandlerBundleSettings->m_convergenceCriteriaMaximumIterations 
+          m_xmlHandlerBundleSettings->m_convergenceCriteriaMaximumIterations
               = toInt(convergenceCriteriaMaximumIterationsStr);
         }
       }
@@ -1467,11 +1207,10 @@ namespace Isis {
 
 
   /**
-   * XML - TBD.
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
+   * @brief Add a character from an XML element to the content handler.
+   *
+   * @param ch charater from XML element
+   * @return true
    */
   bool BundleSettings::XmlHandler::characters(const QString &ch) {
     m_xmlHandlerCharacters += ch;
@@ -1480,20 +1219,18 @@ namespace Isis {
 
 
   /**
-   * XML - TBD.
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
+   * @brief Handle end tags for the BundleSettings serialized XML.
+   *
+   * @param namespaceURI URI of the specified tags namespce
+   * @param localName SAX localName
+   * @param qName SAX qualified name
+   *
+   * @return true
    */
   bool BundleSettings::XmlHandler::endElement(const QString &namespaceURI, const QString &localName,
                                      const QString &qName) {
     if (!m_xmlHandlerCharacters.isEmpty()) {
-      if (localName == "id") {
-        m_xmlHandlerBundleSettings->m_id = NULL;
-        m_xmlHandlerBundleSettings->m_id = new QUuid(m_xmlHandlerCharacters);
-      }
-      else if (localName == "validateNetwork") {
+      if (localName == "validateNetwork") {
         m_xmlHandlerBundleSettings->m_validateNetwork = toBool(m_xmlHandlerCharacters);
       }
       else if (localName == "observationSolveSettingsList") {
@@ -1503,7 +1240,7 @@ namespace Isis {
         }
         m_xmlHandlerObservationSettings.clear();
       }
-  
+
       m_xmlHandlerCharacters = "";
     }
     return XmlStackedHandler::endElement(namespaceURI, localName, qName);
@@ -1511,504 +1248,15 @@ namespace Isis {
 
 
   /**
-   * XML - TBD.
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
+   * @brief Format an error message indicating a problem with BundleSettings.
+   *
+   * @param QXmlParseException Execption thrown by parser.
+   * @return false
    */
   bool BundleSettings::XmlHandler::fatalError(const QXmlParseException &exception) {
-    qDebug() << "Parse error at line " << exception.lineNumber()
+    qDebug() << "Parse error with BundleSettings at line " << exception.lineNumber()
              << ", " << "column " << exception.columnNumber() << ": "
              << qPrintable(exception.message());
     return false;
   }
-
-
-  /**
-   * Writes BundleSettings object to a binary data stream. May be used for 
-   * HDF5. 
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
-   */
-  QDataStream &BundleSettings::write(QDataStream &stream) const {
-
-    stream << m_id->toString()
-           << m_validateNetwork
-           << m_solveObservationMode
-           << m_solveRadius
-           << m_updateCubeLabel
-           << m_errorPropagation
-           << m_createInverseMatrix
-           << m_outlierRejection
-           << m_outlierRejectionMultiplier
-           << m_globalLatitudeAprioriSigma
-           << m_globalLongitudeAprioriSigma
-           << m_globalRadiusAprioriSigma
-           << m_observationSolveSettings
-           << (qint32)m_convergenceCriteria
-           << m_convergenceCriteriaThreshold
-           << (qint32)m_convergenceCriteriaMaximumIterations
-           << m_maximumLikelihood
-           << m_outputFilePrefix;
-
-    return stream;
-
-  }
-
-
-  /**
-   * Reads BundleSettings object from a binary data stream. May be used for 
-   * HDF5. 
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
-   */
-  QDataStream &BundleSettings::read(QDataStream &stream) {
-
-    QString id;
-    qint32 convergenceCriteria, convergenceCriteriaMaximumIterations;
-
-    stream >> id 
-           >> m_validateNetwork
-           >> m_solveObservationMode
-           >> m_solveRadius
-           >> m_updateCubeLabel
-           >> m_errorPropagation
-           >> m_createInverseMatrix
-           >> m_outlierRejection
-           >> m_outlierRejectionMultiplier
-           >> m_globalLatitudeAprioriSigma
-           >> m_globalLongitudeAprioriSigma
-           >> m_globalRadiusAprioriSigma
-           >> m_observationSolveSettings
-           >> convergenceCriteria
-           >> m_convergenceCriteriaThreshold
-           >> convergenceCriteriaMaximumIterations
-           >> m_maximumLikelihood
-           >> m_outputFilePrefix;
-
-    delete m_id;
-    m_id = NULL;
-    m_id = new QUuid(id);
-
-    m_convergenceCriteria = (BundleSettings::ConvergenceCriteria)convergenceCriteria;
-    m_convergenceCriteriaMaximumIterations = (int)convergenceCriteriaMaximumIterations;
-
-    return stream;
-  }
-
-
-  /**
-   * Writes BundleSettings object to a binary data stream. May be used for 
-   * HDF5. 
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
-   */
-  QDataStream &operator<<(QDataStream &stream, const BundleSettings &settings) {
-    return settings.write(stream);
-  }
-
-
-  /**
-   * Reads BundleSettings object from a binary data stream. May be used for 
-   * HDF5. 
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
-   */
-  QDataStream &operator>>(QDataStream &stream, BundleSettings &settings) {
-    return settings.read(stream);
-  }
-
-
-  /**
-   * HDF5 - TBD. 
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
-   * @param 
-   * @param 
-   *  
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   */
-  void BundleSettings::createH5Group(H5::CommonFG &locationObject, QString locationName) const {
-    try {
-      // Try block to detect exceptions raised by any of the calls inside it
-      try {
-        /*
-         * Turn off the auto-printing when failure occurs so that we can
-         * handle the errors appropriately
-         */
-//        H5::Exception::dontPrint();
-
-        // create a settings group to add to the given H5 object
-        QString settingsGroupName = locationName + "/BundleSettings"; 
-        H5::Group settingsGroup = locationObject.createGroup(settingsGroupName.toLatin1());
-
-        // use H5S_SCALAR data space type for single valued spaces
-        H5::DataSpace spc;
-        Attribute att;
-        #if 0
-        hsize_t dims[1] = {2};
-        H5::DataSpace simple1x2Space(1, dims);
-        dims[0] = 1;
-        H5::DataSpace simple1DSpace(1, dims);
-
-        hsize_t dims2D[2] = {{2}, {2}};
-        H5::DataSpace simple2x2Space(2, dims);
-        dims2D[2] = {1, 1};
-        H5::DataSpace simple2x1Space(2, dims);
-        #endif
-
-        /*
-         * Add bool attributes as predefined data type PredType::NATIVE_HBOOL
-         */ 
-        int intFromBool = (int)m_validateNetwork;
-        att = settingsGroup.createAttribute("validateNetwork", PredType::NATIVE_HBOOL, spc);
-        att.write(PredType::NATIVE_HBOOL, &intFromBool);
-
-        intFromBool = (int)m_solveObservationMode;
-        att = settingsGroup.createAttribute("solveObservationMode", PredType::NATIVE_HBOOL, spc);
-        att.write(PredType::NATIVE_HBOOL, &intFromBool);
-
-        intFromBool = (int)m_solveRadius;
-        att = settingsGroup.createAttribute("solveRadius", PredType::NATIVE_HBOOL, spc);
-        att.write(PredType::NATIVE_HBOOL, &intFromBool);
-
-        intFromBool = (int)m_updateCubeLabel;
-        att = settingsGroup.createAttribute("updateCubeLabel", PredType::NATIVE_HBOOL, spc);
-        att.write(PredType::NATIVE_HBOOL, &intFromBool);
-
-        intFromBool = (int)m_errorPropagation;
-        att = settingsGroup.createAttribute("errorPropagation", PredType::NATIVE_HBOOL, spc);
-        att.write(PredType::NATIVE_HBOOL, &intFromBool);
-
-        intFromBool = (int)m_createInverseMatrix;
-        att = settingsGroup.createAttribute("createInverseMatrix", PredType::NATIVE_HBOOL, spc);
-        att.write(PredType::NATIVE_HBOOL, &intFromBool);
-
-        intFromBool = (int)m_outlierRejection;
-        att = settingsGroup.createAttribute("outlierRejection", PredType::NATIVE_HBOOL, spc);
-        att.write(PredType::NATIVE_HBOOL, &intFromBool);
-
-        /* 
-         * Add enum attributes as predefined data type PredType::C_S1 (string)
-         */ 
-        QString enumToStringValue = "";
-        int stringSize = 0;
-        H5::StrType strDataType;
-
-        enumToStringValue = convergenceCriteriaToString(m_convergenceCriteria);
-        stringSize = enumToStringValue.length();
-        strDataType = H5::StrType(PredType::C_S1, stringSize); 
-        att = settingsGroup.createAttribute("convergenceCriteria", strDataType, spc);
-        att.write(strDataType, enumToStringValue.toStdString());
-
-        /* 
-         * Add string attributes as predefined data type PredType::C_S1 (string)
-         */ 
-        stringSize = qMax(m_outputFilePrefix.length(), 1); // if empty string, set size to 1
-        strDataType = H5::StrType(PredType::C_S1, stringSize); 
-        att = settingsGroup.createAttribute("outputFilePrefix", strDataType, spc);
-        att.write(strDataType, m_outputFilePrefix.toStdString());
-
-        /* 
-         * Add double attributes as predefined data type PredType::NATIVE_DOUBLE
-         */ 
-        att = settingsGroup.createAttribute("outlierRejectionMultiplier",
-                                            PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(PredType::NATIVE_DOUBLE, &m_outlierRejectionMultiplier);
-
-        att = settingsGroup.createAttribute("globalLatitudeAprioriSigma", 
-                                            PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(PredType::NATIVE_DOUBLE, &m_globalLatitudeAprioriSigma);
-
-        att = settingsGroup.createAttribute("globalLongitudeAprioriSigma", 
-                                            PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(PredType::NATIVE_DOUBLE, &m_globalLongitudeAprioriSigma);
-
-        att = settingsGroup.createAttribute("globalRadiusAprioriSigma", 
-                                            PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(PredType::NATIVE_DOUBLE, &m_globalRadiusAprioriSigma);
-
-        att = settingsGroup.createAttribute("convergenceCriteriaThreshold", 
-                                            PredType::NATIVE_DOUBLE,
-                                            spc);
-        att.write(PredType::NATIVE_DOUBLE, &m_convergenceCriteriaThreshold);
-
-        /* 
-         * Add integer attributes as predefined data type PredType::NATIVE_INT
-         */ 
-        att = settingsGroup.createAttribute("convergenceCriteriaMaximumIterations", 
-                                            PredType::NATIVE_INT,
-                                            spc);
-        att.write(PredType::NATIVE_INT, &m_convergenceCriteriaMaximumIterations);
-
-        // Data sets??? tables???
-        // ??? QList m_observationSolveSettings; // TODO: pointer???
-        // ??? QList< QPair< MaximumLikelihoodWFunctions::Model, double > > m_maximumLikelihood;
-        // // TODO: pointer???
-//        return locationObject; 
-      }
-      // catch failure caused by the Attribute operations
-      catch ( H5::AttributeIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 ATTRIBUTE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataSet operations
-      catch ( H5::DataSetIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA SET exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataSpace operations
-      catch ( H5::DataSpaceIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA SPACE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataType operations
-      catch ( H5::DataTypeIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA TYPE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the H5File operations
-      catch ( H5::FileIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 FILE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the Group operations
-      catch ( H5::GroupIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 GROUP exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      catch (H5::Exception error) {  //??? how to improve printed msg using major/minor error codes?
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 GENERAL exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-    } 
-    catch (IException &e) {
-      throw IException(e,
-                       IException::Unknown, 
-                       "Unable to save bundle settings information to an HDF5 group.",
-                       _FILEINFO_);
-    }
-  }
-
-
-  /**
-   * HDF5 - TBD. 
-   *  
-   * NOTE: Currently this method is not used and may be deleted. Documentation 
-   * and testing to be completed if called. TargetBody info should be added 
-   * also. 
-   * @param 
-   * @param 
-   *  
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   * @throw 
-   */
-  void BundleSettings::openH5Group(H5::CommonFG &locationObject, QString locationName) {
-    try {
-      // Try block to detect exceptions raised by any of the calls inside it
-      try {
-        /*
-         * Turn off the auto-printing when failure occurs so that we can
-         * handle the errors appropriately
-         */
-//        H5::Exception::dontPrint();
-
-        // create a settings group to add to the given H5 object
-        QString settingsGroupName = locationName + "/BundleSettings"; 
-        H5::Group settingsGroup = locationObject.openGroup(settingsGroupName.toLatin1());
-
-        Attribute att;
-
-        /* 
-         * read bool attributes as predefined data type PredType::NATIVE_HBOOL
-         */ 
-        int boolAttValue = 0;
-        att = settingsGroup.openAttribute("validateNetwork");
-        att.read(PredType::NATIVE_HBOOL, &boolAttValue);
-        m_validateNetwork = (bool)boolAttValue;
-
-        att = settingsGroup.openAttribute("solveObservationMode");
-        att.read(PredType::NATIVE_HBOOL, &boolAttValue);
-        m_solveObservationMode = (bool)boolAttValue;
-
-        att = settingsGroup.openAttribute("solveRadius");
-        att.read(PredType::NATIVE_HBOOL, &boolAttValue);
-        m_solveRadius = (bool)boolAttValue;
-
-        att = settingsGroup.openAttribute("updateCubeLabel");
-        att.read(PredType::NATIVE_HBOOL, &boolAttValue);
-        m_updateCubeLabel = (bool)boolAttValue;
-
-        att = settingsGroup.openAttribute("errorPropagation");
-        att.read(PredType::NATIVE_HBOOL, &boolAttValue);
-        m_errorPropagation = (bool)boolAttValue;
-
-        att = settingsGroup.openAttribute("createInverseMatrix");
-        att.read(PredType::NATIVE_HBOOL, &boolAttValue);
-        m_createInverseMatrix = (bool)boolAttValue;
-
-        att = settingsGroup.openAttribute("outlierRejection");
-        att.read(PredType::NATIVE_HBOOL, &boolAttValue);
-        m_outlierRejection = (bool)boolAttValue;
-
-        /* 
-         * read enum attributes as predefined data type PredType::C_S1 (string)
-         */ 
-        H5std_string strAttValue;
-        H5::StrType strDataType;
-
-        att = settingsGroup.openAttribute("convergenceCriteria");
-        strDataType = H5::StrType(PredType::C_S1, att.getStorageSize());
-        att.read(strDataType, strAttValue);
-        m_convergenceCriteria = stringToConvergenceCriteria(QString::fromStdString(strAttValue));
-
-        /* 
-         * read string attributes as predefined data type PredType::C_S1 (string)
-         */ 
-        att = settingsGroup.openAttribute("outputFilePrefix");
-        strDataType = H5::StrType(PredType::C_S1, att.getStorageSize());
-        att.read(strDataType, strAttValue);
-        m_outputFilePrefix = QString::fromStdString(strAttValue);
-
-        /* 
-         * read double attributes as predefined data type PredType::NATIVE_DOUBLE
-         */ 
-        att = settingsGroup.openAttribute("outlierRejectionMultiplier");
-        att.read(PredType::NATIVE_DOUBLE, &m_outlierRejectionMultiplier);
-
-        att = settingsGroup.openAttribute("globalLatitudeAprioriSigma");
-        att.read(PredType::NATIVE_DOUBLE, &m_globalLatitudeAprioriSigma);
-
-        att = settingsGroup.openAttribute("globalLongitudeAprioriSigma");
-        att.read(PredType::NATIVE_DOUBLE, &m_globalLongitudeAprioriSigma);
-
-        att = settingsGroup.openAttribute("globalRadiusAprioriSigma");
-        att.read(PredType::NATIVE_DOUBLE, &m_globalRadiusAprioriSigma);
-
-        att = settingsGroup.openAttribute("convergenceCriteriaThreshold");
-        att.read(PredType::NATIVE_DOUBLE, &m_convergenceCriteriaThreshold);
-
-        /* 
-         * read int attributes as predefined data type PredType::NATIVE_INT
-         */ 
-        att = settingsGroup.openAttribute("convergenceCriteriaMaximumIterations");
-        att.read(PredType::NATIVE_INT, &m_convergenceCriteriaMaximumIterations);
-
-        // Data sets??? tables???
-        // ??? QList m_observationSolveSettings; // TODO: pointer???
-        // ??? QList< QPair< MaximumLikelihoodWFunctions::Model, double > > m_maximumLikelihood;
-        // // TODO: pointer???
-      }
-      // catch failure caused by the Attribute operations
-      catch ( H5::AttributeIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 ATTRIBUTE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataSet operations
-      catch ( H5::DataSetIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA SET exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataSpace operations
-      catch ( H5::DataSpaceIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA SPACE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the DataType operations
-      catch ( H5::DataTypeIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 DATA TYPE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the H5File operations
-      catch ( H5::FileIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 FILE exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      // catch failure caused by the Group operations
-      catch ( H5::GroupIException error ) {
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 GROUP exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-      catch (H5::Exception error) {  //??? how to improve printed msg using major/minor error codes?
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 GENERAL exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
-    } 
-    catch (IException &e) {
-      throw IException(e,
-                       IException::Unknown, 
-                       "Unable to read bundle settings information from an HDF5 group.",
-                       _FILEINFO_);
-    }
-  }
 }
diff --git a/isis/src/control/objs/BundleSettings/BundleSettings.h b/isis/src/control/objs/BundleSettings/BundleSettings.h
index 64017e9dfe4db94fce772ae20fa23a2486e24a80..3475474b7f40e779fc0247de3bc46206a3ebd750 100644
--- a/isis/src/control/objs/BundleSettings/BundleSettings.h
+++ b/isis/src/control/objs/BundleSettings/BundleSettings.h
@@ -28,10 +28,7 @@
 #include 
 #include 
 
-// hdf5 library
-#include 
-#include 
-#include 
+
 
 // ISIS library
 #include "BundleTargetBody.h"
@@ -44,7 +41,7 @@ class QDataStream;
 class QUuid;
 class QXmlStreamWriter;
 
-using namespace H5;
+
 using namespace Isis;
 
 namespace Isis {
@@ -54,10 +51,10 @@ namespace Isis {
   class XmlStackedHandlerReader;
 
   /**
-   * @brief Container class for BundleAdjustment settings. 
-   * This class contains all of the settings needed to run a bundle adjustment. 
-   * A BundleSettings object is passed into the BundleAdjustment constructor.  
-   *  
+   * @brief Container class for BundleAdjustment settings.
+   * This class contains all of the settings needed to run a bundle adjustment.
+   * A BundleSettings object is passed into the BundleAdjustment constructor.
+   *
    * @ingroup ControlNetworks
    *
    * @author 2014-05-14 Jeannie Backer
@@ -103,7 +100,8 @@ namespace Isis {
    *                           are acquired by an associated observation number. References #4293.
    *   @history 2016-10-17 Jesse Mapel - Removed m_SCPVLFilename parameter in accordance with
    *                           USEPVL being removed from jigsaw.  References #4316.
-   *  
+   *   @history 2017-04-24 Ian Humphrey - Removed pvlObject(). Fixes #4797.
+   *
    *   @todo Determine which XmlStackedHandlerReader constructor is preferred
    *   @todo Determine which XmlStackedHandler needs a Project pointer (see constructors)
    *   @todo Determine whether QList m_observationSolveSettings
@@ -112,9 +110,8 @@ namespace Isis {
    *   @todo Determine whether QList< QPair< MaximumLikelihoodWFunctions::Model, double > >
    *         m_maximumLikelihood should be a list of pointers, or a pointer to a list, or a pointer
    *         to a list of pointers, etc...
-      ; 
-   *   @todo Determine which to use or delete: XML or HDF5. Whichever is used needs to be fully
-   *         documented, tested
+   *   @todo TargetBody information is not being serialized. A determination needs to
+   *         be made as to where it will be stored.
    */
   class BundleSettings {
     public:
@@ -124,14 +121,14 @@ namespace Isis {
       //=====================================================================//
       BundleSettings();
       BundleSettings(const BundleSettings &other);
-      BundleSettings(Project *project, 
+      BundleSettings(Project *project,
                      XmlStackedHandlerReader *xmlReader);
 #if 0
       BundleSettings(FileName xmlFile,
-                     Project *project, 
-                     XmlStackedHandlerReader *xmlReader, 
+                     Project *project,
+                     XmlStackedHandlerReader *xmlReader,
                      QObject *parent = NULL);
-      BundleSettings(XmlStackedHandlerReader *xmlReader, 
+      BundleSettings(XmlStackedHandlerReader *xmlReader,
                      QObject *parent = NULL);
 #endif
       ~BundleSettings();
@@ -147,13 +144,13 @@ namespace Isis {
 
       // mutators
       void setSolveOptions(bool solveObservationMode = false,
-                           bool updateCubeLabel = false, 
+                           bool updateCubeLabel = false,
                            bool errorPropagation = false,
-                           bool solveRadius = false, 
-                           double globalLatitudeAprioriSigma = Isis::Null, 
-                           double globalLongitudeAprioriSigma = Isis::Null, 
+                           bool solveRadius = false,
+                           double globalLatitudeAprioriSigma = Isis::Null,
+                           double globalLongitudeAprioriSigma = Isis::Null,
                            double globalRadiusAprioriSigma = Isis::Null);
-      void setOutlierRejection(bool outlierRejection, 
+      void setOutlierRejection(bool outlierRejection,
                                double multiplier = 1.0);
       void setObservationSolveOptions(QList obsSolveSettingsList);
       void setCreateInverseMatrix(bool createMatrix);
@@ -180,20 +177,20 @@ namespace Isis {
       //=====================================================================//
 
       /**
-       * This enum defines the options for the bundle adjustment's convergence. 
+       * This enum defines the options for the bundle adjustment's convergence.
        */
       enum ConvergenceCriteria {
-        Sigma0,              /**< The value of sigma0 will be used to determine that the bundle 
+        Sigma0,              /**< The value of sigma0 will be used to determine that the bundle
                                   adjustment has converged.*/
-        ParameterCorrections /**< All parameter corrections will be used to determine that the 
+        ParameterCorrections /**< All parameter corrections will be used to determine that the
                                   bundle adjustment has converged.*/
       };
 
 
       static ConvergenceCriteria stringToConvergenceCriteria(QString criteria);
       static QString convergenceCriteriaToString(ConvergenceCriteria criteria);
-      void setConvergenceCriteria(ConvergenceCriteria criteria, 
-                                  double threshold, 
+      void setConvergenceCriteria(ConvergenceCriteria criteria,
+                                  double threshold,
                                   int maximumIterations);
       ConvergenceCriteria convergenceCriteria() const;
       double convergenceCriteriaThreshold() const;
@@ -209,11 +206,11 @@ namespace Isis {
 
 
       //=====================================================================//
-      //=============== Maximum Likelihood Estimation Options ===============// 
-      //=====================================================================// 
+      //=============== Maximum Likelihood Estimation Options ===============//
+      //=====================================================================//
 
       /**
-       * This enum defines the options for maximum likelihood estimation. 
+       * This enum defines the options for maximum likelihood estimation.
        */
       enum MaximumLikelihoodModel {
         NoMaximumLikelihoodEstimator, /**< Do not use a maximum likelihood model.*/
@@ -232,9 +229,9 @@ namespace Isis {
       };
 
 
-      void addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Model model, 
+      void addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Model model,
                                               double cQuantile);
-      QList< QPair< MaximumLikelihoodWFunctions::Model, double > > 
+      QList< QPair< MaximumLikelihoodWFunctions::Model, double > >
           maximumLikelihoodEstimatorModels() const;
 
       //=====================================================================//
@@ -245,6 +242,7 @@ namespace Isis {
       //=====================================================================//
       //============================== Target Body ==========================//
       //=====================================================================//
+      // Note targeBody information is not currently serialized.
       void setBundleTargetBody(BundleTargetBodyQsp bundleTargetBody);
       BundleTargetBodyQsp bundleTargetBody() const;
 //      bool solveTargetBodyPolePosition() const;
@@ -265,69 +263,51 @@ namespace Isis {
 
 
       //=====================================================================//
-      //================== Output Options ??? (from Jigsaw only)=============// 
-      //=====================================================================// 
+      //================== Output Options ??? (from Jigsaw only)=============//
+      //=====================================================================//
       void setOutputFilePrefix(QString outputFilePrefix);
       void setSCPVLFilename(QString SCParamFilename);
       QString outputFilePrefix() const;
       QString SCPVLFilename() const;
 
-      PvlObject pvlObject(QString name = "BundleSettings") const;
-
       void save(QXmlStreamWriter &stream, const Project *project) const;
 
-      QDataStream &write(QDataStream &stream) const;
-      QDataStream &read(QDataStream &stream);
-
-      void createH5Group(hid_t locationId, 
-                         QString locationName) const; //delete
-      void parseH5Group(hid_t locationId, 
-                        QString locationName);        //delete
-
-      void createH5Group(H5::CommonFG &locationObject, 
-                         QString locationName) const;
-      H5::Group createH5Group2(H5::Group locationGroup, 
-                               QString locationName);
-      void openH5Group(H5::CommonFG &locationObject, 
-                       QString locationName);
-      BundleSettings(H5::CommonFG &locationObject, 
-                     QString locationName);
-
     private:
+      void init();
 
       //=====================================================================//
       //============= Saving/Restoring a BundleSettings object ==============//
       //=====================================================================//
 
       /**
-       * This class is needed to read/write BundleSettings from/to an XML 
-       * formateed file. 
-       *  
+       * This class is needed to read/write BundleSettings from/to an XML
+       * formateed file.
+       *
        * @author 2014-07-21 Ken Edmundson
        *
-       * @internal 
+       * @internal
        *   @history 2014-07-21 Ken Edmundson - Original version.
        */
       class XmlHandler : public XmlStackedHandler {
         public:
-          XmlHandler(BundleSettings *bundleSettings, 
+          XmlHandler(BundleSettings *bundleSettings,
                      Project *project);
           XmlHandler(BundleSettings *bundleSettings);
           ~XmlHandler();
-   
-          virtual bool startElement(const QString &namespaceURI, 
+
+          virtual bool startElement(const QString &namespaceURI,
                                     const QString &localName,
-                                    const QString &qName, 
+                                    const QString &qName,
                                     const QXmlAttributes &atts);
           virtual bool characters(const QString &ch);
-          virtual bool endElement(const QString &namespaceURI, 
+          virtual bool endElement(const QString &namespaceURI,
                                   const QString &localName,
                                   const QString &qName);
           bool fatalError(const QXmlParseException &exception);
 
         private:
           Q_DISABLE_COPY(XmlHandler);
-   
+
           BundleSettings *m_xmlHandlerBundleSettings ;
           Project *m_xmlHandlerProject; // TODO: does xml stuff need project???
           QString m_xmlHandlerCharacters;
@@ -335,10 +315,10 @@ namespace Isis {
       };
 
 
-      /** 
-       * This struct is needed to write the m_maximumLikelihood variable as an 
-       * HDF5 table. Each table record has 3 field values: index, name, and 
-       * quantile. 
+      /**
+       * This struct is needed to write the m_maximumLikelihood variable as an
+       * HDF5 table. Each table record has 3 field values: index, name, and
+       * quantile.
        */
       struct MaximumLikelihoodModelTableRecord {
           unsigned int indexFieldValue; //!< The index of the TableRecord.???
@@ -346,15 +326,13 @@ namespace Isis {
           double quantileFieldValue; //!< The quantile of the TableRecord.???
       };
 
-      QUuid *m_id; /**< A unique ID for this BundleSettings object. 
-                        Used to reference this object when saving to disk.*/
       bool m_validateNetwork; //!< Indicates whether the network should be validated.
       bool m_solveObservationMode; //!< Indicates whether to solve for observation mode.
       bool m_solveRadius; //!< Indicates whether to solve for point radii.
       bool m_updateCubeLabel; //!< Indicates whether to update cubes.
       bool m_errorPropagation; //!< Indicates whether to perform error propagation.
       bool m_createInverseMatrix; //!< Indicates whether to create the inverse matrix file.
-      bool m_outlierRejection; /**< Indicates whether to perform automatic 
+      bool m_outlierRejection; /**< Indicates whether to perform automatic
                                     outlier detection/rejection.*/
       double m_outlierRejectionMultiplier; /**< The multiplier value for outlier rejection.
                                                 Defaults to 1, so no change if rejection = false.*/
@@ -368,24 +346,24 @@ namespace Isis {
       QList m_observationSolveSettings; //!<
 
       // Convergence Criteria
-      ConvergenceCriteria m_convergenceCriteria;  /**< Enumeration used to indicate what criteria 
-                                                       to use to determine bundle 
+      ConvergenceCriteria m_convergenceCriteria;  /**< Enumeration used to indicate what criteria
+                                                       to use to determine bundle
                                                        adjustment convergence.*/
-      double m_convergenceCriteriaThreshold;      /**< Tolerance value corresponding to the selected 
+      double m_convergenceCriteriaThreshold;      /**< Tolerance value corresponding to the selected
                                                        convergence criteria.*/
-      int m_convergenceCriteriaMaximumIterations; /**< Maximum number of iterations before 
-                                                       quitting the bundle adjustment if it has 
+      int m_convergenceCriteriaMaximumIterations; /**< Maximum number of iterations before
+                                                       quitting the bundle adjustment if it has
                                                        not yet converged to the given threshold.*/
 
       // Maximum Likelihood Estimation Options
       /**
-       * Model and C-Quantile for each of the three maximum likelihood 
-       * estimations. The C-Quantile is the quantile of the residual used 
-       * to compute the tweaking constant. Note that this is an ordered 
-       * list and that the Welsch and Chen models can not be used for the 
+       * Model and C-Quantile for each of the three maximum likelihood
+       * estimations. The C-Quantile is the quantile of the residual used
+       * to compute the tweaking constant. Note that this is an ordered
+       * list and that the Welsch and Chen models can not be used for the
        * first model.
        */
-      QList< QPair< MaximumLikelihoodWFunctions::Model, double > > m_maximumLikelihood; 
+      QList< QPair< MaximumLikelihoodWFunctions::Model, double > > m_maximumLikelihood;
 
       // Self Calibration
 
@@ -396,19 +374,16 @@ namespace Isis {
 
       // Output Options
       QString m_outputFilePrefix;    /**< The prefix for all output files. If the user does not want
-                                          output files to be written to the current directory, the 
+                                          output files to be written to the current directory, the
                                           output directory path should be included in this prefix.*/
  };
   // typedefs
   //! Definition for a BundleSettingsQsp, a shared pointer to a BundleSettings object.
   typedef QSharedPointer BundleSettingsQsp;
 
-  // operators to read/write BundleResults to/from binary data
-  QDataStream &operator<<(QDataStream &stream, const BundleSettings &settings);
-  QDataStream &operator>>(QDataStream &stream, BundleSettings &settings);
+
 };
 
 Q_DECLARE_METATYPE(Isis::BundleSettingsQsp);
 
 #endif
-
diff --git a/isis/src/control/objs/BundleSettings/BundleSettings.truth b/isis/src/control/objs/BundleSettings/BundleSettings.truth
index cfe4568838b1f371ddaf5a77486ffb79b4224369..29abea63bdc5a8b29e789e0b127615d58d8b4688 100644
--- a/isis/src/control/objs/BundleSettings/BundleSettings.truth
+++ b/isis/src/control/objs/BundleSettings/BundleSettings.truth
@@ -1,391 +1,264 @@
 Unit test for BundleSettings...
 Printing PVL group with settings from the default constructor...
-Object = DefaultSettingsObject
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = No
-  SolveRadius                          = No
-  UpdateCubeLabel                      = No
-  ErrorPropagation                     = No
-  CreateInverseMatrix                  = No
-  OutlierRejection                     = No
-  GlobalLatitudeAprioriSigma           = None
-  GlobalLongitudeAprioriSigma          = None
-  ConvergenceCriteria                  = Sigma0
-  ConvergenceCriteriaThreshold         = 1.0e-10
-  ConvergenceCriteriaMaximumIterations = 50
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = Null
-  NumberObservationSolveSettings       = 1
-
-  Object = Null
-    InstrumentPointingSolveOption       = AnglesOnly
-    NumberAngleCoefficientsSolved       = 1
-    CKDegree                            = 2
-    CKSolveDegree                       = 2
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = No
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = 3
-    InstrumentPositionSolveOption       = None
-    NumberPositionCoefficientsSolved    = N/A
-    SPKDegree                           = N/A
-    SPKSolveDegree                      = N/A
-    SolvePositionOverHermiteSpline      = N/A
-    PositionAprioriSigmas               = N/A
-    InstrumentPositionInterpolationType = N/A
-  End_Object
-End_Object
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
 
 Testing copy constructor...
-Object = CopySettingsObject
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = No
-  SolveRadius                          = No
-  UpdateCubeLabel                      = No
-  ErrorPropagation                     = No
-  CreateInverseMatrix                  = No
-  OutlierRejection                     = No
-  GlobalLatitudeAprioriSigma           = None
-  GlobalLongitudeAprioriSigma          = None
-  ConvergenceCriteria                  = Sigma0
-  ConvergenceCriteriaThreshold         = 1.0e-10
-  ConvergenceCriteriaMaximumIterations = 50
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = Null
-  NumberObservationSolveSettings       = 1
-
-  Object = Null
-    InstrumentPointingSolveOption       = AnglesOnly
-    NumberAngleCoefficientsSolved       = 1
-    CKDegree                            = 2
-    CKSolveDegree                       = 2
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = No
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = 3
-    InstrumentPositionSolveOption       = None
-    NumberPositionCoefficientsSolved    = N/A
-    SPKDegree                           = N/A
-    SPKSolveDegree                      = N/A
-    SolvePositionOverHermiteSpline      = N/A
-    PositionAprioriSigmas               = N/A
-    InstrumentPositionInterpolationType = N/A
-  End_Object
-End_Object
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
 
 Testing assignment operator to set this equal to itself...
-Object = SelfAssignedSettingsObject
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = No
-  SolveRadius                          = No
-  UpdateCubeLabel                      = No
-  ErrorPropagation                     = No
-  CreateInverseMatrix                  = No
-  OutlierRejection                     = No
-  GlobalLatitudeAprioriSigma           = None
-  GlobalLongitudeAprioriSigma          = None
-  ConvergenceCriteria                  = Sigma0
-  ConvergenceCriteriaThreshold         = 1.0e-10
-  ConvergenceCriteriaMaximumIterations = 50
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = Null
-  NumberObservationSolveSettings       = 1
-
-  Object = Null
-    InstrumentPointingSolveOption       = AnglesOnly
-    NumberAngleCoefficientsSolved       = 1
-    CKDegree                            = 2
-    CKSolveDegree                       = 2
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = No
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = 3
-    InstrumentPositionSolveOption       = None
-    NumberPositionCoefficientsSolved    = N/A
-    SPKDegree                           = N/A
-    SPKSolveDegree                      = N/A
-    SolvePositionOverHermiteSpline      = N/A
-    PositionAprioriSigmas               = N/A
-    InstrumentPositionInterpolationType = N/A
-  End_Object
-End_Object
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
 
 Testing assignment operator to create a new settings object...
-Object = AssignedSettingsObject
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = No
-  SolveRadius                          = No
-  UpdateCubeLabel                      = No
-  ErrorPropagation                     = No
-  CreateInverseMatrix                  = No
-  OutlierRejection                     = No
-  GlobalLatitudeAprioriSigma           = None
-  GlobalLongitudeAprioriSigma          = None
-  ConvergenceCriteria                  = Sigma0
-  ConvergenceCriteriaThreshold         = 1.0e-10
-  ConvergenceCriteriaMaximumIterations = 50
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = Null
-  NumberObservationSolveSettings       = 1
-
-  Object = Null
-    InstrumentPointingSolveOption       = AnglesOnly
-    NumberAngleCoefficientsSolved       = 1
-    CKDegree                            = 2
-    CKSolveDegree                       = 2
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = No
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = 3
-    InstrumentPositionSolveOption       = None
-    NumberPositionCoefficientsSolved    = N/A
-    SPKDegree                           = N/A
-    SPKSolveDegree                      = N/A
-    SolvePositionOverHermiteSpline      = N/A
-    PositionAprioriSigmas               = N/A
-    InstrumentPositionInterpolationType = N/A
-  End_Object
-End_Object
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
 
 Testing mutator methods...
-Object = ResetAllOptions
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = Yes
-  SolveRadius                          = Yes
-  UpdateCubeLabel                      = Yes
-  ErrorPropagation                     = Yes
-  CreateInverseMatrix                  = Yes
-  OutlierRejection                     = Yes
-  OutlierMultiplier                    = 4.0
-  GlobalLatitudeAprioriSigma           = 1000.0
-  GlobalLongitudeAprioriSigma          = 2000.0
-  GlobalRadiiAprioriSigma              = 3000.0
-  ConvergenceCriteria                  = ParameterCorrections
-  ConvergenceCriteriaThreshold         = 0.25
-  ConvergenceCriteriaMaximumIterations = 26
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = TestFilePrefix
-  MaximumLikelihoodModels              = (Huber, Welsch, HuberModified, Chen)
-  MaximumLikelihoodQuantiles           = (0.27, 28.0, 29.0, 30.0)
-  NumberObservationSolveSettings       = 2
-
-  Object = Null
-    InstrumentPointingSolveOption       = None
-    NumberAngleCoefficientsSolved       = N/A
-    CKDegree                            = N/A
-    CKSolveDegree                       = N/A
-    SolveTwist                          = N/A
-    SolvePointingPolynomialOverExisting = N/A
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = N/A
-    InstrumentPositionSolveOption       = AllPolynomialCoefficients
-    NumberPositionCoefficientsSolved    = 7
-    SPKDegree                           = 5
-    SPKSolveDegree                      = 6
-    SolvePositionOverHermiteSpline      = Yes
-    PositionAprioriSigmas               = (7000.0, 8000.0, 9000.0)
-    InstrumentPositionInterpolationType = 4
-  End_Object
-
-  Object = Null
-    InstrumentPointingSolveOption       = AllPolynomialCoefficients
-    NumberAngleCoefficientsSolved       = 2
-    CKDegree                            = 21
-    CKSolveDegree                       = 1
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = Yes
-    AngleAprioriSigmas                  = (22.0, 23.0)
-    InstrumentPointingInterpolationType = 4
-    InstrumentPositionSolveOption       = PositionOnly
-    NumberPositionCoefficientsSolved    = 1
-    SPKDegree                           = 2
-    SPKSolveDegree                      = 2
-    SolvePositionOverHermiteSpline      = Yes
-    PositionAprioriSigmas               = 17000.0
-    InstrumentPositionInterpolationType = 4
-  End_Object
-End_Object
-
-Object = ResetSolveOptions
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = Yes
-  SolveRadius                          = No
-  UpdateCubeLabel                      = Yes
-  ErrorPropagation                     = Yes
-  CreateInverseMatrix                  = Yes
-  OutlierRejection                     = No
-  GlobalLatitudeAprioriSigma           = None
-  GlobalLongitudeAprioriSigma          = None
-  ConvergenceCriteria                  = Sigma0
-  ConvergenceCriteriaThreshold         = 1.0e-10
-  ConvergenceCriteriaMaximumIterations = 50
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = TestFilePrefix
-  NumberObservationSolveSettings       = 1
-
-  Object = Null
-    InstrumentPointingSolveOption       = AnglesOnly
-    NumberAngleCoefficientsSolved       = 1
-    CKDegree                            = 2
-    CKSolveDegree                       = 2
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = No
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = 3
-    InstrumentPositionSolveOption       = None
-    NumberPositionCoefficientsSolved    = N/A
-    SPKDegree                           = N/A
-    SPKSolveDegree                      = N/A
-    SolvePositionOverHermiteSpline      = N/A
-    PositionAprioriSigmas               = N/A
-    InstrumentPositionInterpolationType = N/A
-  End_Object
-End_Object
-
-Object = ResetOutputOptions
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = Yes
-  SolveRadius                          = No
-  UpdateCubeLabel                      = Yes
-  ErrorPropagation                     = Yes
-  CreateInverseMatrix                  = Yes
-  OutlierRejection                     = No
-  GlobalLatitudeAprioriSigma           = None
-  GlobalLongitudeAprioriSigma          = None
-  ConvergenceCriteria                  = Sigma0
-  ConvergenceCriteriaThreshold         = 1.0e-10
-  ConvergenceCriteriaMaximumIterations = 50
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = TestFilePrefix
-  NumberObservationSolveSettings       = 1
-
-  Object = Null
-    InstrumentPointingSolveOption       = AnglesOnly
-    NumberAngleCoefficientsSolved       = 1
-    CKDegree                            = 2
-    CKSolveDegree                       = 2
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = No
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = 3
-    InstrumentPositionSolveOption       = None
-    NumberPositionCoefficientsSolved    = N/A
-    SPKDegree                           = N/A
-    SPKSolveDegree                      = N/A
-    SolvePositionOverHermiteSpline      = N/A
-    PositionAprioriSigmas               = N/A
-    InstrumentPositionInterpolationType = N/A
-  End_Object
-End_Object
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+            
+            
+            
+            
+        
+        
+    
+    
+        
+            
+            
+            
+                
+            
+            
+                
+                    7000.0
+                    8000.0
+                    9000.0
+                
+            
+        
+        
+            
+            
+            
+                
+                    22.0
+                    23.0
+                
+            
+            
+                
+                    17000.0
+                
+            
+        
+    
+ 
+
+
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
+
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
 
 Testing accessor methods...
 Get BundleObservationSolveSettings with name InstrumentId = Instrument1
-Object = Null
-  InstrumentPointingSolveOption       = None
-  NumberAngleCoefficientsSolved       = N/A
-  CKDegree                            = N/A
-  CKSolveDegree                       = N/A
-  SolveTwist                          = N/A
-  SolvePointingPolynomialOverExisting = N/A
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = N/A
-  InstrumentPositionSolveOption       = AllPolynomialCoefficients
-  NumberPositionCoefficientsSolved    = 7
-  SPKDegree                           = 5
-  SPKSolveDegree                      = 6
-  SolvePositionOverHermiteSpline      = Yes
-  PositionAprioriSigmas               = (7000.0, 8000.0, 9000.0)
-  InstrumentPositionInterpolationType = 4
-End_Object
+
+
+    
+    
+    
+        
+    
+    
+        
+            7000.0
+            8000.0
+            9000.0
+        
+    
+ 
+
 
 Now get BundleObservationSolveSettings at index 1
-Object = Null
-  InstrumentPointingSolveOption       = AllPolynomialCoefficients
-  NumberAngleCoefficientsSolved       = 2
-  CKDegree                            = 21
-  CKSolveDegree                       = 1
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = Yes
-  AngleAprioriSigmas                  = (22.0, 23.0)
-  InstrumentPointingInterpolationType = 4
-  InstrumentPositionSolveOption       = PositionOnly
-  NumberPositionCoefficientsSolved    = 1
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = Yes
-  PositionAprioriSigmas               = 17000.0
-  InstrumentPositionInterpolationType = 4
-End_Object
+
+
+    
+    
+    
+        
+            22.0
+            23.0
+        
+    
+    
+        
+            17000.0
+        
+    
+ 
+
 
 "Huber" "0.27"
 "Welsch" "28.0"
@@ -396,155 +269,169 @@ Testing static enum-to-string and string-to-enum methods...
 "Sigma0"
 "ParameterCorrections"
 
-Testing serialization...
-Object = BundleSettings
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = Yes
-  SolveRadius                          = Yes
-  UpdateCubeLabel                      = Yes
-  ErrorPropagation                     = Yes
-  CreateInverseMatrix                  = Yes
-  OutlierRejection                     = Yes
-  OutlierMultiplier                    = 4.0
-  GlobalLatitudeAprioriSigma           = 1000.0
-  GlobalLongitudeAprioriSigma          = 2000.0
-  GlobalRadiiAprioriSigma              = 3000.0
-  ConvergenceCriteria                  = ParameterCorrections
-  ConvergenceCriteriaThreshold         = 0.25
-  ConvergenceCriteriaMaximumIterations = 26
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = TestFilePrefix
-  MaximumLikelihoodModels              = (Huber, Welsch, HuberModified, Chen)
-  MaximumLikelihoodQuantiles           = (0.27, 28.0, 29.0, 30.0)
-  NumberObservationSolveSettings       = 2
-
-  Object = Null
-    InstrumentPointingSolveOption       = None
-    NumberAngleCoefficientsSolved       = N/A
-    CKDegree                            = N/A
-    CKSolveDegree                       = N/A
-    SolveTwist                          = N/A
-    SolvePointingPolynomialOverExisting = N/A
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = N/A
-    InstrumentPositionSolveOption       = AllPolynomialCoefficients
-    NumberPositionCoefficientsSolved    = 7
-    SPKDegree                           = 5
-    SPKSolveDegree                      = 6
-    SolvePositionOverHermiteSpline      = Yes
-    PositionAprioriSigmas               = (7000.0, 8000.0, 9000.0)
-    InstrumentPositionInterpolationType = 4
-  End_Object
-
-  Object = Null
-    InstrumentPointingSolveOption       = AllPolynomialCoefficients
-    NumberAngleCoefficientsSolved       = 2
-    CKDegree                            = 21
-    CKSolveDegree                       = 1
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = Yes
-    AngleAprioriSigmas                  = (22.0, 23.0)
-    InstrumentPointingInterpolationType = 4
-    InstrumentPositionSolveOption       = PositionOnly
-    NumberPositionCoefficientsSolved    = 1
-    SPKDegree                           = 2
-    SPKSolveDegree                      = 2
-    SolvePositionOverHermiteSpline      = Yes
-    PositionAprioriSigmas               = 17000.0
-    InstrumentPositionInterpolationType = 4
-  End_Object
-End_Object
-
-Testing XML: write XML from BundleSettings object...
-Testing XML: read XML to BundleSettings object...
-Object = BundleSettingsFromXml
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = Yes
-  SolveRadius                          = No
-  UpdateCubeLabel                      = Yes
-  ErrorPropagation                     = Yes
-  CreateInverseMatrix                  = Yes
-  OutlierRejection                     = No
-  GlobalLatitudeAprioriSigma           = None
-  GlobalLongitudeAprioriSigma          = None
-  ConvergenceCriteria                  = Sigma0
-  ConvergenceCriteriaThreshold         = 1.0e-10
-  ConvergenceCriteriaMaximumIterations = 50
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = TestFilePrefix
-  NumberObservationSolveSettings       = 1
-
-  Object = Null
-    InstrumentPointingSolveOption       = AnglesOnly
-    NumberAngleCoefficientsSolved       = 1
-    CKDegree                            = 2
-    CKSolveDegree                       = 2
-    SolveTwist                          = Yes
-    SolvePointingPolynomialOverExisting = No
-    AngleAprioriSigmas                  = N/A
-    InstrumentPointingInterpolationType = 3
-    InstrumentPositionSolveOption       = None
-    NumberPositionCoefficientsSolved    = N/A
-    SPKDegree                           = N/A
-    SPKSolveDegree                      = N/A
-    SolvePositionOverHermiteSpline      = N/A
-    PositionAprioriSigmas               = N/A
-    InstrumentPositionInterpolationType = N/A
-  End_Object
-End_Object
-
-Testing XML: read XML to BundleSettings object...
-Object = BundleSettingsFromXml
-  NetworkValidated                     = Yes
-  SolveObservationMode                 = Yes
-  SolveRadius                          = Yes
-  UpdateCubeLabel                      = Yes
-  ErrorPropagation                     = Yes
-  CreateInverseMatrix                  = Yes
-  OutlierRejection                     = Yes
-  OutlierMultiplier                    = 4.0
-  GlobalLatitudeAprioriSigma           = 1000.0
-  GlobalLongitudeAprioriSigma          = 2000.0
-  GlobalRadiiAprioriSigma              = 3000.0
-  ConvergenceCriteria                  = ParameterCorrections
-  ConvergenceCriteriaThreshold         = 0.25
-  ConvergenceCriteriaMaximumIterations = 26
-  SolveTargetBody                      = No
-  NumberTargetBodyParameters           = 0
-  SolvePoleRightAscension              = No
-  SolvePoleRightAscensionVelocity      = No
-  SolvePoleDeclination                 = No
-  SolvePoleDeclinationVelocity         = No
-  SolvePolePrimeMeridian               = No
-  SolvePolePrimeMeridianVelocity       = No
-  SolvePolePrimeMeridianAcceleration   = No
-  solveTriaxialRadii                   = No
-  solveMeanRadius                      = No
-  FilePrefix                           = TestFilePrefix
-  MaximumLikelihoodModels              = (Huber, Welsch, HuberModified, Chen)
-  MaximumLikelihoodQuantiles           = (0.27, 28.0, 29.0, 30.0)
-  NumberObservationSolveSettings       = 0
-End_Object
+Testing XML serialization 1: write XML from BundleSettings object...
+Serializing test XML object to file:
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
+
+Testing XML: Object deserialized as (should match object above):
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+            
+        
+    
+ 
+
+
+Testing XML serialization 2: write XML from BundleSettings object...
+Serializing test XML object to file:
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+            
+            
+            
+            
+        
+        
+    
+    
+        
+            
+            
+            
+                
+            
+            
+                
+                    7000.0
+                    8000.0
+                    9000.0
+                
+            
+        
+        
+            
+            
+            
+                
+                    22.0
+                    23.0
+                
+            
+            
+                
+                    17000.0
+                
+            
+        
+    
+ 
+
+
+Testing XML: Object deserialized as (should match object above):
+
+
+    
+        Yes
+        
+        
+        
+        
+        
+            
+            
+            
+            
+        
+        
+    
+    
+        
+            
+            
+            
+                
+                    N/A
+                
+            
+            
+                
+                    7000.0
+                    8000.0
+                    9000.0
+                
+            
+        
+        
+            
+            
+            
+                
+                    22.0
+                    23.0
+                
+            
+            
+                
+                    17000.0
+                
+            
+        
+    
+ 
+
 
 Testing error throws...
 **ERROR** Unable to find BundleObservationSolveSettings for observation number [UnassociatedObservationNumber].
@@ -553,5 +440,3 @@ Testing error throws...
 **PROGRAMMER ERROR** Unknown bundle convergence criteria [Pickles].
 **PROGRAMMER ERROR** Unknown convergence criteria enum [33].
 **PROGRAMMER ERROR** For bundle adjustments with multiple maximum likelihood estimators, the first model must be of type HUBER or HUBER_MODIFIED.
-
-Testing HDF5 write/read...
diff --git a/isis/src/control/objs/BundleSettings/unitTest.cpp b/isis/src/control/objs/BundleSettings/unitTest.cpp
index c26749af576ed2b4b1973a8bda6a6bec1c0decdc..b8811df68fc3d583be0cfde31d8b88512443165a 100755
--- a/isis/src/control/objs/BundleSettings/unitTest.cpp
+++ b/isis/src/control/objs/BundleSettings/unitTest.cpp
@@ -3,6 +3,7 @@
 #include 
 #include 
 #include 
+#include 
 #include 
 #include 
 #include 
@@ -21,9 +22,12 @@
 using namespace std;
 using namespace Isis;
 
+template
+void printXml(const T &);
+
 /**
-  * Test BundleSettings 
-  *  
+  * Test BundleSettings
+  *
   *
   * @author 2014-05-14 Jeannie Backer
   * @internal
@@ -37,24 +41,26 @@ using namespace Isis;
   *   @history 2016-10-13 Ian Humphrey - Replaced setInstrumentId() with addObservationNumber()
   *                           to associate the bundle observation solve settings with an
   *                           observation number. References #4293.
-  *   @history 2016-10-24 Makayla Shepherd - Commented out the test for setting the default settings 
-  *                           when reading from an empty XML. This test was failing on prog24 and we 
-  *                           are not sure if we are going to allow XML reading/writing as we are 
+  *   @history 2016-10-24 Makayla Shepherd - Commented out the test for setting the default settings
+  *                           when reading from an empty XML. This test was failing on prog24 and we
+  *                           are not sure if we are going to allow XML reading/writing as we are
   *                           most likely going to move to HDF5. Fixes #4327.
+  *   @history 2017-04-24 Ian Humphrey - Removed pvlObject() and replaced with the XML save().
+  *                           Fixes #4797.
   *
   *   @todo Truth updated so that the name of the BundleObservationSolveSettings object is Null,
   *         this should be fixed as part of #4292.
   *   @todo Test hdf5 methods when added.
   *   @todo Test setBundleTargetBody()
   *   @todo Test non-null bundleTargetBody()
-  *  
+  *
   */
 
 
 namespace Isis {
   /**
    * Child class of BundleSettings used to test the embedded XML handler class.
-   *  
+   *
    * @author 2014-05-14 Jeannie Backer
    * @internal
    *   @history 2014-05-14 Jeannie Backer - Original version.
@@ -62,18 +68,18 @@ namespace Isis {
   class BundleSettingsXmlHandlerTester : public BundleSettings {
     public:
       /**
-       * Constructs BundleSettings using XML handler. 
-       *  
+       * Constructs BundleSettings using XML handler.
+       *
        * @param project A pointer to the project.
        * @param reader A pointer to a XmlStackedHandlerReader.
-       * @param xmlFile The name of the XML file to be used to create a 
+       * @param xmlFile The name of the XML file to be used to create a
        *                BundleSettings object.
-       * 
-       * 
+       *
+       *
        * @throw Isis::Exception::Io "Unable to open XML file with read access."
        * @throw Isis::Exception::Unknown "Failed to parse XML file."
        */
-      BundleSettingsXmlHandlerTester(Project *project, XmlStackedHandlerReader *reader, 
+      BundleSettingsXmlHandlerTester(Project *project, XmlStackedHandlerReader *reader,
                                      FileName xmlFile) : BundleSettings(project, reader) {
 
         QString xmlPath(xmlFile.expanded());
@@ -88,7 +94,7 @@ namespace Isis {
         QXmlInputSource xmlInputSource(&file);
         bool success = reader->parse(xmlInputSource);
         if (!success) {
-          throw IException(IException::Unknown, 
+          throw IException(IException::Unknown,
                            QString("Failed to parse xml file, [%1]").arg(xmlPath),
                             _FILEINFO_);
         }
@@ -127,36 +133,34 @@ int main(int argc, char *argv[]) {
     //      int convergenceCriteriaMaximumIterations() const;
     //      QString outputFilePrefix() const;
     //      int numberSolveSettings();
-    //      int numberTargetBodyParameters() 
-    //      bool solveTargetBody()            
-    //      bool solvePoleRA()                
-    //      bool solvePoleRAVelocity()        
-    //      bool solvePoleDec()               
-    //      bool solvePoleDecVelocity()       
-    //      bool solvePM()                    
-    //      bool solvePMVelocity()   
+    //      int numberTargetBodyParameters()
+    //      bool solveTargetBody()
+    //      bool solvePoleRA()
+    //      bool solvePoleRAVelocity()
+    //      bool solvePoleDec()
+    //      bool solvePoleDecVelocity()
+    //      bool solvePM()
+    //      bool solvePMVelocity()
     //      bool solvePMAcceleration()
     //      bool solveTriaxialRadii()
     //      bool solveMeanRadius()
 
-    PvlObject pvl = settings.pvlObject("DefaultSettingsObject");
-    cout << pvl << endl << endl;
+    // Default bundle settings
+    printXml(settings);
+
 
     qDebug() << "Testing copy constructor...";
     BundleSettings copySettings(settings);
-    pvl = copySettings.pvlObject("CopySettingsObject");
-    cout << pvl << endl << endl;
+    printXml(copySettings);
 
     qDebug() << "Testing assignment operator to set this equal to itself...";
     settings = settings;
-    pvl = settings.pvlObject("SelfAssignedSettingsObject");
-    cout << pvl << endl << endl;
+    printXml(settings);
 
     qDebug() << "Testing assignment operator to create a new settings object...";
     BundleSettings assignmentOpSettings;
     assignmentOpSettings = settings;
-    pvl = assignmentOpSettings.pvlObject("AssignedSettingsObject");
-    cout << pvl << endl << endl;
+    printXml(assignmentOpSettings);
 
     qDebug() << "Testing mutator methods...";
     // reset all...
@@ -171,37 +175,30 @@ int main(int argc, char *argv[]) {
     boss1.addObservationNumber("Instrument1");
     boss1.setInstrumentPositionSettings(BundleObservationSolveSettings::AllPositionCoefficients,
                                         5, 6, true, 7000.0, 8000.0, 9000.0);
-    boss1.setInstrumentPointingSettings(BundleObservationSolveSettings::NoPointingFactors, 
+    boss1.setInstrumentPointingSettings(BundleObservationSolveSettings::NoPointingFactors,
                                         10, 11, true, true, 12.0, 13.0, 14.0);
-    // TODO: why am i getting QList index error???
-//    pvl = boss1.pvlObject();
-//    cout << pvl << endl << endl;
     QList observationSolveSettings;
     observationSolveSettings.append(boss1);
     boss1.addObservationNumber("Instrument2");
     boss1.setInstrumentPositionSettings(BundleObservationSolveSettings::PositionOnly,
                                         15, 16, true, 17000.0, 18000.0, 19000.0);
-    boss1.setInstrumentPointingSettings(BundleObservationSolveSettings::AllPointingCoefficients, 
+    boss1.setInstrumentPointingSettings(BundleObservationSolveSettings::AllPointingCoefficients,
                                         20, 21, true, true, 22.0, 23.0, 24.0);
-    // TODO: why am i getting QList index error???
-//    pvl = boss1.pvlObject();
-//    cout << pvl << endl << endl;
     observationSolveSettings.append(boss1);
     copySettings.setObservationSolveOptions(observationSolveSettings);
     // set convergence criteria values
     copySettings.setConvergenceCriteria(
                      BundleSettings::stringToConvergenceCriteria("parametercorrections"), 0.25, 26);
     // set maximum likelihood models
-    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Huber, 0.27); 
-    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Welsch, 28); 
-    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::HuberModified, 29); 
-    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Chen, 30); 
+    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Huber, 0.27);
+    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Welsch, 28);
+    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::HuberModified, 29);
+    copySettings.addMaximumLikelihoodEstimatorModel(MaximumLikelihoodWFunctions::Chen, 30);
     // set target body
     // TODO
     // set output file options
     copySettings.setOutputFilePrefix("TestFilePrefix");
-    pvl = copySettings.pvlObject("ResetAllOptions");
-    cout << pvl << endl << endl;
+    printXml(copySettings);
 
     // now for test coverage, call some more resets
     // SolveObservationMode = UpdateCubeLabel = ErrorPropagation = true and
@@ -209,24 +206,20 @@ int main(int argc, char *argv[]) {
     settings.setSolveOptions(true, true, true, false);
     settings.setOutlierRejection(false);
     settings.setOutputFilePrefix("TestFilePrefix");
-    pvl = settings.pvlObject("ResetSolveOptions");
-    cout << pvl << endl << endl;
+    printXml(settings);
 
     // reset output options - test coverage
     settings.setOutputFilePrefix("TestFilePrefix");
-    pvl = settings.pvlObject("ResetOutputOptions");
-    cout << pvl << endl << endl;
-
+    printXml(settings);
 
     qDebug() << "Testing accessor methods...";
     BundleObservationSolveSettings boss2 = copySettings.observationSolveSettings("Instrument1");
     qDebug() << "Get BundleObservationSolveSettings with name InstrumentId = Instrument1";
-    pvl = boss2.pvlObject();
-    cout << pvl << endl << endl;
+    printXml(boss2);
+
     boss2 = copySettings.observationSolveSettings(1);
     qDebug() << "Now get BundleObservationSolveSettings at index 1";
-    pvl = boss2.pvlObject();
-    cout << pvl << endl << endl;
+    printXml(boss2);
 
     QList< QPair< MaximumLikelihoodWFunctions::Model, double > > models
             = copySettings.maximumLikelihoodEstimatorModels();
@@ -238,25 +231,17 @@ int main(int argc, char *argv[]) {
 
     qDebug() << "Testing static enum-to-string and string-to-enum methods...";
     qDebug() << BundleSettings::convergenceCriteriaToString(
-                               BundleSettings::stringToConvergenceCriteria("SIGMA0")); 
+                               BundleSettings::stringToConvergenceCriteria("SIGMA0"));
     qDebug() << BundleSettings::convergenceCriteriaToString(
-                               BundleSettings::stringToConvergenceCriteria("PARAMETERCORRECTIONS")); 
-    qDebug() << "";
- 
-    qDebug() << "Testing serialization...";
-    QByteArray byteArray;
-    QDataStream outputData(&byteArray, QIODevice::WriteOnly);
-    outputData << copySettings;
-    QDataStream inputData(byteArray);
-    BundleSettings newSettings;
-    inputData >> newSettings;
-    pvl = newSettings.pvlObject();
-    cout << pvl << endl;
+                               BundleSettings::stringToConvergenceCriteria("PARAMETERCORRECTIONS"));
     qDebug() << "";
 
-    qDebug() << "Testing XML: write XML from BundleSettings object...";
-    // write xml 
-    FileName xmlFile("./BundleSettings.xml");
+    qDebug() << "Testing XML serialization 1: write XML from BundleSettings object...";
+    // write xml to test output file for comparison
+    qDebug() << "Serializing test XML object to file:";
+    printXml(settings);
+    // now write the object to serialization file
+    FileName xmlFile("./BundleSettings2.xml");
     QString xmlPath = xmlFile.expanded();
     QFile qXmlFile(xmlPath);
     if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
@@ -271,81 +256,82 @@ int main(int argc, char *argv[]) {
     settings.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
-    qDebug() << "Testing XML: read XML to BundleSettings object...";
+
+    // read serialized xml into object and then write object to log file
+    qDebug() << "Testing XML: Object deserialized as (should match object above):";
     XmlStackedHandlerReader reader;
     BundleSettingsXmlHandlerTester bsFromXml(project, &reader, xmlFile);
-    //BundleSettings bsFromXml(xmlFile, project, &reader);
-    pvl = bsFromXml.pvlObject("BundleSettingsFromXml");
-    cout << pvl << endl << endl;
+    printXml(bsFromXml);
 
+    qDebug() << "Testing XML serialization 2: write XML from BundleSettings object...";
     // for test coverage, read/write the copySettings object with
     // solveRadius=true, outlierRejection=true, no observationSolveSettings,
     // globalRadiusAprioriSigma != N/A, outlierRejectionMultiplier != N/A
-    copySettings.setObservationSolveOptions(QList());
     if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
       throw IException(IException::Io,
                        QString("Unable to open xml file, [%1],  with write access").arg(xmlPath),
                        _FILEINFO_);
     }
+    // write xml to test output file for comparison
+    qDebug() << "Serializing test XML object to file:";
+    printXml(copySettings);
     writer.setAutoFormatting(true);
     writer.writeStartDocument();
     copySettings.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
-    qDebug() << "Testing XML: read XML to BundleSettings object...";
+
+    // read serialized xml into object and then write object to log file
+    qDebug() << "Testing XML: Object deserialized as (should match object above):";
     BundleSettingsXmlHandlerTester bsFromXml2(project, &reader, xmlFile);
-    //BundleSettings bsFromXml(xmlFile, project, &reader);
-    pvl = bsFromXml2.pvlObject("BundleSettingsFromXml");
-    cout << pvl << endl << endl;
+    printXml(bsFromXml2);
     qXmlFile.remove();
 
 
     qDebug() << "Testing error throws..."; // ??? weird error if i move this after read from empty???
     try {
       settings.observationSolveSettings("UnassociatedObservationNumber");
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       settings.observationSolveSettings(32);
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       settings.observationSolveSettings(-1.0);
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       BundleSettings::stringToConvergenceCriteria("Pickles");
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       BundleSettings::convergenceCriteriaToString(BundleSettings::ConvergenceCriteria(33));
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       BundleSettings invalidMaxLikelihoodModel1;
       invalidMaxLikelihoodModel1.addMaximumLikelihoodEstimatorModel(
-          MaximumLikelihoodWFunctions::Chen, 33); 
-    } 
+          MaximumLikelihoodWFunctions::Chen, 33);
+    }
     catch (IException &e) {
       e.print();
     }
-    
-    /* 
+
+    /*
      * Commenting out this test because it is causing an error on prog24 and we are not sure
      * if we are going to include XML reading/writing
-     * 
+     *
      * qDebug() << "";    // read xml with no attributes or values
      * qDebug() << "Testing XML: read XML with no attributes or values to object...";
      * FileName emptyXmlFile("./unitTest_NoElementValues.xml");
@@ -353,28 +339,27 @@ int main(int argc, char *argv[]) {
      * pvl = bsFromEmptyXml.pvlObject("DefaultBundleSettingsFromEmptyXml");
      * cout << pvl << endl << endl;
     */
-    
-    qDebug() << "";
-    qDebug() << "Testing HDF5 write/read...";
-    FileName hdfFile("./BundleSettings.hdf");
-    if (hdfFile.fileExists()) {
-      QFile::remove(hdfFile.expanded());
-    }
-//    newSettings.createH5Group(hdfFile, "/");
-//    BundleSettings fromHDF(hdfFile);
-//    pvl = fromHDF.pvlObject("BundleSolutionInfoFromHDF");
-//    cout << pvl << endl << endl;
-//    QFile::remove(hdfFile.expanded());
 
-  } 
+  }
   catch (IException &e) {
     e.print();
   }
 }
-#if 0
-still need test coverage for
 
-commented out bundlesettings constructors, commented out xmlhandler constructor
 
-fatalError
-#endif
+/**
+ * Prints the serialized BundleSettings as XML.
+ *
+ * @param const T &printable The BundleSettings to print.
+ */
+template
+void printXml(const T &printable) {
+  QString output;
+  QXmlStreamWriter writer(&output);
+  writer.setAutoFormatting(true);
+  printable.save(writer, NULL);
+  // needed to remove UUids from sub-object serialization.
+  output.remove(QRegExp("[^<]*"));
+  qDebug().noquote() << output << endl << endl;
+}
+
diff --git a/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.cpp b/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.cpp
index 1d525b314d3a80cdf82baacfcb2d2f392e64fbc2..d526c9974710ebc24f61e42f8f42c2403ed0f4a2 100755
--- a/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.cpp
+++ b/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.cpp
@@ -3,14 +3,11 @@
 #include 
 #include 
 #include 
+#include 
 #include 
 #include 
 #include 
 
-#include  // in the hdf5 library
-#include 
-#include 
-
 #include "BundleResults.h"
 #include "ControlMeasure.h"
 #include "ControlNet.h"
@@ -26,10 +23,10 @@
 #include "XmlStackedHandlerReader.h"
 
 namespace Isis {
-  
+
   /**
    * Constructor. Creates a BundleSolutionInfo.
-   * 
+   *
    * @param inputSettings The settings saved in BundleSolutionInfo
    * @param controlNetworkFileName The file name and path of the control network
    * @param outputStatistics The results of the BundleAdjust
@@ -37,84 +34,61 @@ namespace Isis {
    */
   BundleSolutionInfo::BundleSolutionInfo(BundleSettingsQsp inputSettings,
                                          FileName controlNetworkFileName,
-                                         BundleResults outputStatistics, 
+                                         BundleResults outputStatistics,
+                                         QList imgList,
                                          QObject *parent) : QObject(parent) {
-    m_id = NULL;
     m_id = new QUuid(QUuid::createUuid());
 
     m_runTime = "";
 
-    m_controlNetworkFileName = NULL;
     m_controlNetworkFileName = new FileName(controlNetworkFileName);
 
     m_settings = inputSettings;
 
-    m_statisticsResults = NULL;
     m_statisticsResults = new BundleResults(outputStatistics);
 
-    m_images = NULL;
-    m_images = new QList;
+    m_images = new QList(imgList);
   }
 
 
   /**
    * Constructor. Creates a BundleSolutionInfo.
-   * 
+   *
    * @param project The current project
    * @param xmlReader An XML reader that's up to an  tag.
    * @param parent The Qt-relationship parent
    */
-  BundleSolutionInfo::BundleSolutionInfo(Project *project, 
-                                         XmlStackedHandlerReader *xmlReader, 
-                                         QObject *parent) : QObject(parent) {   
+  BundleSolutionInfo::BundleSolutionInfo(Project *project,
+                                         XmlStackedHandlerReader *xmlReader,
+                                         QObject *parent) : QObject(parent) {
                                          //TODO does xml stuff need project???
-    m_id = NULL;
+    m_id = new QUuid(QUuid::createUuid());
+    m_runTime = "";
+    m_controlNetworkFileName = NULL;
+    m_statisticsResults = NULL;
     // what about the rest of the member data ? should we set defaults ??? CREATE INITIALIZE METHOD
+    m_images = new QList;
 
-    xmlReader->pushContentHandler(new XmlHandler(this, project));
     xmlReader->setErrorHandler(new XmlHandler(this, project));
+    xmlReader->pushContentHandler(new XmlHandler(this, project));
   }
 
-  /**
-   * Constructor. Creates a BundleSolutionInfo.
-   * 
-   * @param bundleSolutionInfo Filename of another BundleSolutionInfo and reads the settings and 
-   *        BundleResults from that.
-   */
-  BundleSolutionInfo::BundleSolutionInfo(FileName bundleSolutionInfoFile) {
-    m_id = NULL;
-    m_id = new QUuid(QUuid::createUuid());
-
-    m_statisticsResults = NULL;
-    m_statisticsResults = new BundleResults();
-
-    m_settings = BundleSettingsQsp(new BundleSettings);
-
-    m_images = NULL;
-    m_images = new QList;// change to QList ???
-
-    openH5File(bundleSolutionInfoFile);
-  }
 
   /**
    * Constructor. Creates a BundleSolutionInfo.
-   * 
+   *
    * @param src BundleSolutionInfo where the settings and BundleResults are read from.
    */
   BundleSolutionInfo::BundleSolutionInfo(const BundleSolutionInfo &src)
-      : m_id(new QUuid(src.m_id->toString())),
+      : m_id(new QUuid(QUuid::createUuid())),
         m_runTime(src.m_runTime),
         m_controlNetworkFileName(new FileName(src.m_controlNetworkFileName->expanded())),
         m_settings(new BundleSettings(*src.m_settings)),
         m_statisticsResults(new BundleResults(*src.m_statisticsResults)),
-        m_images(new QList(*src.m_images)) { // is this correct???
-
-    // m_images = NULL;
-    // m_images = new QList;
-    // for (int i = 0; i < src.m_images->size(); i++) {
-    //   m_images->append(src.m_images->at(i));
-    // }
-
+        m_images(new QList(*src.m_images)),
+        m_csvSavedImagesFilename(src.m_csvSavedImagesFilename),
+        m_csvSavedPointsFilename(src.m_csvSavedPointsFilename),
+        m_csvSavedResidualsFilename(src.m_csvSavedResidualsFilename) {
   }
 
 
@@ -123,7 +97,6 @@ namespace Isis {
    */
   BundleSolutionInfo::~BundleSolutionInfo() {
     delete m_id;
-    m_id = NULL;
 
     delete m_controlNetworkFileName;
     m_controlNetworkFileName = NULL;
@@ -131,16 +104,18 @@ namespace Isis {
     delete m_statisticsResults;
     m_statisticsResults = NULL;
 
-    delete m_images;
-    m_images = NULL;
+    if (m_images != NULL) {
+      delete m_images;
+      m_images = NULL;
+    }
   }
 
 
   /**
    * Creates an equal operator for BundleSolutionInfos.
-   * 
+   *
    * @param src the BundleSolutionInfo that we are comparing the current BundleSolutionInfo to.
-   * 
+   *
    * @return @b BundleSolutionInfo Reference to the current BundleSolutionInfo
    */
   BundleSolutionInfo &BundleSolutionInfo::operator=(const BundleSolutionInfo &src) {
@@ -148,32 +123,39 @@ namespace Isis {
     if (&src != this) {
 
       delete m_id;
-      m_id = NULL;
-      m_id = new QUuid(src.m_id->toString());
+      m_id = new QUuid(QUuid::createUuid());
 
       m_runTime = src.m_runTime;
 
       delete m_controlNetworkFileName;
-      m_controlNetworkFileName = NULL;
       m_controlNetworkFileName = new FileName(src.m_controlNetworkFileName->expanded());
 
       m_settings = src.m_settings;
 
       delete m_statisticsResults;
-      m_statisticsResults = NULL;
       m_statisticsResults = new BundleResults(*src.m_statisticsResults);
 
       delete m_images;
-      m_images = NULL;
       m_images = new QList(*src.m_images);
     }
     return *this;
   }
 
+  QString BundleSolutionInfo::savedImagesFilename() {
+    return m_csvSavedImagesFilename;
+  }
+
+  QString BundleSolutionInfo::savedPointsFilename() {
+    return m_csvSavedPointsFilename;
+  }
+
+  QString BundleSolutionInfo::savedResidualsFilename() {
+    return m_csvSavedResidualsFilename;
+  }
 
   /**
    * Sets the stat results.
-   * 
+   *
    * @param statisticsResults The new BundleResults
    */
   void BundleSolutionInfo::setOutputStatistics(BundleResults statisticsResults) {
@@ -182,127 +164,21 @@ namespace Isis {
     m_statisticsResults = new BundleResults(statisticsResults);
   }
 
-  /**
-   * Writes the results from BundleAdjust to a Pvl.
-   * 
-   * @param resultsName The name of the results
-   * @param settingsName The name of the settings
-   * @param statisticsName The name of the statistics
-   * 
-   * @return @b PvlObject The PvlObject that we are writing to
-   */
-  PvlObject BundleSolutionInfo::pvlObject(QString resultsName, QString settingsName, 
-                                          QString statisticsName) {
-
-    PvlObject pvl(resultsName);
-    pvl += PvlKeyword("RunTime", runTime());
-    if (m_controlNetworkFileName->expanded() != "") {
-      pvl += PvlKeyword("OutputControlNetwork", controlNetworkFileName());
-    }
-    pvl += bundleSettings()->pvlObject(settingsName);
-    pvl += bundleResults().pvlObject(statisticsName);
-    return pvl;
-
-  }
-
-
-
-  /**
-   * Saves the BundleSolutionInfo to the project
-   * 
-   * Output format:
-   *
-   *
-   * 
-   *   ...
-   * 
-   *
-   * (fileName attribute is just the base name)
-   * 
-   * @param stream The stream to which the BundleSolutionInfo will be saved
-   * @param project The project to which this BundleSolutionInfo will be saved
-   * @param newProjectRoot The location of the project root directory. This is not used.
-   */
-  void BundleSolutionInfo::save(QXmlStreamWriter &stream, const Project *project,
-                                FileName newProjectRoot) const {
-
-    stream.writeStartElement("bundleSolutionInfo");
-    // save ID, cnet file name, and run time to stream
-    stream.writeStartElement("generalAttributes");
-    stream.writeTextElement("id", m_id->toString());
-    stream.writeTextElement("runTime", runTime());
-    stream.writeTextElement("fileName", m_controlNetworkFileName->expanded());
-    stream.writeEndElement(); // end general attributes
-
-    // save settings to stream
-    m_settings->save(stream, project);
-
-    // save statistics to stream
-    m_statisticsResults->save(stream, project);
-
-    // save image lists to stream
-    if ( !m_images->isEmpty() ) {
-      stream.writeStartElement("imageLists");
-
-      for (int i = 0; i < m_images->count(); i++) {
-        m_images->at(i)->save(stream, project, "");
-      }
-
-      stream.writeEndElement();
-    }
-    stream.writeEndElement(); //end bundleSolutionInfo
-  }
-
 
   /**
-   * Saves the BundleSolutionInfo to the project
-   * 
-   * @param stream The stream to which the BundleSolutionInfo will be saved
-   * @param project The project to which this BundleSolutionInfo will be saved
-   */
-  void BundleSolutionInfo::save(QXmlStreamWriter &stream, const Project *project) const {
-
-    stream.writeStartElement("bundleSolutionInfo");
-    // save ID, cnet file name, and run time to stream
-    stream.writeStartElement("generalAttributes");
-    stream.writeTextElement("id", m_id->toString());
-    stream.writeTextElement("runTime", runTime());
-    stream.writeTextElement("fileName", m_controlNetworkFileName->expanded());
-    stream.writeEndElement(); // end general attributes
-
-    // save settings to stream
-    m_settings->save(stream, project);
-
-    // save statistics to stream
-    m_statisticsResults->save(stream, project);
-
-    // save image lists to stream
-    if ( !m_images->isEmpty() ) {
-      stream.writeStartElement("imageLists");
-
-      for (int i = 0; i < m_images->count(); i++) {
-        m_images->at(i)->save(stream, project, "");
-      }
-
-      stream.writeEndElement();
-    }
-    stream.writeEndElement(); //end bundleSolutionInfo
-  }
-  
-  /**
-   * Change the on-disk file name for the control network used to be where the control network 
+   * Change the on-disk file name for the control network used to be where the control network
    * ought to be in the given project.
-   * 
+   *
    * This method is modelled after the updateFileName() methods in Image and Control. Those methods
-   * close something (cubes for Image and a control net for control) but there is not a close 
-   * method in BundleSolutionInfo. 
+   * close something (cubes for Image and a control net for control) but there is not a close
+   * method in BundleSolutionInfo.
    *
    * @param project The project that this BundleSolutionInfo is stored in
    */
   void BundleSolutionInfo::updateFileName(Project *project) {
-    
+
     //TODO do we need to close anything here?
-    
+
     FileName oldFileName(*m_controlNetworkFileName);
     FileName newName(project->cnetRoot() + "/" +
                      oldFileName.dir().dirName() + "/" + oldFileName.name());
@@ -310,139 +186,6 @@ namespace Isis {
   }
 
 
-
-  /**
-   * Create an XML Handler (reader) that can populate the BundleSolutionInfo class data. See
-   *   BundleSolutionInfo::save() for the expected format.
-   *
-   * @param bundleSolutionInfo The bundle solution we're going to be initializing
-   * @param project The project we are working in
-   */
-  BundleSolutionInfo::XmlHandler::XmlHandler(BundleSolutionInfo *bundleSolutionInfo, 
-                                             Project *project) {
-    m_xmlHandlerBundleSolutionInfo = bundleSolutionInfo;
-    m_xmlHandlerProject = NULL;
-    m_xmlHandlerProject = project;
-    m_xmlHandlerCharacters = "";
-    m_xmlHandlerImages = NULL;
-    m_xmlHandlerBundleResults = NULL;
-  }
-
-
-  /**
-   * Destructor
-   */
-  BundleSolutionInfo::XmlHandler::~XmlHandler() {
-    // bundleSolutionInfo passed in is "this" delete+null will cause problems,no?
-//    delete m_xmlHandlerBundleSolutionInfo;
-//    m_xmlHandlerBundleSolutionInfo = NULL;
-
-    // we do not delete this pointer since it was set to a passed in pointer in constructor and we
-    // don't own it... is that right???
-//    delete m_xmlHandlerProject;
-    m_xmlHandlerProject = NULL;
-
-    delete m_xmlHandlerImages;
-    m_xmlHandlerImages = NULL;
-
-    delete m_xmlHandlerBundleResults;
-    m_xmlHandlerBundleResults = NULL;
-  }
-
-
-  /**
-   * Handle an XML start element. This expects  and  elements.
-   *
-   * @param namespaceURI ???
-   * @param localName The keyword name given to the member variable in the XML.
-   * @param qName ???
-   * @param atts The attribute containing the keyword value for the given local name.
-   * 
-   * @return @b bool True if we should continue reading the XML.
-   */
-  bool BundleSolutionInfo::XmlHandler::startElement(const QString &namespaceURI, 
-                                                    const QString &localName,
-                                                    const QString &qName,
-                                                    const QXmlAttributes &atts) {
-    m_xmlHandlerCharacters = "";
-
-    if (XmlStackedHandler::startElement(namespaceURI, localName, qName, atts)) {
-
-      if (localName == "bundleSettings") {
-        m_xmlHandlerBundleSettings =
-            BundleSettingsQsp(new BundleSettings(m_xmlHandlerProject, reader()));
-      }
-      else if (localName == "bundleResults") {
-        delete m_xmlHandlerBundleResults;
-        m_xmlHandlerBundleResults = NULL;
-
-        //TODO need to add constructor for this???
-        m_xmlHandlerBundleResults = new BundleResults(m_xmlHandlerProject, reader()); 
-      }
-      else if (localName == "imageList") {
-        m_xmlHandlerImages->append(new ImageList(m_xmlHandlerProject, reader()));
-      }
-    }
-    return true;
-  }
-
-
-  /**
-   * Adds characters to m_xmlHandlerCharacters
-   * 
-   * @param ch QString of characters to add
-   * 
-   * @return @b bool Almost always true. Only false if the characters cannot be read
-   */
-  bool BundleSolutionInfo::XmlHandler::characters(const QString &ch) {
-    m_xmlHandlerCharacters += ch;
-    return XmlStackedHandler::characters(ch);
-  }
-
-
-  /**
-   * Handle an XML end element.
-   * 
-   * @param namespaceURI ???
-   * @param localName The keyword name given to the member variable in the XML.
-   * @param qName ???
-   * 
-   * @return @b bool Returns XmlStackedHandler's endElement()
-   */  
-  bool BundleSolutionInfo::XmlHandler::endElement(const QString &namespaceURI, 
-                                                  const QString &localName,
-                                                  const QString &qName) {
-    if (localName == "id") {
-      m_xmlHandlerBundleSolutionInfo->m_id = NULL;
-      m_xmlHandlerBundleSolutionInfo->m_id = new QUuid(m_xmlHandlerCharacters);
-    }
-    else if (localName == "runTime") {
-      m_xmlHandlerBundleSolutionInfo->m_runTime = m_xmlHandlerCharacters;
-    }
-    else if (localName == "fileName") {
-      m_xmlHandlerBundleSolutionInfo->m_controlNetworkFileName = NULL;
-      m_xmlHandlerBundleSolutionInfo->m_controlNetworkFileName = new FileName(m_xmlHandlerCharacters);
-    }
-    else if (localName == "bundleSettings") {
-      m_xmlHandlerBundleSolutionInfo->m_settings =
-          BundleSettingsQsp(new BundleSettings(*m_xmlHandlerBundleSettings));
-    }
-    else if (localName == "bundleResults") {
-      m_xmlHandlerBundleSolutionInfo->m_statisticsResults = new BundleResults(*m_xmlHandlerBundleResults);
-      delete m_xmlHandlerBundleResults;
-      m_xmlHandlerBundleResults = NULL;
-    }
-    if (localName == "imageLists") {
-      for (int i = 0; i < m_xmlHandlerImages->size(); i++) {
-        m_xmlHandlerBundleSolutionInfo->m_images->append(m_xmlHandlerImages->at(i));
-      }
-      m_xmlHandlerImages->clear();
-    }
-    m_xmlHandlerCharacters = "";
-    return XmlStackedHandler::endElement(namespaceURI, localName, qName);
-  }
-
-
   /**
    * Get a unique, identifying string associated with this BundleSolutionInfo object.
    *
@@ -455,10 +198,10 @@ namespace Isis {
 
   /**
    * Sets the run time
-   * 
+   *
    * @param runTime The run time.
    */
-  void BundleSolutionInfo::setRunTime(QString runTime) { 
+  void BundleSolutionInfo::setRunTime(QString runTime) {
     // ??? validate that a valid time has been given???
     // try {
     //   iTime time(runTime);
@@ -474,7 +217,7 @@ namespace Isis {
 
   /**
    * Returns the run time.
-   * 
+   *
    * @return @b QString The run time.
    */
   QString BundleSolutionInfo::runTime() const {
@@ -484,7 +227,7 @@ namespace Isis {
 
   /**
    * Returns the name of the control network.
-   * 
+   *
    * @return @b QString The name of the control network.
    */
   QString BundleSolutionInfo::controlNetworkFileName() const {
@@ -494,7 +237,7 @@ namespace Isis {
 
   /**
    * Returns the bundle settings.
-   * 
+   *
    * @return @b BundleSettingsQsp The bundle settings.
    */
   BundleSettingsQsp BundleSolutionInfo::bundleSettings() {
@@ -504,9 +247,9 @@ namespace Isis {
 
   /**
    * Returns the bundle results.
-   * 
+   *
    * @throws IException::Unknown "Results for this bundle is NULL."
-   * 
+   *
    * @return @b BundleResults The bundle results.
    */
   BundleResults BundleSolutionInfo::bundleResults() {
@@ -514,21 +257,31 @@ namespace Isis {
       return *m_statisticsResults;
     }
     else {
-      throw IException(IException::Unknown, 
+      throw IException(IException::Unknown,
                        "Results for this bundle is NULL.",
                        _FILEINFO_);
     }
   }
 
-
-
-
+/**
+* Returns the images used in the bundle
+*
+* @return m_imageList The image list used in the bundle
+*/
+  QList BundleSolutionInfo::imageList() {
+    return *m_images;
+  }
 
 
   /**
    * @brief Outputs the header for the bundleout_images.csv file
    * @param fpOut The output file stream.
    * @return True if the write is successful, False otherwise.
+   *
+   * @internal
+   *   @history 2016-12-08 Ian Humphrey - Removed conditions that handle TWIST headers differently
+   *                           than the other headers. The number of TWIST headers will be the same
+   *                           as each of the other angle headers. Fixes #4557.
    */
   bool BundleSolutionInfo::outputImagesCSVHeader(std::ofstream &fpOut) {
 
@@ -550,7 +303,6 @@ namespace Isis {
 
     int numberCamPosCoefSolved = obsSettings.numberCameraPositionCoefficientsSolved();
     int numberCamAngleCoefSolved  = obsSettings.numberCameraAngleCoefficientsSolved();
-    bool solveTwist = obsSettings.solveTwist();
 
     int nCoeff = 1;
     if (numberCamPosCoefSolved > 0)
@@ -612,7 +364,7 @@ namespace Isis {
     }
     for (int i = 0; i < numberCamAngleCoefSolved; i++) {
       for (int j = 0; j < 5; j++) {
-        if (numberCamAngleCoefSolved == 1 || !solveTwist) {
+        if (numberCamAngleCoefSolved == 1) {
           outputColumns.push_back("TWIST,");
         }
         else {
@@ -620,8 +372,6 @@ namespace Isis {
           outputColumns.push_back(str);
         }
       }
-      if (!solveTwist)
-        break;
     }
 
     // print first column header to buffer and output to file
@@ -641,14 +391,16 @@ namespace Isis {
     outputColumns.push_back("line res,");
     outputColumns.push_back("total res,");
 
+    // Initially account for X,Y,Z (3)
     int nparams = 3;
+    // See how many position coeffients we solved for to make more headers (t0, t1, ...)
     if (numberCamPosCoefSolved)
       nparams = 3 * numberCamPosCoefSolved;
 
-    int numCameraAnglesSolved = 2;
-    if (solveTwist) numCameraAnglesSolved++;
+    // Initially account for RA,DEC,TWIST (3)
+    int numCameraAnglesSolved = 3;
+    // See how many angle coefficients we solved for to make more headers (t0, t1, ...)
     nparams += numCameraAnglesSolved*numberCamAngleCoefSolved;
-    if (!solveTwist) nparams += 1; // Report on twist only
     for (int i = 0; i < nparams; i++) {
       outputColumns.push_back("Initial,");
       outputColumns.push_back("Correction,");
@@ -674,14 +426,14 @@ namespace Isis {
 
   /**
    * Output header for bundle results file.
-   * 
+   *
    * @param fpOut The output stream that the header will be sent to.
-   * 
+   *
    * @return @b bool If the header was successfully output to the output stream.
-   * 
+   *
    * @throws IException::Io "Failed to output residual percentiles for bundleout"
    * @throws IException::Io "Failed to output residual box plot for bundleout"
-   * 
+   *
    * @todo Determine how multiple sensor solve settings should be output.
    */
   bool BundleSolutionInfo::outputHeader(std::ofstream &fpOut) {
@@ -1069,7 +821,7 @@ namespace Isis {
     sprintf(buf, "             Total Elapsed Time: %6.4lf (seconds)\n",
                   m_statisticsResults->elapsedTime());
     fpOut << buf;
-    if (m_statisticsResults->numberObservations() 
+    if (m_statisticsResults->numberObservations()
         + m_statisticsResults->numberRejectedObservations()
         > 100) {
       sprintf(buf, "\n           Residual Percentiles:\n");
@@ -1136,13 +888,13 @@ namespace Isis {
     int imageIndex = 0;
 
     for (int i = 0; i < numObservations; i++) {
-      
+
       int numImagesInObservation = m_statisticsResults->observations().at(i)->size();
-      
+
       for (int j = 0; j < numImagesInObservation; j++) {
-        
+
         BundleImageQsp bundleImage = m_statisticsResults->observations().at(i)->at(j);
-        
+
         double rmsSampleResiduals = m_statisticsResults->
                                         rmsImageSampleResiduals()[imageIndex].Rms();
         double rmsLineResiduals =   m_statisticsResults->
@@ -1185,6 +937,12 @@ namespace Isis {
    * @brief Outputs the bundleout_images.csv file which contains Jigsaw data about the images
    * within each observation.
    * @return True upon success, False if something went wrong.
+   *
+   * @internal
+   *   @history 2016-12-01 Ian Humphrey - Added %s as second argument to sprintf() call to prevent
+   *                           -Wformat-security warning. Since image->fileName().toLatin1().data()
+   *                           returns a char* at runtime, the compiler does not know if it will
+   *                           contain format specifiers and produces the mentioned warning.
    */
   bool BundleSolutionInfo::outputImagesCSV() {
 
@@ -1197,6 +955,7 @@ namespace Isis {
 
     QString ofname = "bundleout_images.csv";
     ofname = m_settings->outputFilePrefix() + ofname;
+    m_csvSavedImagesFilename = ofname;
 
     std::ofstream fpOut(ofname.toLatin1().data(), std::ios::out);
     if (!fpOut) {
@@ -1229,7 +988,7 @@ namespace Isis {
         BundleImageQsp image = observation->at(j);
 
 
-        sprintf(buf,image->fileName().toLatin1().data());
+        sprintf(buf, "%s", image->fileName().toLatin1().data());
         fpOut << buf;
         sprintf(buf,",");
         fpOut << buf;
@@ -1271,7 +1030,7 @@ namespace Isis {
 
   /**
    * Outputs a text file with the results of the BundleAdjust.
-   * 
+   *
    * @return @b bool If the text file was successfully output.
    */
   bool BundleSolutionInfo::outputText() {
@@ -1353,7 +1112,7 @@ namespace Isis {
         }
       }
     }
-        
+
     // Save list of images and their associated parameters for CorrelationMatrix to use in ice.
     m_statisticsResults->setCorrMatImgsAndParams(imagesAndParameters);
 
@@ -1450,7 +1209,7 @@ namespace Isis {
 
   /**
    * Outputs point data to a csv file.
-   * 
+   *
    * @return @b bool If the point data was successfully output.
    */
   bool BundleSolutionInfo::outputPointsCSV() {
@@ -1458,6 +1217,7 @@ namespace Isis {
 
     QString ofname = "bundleout_points.csv";
     ofname = m_settings->outputFilePrefix() + ofname;
+    m_csvSavedPointsFilename = ofname;
 
     std::ofstream fpOut(ofname.toLatin1().data(), std::ios::out);
     if (!fpOut) {
@@ -1564,7 +1324,7 @@ namespace Isis {
 
   /**
    * Outputs image coordinate residuals to a csv file.
-   * 
+   *
    * @return @b bool If the residuals were successfully output.
    */
   bool BundleSolutionInfo::outputResiduals() {
@@ -1572,6 +1332,7 @@ namespace Isis {
 
     QString ofname = "residuals.csv";
     ofname = m_settings->outputFilePrefix() + ofname;
+    m_csvSavedResidualsFilename = ofname;
 
     std::ofstream fpOut(ofname.toLatin1().data(), std::ios::out);
     if (!fpOut) {
@@ -1596,7 +1357,7 @@ namespace Isis {
 
     BundleControlPointQsp bundleControlPoint;
     BundleMeasureQsp bundleMeasure;
-    
+
     for (int i = 0; i < numPoints; i++) {
       bundleControlPoint = m_statisticsResults->bundleControlPoints().at(i);
       numMeasures = bundleControlPoint->size();
@@ -1604,7 +1365,7 @@ namespace Isis {
       if (bundleControlPoint->rawControlPoint()->IsIgnored()) {
         continue;
       }
-      
+
       for (int j = 0; j < numMeasures; j++) {
         bundleMeasure = bundleControlPoint->at(j);
 
@@ -1650,337 +1411,161 @@ namespace Isis {
 
 
   /**
-   * Writes the data to the stream.
-   * 
-   * @param stream The stream we are writing to and returning
-   * 
-   * @return @b QDataStream The stream we wrote to
+   * Saves the BundleSolutionInfo to the project
+   *
+   * Output format:
+   *
+   *
+   * 
+   *   ...
+   * 
+   *
+   * (fileName attribute is just the base name)
+   *
+   * @param stream The stream to which the BundleSolutionInfo will be saved
+   * @param project The project to which this BundleSolutionInfo will be saved
+   * @param newProjectRoot The location of the project root directory. This is not used.
    */
-  QDataStream &BundleSolutionInfo::write(QDataStream &stream) const {
-    stream << m_id->toString()
-           << m_runTime
-           << m_controlNetworkFileName->expanded()
-           << *m_settings
-           << *m_statisticsResults;
-  //TODO add this capability to Image and ImageList
-  //          << *m_images;
-    return stream;
-  }
-
+  void BundleSolutionInfo::save(QXmlStreamWriter &stream, const Project *project,
+                                FileName newProjectRoot) const {
 
-  /**
-   * Reads the data from the stream
-   * 
-   * @param stream The stream we are reading from
-   * 
-   * @return @b QDataStream The stream we read from
-   */
-  QDataStream &BundleSolutionInfo::read(QDataStream &stream) {
+    stream.writeStartElement("bundleSolutionInfo");
+    // save ID, cnet file name, and run time to stream
+    stream.writeStartElement("generalAttributes");
+    stream.writeTextElement("id", m_id->toString());
+    stream.writeTextElement("runTime", runTime());
+    stream.writeTextElement("fileName", m_controlNetworkFileName->expanded());
+    stream.writeTextElement("imagesCSV", m_csvSavedImagesFilename);
+    stream.writeTextElement("pointsCSV", m_csvSavedPointsFilename);
+    stream.writeTextElement("residualsCSV", m_csvSavedResidualsFilename);
+    stream.writeEndElement(); // end general attributes
 
-    QString id;
-    stream >> id;
-    delete m_id;
-    m_id = NULL;
-    m_id = new QUuid(id);
+    // save settings to stream
+    m_settings->save(stream, project);
 
-    stream >> m_runTime;
+    // save statistics to stream
+    m_statisticsResults->save(stream, project);
 
-    QString controlNetworkFileName;
-    stream >> controlNetworkFileName;
-    delete m_controlNetworkFileName;
-    m_controlNetworkFileName = NULL;
-    m_controlNetworkFileName = new FileName(controlNetworkFileName);
+    // save image lists to stream
+    if ( !m_images->isEmpty() ) {
+      stream.writeStartElement("imageLists");
 
-    BundleSettings settings;
-    stream >> settings;
-    m_settings = BundleSettingsQsp(new BundleSettings(settings));
+      FileName newResultsRoot(Project::bundleSolutionInfoRoot(newProjectRoot.expanded()) +
+                              "/" + runTime());
+      for (int i = 0; i < m_images->count(); i++) {
+        m_images->at(i)->save(stream, project, newResultsRoot);
+      }
 
-    BundleResults statisticsResults;
-    stream >> statisticsResults;
-    delete m_statisticsResults;
-    m_statisticsResults = NULL;
-    m_statisticsResults = new BundleResults(statisticsResults);
+      stream.writeEndElement();
+    }
+    stream.writeEndElement(); //end bundleSolutionInfo
+  }
 
-    //TODO add this capability to Image and ImageList
-    // QList imageLists;
-    // stream >> imageLists;
-    // delete m_images;
-    // m_images = NULL;
-    // m_images = new QList(imageLists);
 
-    return stream;
+  /**
+   * Create an XML Handler (reader) that can populate the BundleSolutionInfo class data. See
+   *   BundleSolutionInfo::save() for the expected format.
+   *
+   * @param bundleSolutionInfo The bundle solution we're going to be initializing
+   * @param project The project we are working in
+   */
+  BundleSolutionInfo::XmlHandler::XmlHandler(BundleSolutionInfo *bundleSolutionInfo,
+                                             Project *project) {
+    m_xmlHandlerBundleSolutionInfo = bundleSolutionInfo;
+    m_xmlHandlerProject = project;
+    m_xmlHandlerCharacters = "";
   }
 
 
   /**
-   * Creates the write operator for BundleSolutionInfo
-   * 
-   * @param stream The stream we are writing to
-   * @param bundleSolutionInfo The BundleSolutionInfo we are writing
-   * 
-   * @return @b QDataStream The stream we wrote to
+   * Destructor
    */
-  QDataStream &operator<<(QDataStream &stream, const BundleSolutionInfo &bundleSolutionInfo) {
-    return bundleSolutionInfo.write(stream);
+  BundleSolutionInfo::XmlHandler::~XmlHandler() {
   }
 
 
   /**
-   * Creates the read operator for BundleSolutionInfo
-   * 
-   * @param stream The stream we are reading to
-   * @param bundleSolutionInfo The BundleSolutionInfo we are reading
-   * 
-   * @return @b QDataStream The stream we read from
+   * Adds characters to m_xmlHandlerCharacters
+   *
+   * @param ch QString of characters to add
+   *
+   * @return @b bool Almost always true. Only false if the characters cannot be read
    */
-  QDataStream &operator>>(QDataStream &stream, BundleSolutionInfo &bundleSolutionInfo) {
-    return bundleSolutionInfo.read(stream);
+  bool BundleSolutionInfo::XmlHandler::characters(const QString &ch) {
+    m_xmlHandlerCharacters += ch;
+    return XmlStackedHandler::characters(ch);
   }
 
 
   /**
-   * Reads the settings and results from another BundleSolutionInfo
-   * 
-   * @throws IException::Io "No file with the given name was found."
-   * @throws IException::Io "The given file is unsupported for constructing BundleSolutionInfo 
-   *                        objects. Supported file types include [hdf]."
-   * @throws IException::Unknown "H5 exception handler has detected an error when invoking the 
-   *                             function"
-   * @throws IException::Unknown "Unable to read bundle solution information from the given HDF5 
-   *                             file"
-   * 
-   * @param bundleSolutionInfoFile The name of the BundleSolutionInfo we are reading from
+   * Handle an XML start element. This expects  and  elements.
+   *
+   * @param namespaceURI ???
+   * @param localName The keyword name given to the member variable in the XML.
+   * @param qName ???
+   * @param atts The attribute containing the keyword value for the given local name.
+   *
+   * @return @b bool True if we should continue reading the XML.
    */
-  void BundleSolutionInfo::openH5File(FileName bundleSolutionInfoFile) {
+  bool BundleSolutionInfo::XmlHandler::startElement(const QString &namespaceURI,
+                                                    const QString &localName,
+                                                    const QString &qName,
+                                                    const QXmlAttributes &atts) {
+    m_xmlHandlerCharacters = "";
 
-    try {
-      if (!bundleSolutionInfoFile.fileExists()) {
-        QString msg = "No file with the given name was found.";
-        throw IException(IException::Io, msg, _FILEINFO_);
-      }
+    if (XmlStackedHandler::startElement(namespaceURI, localName, qName, atts)) {
 
-      if (QString::compare(bundleSolutionInfoFile.extension(), "hdf", Qt::CaseInsensitive) != 0) {
-        QString msg = "The given file is unsupported for constructing BundleSolutionInfo objects. "
-                      "Supported file types include [hdf].";
-        throw IException(IException::Io, msg, _FILEINFO_);
+      if (localName == "bundleSettings") {
+        m_xmlHandlerBundleSolutionInfo->m_settings =
+            BundleSettingsQsp(new BundleSettings(m_xmlHandlerProject, reader()));
       }
-
-      // catch H5 exceptions and rethrow
-      try {
-        /*
-         * Turn off the auto-printing when failure occurs so that we can
-         * handle the errors appropriately
-         */
-//        H5::Exception::dontPrint();//??? uncomment
-    
-        /* 
-         * Create and open an H5File object with read-only access. This will throw an
-         * H5 exception if the open fails.
-         * 
-         * The static H5Fopen() function will returns a negative file ID if it fails. So, in this
-         * case, we would have to take the extra step of checking whether the return
-         * is negative.
-         */
-
-        const H5std_string hdfFileName(bundleSolutionInfoFile.expanded().toStdString()); 
-        H5::H5File hdfFile( hdfFileName, H5F_ACC_RDONLY ); // valgrind: Invalid read of size 4
-
-        // get the BundleSolutionInfo group
-        QString root = "/";
-        QString bundleRunGroupName = root + "BundleSolutionInfo";
-        H5::Group bundleRunGroup = hdfFile.openGroup(bundleRunGroupName.toLatin1());
-
-        /* 
-         * Add basic attributes
-         */ 
-        H5std_string attValue;
-
-        Attribute att = bundleRunGroup.openAttribute("runTime");
-        H5::StrType strDataType(H5::PredType::C_S1, att.getStorageSize());
-        att.read(strDataType, attValue);
-        m_runTime = QString::fromStdString(attValue);
-
-        att = bundleRunGroup.openAttribute("controlNetworkFileName");
-        strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());
-        att.read(strDataType, attValue);
-        m_controlNetworkFileName = new FileName(QString::fromStdString(attValue));
-
-        m_settings->openH5Group(bundleRunGroup, bundleRunGroupName);
-        m_statisticsResults->openH5Group(bundleRunGroup, bundleRunGroupName);
-
-        // ???Let's just save off the image list file names for now...
-        QString   imagesGroupName = bundleRunGroupName + "/imageLists";
-        H5::Group imagesGroup     = bundleRunGroup.openGroup(imagesGroupName.toLatin1());
-        int imagesGroupSize = (int)imagesGroup.getNumObjs();
-
-        for (int i = 0; i < imagesGroupSize; i++) {
-          H5std_string listGroupName = imagesGroup.getObjnameByIdx(i);
-          H5::Group listGroup = imagesGroup.openGroup(listGroupName);
-          
-          H5std_string attValue;
-          att = listGroup.openAttribute("path");
-          strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());
-          att.read(strDataType, attValue);
-          QString listPath = QString::fromStdString(attValue);
-          QString listName = QString::fromStdString(listGroupName).remove(imagesGroupName + "/");
-
-          ImageList *imageList = new ImageList(listName, listPath);
-
-          att = listGroup.openAttribute("fileNames");
-          strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());
-          att.read(strDataType, attValue);
-          QStringList fileList = QString::fromStdString(attValue).split(",");
-          for (int j = 0; j < fileList.size();j++) {
-            imageList->append(new Image(fileList[j]));
-          }
-
-          m_images->append(imageList);// delete and null imageList???
-
-        }
-  #if 0
-        
-        QString   imagesGroupName = bundleRunGroupName + "/imageLists";
-        H5::Group imagesGroup     = bundleRunGroup.openGroup(imagesGroupName.toLatin1());
-        int imagesGroupSize = (int)imagesGroup.getNumObjs();
-
-        for (int i = 0; i < imagesGroupSize; i++) {
-          H5std_string listGroupName = imagesGroup.getObjnameByIdx(i);
-          H5::Group listGroup = imagesGroup.openGroup(listGroupName);
-
-          H5std_string attValue;
-          att = listGroup.openAttribute("path");
-          strDataType = H5::StrType(H5::PredType::C_S1, att.getStorageSize());
-          att.read(strDataType, attValue);
-          QString listPath = QString::fromStdString(attValue);
-          QString listName = QString::fromStdString(listGroupName).remove(imagesGroupName + "/");
-
-          ImageList *imageList = new ImageList(listName, listPath);
-          imageList->openH5Group(bundleRunGroup, bundleRunGroupName);
-          m_images.append(imageList);
-        }
-#endif
-
+      else if (localName == "bundleResults") {
+        m_xmlHandlerBundleSolutionInfo->m_statisticsResults = new BundleResults(m_xmlHandlerProject, reader());
       }
-      catch (H5::Exception error) {  //?? how to improve printed msg using major/minor error codes?
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 exception handler has detected an error when invoking the function " 
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
+      else if (localName == "imageList") {
+        m_xmlHandlerBundleSolutionInfo->m_images->append(new ImageList(m_xmlHandlerProject, reader()));
       }
     }
-    catch (IException &e) {
-      QString msg = "Unable to read bundle solution information from the given HDF5 file ["
-                    + bundleSolutionInfoFile.expanded() + "].";
-      throw IException(e, IException::Unknown, msg, _FILEINFO_);
-    }
+    return true;
   }
 
 
   /**
-   * Creates a new file using H5F_ACC_EXCL
-   * 
-   * @throws IException::Io "A file already exists with the given name ["
-   * @throws IException::Unknown "H5 exception handler has detected an error when invoking the 
-   *                             function"
-   * @throws IException::Unknown "Unable to save bundle solution information to an HDF5 file."
-   * 
-   * @param outputFileName The name of the file we are creating.
+   * Handle an XML end element.
+   *
+   * @param namespaceURI ???
+   * @param localName The keyword name given to the member variable in the XML.
+   * @param qName ???
+   *
+   * @return @b bool Returns XmlStackedHandler's endElement()
    */
-  void BundleSolutionInfo::createH5File(FileName outputFileName) const {
-
-    try {
-      if (outputFileName.fileExists()) {
-        QString msg = "A file already exists with the given name ["
-                      + outputFileName.expanded() + "].";
-        throw IException(IException::Io, msg, _FILEINFO_);
-      }
-
-      // Try block to detect exceptions raised by any of the calls inside it
-      try {
-        /*
-         * Turn off the auto-printing when failure occurs so that we can
-         * handle the errors appropriately
-         */
-        //H5::Exception::dontPrint();
-
-        /*
-         * Create a new file using H5F_ACC_EXCL access,
-         * default file creation properties, and default file
-         * access properties.
-         */
-        const H5std_string hdfFileName(outputFileName.expanded().toStdString());
-//        const H5std_string hdfFileName("./BundleSolutionInfo.hdf");
-        H5::H5File hdfFile(hdfFileName, H5F_ACC_EXCL); // valgrind: Invalid read of size 4???
-
-        // create BundleSolutionInfo group
-        QString   root               = "/";
-        QString   bundleRunGroupName = root + "BundleSolutionInfo";
-        H5::Group bundleRunGroup     = hdfFile.createGroup(bundleRunGroupName.toLatin1());
-
-        /* 
-         * Add basic attributes
-         */
-        Attribute     att;
-        H5::DataSpace spc(H5S_SCALAR); // single value space
-        QString       attValue    = "";
-
-        H5::StrType   strDataType(H5::PredType::C_S1, m_runTime.length());
-        att = bundleRunGroup.createAttribute("runTime", strDataType, spc);
-        att.write(strDataType, m_runTime.toStdString());
-
-        attValue = m_controlNetworkFileName->expanded();
-        strDataType = H5::StrType(H5::PredType::C_S1, attValue.length());
-        att = bundleRunGroup.createAttribute("controlNetworkFileName", strDataType, spc);
-        att.write(strDataType, attValue.toStdString());
-
-        m_settings->createH5Group(bundleRunGroup, bundleRunGroupName);
-        m_statisticsResults->createH5Group(bundleRunGroup, bundleRunGroupName);
-
-        // Let's just save off the image list file names for now...
-        QString   imagesGroupName = bundleRunGroupName + "/imageLists";
-        H5::Group imagesGroup     = bundleRunGroup.createGroup(imagesGroupName.toLatin1());
-
-        QString listGroupName = "";
-        int     stringSize    = 0;
-
-        for (int i = 0; i < m_images->size(); i++) {
-          listGroupName = imagesGroupName + "/" + (*m_images)[i]->name();
-
-          H5::Group listGroup = imagesGroup.createGroup(listGroupName.toLatin1());
-
-          attValue = (*m_images)[i]->path();
-          strDataType = H5::StrType(H5::PredType::C_S1, attValue.length());
-          att = listGroup.createAttribute("path", strDataType, spc);
-          att.write(strDataType, attValue.toStdString());
-
-          QStringList fileList;
-          for (int j = 0; j < (*m_images)[i]->size(); j++) {
-            fileList += (*(*m_images)[i])[j]->fileName(); //???
-          }
-
-          QString fileNames = fileList.join(",");
-          stringSize = qMax(fileNames.length(), 1);
-          strDataType = H5::StrType(H5::PredType::C_S1, stringSize);
-          att = listGroup.createAttribute("fileNames", strDataType, spc);
-          att.write(strDataType, fileNames.toStdString());
-
-        }
-      }
-      catch (H5::Exception error) {  //??? how to improve printed msg using major/minor error codes?
-        QString msg = "H5 Exception Message: " + QString::fromStdString(error.getDetailMsg());
-        IException hpfError(IException::Unknown, msg, _FILEINFO_);
-        msg = "H5 exception handler has detected an error when invoking the function "
-              + QString::fromStdString(error.getFuncName()) + ".";
-        throw IException(hpfError, IException::Unknown, msg, _FILEINFO_);
-      }
+  bool BundleSolutionInfo::XmlHandler::endElement(const QString &namespaceURI,
+                                                  const QString &localName,
+                                                  const QString &qName) {
+    if (localName == "id") {
+      // all constructors assign a Uuid - we need to give it a one from the XML
+      assert(m_xmlHandlerBundleSolutionInfo->m_id);
+      delete m_xmlHandlerBundleSolutionInfo->m_id;
+      m_xmlHandlerBundleSolutionInfo->m_id = new QUuid(m_xmlHandlerCharacters);
     }
-    catch (IException &e) {
-      throw IException(e,
-                       IException::Unknown,
-                       "Unable to save bundle solution information to an HDF5 file.",
-                       _FILEINFO_);
+    else if (localName == "runTime") {
+      m_xmlHandlerBundleSolutionInfo->m_runTime = m_xmlHandlerCharacters;
+    }
+    else if (localName == "fileName") {
+      assert(m_xmlHandlerBundleSolutionInfo->m_controlNetworkFileName == NULL);
+      m_xmlHandlerBundleSolutionInfo->m_controlNetworkFileName = new FileName(m_xmlHandlerCharacters);
+    }
+    else if (localName == "imagesCSV") {
+      m_xmlHandlerBundleSolutionInfo->m_csvSavedImagesFilename = m_xmlHandlerCharacters;
+    }
+    else if (localName == "pointsCSV") {
+      m_xmlHandlerBundleSolutionInfo->m_csvSavedPointsFilename = m_xmlHandlerCharacters;
+    }
+    else if (localName == "residualsCSV") {
+      m_xmlHandlerBundleSolutionInfo->m_csvSavedResidualsFilename = m_xmlHandlerCharacters;
     }
-  }
 
+    m_xmlHandlerCharacters = "";
+    return XmlStackedHandler::endElement(namespaceURI, localName, qName);
+  }
 }
diff --git a/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.h b/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.h
index a7b0fbf5b3ab83ae3fd57e69a833fc2502eecece..e89fb574a1fdcc79525bd74401b8f6fe9d8e79ad 100755
--- a/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.h
+++ b/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.h
@@ -3,8 +3,6 @@
 
 /**
  * @file
- * $Revision: 1.20 $
- * $Date: 2009/10/15 01:35:17 $
  *
  *   Unless noted otherwise, the portions of Isis written by the USGS are
  *   public domain. See individual third-party library and package descriptions
@@ -45,10 +43,10 @@ namespace Isis {
   class XmlStackedHandlerReader;
 
   /**
-   * @brief Container class for BundleAdjustment results. 
-   * This class includes the settings used to run the bundle adjustment, the resulting statistics 
+   * @brief Container class for BundleAdjustment results.
+   * This class includes the settings used to run the bundle adjustment, the resulting statistics
    * values, and the name of the control network used.
-   *  
+   *
    * @ingroup ControlNetworks
    *
    * @author 2014-07-08 Jeannie Backer
@@ -59,7 +57,7 @@ namespace Isis {
    *                           operators and the read/write methods.
    *   @history 2014-12-04 Jeannie Backer - Renamed from BundleResults to BundleSolutionInfo.
    *   @history 2015-09-03 Jeannie Backer - Added preliminary hdf5 read/write capabilities.
-   *   @history 2015-10-14 Jeffrey Covington - Declared BundleSolutionInfo * as 
+   *   @history 2015-10-14 Jeffrey Covington - Declared BundleSolutionInfo * as
    *                           a Qt metatype for use with QVariant.
    *   @history 2016-06-13 Makayla Shepherd - Added updateFileName() and updated documentation.
    *                           Fixes #2298.
@@ -88,23 +86,44 @@ namespace Isis {
    *                            "CAMSOLVE: All POLYNOMIAL COEFFICIENTS"
    *                           -modified output of image EO in bundleout.txt for images solved with
    *                            observation mode; previously one entry per observation was written,
-   *                            now all images in the observation are written separately. 
+   *                            now all images in the observation are written separately.
+   *   @history 2016-12-01 Ian Humphrey - Modified an sprintf() call in outputImagesCSV() to
+   *                           prevent a -Wformat-security warning from occurring.
+   *   @history 2016-12-08 Ian Humphrey - Modified outputImagesCSVHeader() to treat TWIST the same
+   *                           as the other angles when determining how many headers to create.
+   *                           Fixes #4557.
+   *   @history 2017-04-24 Ian Humphrey - Removed pvlObject(). Fixes #4797.
+   *   @history 2017-05-01 Makayla Shepherd - Added imageList() to track and return the images used
+   *                           in the bundle adjustment. These images will be displayed on the
+   *                           project tree under results/bundle/ and will keep the same
+   *                           structure as the input on the project tree. Fixes #4818.
+   *   @history 2017-05-02 J Bonn - Fixed XML serialzation and code cleanup.  Fixes #4835.
+   *   @history 2017-05-02 Tracie Sucharski - Moved XMLHandler code to bottom of file for
+   *                           consistency;  all other classes have the XmlHandler at end of file.
+   *                           Fixes #4822.
+   *   @history 2017-05-04 Ian Humphrey & Makayla Shepherd - Modified save() to write the bundle
+   *                           solution info images to the correct directory in the project on disk.
+   *                           Fixes #4804, #4837.
    */
   class BundleSolutionInfo : public QObject {
     Q_OBJECT
     public:
       BundleSolutionInfo(BundleSettingsQsp inputSettings,
-                    FileName controlNetworkFileName, 
-                    BundleResults outputStatistics, 
+                    FileName controlNetworkFileName,
+                    BundleResults outputStatistics,
+                    QList imgList,
                     QObject *parent = 0);
-      BundleSolutionInfo(Project *project, 
-                    XmlStackedHandlerReader *xmlReader, 
+      BundleSolutionInfo(Project *project,
+                    XmlStackedHandlerReader *xmlReader,
                     QObject *parent = 0);  //TODO does xml stuff need project???
-      BundleSolutionInfo(FileName bundleSolutionInfoFile);
       BundleSolutionInfo(const BundleSolutionInfo &src);
       ~BundleSolutionInfo();
       BundleSolutionInfo &operator=(const BundleSolutionInfo &src);
 
+      QString savedImagesFilename();
+      QString savedPointsFilename();
+      QString savedResidualsFilename();
+
       void setOutputStatistics(BundleResults statisticsResults);
       void setRunTime(QString runTime);
 
@@ -112,43 +131,26 @@ namespace Isis {
       QString controlNetworkFileName() const;
       BundleSettingsQsp bundleSettings();
       BundleResults bundleResults();
+      QList imageList();
       QString runTime() const;
 
 
-      bool outputImagesCSVHeader(std::ofstream &fpOut);     
+      bool outputImagesCSVHeader(std::ofstream &fpOut);
       bool outputHeader(std::ofstream &fpOut);
       bool outputText();
       bool outputImagesCSV();
       bool outputPointsCSV();
       bool outputResiduals();
 
-      PvlObject pvlObject(QString resultsName = "BundleSolutionInfo",
-                          QString settingsName = "InputSettings",
-                          QString statisticsName = "StatisticsResults");
-       
-      //TODO does xml stuff need project and newRoot???
-      void save(QXmlStreamWriter &stream, const Project *project, FileName newProjectRoot) const;  
-      
-      //TODO does xml stuff need project???
-      void save(QXmlStreamWriter &stream, const Project *project) const;  
-
-      QDataStream &write(QDataStream &stream) const;
-      QDataStream &read(QDataStream &stream);
-
-      void writeH5File(FileName outputFileName) const;
-      void readH5File(FileName outputFileName) const;
-
-      void createH5File(FileName outputFileName) const;
-      void openH5File(FileName outputFileName);
-//      BundleSolutionInfo(FileName bundleSolutionInfoFile);
-      
-      public slots:
+      void save(QXmlStreamWriter &stream, const Project *project, FileName newProjectRoot) const;
+
+    public slots:
       void updateFileName(Project *);
 
     private:
       /**
        * This class is used to read an images.xml file into an image list
-       * 
+       *
        * @see QXmlDefaultHandler documentation
        * @author 2014-07-21 Ken Edmundson
        *
@@ -159,7 +161,7 @@ namespace Isis {
       class XmlHandler : public XmlStackedHandler {
         public:
           //TODO does xml stuff need project???
-          XmlHandler(BundleSolutionInfo *bundleSolutionInfo, Project *project);  
+          XmlHandler(BundleSolutionInfo *bundleSolutionInfo, Project *project);
           ~XmlHandler();
 
           virtual bool startElement(const QString &namespaceURI, const QString &localName,
@@ -174,9 +176,6 @@ namespace Isis {
           BundleSolutionInfo *m_xmlHandlerBundleSolutionInfo; //!< The bundleSolutionInfo object
           Project *m_xmlHandlerProject;  //TODO does xml stuff need project???
           QString m_xmlHandlerCharacters; //!< List of characters that have been handled
-          QList *m_xmlHandlerImages; //!< List of pointers to images
-          BundleSettingsQsp m_xmlHandlerBundleSettings; //!< Settings used to run the bundle adjust
-          BundleResults *m_xmlHandlerBundleResults; //!< Results from the bundle adjust
       };
 
     private:
@@ -190,13 +189,17 @@ namespace Isis {
       BundleSettingsQsp   m_settings; //!< The settings from the bundle adjust
       BundleResults      *m_statisticsResults; //!< The results of the bundle adjust
       QList *m_images; //!< The list of images that were adjusted
+
+      // In theory the path in the BundlesSettings can change while running.  So we save the
+      // filenames actually used when the most recent save of the file was done.
+      QString m_csvSavedImagesFilename;
+      QString m_csvSavedPointsFilename;
+      QString m_csvSavedResidualsFilename;
+
   }; // end BundleSolutionInfo class
 
-  // operators to read/write BundleSolutionInfo to/from binary data
-  QDataStream &operator<<(QDataStream &stream, const BundleSolutionInfo &bundleSolutionInfo);
-  QDataStream &operator>>(QDataStream &stream, BundleSolutionInfo &bundleSolutionInfo);
 
-  void setStringAttribute(int locationId, QString locationName, 
+  void setStringAttribute(int locationId, QString locationName,
                           QString attributeName, QString attributeValue);
   QString getStringAttribute(int locationId, QString locationName, QString attributeName);
 }; // end namespace Isis
diff --git a/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.truth b/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.truth
old mode 100755
new mode 100644
index ae84e2cca19a8c28376a26850cedd92d8e074455..c05ed0149654eafb831a57eba2f032327839ee00
--- a/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.truth
+++ b/isis/src/control/objs/BundleSolutionInfo/BundleSolutionInfo.truth
@@ -1,503 +1,636 @@
 Unit test for BundleSolutionInfo...
-Printing PVL group with results from the settings/cnet/statistics constructor...
-Object = DefaultSolutionInfoObject
-  RunTime              = Null
-  OutputControlNetwork = cnetfile.net
-
-  Object = InputSettings
-    NetworkValidated                     = Yes
-    SolveObservationMode                 = No
-    SolveRadius                          = No
-    UpdateCubeLabel                      = No
-    ErrorPropagation                     = No
-    CreateInverseMatrix                  = No
-    OutlierRejection                     = No
-    GlobalLatitudeAprioriSigma           = None
-    GlobalLongitudeAprioriSigma          = None
-    ConvergenceCriteria                  = Sigma0
-    ConvergenceCriteriaThreshold         = 1.0e-10
-    ConvergenceCriteriaMaximumIterations = 50
-    SolveTargetBody                      = No
-    NumberTargetBodyParameters           = 0
-    SolvePoleRightAscension              = No
-    SolvePoleRightAscensionVelocity      = No
-    SolvePoleDeclination                 = No
-    SolvePoleDeclinationVelocity         = No
-    SolvePolePrimeMeridian               = No
-    SolvePolePrimeMeridianVelocity       = No
-    SolvePolePrimeMeridianAcceleration   = No
-    solveTriaxialRadii                   = No
-    solveMeanRadius                      = No
-    FilePrefix                           = Null
-    NumberObservationSolveSettings       = 1
-
-    Object = Null
-      InstrumentPointingSolveOption       = AnglesOnly
-      NumberAngleCoefficientsSolved       = 1
-      CKDegree                            = 2
-      CKSolveDegree                       = 2
-      SolveTwist                          = Yes
-      SolvePointingPolynomialOverExisting = No
-      AngleAprioriSigmas                  = N/A
-      InstrumentPointingInterpolationType = 3
-      InstrumentPositionSolveOption       = None
-      NumberPositionCoefficientsSolved    = N/A
-      SPKDegree                           = N/A
-      SPKSolveDegree                      = N/A
-      SolvePositionOverHermiteSpline      = N/A
-      PositionAprioriSigmas               = N/A
-      InstrumentPositionInterpolationType = N/A
-    End_Object
-  End_Object
-
-  Object = StatisticsResults
-    NumberFixedPoints                 = 0
-    NumberIgnoredPoints               = 0
-    NumberHeldImages                  = 0
-    RMSResidualX                      = 0.0
-    RMSResidualY                      = 0.0
-    RMSResidualXY                     = 0.0
-    RejectionLimit                    = 0.0
-    RadiansToMeters                   = 0.0
-    NumberRejectedObservations        = 0
-    NumberObservations                = 0
-    NumberImageParameters             = 0
-    NumberConstrainedPointParameters  = 0
-    NumberConstrainedImageParameters  = 0
-    NumberConstrainedTargetParameters = 0
-    NumberUnknownParameters           = 0
-    DegreesOfFreedom                  = -1
-    Sigma0                            = 0.0
-    ElapsedTime                       = 0.0
-    ElapsedTimeErrorProp              = 0.0
-    Iterations                        = 0
-    Converged                         = No
-    MinSigmaLatitude                  = 1000000000000.0
-    MinSigmaLatitudePointId           = Null
-    MaxSigmaLatitude                  = 0.0
-    MaxSigmaLatitudePointId           = Null
-    MinSigmaLongitude                 = 1000000000000.0
-    MinSigmaLongitudePointId          = Null
-    MaxSigmaLongitude                 = 0.0
-    MaxSigmaLongitudePointId          = Null
-    MinSigmaRadius                    = 1000000000000.0
-    MinSigmaRadiusPointId             = Null
-    MaxSigmaRadius                    = 0.0
-    MaxSigmaRadiusPointId             = Null
-    RmsSigmaLat                       = 0.0
-    RmsSigmaLon                       = 0.0
-    RmsSigmaRad                       = 0.0
-    NumberMaximumLikelihoodModels     = 0
-
-    Object = CorrelationMatrixData
-      CovarianceMatrixFileName  = Null
-      CorrelationMatrixFileName = Null
-
-      Group = ImagesAndParameters
-      End_Group
-    End_Object
-  End_Object
-End_Object
+Serializing results from the settings/cnet/statistics constructor...
+
+
+    
+        
+        
+        cnetfile.net
+        
+        
+        
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+        
+        
+            0
+            0
+            0
+            0.0
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
+
+
+Testing XML serialization 1: round trip serialization of BundleSolution object...
+Serializing test XML object to file...
+
+
+    
+        
+        
+        cnetfile.net
+        
+        
+        
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+        
+        
+            0
+            0
+            0
+            0.0
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
+
+Testing XML: reading serialized BundleResults back in...
+Testing XML: Object deserialized as (should match object above):
+
+
+    
+        
+        
+        cnetfile.net
+        
+        
+        
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+        
+        
+            0
+            0
+            0
+            0.0
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
 
 Testing copy constructor...
-Object = CopySolutionInfoObject
-  RunTime              = Null
-  OutputControlNetwork = cnetfile.net
-
-  Object = InputSettings
-    NetworkValidated                     = Yes
-    SolveObservationMode                 = No
-    SolveRadius                          = No
-    UpdateCubeLabel                      = No
-    ErrorPropagation                     = No
-    CreateInverseMatrix                  = No
-    OutlierRejection                     = No
-    GlobalLatitudeAprioriSigma           = None
-    GlobalLongitudeAprioriSigma          = None
-    ConvergenceCriteria                  = Sigma0
-    ConvergenceCriteriaThreshold         = 1.0e-10
-    ConvergenceCriteriaMaximumIterations = 50
-    SolveTargetBody                      = No
-    NumberTargetBodyParameters           = 0
-    SolvePoleRightAscension              = No
-    SolvePoleRightAscensionVelocity      = No
-    SolvePoleDeclination                 = No
-    SolvePoleDeclinationVelocity         = No
-    SolvePolePrimeMeridian               = No
-    SolvePolePrimeMeridianVelocity       = No
-    SolvePolePrimeMeridianAcceleration   = No
-    solveTriaxialRadii                   = No
-    solveMeanRadius                      = No
-    FilePrefix                           = Null
-    NumberObservationSolveSettings       = 1
-
-    Object = Null
-      InstrumentPointingSolveOption       = AnglesOnly
-      NumberAngleCoefficientsSolved       = 1
-      CKDegree                            = 2
-      CKSolveDegree                       = 2
-      SolveTwist                          = Yes
-      SolvePointingPolynomialOverExisting = No
-      AngleAprioriSigmas                  = N/A
-      InstrumentPointingInterpolationType = 3
-      InstrumentPositionSolveOption       = None
-      NumberPositionCoefficientsSolved    = N/A
-      SPKDegree                           = N/A
-      SPKSolveDegree                      = N/A
-      SolvePositionOverHermiteSpline      = N/A
-      PositionAprioriSigmas               = N/A
-      InstrumentPositionInterpolationType = N/A
-    End_Object
-  End_Object
-
-  Object = StatisticsResults
-    NumberFixedPoints                 = 0
-    NumberIgnoredPoints               = 0
-    NumberHeldImages                  = 0
-    RMSResidualX                      = 0.0
-    RMSResidualY                      = 0.0
-    RMSResidualXY                     = 0.0
-    RejectionLimit                    = 0.0
-    RadiansToMeters                   = 0.0
-    NumberRejectedObservations        = 0
-    NumberObservations                = 0
-    NumberImageParameters             = 0
-    NumberConstrainedPointParameters  = 0
-    NumberConstrainedImageParameters  = 0
-    NumberConstrainedTargetParameters = 0
-    NumberUnknownParameters           = 0
-    DegreesOfFreedom                  = -1
-    Sigma0                            = 0.0
-    ElapsedTime                       = 0.0
-    ElapsedTimeErrorProp              = 0.0
-    Iterations                        = 0
-    Converged                         = No
-    MinSigmaLatitude                  = 1000000000000.0
-    MinSigmaLatitudePointId           = Null
-    MaxSigmaLatitude                  = 0.0
-    MaxSigmaLatitudePointId           = Null
-    MinSigmaLongitude                 = 1000000000000.0
-    MinSigmaLongitudePointId          = Null
-    MaxSigmaLongitude                 = 0.0
-    MaxSigmaLongitudePointId          = Null
-    MinSigmaRadius                    = 1000000000000.0
-    MinSigmaRadiusPointId             = Null
-    MaxSigmaRadius                    = 0.0
-    MaxSigmaRadiusPointId             = Null
-    RmsSigmaLat                       = 0.0
-    RmsSigmaLon                       = 0.0
-    RmsSigmaRad                       = 0.0
-    NumberMaximumLikelihoodModels     = 0
-
-    Object = CorrelationMatrixData
-      CovarianceMatrixFileName  = Null
-      CorrelationMatrixFileName = Null
-
-      Group = ImagesAndParameters
-      End_Group
-    End_Object
-  End_Object
-End_Object
+
+
+    
+        
+        
+        cnetfile.net
+        
+        
+        
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+        
+        
+            0
+            0
+            0
+            0.0
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
 
 Testing assignment operator to set this equal to itself...
-Object = SelfAssignedSolutionInfoObject
-  RunTime              = Null
-  OutputControlNetwork = cnetfile.net
-
-  Object = InputSettings
-    NetworkValidated                     = Yes
-    SolveObservationMode                 = No
-    SolveRadius                          = No
-    UpdateCubeLabel                      = No
-    ErrorPropagation                     = No
-    CreateInverseMatrix                  = No
-    OutlierRejection                     = No
-    GlobalLatitudeAprioriSigma           = None
-    GlobalLongitudeAprioriSigma          = None
-    ConvergenceCriteria                  = Sigma0
-    ConvergenceCriteriaThreshold         = 1.0e-10
-    ConvergenceCriteriaMaximumIterations = 50
-    SolveTargetBody                      = No
-    NumberTargetBodyParameters           = 0
-    SolvePoleRightAscension              = No
-    SolvePoleRightAscensionVelocity      = No
-    SolvePoleDeclination                 = No
-    SolvePoleDeclinationVelocity         = No
-    SolvePolePrimeMeridian               = No
-    SolvePolePrimeMeridianVelocity       = No
-    SolvePolePrimeMeridianAcceleration   = No
-    solveTriaxialRadii                   = No
-    solveMeanRadius                      = No
-    FilePrefix                           = Null
-    NumberObservationSolveSettings       = 1
-
-    Object = Null
-      InstrumentPointingSolveOption       = AnglesOnly
-      NumberAngleCoefficientsSolved       = 1
-      CKDegree                            = 2
-      CKSolveDegree                       = 2
-      SolveTwist                          = Yes
-      SolvePointingPolynomialOverExisting = No
-      AngleAprioriSigmas                  = N/A
-      InstrumentPointingInterpolationType = 3
-      InstrumentPositionSolveOption       = None
-      NumberPositionCoefficientsSolved    = N/A
-      SPKDegree                           = N/A
-      SPKSolveDegree                      = N/A
-      SolvePositionOverHermiteSpline      = N/A
-      PositionAprioriSigmas               = N/A
-      InstrumentPositionInterpolationType = N/A
-    End_Object
-  End_Object
-
-  Object = StatisticsResults
-    NumberFixedPoints                 = 0
-    NumberIgnoredPoints               = 0
-    NumberHeldImages                  = 0
-    RMSResidualX                      = 0.0
-    RMSResidualY                      = 0.0
-    RMSResidualXY                     = 0.0
-    RejectionLimit                    = 0.0
-    RadiansToMeters                   = 0.0
-    NumberRejectedObservations        = 0
-    NumberObservations                = 0
-    NumberImageParameters             = 0
-    NumberConstrainedPointParameters  = 0
-    NumberConstrainedImageParameters  = 0
-    NumberConstrainedTargetParameters = 0
-    NumberUnknownParameters           = 0
-    DegreesOfFreedom                  = -1
-    Sigma0                            = 0.0
-    ElapsedTime                       = 0.0
-    ElapsedTimeErrorProp              = 0.0
-    Iterations                        = 0
-    Converged                         = No
-    MinSigmaLatitude                  = 1000000000000.0
-    MinSigmaLatitudePointId           = Null
-    MaxSigmaLatitude                  = 0.0
-    MaxSigmaLatitudePointId           = Null
-    MinSigmaLongitude                 = 1000000000000.0
-    MinSigmaLongitudePointId          = Null
-    MaxSigmaLongitude                 = 0.0
-    MaxSigmaLongitudePointId          = Null
-    MinSigmaRadius                    = 1000000000000.0
-    MinSigmaRadiusPointId             = Null
-    MaxSigmaRadius                    = 0.0
-    MaxSigmaRadiusPointId             = Null
-    RmsSigmaLat                       = 0.0
-    RmsSigmaLon                       = 0.0
-    RmsSigmaRad                       = 0.0
-    NumberMaximumLikelihoodModels     = 0
-
-    Object = CorrelationMatrixData
-      CovarianceMatrixFileName  = Null
-      CorrelationMatrixFileName = Null
-
-      Group = ImagesAndParameters
-      End_Group
-    End_Object
-  End_Object
-End_Object
+
+
+    
+        
+        
+        cnetfile.net
+        
+        
+        
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+        
+        
+            0
+            0
+            0
+            0.0
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
 
 Testing assignment operator to create a new results object...
-Object = AssignedSolutionInfoObject
-  RunTime              = Null
-  OutputControlNetwork = cnetfile.net
-
-  Object = InputSettings
-    NetworkValidated                     = Yes
-    SolveObservationMode                 = No
-    SolveRadius                          = No
-    UpdateCubeLabel                      = No
-    ErrorPropagation                     = No
-    CreateInverseMatrix                  = No
-    OutlierRejection                     = No
-    GlobalLatitudeAprioriSigma           = None
-    GlobalLongitudeAprioriSigma          = None
-    ConvergenceCriteria                  = Sigma0
-    ConvergenceCriteriaThreshold         = 1.0e-10
-    ConvergenceCriteriaMaximumIterations = 50
-    SolveTargetBody                      = No
-    NumberTargetBodyParameters           = 0
-    SolvePoleRightAscension              = No
-    SolvePoleRightAscensionVelocity      = No
-    SolvePoleDeclination                 = No
-    SolvePoleDeclinationVelocity         = No
-    SolvePolePrimeMeridian               = No
-    SolvePolePrimeMeridianVelocity       = No
-    SolvePolePrimeMeridianAcceleration   = No
-    solveTriaxialRadii                   = No
-    solveMeanRadius                      = No
-    FilePrefix                           = Null
-    NumberObservationSolveSettings       = 1
-
-    Object = Null
-      InstrumentPointingSolveOption       = AnglesOnly
-      NumberAngleCoefficientsSolved       = 1
-      CKDegree                            = 2
-      CKSolveDegree                       = 2
-      SolveTwist                          = Yes
-      SolvePointingPolynomialOverExisting = No
-      AngleAprioriSigmas                  = N/A
-      InstrumentPointingInterpolationType = 3
-      InstrumentPositionSolveOption       = None
-      NumberPositionCoefficientsSolved    = N/A
-      SPKDegree                           = N/A
-      SPKSolveDegree                      = N/A
-      SolvePositionOverHermiteSpline      = N/A
-      PositionAprioriSigmas               = N/A
-      InstrumentPositionInterpolationType = N/A
-    End_Object
-  End_Object
-
-  Object = StatisticsResults
-    NumberFixedPoints                 = 0
-    NumberIgnoredPoints               = 0
-    NumberHeldImages                  = 0
-    RMSResidualX                      = 0.0
-    RMSResidualY                      = 0.0
-    RMSResidualXY                     = 0.0
-    RejectionLimit                    = 0.0
-    RadiansToMeters                   = 0.0
-    NumberRejectedObservations        = 0
-    NumberObservations                = 0
-    NumberImageParameters             = 0
-    NumberConstrainedPointParameters  = 0
-    NumberConstrainedImageParameters  = 0
-    NumberConstrainedTargetParameters = 0
-    NumberUnknownParameters           = 0
-    DegreesOfFreedom                  = -1
-    Sigma0                            = 0.0
-    ElapsedTime                       = 0.0
-    ElapsedTimeErrorProp              = 0.0
-    Iterations                        = 0
-    Converged                         = No
-    MinSigmaLatitude                  = 1000000000000.0
-    MinSigmaLatitudePointId           = Null
-    MaxSigmaLatitude                  = 0.0
-    MaxSigmaLatitudePointId           = Null
-    MinSigmaLongitude                 = 1000000000000.0
-    MinSigmaLongitudePointId          = Null
-    MaxSigmaLongitude                 = 0.0
-    MaxSigmaLongitudePointId          = Null
-    MinSigmaRadius                    = 1000000000000.0
-    MinSigmaRadiusPointId             = Null
-    MaxSigmaRadius                    = 0.0
-    MaxSigmaRadiusPointId             = Null
-    RmsSigmaLat                       = 0.0
-    RmsSigmaLon                       = 0.0
-    RmsSigmaRad                       = 0.0
-    NumberMaximumLikelihoodModels     = 0
-
-    Object = CorrelationMatrixData
-      CovarianceMatrixFileName  = Null
-      CorrelationMatrixFileName = Null
-
-      Group = ImagesAndParameters
-      End_Group
-    End_Object
-  End_Object
-End_Object
+
+
+    
+        
+        
+        cnetfile.net
+        
+        
+        
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+        
+        
+            0
+            0
+            0
+            0.0
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
 
 Testing mutator methods...
-Object = MutatorTest
-  RunTime              = xxx
-  OutputControlNetwork = cnetfile.net
-
-  Object = InputSettings
-    NetworkValidated                     = Yes
-    SolveObservationMode                 = No
-    SolveRadius                          = No
-    UpdateCubeLabel                      = No
-    ErrorPropagation                     = No
-    CreateInverseMatrix                  = No
-    OutlierRejection                     = No
-    GlobalLatitudeAprioriSigma           = None
-    GlobalLongitudeAprioriSigma          = None
-    ConvergenceCriteria                  = Sigma0
-    ConvergenceCriteriaThreshold         = 1.0e-10
-    ConvergenceCriteriaMaximumIterations = 50
-    SolveTargetBody                      = No
-    NumberTargetBodyParameters           = 0
-    SolvePoleRightAscension              = No
-    SolvePoleRightAscensionVelocity      = No
-    SolvePoleDeclination                 = No
-    SolvePoleDeclinationVelocity         = No
-    SolvePolePrimeMeridian               = No
-    SolvePolePrimeMeridianVelocity       = No
-    SolvePolePrimeMeridianAcceleration   = No
-    solveTriaxialRadii                   = No
-    solveMeanRadius                      = No
-    FilePrefix                           = Null
-    NumberObservationSolveSettings       = 1
-
-    Object = Null
-      InstrumentPointingSolveOption       = AnglesOnly
-      NumberAngleCoefficientsSolved       = 1
-      CKDegree                            = 2
-      CKSolveDegree                       = 2
-      SolveTwist                          = Yes
-      SolvePointingPolynomialOverExisting = No
-      AngleAprioriSigmas                  = N/A
-      InstrumentPointingInterpolationType = 3
-      InstrumentPositionSolveOption       = None
-      NumberPositionCoefficientsSolved    = N/A
-      SPKDegree                           = N/A
-      SPKSolveDegree                      = N/A
-      SolvePositionOverHermiteSpline      = N/A
-      PositionAprioriSigmas               = N/A
-      InstrumentPositionInterpolationType = N/A
-    End_Object
-  End_Object
-
-  Object = StatisticsResults
-    NumberFixedPoints                 = 0
-    NumberIgnoredPoints               = 0
-    NumberHeldImages                  = 0
-    RMSResidualX                      = 0.0
-    RMSResidualY                      = 0.0
-    RMSResidualXY                     = 0.0
-    RejectionLimit                    = 0.5
-    RadiansToMeters                   = 0.0
-    NumberRejectedObservations        = 0
-    NumberObservations                = 0
-    NumberImageParameters             = 0
-    NumberConstrainedPointParameters  = 0
-    NumberConstrainedImageParameters  = 0
-    NumberConstrainedTargetParameters = 0
-    NumberUnknownParameters           = 0
-    DegreesOfFreedom                  = -1
-    Sigma0                            = 0.0
-    ElapsedTime                       = 0.0
-    ElapsedTimeErrorProp              = 0.0
-    Iterations                        = 0
-    Converged                         = No
-    MinSigmaLatitude                  = 1000000000000.0
-    MinSigmaLatitudePointId           = Null
-    MaxSigmaLatitude                  = 0.0
-    MaxSigmaLatitudePointId           = Null
-    MinSigmaLongitude                 = 1000000000000.0
-    MinSigmaLongitudePointId          = Null
-    MaxSigmaLongitude                 = 0.0
-    MaxSigmaLongitudePointId          = Null
-    MinSigmaRadius                    = 1000000000000.0
-    MinSigmaRadiusPointId             = Null
-    MaxSigmaRadius                    = 0.0
-    MaxSigmaRadiusPointId             = Null
-    RmsSigmaLat                       = 0.0
-    RmsSigmaLon                       = 0.0
-    RmsSigmaRad                       = 0.0
-    NumberMaximumLikelihoodModels     = 0
-
-    Object = CorrelationMatrixData
-      CovarianceMatrixFileName  = Null
-      CorrelationMatrixFileName = Null
-
-      Group = ImagesAndParameters
-      End_Group
-    End_Object
-  End_Object
-End_Object
+
+
+    
+        
+        xxx
+        cnetfile.net
+        
+        
+        
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+        
+        
+            0
+            0
+            0
+            0.5
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
 
 Testing accessor methods...
 runTime =  "xxx"
@@ -508,105 +641,211 @@ we cannot test updateFileName().
 Testing error throws...
 
 Testing output methods
-Testing XML write/read...
-
-Testing HDF5 write/read...
-Object = BundleSolutionInfoFromHDF
-  RunTime              = xxx
-  OutputControlNetwork = cnetfile.net
-
-  Object = InputSettings
-    NetworkValidated                     = Yes
-    SolveObservationMode                 = No
-    SolveRadius                          = No
-    UpdateCubeLabel                      = No
-    ErrorPropagation                     = No
-    CreateInverseMatrix                  = No
-    OutlierRejection                     = No
-    GlobalLatitudeAprioriSigma           = None
-    GlobalLongitudeAprioriSigma          = None
-    ConvergenceCriteria                  = Sigma0
-    ConvergenceCriteriaThreshold         = 1.0e-10
-    ConvergenceCriteriaMaximumIterations = 50
-    SolveTargetBody                      = No
-    NumberTargetBodyParameters           = 0
-    SolvePoleRightAscension              = No
-    SolvePoleRightAscensionVelocity      = No
-    SolvePoleDeclination                 = No
-    SolvePoleDeclinationVelocity         = No
-    SolvePolePrimeMeridian               = No
-    SolvePolePrimeMeridianVelocity       = No
-    SolvePolePrimeMeridianAcceleration   = No
-    solveTriaxialRadii                   = No
-    solveMeanRadius                      = No
-    FilePrefix                           = Null
-    NumberObservationSolveSettings       = 1
-
-    Object = Null
-      InstrumentPointingSolveOption       = AnglesOnly
-      NumberAngleCoefficientsSolved       = 1
-      CKDegree                            = 2
-      CKSolveDegree                       = 2
-      SolveTwist                          = Yes
-      SolvePointingPolynomialOverExisting = No
-      AngleAprioriSigmas                  = N/A
-      InstrumentPointingInterpolationType = 3
-      InstrumentPositionSolveOption       = None
-      NumberPositionCoefficientsSolved    = N/A
-      SPKDegree                           = N/A
-      SPKSolveDegree                      = N/A
-      SolvePositionOverHermiteSpline      = N/A
-      PositionAprioriSigmas               = N/A
-      InstrumentPositionInterpolationType = N/A
-    End_Object
-  End_Object
-
-  Object = StatisticsResults
-    NumberFixedPoints                 = 0
-    NumberIgnoredPoints               = 0
-    NumberHeldImages                  = 0
-    RMSResidualX                      = 0.0
-    RMSResidualY                      = 0.0
-    RMSResidualXY                     = 0.0
-    RejectionLimit                    = 0.5
-    RadiansToMeters                   = 0.0
-    NumberRejectedObservations        = 0
-    NumberObservations                = 0
-    NumberImageParameters             = 0
-    NumberConstrainedPointParameters  = 0
-    NumberConstrainedImageParameters  = 0
-    NumberConstrainedTargetParameters = 0
-    NumberUnknownParameters           = 0
-    DegreesOfFreedom                  = -1
-    Sigma0                            = 0.0
-    ElapsedTime                       = 0.0
-    ElapsedTimeErrorProp              = 0.0
-    Iterations                        = 0
-    Converged                         = No
-    MinSigmaLatitude                  = 1000000000000.0
-    MinSigmaLatitudePointId           = Null
-    MaxSigmaLatitude                  = 0.0
-    MaxSigmaLatitudePointId           = Null
-    MinSigmaLongitude                 = 1000000000000.0
-    MinSigmaLongitudePointId          = Null
-    MaxSigmaLongitude                 = 0.0
-    MaxSigmaLongitudePointId          = Null
-    MinSigmaRadius                    = 1000000000000.0
-    MinSigmaRadiusPointId             = Null
-    MaxSigmaRadius                    = 0.0
-    MaxSigmaRadiusPointId             = Null
-    RmsSigmaLat                       = 0.0
-    RmsSigmaLon                       = 0.0
-    RmsSigmaRad                       = 0.0
-    NumberMaximumLikelihoodModels     = 0
-
-    Object = CorrelationMatrixData
-      CovarianceMatrixFileName  = Null
-      CorrelationMatrixFileName = Null
-
-      Group = ImagesAndParameters
-      End_Group
-    End_Object
-  End_Object
-End_Object
 
+Testing XML serialization 2: round trip serialization of fully populated BundleSolution object...
+Serializing test XML object to file...
+
+
+    
+        
+        xxx
+        cnetfile.net
+        bundleout_images.csv
+        bundleout_points.csv
+        residuals.csv
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+                
+                      X  (t0)
+                      Y  (t0)
+                      Z  (t0)
+                     RA  (t0)
+                    DEC  (t0)
+                    TWI  (t0)
+                
+            
+        
+        
+            0
+            0
+            0
+            0.5
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                    
+                        
+                    
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
+
+Testing XML: reading serialized BundleResults back in...
+Testing XML: Object deserialized as (should match object above):
+
+
+    
+        
+        xxx
+        cnetfile.net
+        bundleout_images.csv
+        bundleout_points.csv
+        residuals.csv
+    
+    
+        
+            Yes
+            
+            
+            
+            
+            
+            
+        
+        
+            
+                
+                
+                
+                    
+                        N/A
+                    
+                
+                
+                    
+                
+            
+        
+    
+    
+        
+            
+                
+                      X  (t0)
+                      Y  (t0)
+                      Z  (t0)
+                     RA  (t0)
+                    DEC  (t0)
+                    TWI  (t0)
+                
+            
+        
+        
+            0
+            0
+            0
+            0.5
+            0
+            0
+            0
+            0
+            0
+            0
+            0
+            -1
+            0.0
+            No
+        
+        
+            
+            
+            
+                
+                    
+                        
+                    
+                
+            
+            
+                
+                
+                
+                
+                
+                
+            
+        
+        
+        
+            
+            
+            
+            
+            
+            
+        
+        
+            
+            
+        
+    
+ 
+
+
+
+Writing text ouput file...
+Writing csv ouput files...
diff --git a/isis/src/control/objs/BundleSolutionInfo/unitTest.cpp b/isis/src/control/objs/BundleSolutionInfo/unitTest.cpp
index c58ad5b1d50a1007e8383a126688490bce5999e2..ab2043f0c29842fc59d12191af7aa0548737ab24 100755
--- a/isis/src/control/objs/BundleSolutionInfo/unitTest.cpp
+++ b/isis/src/control/objs/BundleSolutionInfo/unitTest.cpp
@@ -29,6 +29,7 @@
 using namespace std;
 using namespace Isis;
 
+void printXml(const BundleSolutionInfo &);
 
 /**
  * This class is needed to test the xml read/write methods.
@@ -40,7 +41,7 @@ using namespace Isis;
 namespace Isis {
   class BundleSolutionInfoXmlHandlerTester : public BundleSolutionInfo {
     public:
-      BundleSolutionInfoXmlHandlerTester(Project *project, XmlStackedHandlerReader *reader, 
+      BundleSolutionInfoXmlHandlerTester(Project *project, XmlStackedHandlerReader *reader,
                                      FileName xmlFile) : BundleSolutionInfo(project, reader) {
 
         QString xmlPath(xmlFile.expanded());
@@ -55,7 +56,7 @@ namespace Isis {
         QXmlInputSource xmlInputSource(&file);
         bool success = reader->parse(xmlInputSource);
         if (!success) {
-          throw IException(IException::Unknown, 
+          throw IException(IException::Unknown,
                            QString("Failed to parse xml file, [%1]").arg(xmlPath),
                             _FILEINFO_);
         }
@@ -76,6 +77,7 @@ namespace Isis {
  *   @history 2015-09-03 Jeannie Backer - Commented out xml code test until we determine whether
  *                           we will keep this code.
  *   @history 2016-10-13 Ian Humphrey - Changed addnew call to addNew(). References #4293.
+ *   @history 2017-04-24 Ian Humphrey - Replaced pvlObject() with XML save(). Fixes #4797.
  */
 int main(int argc, char *argv[]) {
   Preference::Preferences(true);
@@ -84,7 +86,7 @@ int main(int argc, char *argv[]) {
 
   try {
     qDebug() << "Unit test for BundleSolutionInfo...";
-    qDebug() << "Printing PVL group with results from the settings/cnet/statistics constructor...";
+    qDebug() << "Serializing results from the settings/cnet/statistics constructor...";
 
     // create default settings and statistics objects to pass into results object
     BundleSettingsQsp settings = BundleSettingsQsp(new BundleSettings);
@@ -102,14 +104,14 @@ int main(int argc, char *argv[]) {
     freeMeasure2->SetCoordinate(1.0, 2.0);
     freeMeasure2->SetResidual(-3.0, 4.0);
     freePoint->Add(freeMeasure2);
-    SurfacePoint freeSurfacePoint(Latitude(45.0, Angle::Degrees), 
-                                  Longitude(120.0, Angle::Degrees), 
+    SurfacePoint freeSurfacePoint(Latitude(45.0, Angle::Degrees),
+                                  Longitude(120.0, Angle::Degrees),
                                   Distance(6.0, Distance::Meters));
     freePoint->SetAdjustedSurfacePoint(freeSurfacePoint);
     ControlPoint *fixedPoint = new ControlPoint("FixedPoint");
     fixedPoint->SetType(ControlPoint::Fixed);
-    SurfacePoint fixedSurfacePoint(Latitude(90.0, Angle::Degrees), 
-                                   Longitude(180.0, Angle::Degrees), 
+    SurfacePoint fixedSurfacePoint(Latitude(90.0, Angle::Degrees),
+                                   Longitude(180.0, Angle::Degrees),
                                    Distance(10.0, Distance::Meters));
     fixedPoint->SetAdjustedSurfacePoint(fixedSurfacePoint);
     ControlNet outNet;
@@ -134,35 +136,60 @@ int main(int argc, char *argv[]) {
     statistics.setBundleControlPoints(bundleControlPointVector);
     statistics.setOutputControlNet(ControlNetQsp(new ControlNet(outNet)));
     statistics.setObservations(observationVector);
-    BundleSolutionInfo results(settings, cnetFile, statistics, parent);
+    QList imgList;
+    BundleSolutionInfo results(settings, cnetFile, statistics, imgList, parent);
+
+    printXml(results);
+
+
+    qDebug() << "";
+    qDebug() << "Testing XML serialization 1: round trip serialization of BundleSolution object...";
+    qDebug() << "Serializing test XML object to file...";
+    printXml(results);    // save XML to test log for comparison
+    FileName xmlFile1("./BundleSolutionInfo1.xml");
+    QString xmlPath1 = xmlFile1.expanded();
+    QFile qXmlFile1(xmlPath1);
+    if (!qXmlFile1.open(QIODevice::WriteOnly|QIODevice::Text)) {
+      throw IException(IException::Io,
+                       QString("Unable to open xml file, [%1],  with write access").arg(xmlPath1),
+                       _FILEINFO_);
+    }
+    QXmlStreamWriter writer(&qXmlFile1);
+    writer.setAutoFormatting(true);
+    writer.writeStartDocument();
+    Project *project = NULL;
+    results.save(writer, project, "");
+    writer.writeEndDocument();
+    qXmlFile1.close();
+
+    qDebug() << "Testing XML: reading serialized BundleResults back in...";
+    XmlStackedHandlerReader reader1;
+    BundleSolutionInfoXmlHandlerTester bsFromXml1(project, &reader1, xmlFile1);
+    qDebug() << "Testing XML: Object deserialized as (should match object above):";
+    printXml(bsFromXml1);  // Save comparison output to log file
+
 
-    PvlObject pvl = results.pvlObject("DefaultSolutionInfoObject");
-    cout << pvl << endl << endl;
 
     qDebug() << "Testing copy constructor...";
 
     BundleSolutionInfo copySolutionInfo(results);
-    pvl = copySolutionInfo.pvlObject("CopySolutionInfoObject");
-    cout << pvl << endl << endl;
+    printXml(copySolutionInfo);
 
     qDebug() << "Testing assignment operator to set this equal to itself...";
     results = results;
-    pvl = results.pvlObject("SelfAssignedSolutionInfoObject");
-    cout << pvl << endl << endl;
+    printXml(results);
 
     qDebug() << "Testing assignment operator to create a new results object...";
 
     BundleSolutionInfo assignmentOpSolutionInfo = results;
     assignmentOpSolutionInfo = results;
-    pvl = assignmentOpSolutionInfo.pvlObject("AssignedSolutionInfoObject");
-    cout << pvl << endl << endl;
+    printXml(assignmentOpSolutionInfo);
 
     qDebug() << "Testing mutator methods...";
     statistics.setRejectionLimit(0.5);
     results.setOutputStatistics(statistics);
     results.setRunTime("xxx"); //???
-    pvl = results.pvlObject("MutatorTest");
-    cout << pvl << endl << endl;
+    printXml(results);
 
     qDebug() << "Testing accessor methods...";
     // Can't print this value out since it changes for every run,
@@ -211,16 +238,16 @@ int main(int argc, char *argv[]) {
     rmsStats.AddData(-1);        // 1 below range
     rmsStats.AddData(1000);      // 2 above range
     rmsStats.AddData(1001);
-    // 6, 14, 0, 3, 0, 100, 22, 4, 1, 2, 3, 4, 5, 1, 2, false 
-     
+    // 6, 14, 0, 3, 0, 100, 22, 4, 1, 2, 3, 4, 5, 1, 2, false
+
     QList rmsImageLineResiduals;
     rmsImageLineResiduals += rmsStats;
     rmsStats.AddData(4);
-    // 10, 30, 0, 4, 0, 100, 23, 5, 1, 2, 3, 4, 5, 1, 2, false 
+    // 10, 30, 0, 4, 0, 100, 23, 5, 1, 2, 3, 4, 5, 1, 2, false
     rmsImageLineResiduals += rmsStats;
     rmsStats.AddData(5);
     rmsStats.RemoveData(5);
-    // 10, 30, 0, 5, 0, 100, 23, 5, 1, 2, 3, 4, 5, 1, 2, true 
+    // 10, 30, 0, 5, 0, 100, 23, 5, 1, 2, 3, 4, 5, 1, 2, true
     rmsImageLineResiduals += rmsStats;
 
     QList rmsImageSampleResiduals = rmsImageLineResiduals;
@@ -228,8 +255,8 @@ int main(int argc, char *argv[]) {
     rmsImageSampleResiduals[0].AddData(4);
     rmsImageSampleResiduals[2].RemoveData(2);
     // 10, 30, 0, 3, 0, 100, 22, 4, 1, 2, 3, 4, 5, 1, 2, true
-    // 10, 30, 0, 4, 0, 100, 23, 5, 1, 2, 3, 4, 5, 1, 2, false 
-    // 8, 26, 0, 5, 0, 100, 22, 4, 1, 2, 3, 4, 5, 1, 2, true 
+    // 10, 30, 0, 4, 0, 100, 23, 5, 1, 2, 3, 4, 5, 1, 2, false
+    // 8, 26, 0, 5, 0, 100, 22, 4, 1, 2, 3, 4, 5, 1, 2, true
 
     QList rmsImageResiduals = rmsImageSampleResiduals;
     rmsImageResiduals[0].AddData(0);
@@ -246,7 +273,7 @@ int main(int argc, char *argv[]) {
     rmsImageResiduals[2].AddData(3);
     // 16, 44, 0, 3, 0, 100, 26, 8, 1, 2, 3, 4, 5, 1, 2, true
     // 16, 44, 0, 4, 0, 100, 27, 9, 1, 2, 3, 4, 5, 1, 2, false
-    // 14, 40, 0, 5, 0, 100, 26, 8, 1, 2, 3, 4, 5, 1, 2, true 
+    // 14, 40, 0, 5, 0, 100, 26, 8, 1, 2, 3, 4, 5, 1, 2, true
 
     statistics.setRmsImageResidualLists(rmsImageLineResiduals,
                                         rmsImageSampleResiduals,
@@ -254,60 +281,47 @@ int main(int argc, char *argv[]) {
     results.setOutputStatistics(statistics);
 
     qDebug() << "Testing output methods";
-    
+
     results.outputText();
     results.outputImagesCSV();
     results.outputPointsCSV();
     results.outputResiduals();
 
 
-
-
-
-
-
-    qDebug() << "Testing XML write/read...";
-    // write xml
-#if 0
-    FileName xmlFile("./BundleSolutionInfo.xml");
-    QString xmlPath = xmlFile.expanded();
-    QFile qXmlFile(xmlPath);
-    if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
+    qDebug() << "";
+    qDebug() << "Testing XML serialization 2: round trip serialization of fully populated BundleSolution object...";
+    qDebug() << "Serializing test XML object to file...";
+    printXml(results);    // save XML to test log for comparison
+    FileName xmlFile2("./BundleSolutionInfo2.xml");
+    QString xmlPath2 = xmlFile2.expanded();
+    QFile qXmlFile2(xmlPath2);
+    if (!qXmlFile2.open(QIODevice::WriteOnly|QIODevice::Text)) {
       throw IException(IException::Io,
-                       QString("Unable to open xml file, [%1],  with write access").arg(xmlPath),
+                       QString("Unable to open xml file, [%1],  with write access").arg(xmlPath2),
                        _FILEINFO_);
     }
-    QXmlStreamWriter writer(&qXmlFile);
-    writer.setAutoFormatting(true);
-    writer.writeStartDocument();
-    Project *project = NULL;
-    results.save(writer, project);
-    writer.writeEndDocument();
-    qXmlFile.close();
-    // read xml
+    QXmlStreamWriter writer2(&qXmlFile2);
+    writer2.setAutoFormatting(true);
+    writer2.writeStartDocument();
+    results.save(writer2, project, "");
+    writer2.writeEndDocument();
+    qXmlFile2.close();
+
+    qDebug() << "Testing XML: reading serialized BundleResults back in...";
     XmlStackedHandlerReader reader;
-// ???     BundleSolutionInfoXmlHandlerTester brToFill(project, &reader, xmlFile);
-// ???     pvl = bsToFill.pvlObject("BundleSolutionInfoFromXml");
-// ???     cout << pvl << endl << endl;
-#endif
-    qDebug() << "";
+    BundleSolutionInfoXmlHandlerTester bsFromXml2(project, &reader, xmlFile2);
+    qDebug() << "Testing XML: Object deserialized as (should match object above):";
+    printXml(bsFromXml2);  // Save comparison output to log file
 
-    qDebug() << "Testing HDF5 write/read...";
-    // write hdf
-    FileName hdfFile("./BundleSolutionInfo.hdf");
-    if (hdfFile.fileExists()) {
-       QFile::remove(hdfFile.expanded());
-    }
-    results.createH5File(hdfFile);
-    BundleSolutionInfo fromHDF(hdfFile);
-    pvl = fromHDF.pvlObject("BundleSolutionInfoFromHDF");
-    cout << pvl << endl << endl;
-//    QFile::remove(hdfFile.expanded());
+
+    qDebug() << "";
+    qDebug() << "Writing text ouput file...";
     FileName txtFile("./bundleout.txt");
     QFile txtOutput(txtFile.expanded());
     if (txtOutput.exists()) {
       txtOutput.remove();
     }
+    qDebug() << "Writing csv ouput files...";
     FileName pointsCsv("./bundleout_points.csv");
     QFile pointsOutput(pointsCsv.expanded());
     if (pointsOutput.exists()) {
@@ -324,3 +338,20 @@ int main(int argc, char *argv[]) {
     e.print();
   }
 }
+
+
+/**
+ * Prints the serialzed BundleSolutionInfo as XML.
+ *
+ * @param const BundleSolutionInfo &printable The BundleSolutionInfo to print.
+ */
+void printXml(const BundleSolutionInfo &printable) {
+  QString output;
+  QXmlStreamWriter writer(&output);
+  writer.setAutoFormatting(true);
+  printable.save(writer, NULL, "");
+  // Note Statistics class does not serialize/restore properly as of 2017-04-27
+  output.remove(QRegExp(".*"));
+  output.remove(QRegExp("[^<]*"));
+  qDebug().noquote() << output << endl << endl;
+}
diff --git a/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.cpp b/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.cpp
index 224848cfb4d4d2cb3278f1bdbd7a2ad6eeb84ff2..6fecb8fd7244297e8232239e1812cc21c702cd2c 100644
--- a/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.cpp
+++ b/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.cpp
@@ -10,11 +10,6 @@
 #include 
 #include 
 
-// in the hdf5 library
-#include 
-#include  
-#include 
-
 #include "BundleImage.h"
 #include "Camera.h"
 #include "FileName.h"
@@ -39,12 +34,12 @@ namespace Isis {
   /**
    * Construct this BundleObservationSolveSettings object from XML.
    *
-   * @param bundleSettingsFolder Where this settings XML resides - 
+   * @param bundleSettingsFolder Where this settings XML resides -
    *                             /work/.../projectRoot/images/import1
    * @param xmlReader An XML reader that's up to an  tag.
    */
   BundleObservationSolveSettings::BundleObservationSolveSettings(
-                                                             Project *project, 
+                                                             Project *project,
                                                              XmlStackedHandlerReader *xmlReader) {
     initialize();
     xmlReader->pushContentHandler(new XmlHandler(this, project));
@@ -61,7 +56,7 @@ namespace Isis {
    */
   BundleObservationSolveSettings::BundleObservationSolveSettings(
                                                              FileName xmlFile,
-                                                             Project *project, 
+                                                             Project *project,
                                                              XmlStackedHandlerReader *xmlReader) {
 
     initialize();
@@ -78,7 +73,7 @@ namespace Isis {
     xmlReader->setErrorHandler(new XmlHandler(this, project));
     bool success = xmlReader->parse(xmlInputSource);
     if (!success) {
-      throw IException(IException::Unknown, 
+      throw IException(IException::Unknown,
                        QString("Failed to parse xml file, [%1]").arg(xmlPath),
                         _FILEINFO_);
     }
@@ -114,7 +109,7 @@ namespace Isis {
 
     m_id = NULL;
     m_id = new QUuid(other.m_id->toString());
-     // TODO: add check to all copy constructors (verify other.xxx is not null) and operator= ??? 
+     // TODO: add check to all copy constructors (verify other.xxx is not null) and operator= ???
      // or intit all variables in all constructors
 
     m_instrumentId = other.m_instrumentId;
@@ -156,16 +151,16 @@ namespace Isis {
    * @internal
    *   @todo Check this (assignment operator)
    */
-  BundleObservationSolveSettings 
+  BundleObservationSolveSettings
       &BundleObservationSolveSettings::operator=(const BundleObservationSolveSettings &other) {
     if (&other != this) {
       delete m_id;
       m_id = NULL;
       m_id = new QUuid(other.m_id->toString());
-      
+
       m_instrumentId = other.m_instrumentId;
       m_observationNumbers = other.m_observationNumbers;
-      
+
       // pointing related
       m_instrumentPointingSolveOption = other.m_instrumentPointingSolveOption;
       m_numberCamAngleCoefSolved = other.m_numberCamAngleCoefSolved;
@@ -184,7 +179,7 @@ namespace Isis {
       m_solvePositionOverHermiteSpline = other.m_solvePositionOverHermiteSpline;
       m_positionInterpolationType = other.m_positionInterpolationType;
       m_positionAprioriSigma = other.m_positionAprioriSigma;
-      
+
     }
 
     return *this;
@@ -198,11 +193,11 @@ namespace Isis {
   void BundleObservationSolveSettings::initialize() {
     m_id = NULL;
     m_id = new QUuid(QUuid::createUuid());
-    
+
     m_instrumentId = "";
 
     // Camera Pointing Options
-    // Defaults: 
+    // Defaults:
     //     m_instrumentPointingSolveOption = AnglesOnly;
     //     m_numberCamAngleCoefSolved = 1; // AnglesOnly;
     //     m_ckDegree = 2;
@@ -245,7 +240,7 @@ namespace Isis {
   /**
    * Accesses the instrument id for this observation.
    *
-   * @return @b QString Returns the instrument id for this observation 
+   * @return @b QString Returns the instrument id for this observation
    */
   QString BundleObservationSolveSettings::instrumentId() const {
     return m_instrumentId;
@@ -254,9 +249,9 @@ namespace Isis {
 
   /**
    * Associates an observation number with these solve settings.
-   * 
+   *
    * These solve settings are to be applied to any associated observations.
-   * 
+   *
    * @param observationNumber QString observation number to associate with these settings.
    */
   void BundleObservationSolveSettings::addObservationNumber(QString observationNumber) {
@@ -266,7 +261,7 @@ namespace Isis {
 
   /**
    * Returns a list of observation numbers associated with these solve settings.
-   * 
+   *
    * @return @b QSet Returns a QSet containing the associated observation numbers.
    */
   QSet BundleObservationSolveSettings::observationNumbers() const {
@@ -279,7 +274,7 @@ namespace Isis {
   // =============================================================================================//
 
 
-  /** 
+  /**
    * Translates a QString InstrumentPointingSolveOption to its enumerated value.
    *
    * @param option QString representation of the instrument pointing solve option
@@ -288,7 +283,7 @@ namespace Isis {
    *
    * @return @b BundleObservationSolveSettings::InstrumentPointingSolveOption Returns the enumerated
    *     value of the instrument pointing solve option
-   */ 
+   */
   BundleObservationSolveSettings::InstrumentPointingSolveOption
       BundleObservationSolveSettings::stringToInstrumentPointingSolveOption(QString option) {
     if (option.compare("NONE", Qt::CaseInsensitive) == 0) {
@@ -359,20 +354,20 @@ namespace Isis {
    * @param solveTwist Whether or not to solve for twist
    * @param ckDegree
    * @param ckSolveDegree
-   * @param solvePolynomialOverExisting Indicates whether the polynomial will be fit over an 
+   * @param solvePolynomialOverExisting Indicates whether the polynomial will be fit over an
    *                                    existing pointing polynomial
    * @param anglesAprioriSigma A priori angle values
    * @param angularVelocityAprioriSigma A priori angular velocity
    * @param angularAccelerationAprioriSigma A priori angular acceleration
-   */  
+   */
   void BundleObservationSolveSettings::setInstrumentPointingSettings(
-                                           InstrumentPointingSolveOption option, 
-                                           bool solveTwist, 
-                                           int ckDegree, 
+                                           InstrumentPointingSolveOption option,
+                                           bool solveTwist,
+                                           int ckDegree,
                                            int ckSolveDegree,
-                                           bool solvePolynomialOverExisting, 
-                                           double anglesAprioriSigma, 
-                                           double angularVelocityAprioriSigma, 
+                                           bool solvePolynomialOverExisting,
+                                           double anglesAprioriSigma,
+                                           double angularVelocityAprioriSigma,
                                            double angularAccelerationAprioriSigma) {
 
     // automatically set the solve option and ck degree to the user entered values
@@ -393,7 +388,7 @@ namespace Isis {
       // let spkDegree and spkSolveDegree default to 2, 2
       m_ckDegree = 2;
       m_ckSolveDegree = 2;
-      
+
       // solve for the appropriate number of coefficients, based on solve option enum
       m_numberCamAngleCoefSolved = ((int) option);
     }
@@ -428,7 +423,7 @@ namespace Isis {
 
     m_solveTwist = solveTwist; // dependent on solve option???
 
-    // Set the SpiceRotation interpolation type enum appropriately 
+    // Set the SpiceRotation interpolation type enum appropriately
     m_solvePointingPolynomialOverExisting = solvePolynomialOverExisting;
     if (m_solvePointingPolynomialOverExisting) {
       m_pointingInterpolationType = SpiceRotation::PolyFunctionOverSpice;
@@ -436,14 +431,14 @@ namespace Isis {
     else {
       m_pointingInterpolationType = SpiceRotation::PolyFunction;
     }
-  
+
   }
 
 
   /**
    * Accesses the instrument pointing solve option.
    *
-   * @return @b BundleObservationSolveSettings::InstrumentPointingSolveOption Returns the 
+   * @return @b BundleObservationSolveSettings::InstrumentPointingSolveOption Returns the
    *     instrument pointing solve option
    */
   BundleObservationSolveSettings::InstrumentPointingSolveOption
@@ -465,7 +460,7 @@ namespace Isis {
   /**
    * Accesses the degree of polynomial fit to original camera angles (ckDegree).
    *
-   * @return @b int Returns the degree of the polynomial fit to the original camera angles 
+   * @return @b int Returns the degree of the polynomial fit to the original camera angles
    */
   int BundleObservationSolveSettings::ckDegree() const {
     return m_ckDegree;
@@ -473,7 +468,7 @@ namespace Isis {
 
 
   /**
-   * Accesses the degree of the camera angles polynomial being fit to in the bundle adjustment 
+   * Accesses the degree of the camera angles polynomial being fit to in the bundle adjustment
    * (ckSolveDegree).
    *
    * @return @b int Returns the degree of the camera angles polynomial in the bundle adjustment
@@ -486,7 +481,7 @@ namespace Isis {
   /**
    * Accesses the number of camera angle coefficients in the solution.
    *
-   * @return @b int Returns the number of camera angle coefficients in the solution 
+   * @return @b int Returns the number of camera angle coefficients in the solution
    */
   int BundleObservationSolveSettings::numberCameraAngleCoefficientsSolved() const {
     return m_numberCamAngleCoefSolved;
@@ -494,7 +489,7 @@ namespace Isis {
 
 
   /**
-   * Whether or not the solve polynomial will be fit over the existing pointing polynomial.  
+   * Whether or not the solve polynomial will be fit over the existing pointing polynomial.
    *
    * @return @b bool Indicates whether the polynomial will be fit over the existing pointing
    *                 polynomial
@@ -515,8 +510,8 @@ namespace Isis {
 
 
   /**
-   * Accesses the SpiceRotation interpolation type for the instrument pointing.  
-   * 
+   * Accesses the SpiceRotation interpolation type for the instrument pointing.
+   *
    * @return @b SpiceRotation::Source Returns the SpiceRotation interpolation type for pointing
    */
   SpiceRotation::Source BundleObservationSolveSettings::pointingInterpolationType() const {
@@ -610,17 +605,17 @@ namespace Isis {
    * @param spkSolveDegree
    * @param positionOverHermite Whether or not the polynomial will be fit over an existing Hermite
    *                            spline
-   * @param positionAprioriSigma A priori position sigma 
+   * @param positionAprioriSigma A priori position sigma
    * @param velocityAprioriSigma A priori velocity sigma
    * @param accelerationAprioriSigma A priori acceleration sigma
    */
   void BundleObservationSolveSettings::setInstrumentPositionSettings(
-                                           InstrumentPositionSolveOption option, 
-                                           int spkDegree, 
-                                           int spkSolveDegree, 
-                                           bool positionOverHermite, 
-                                           double positionAprioriSigma, 
-                                           double velocityAprioriSigma, 
+                                           InstrumentPositionSolveOption option,
+                                           int spkDegree,
+                                           int spkSolveDegree,
+                                           bool positionOverHermite,
+                                           double positionAprioriSigma,
+                                           double velocityAprioriSigma,
                                            double accelerationAprioriSigma) {
     // automatically set the solve option and spk degree to the user entered values
     m_instrumentPositionSolveOption = option;
@@ -672,7 +667,7 @@ namespace Isis {
       }
     }
 
-    // Set the SpicePosition interpolation type enum appropriately 
+    // Set the SpicePosition interpolation type enum appropriately
     m_solvePositionOverHermiteSpline = positionOverHermite;
     if (m_solvePositionOverHermiteSpline) {
       m_positionInterpolationType = SpicePosition::PolyFunctionOverHermiteConstant;
@@ -687,7 +682,7 @@ namespace Isis {
   /**
    * Accesses the instrument position solve option.
    *
-   * @return @b BundleObservationSolveSettings::InstrumentPositionSolveOption Returns the 
+   * @return @b BundleObservationSolveSettings::InstrumentPositionSolveOption Returns the
    *     instrument position solve option
    */
   BundleObservationSolveSettings::InstrumentPositionSolveOption
@@ -741,7 +736,7 @@ namespace Isis {
   /**
    * Accesses the a priori position sigmas.
    *
-   * @return @b QList Returns a QList of the a priori position sigmas 
+   * @return @b QList Returns a QList of the a priori position sigmas
    */
   QList BundleObservationSolveSettings::aprioriPositionSigmas() const {
     return m_positionAprioriSigma;
@@ -763,97 +758,6 @@ namespace Isis {
   // =============================================================================================//
 
 
-  /**
-   * Serializes this BundleObservationSolveSettings into a PvlObject.
-   *
-   * @param name Name of the pvl to create
-   *
-   * @return @b PvlObject Returns the serialized settings as a PvlObject
-   */
-  PvlObject BundleObservationSolveSettings::pvlObject(QString name) const {
-
-    QString pvlName = "";;
-    if (name == "") {
-      pvlName = instrumentId();
-    }
-    else {
-      pvlName = name;
-    }
-    PvlObject pvl(pvlName);
-
-    pvl += PvlKeyword("InstrumentPointingSolveOption", 
-                      instrumentPointingSolveOptionToString(instrumentPointingSolveOption()));
-    if (instrumentPointingSolveOption() > NoPointingFactors) {
-      pvl += PvlKeyword("NumberAngleCoefficientsSolved", 
-                        toString(numberCameraAngleCoefficientsSolved()));
-      pvl += PvlKeyword("CKDegree", toString(ckDegree()));
-      pvl += PvlKeyword("CKSolveDegree", toString(ckSolveDegree()));
-      pvl += PvlKeyword("SolveTwist", toString(solveTwist()));
-      pvl += PvlKeyword("SolvePointingPolynomialOverExisting", 
-                        toString(solvePolyOverPointing())); 
-      PvlKeyword angleSigmas("AngleAprioriSigmas");
-      for (int i = 0; i < aprioriPointingSigmas().size(); i++) {
-        if (IsSpecial(m_anglesAprioriSigma[i])) {
-          angleSigmas.addValue("N/A");
-        }
-        else {
-          angleSigmas.addValue(toString(m_anglesAprioriSigma[i]));
-        }
-      }
-      pvl += angleSigmas;
-      
-      pvl += PvlKeyword("InstrumentPointingInterpolationType",
-                        toString((int)pointingInterpolationType()));  
-                        // TODO: omit from pvl if pointing option == None ??? 
-    }
-    else {
-      pvl += PvlKeyword("NumberAngleCoefficientsSolved", "N/A");
-      pvl += PvlKeyword("CKDegree", "N/A");
-      pvl += PvlKeyword("CKSolveDegree", "N/A");
-      pvl += PvlKeyword("SolveTwist", "N/A");
-      pvl += PvlKeyword("SolvePointingPolynomialOverExisting", "N/A");
-      pvl += PvlKeyword("AngleAprioriSigmas", "N/A");
-      pvl += PvlKeyword("InstrumentPointingInterpolationType", "N/A");
-    }
-
-
-    // position
-
-    pvl += PvlKeyword("InstrumentPositionSolveOption", 
-                      instrumentPositionSolveOptionToString(instrumentPositionSolveOption()));
-    if (instrumentPositionSolveOption() > NoPositionFactors) {
-      pvl += PvlKeyword("NumberPositionCoefficientsSolved", 
-                        toString(numberCameraPositionCoefficientsSolved()));
-      pvl += PvlKeyword("SPKDegree", toString(spkDegree()));
-      pvl += PvlKeyword("SPKSolveDegree", toString(spkSolveDegree()));
-      pvl += PvlKeyword("SolvePositionOverHermiteSpline", toString(solvePositionOverHermite()));
-    
-      PvlKeyword positionSigmas("PositionAprioriSigmas");
-      for (int i = 0; i < aprioriPositionSigmas().size(); i++) {
-        if (IsSpecial(m_positionAprioriSigma[i])) {
-          positionSigmas.addValue("N/A");
-        }
-        else {
-          positionSigmas.addValue(toString(m_positionAprioriSigma[i]));
-        }
-      }
-      pvl += positionSigmas;
-    
-      pvl += PvlKeyword("InstrumentPositionInterpolationType",
-                        toString((int)positionInterpolationType()));
-    }
-    else {
-      pvl += PvlKeyword("NumberPositionCoefficientsSolved", "N/A");
-      pvl += PvlKeyword("SPKDegree", "N/A");
-      pvl += PvlKeyword("SPKSolveDegree", "N/A");
-      pvl += PvlKeyword("SolvePositionOverHermiteSpline", "N/A");
-      pvl += PvlKeyword("PositionAprioriSigmas", "N/A");
-      pvl += PvlKeyword("InstrumentPositionInterpolationType", "N/A");
-    }
-    return pvl;
-  }
-
-
   /**
    * Saves this BundleObservationSolveSettings to an xml stream.
    *
@@ -863,7 +767,7 @@ namespace Isis {
    * @internal
    *   @todo Does xml stuff need project???
    */
-  void BundleObservationSolveSettings::save(QXmlStreamWriter &stream, 
+  void BundleObservationSolveSettings::save(QXmlStreamWriter &stream,
                                             const Project *project) const {
 
     stream.writeStartElement("bundleObservationSolveSettings");
@@ -872,7 +776,7 @@ namespace Isis {
 
     // pointing related
     stream.writeStartElement("instrumentPointingOptions");
-    stream.writeAttribute("solveOption", 
+    stream.writeAttribute("solveOption",
                            instrumentPointingSolveOptionToString(m_instrumentPointingSolveOption));
     stream.writeAttribute("numberCoefSolved", toString(m_numberCamAngleCoefSolved));
     stream.writeAttribute("degree", toString(m_ckDegree));
@@ -895,7 +799,7 @@ namespace Isis {
 
     // position related
     stream.writeStartElement("instrumentPositionOptions");
-    stream.writeAttribute("solveOption", 
+    stream.writeAttribute("solveOption",
                            instrumentPositionSolveOptionToString(m_instrumentPositionSolveOption));
     stream.writeAttribute("numberCoefSolved", toString(m_numberCamPosCoefSolved));
     stream.writeAttribute("degree", toString(m_spkDegree));
@@ -929,7 +833,7 @@ namespace Isis {
    * @internal
    *   @todo Does xml stuff need project???
    */
-  BundleObservationSolveSettings::XmlHandler::XmlHandler(BundleObservationSolveSettings *settings, 
+  BundleObservationSolveSettings::XmlHandler::XmlHandler(BundleObservationSolveSettings *settings,
                                                          Project *project) {
     m_xmlHandlerObservationSettings = settings;
     m_xmlHandlerProject = project;  // TODO: does xml stuff need project???
@@ -941,12 +845,12 @@ namespace Isis {
    * XmlHandler destructor.
    */
   BundleObservationSolveSettings::XmlHandler::~XmlHandler() {
-    // do not delete this pointer... we don't own it, do we??? 
+    // do not delete this pointer... we don't own it, do we???
     // passed into StatCumProbDistDynCalc constructor as pointer
     // delete m_xmlHandlerProject;  // TODO: does xml stuff need project???
     m_xmlHandlerProject = NULL;
   }
-  
+
 
   /**
    * @param namespaceURI
@@ -959,14 +863,14 @@ namespace Isis {
    * @internal
    *   @todo Document if we decide to use Xml handlers for serialization
    */
-  bool BundleObservationSolveSettings::XmlHandler::startElement(const QString &namespaceURI, 
+  bool BundleObservationSolveSettings::XmlHandler::startElement(const QString &namespaceURI,
                                                                 const QString &localName,
                                                                 const QString &qName,
                                                                 const QXmlAttributes &atts) {
     m_xmlHandlerCharacters = "";
     if (XmlStackedHandler::startElement(namespaceURI, localName, qName, atts)) {
       if (localName == "instrumentPointingOptions") {
-        
+
         QString pointingSolveOption = atts.value("solveOption");
         if (!pointingSolveOption.isEmpty()) {
           m_xmlHandlerObservationSettings->m_instrumentPointingSolveOption
@@ -995,13 +899,13 @@ namespace Isis {
 
         QString solveOverExisting = atts.value("solveOverExisting");
         if (!solveOverExisting.isEmpty()) {
-          m_xmlHandlerObservationSettings->m_solvePointingPolynomialOverExisting = 
+          m_xmlHandlerObservationSettings->m_solvePointingPolynomialOverExisting =
               toBool(solveOverExisting);
         }
 
         QString interpolationType = atts.value("interpolationType");
         if (!interpolationType.isEmpty()) {
-          m_xmlHandlerObservationSettings->m_pointingInterpolationType = 
+          m_xmlHandlerObservationSettings->m_pointingInterpolationType =
               SpiceRotation::Source(toInt(interpolationType));
         }
 
@@ -1010,7 +914,7 @@ namespace Isis {
         m_xmlHandlerAprioriSigmas.clear();
       }
       else if (localName == "instrumentPositionOptions") {
-        
+
         QString positionSolveOption = atts.value("solveOption");
         if (!positionSolveOption.isEmpty()) {
           m_xmlHandlerObservationSettings->m_instrumentPositionSolveOption
@@ -1034,13 +938,13 @@ namespace Isis {
 
         QString solveOverHermiteSpline = atts.value("solveOverHermiteSpline");
         if (!solveOverHermiteSpline.isEmpty()) {
-          m_xmlHandlerObservationSettings->m_solvePositionOverHermiteSpline = 
+          m_xmlHandlerObservationSettings->m_solvePositionOverHermiteSpline =
               toBool(solveOverHermiteSpline);
         }
 
         QString interpolationType = atts.value("interpolationType");
         if (!interpolationType.isEmpty()) {
-          m_xmlHandlerObservationSettings->m_positionInterpolationType = 
+          m_xmlHandlerObservationSettings->m_positionInterpolationType =
               SpicePosition::Source(toInt(interpolationType));
         }
       }
@@ -1076,7 +980,7 @@ namespace Isis {
    * @internal
    *   @todo Document if we use Xml handlers for serialization.
    */
-  bool BundleObservationSolveSettings::XmlHandler::endElement(const QString &namespaceURI, 
+  bool BundleObservationSolveSettings::XmlHandler::endElement(const QString &namespaceURI,
                                                               const QString &localName,
                                                               const QString &qName) {
     if (!m_xmlHandlerCharacters.isEmpty()) {
@@ -1122,177 +1026,4 @@ namespace Isis {
     }
     return XmlStackedHandler::endElement(namespaceURI, localName, qName);
   }
-
-
-  /**
-   * Writes this BundleObservationSolveSettings to a stream.
-   *
-   * @param stream QDataStream to write state to
-   */
-  QDataStream &BundleObservationSolveSettings::write(QDataStream &stream) const {
-
-    stream << m_id->toString()
-           << m_instrumentId
-           << (qint32)m_instrumentPointingSolveOption
-           << (qint32)m_numberCamAngleCoefSolved
-           << (qint32)m_ckDegree
-           << (qint32)m_ckSolveDegree
-           << m_solveTwist
-           << m_solvePointingPolynomialOverExisting
-           << m_anglesAprioriSigma
-           << (qint32)m_pointingInterpolationType
-           << (qint32)m_instrumentPositionSolveOption
-           << (qint32)m_numberCamPosCoefSolved 
-           << (qint32)m_spkDegree
-           << (qint32)m_spkSolveDegree
-           << m_solvePositionOverHermiteSpline
-           << m_positionAprioriSigma
-           << (qint32)m_positionInterpolationType;
-
-    return stream;
-
-  }
-
-
-  /**
-   * Reads in the state of a BundleObservationSolveSettings from a stream.
-   *
-   * @param stream QDataStream to read state from
-   */
-  QDataStream &BundleObservationSolveSettings::read(QDataStream &stream) {
-
-    QString id;
-    qint32 anglesSolveOption, ckDegree, ckSolveDegree, numCamAngleCoefSolved, anglesInterpType,
-           positionSolveOption, spkDegree, spkSolveDegree, numCamPosCoefSolved, positionInterpType;
-
-    stream >> id 
-           >> m_instrumentId
-           >> anglesSolveOption
-           >> numCamAngleCoefSolved
-           >> ckDegree
-           >> ckSolveDegree
-           >> m_solveTwist
-           >> m_solvePointingPolynomialOverExisting
-           >> m_anglesAprioriSigma
-           >> anglesInterpType
-           >> positionSolveOption
-           >> numCamPosCoefSolved
-           >> spkDegree
-           >> spkSolveDegree
-           >> m_solvePositionOverHermiteSpline
-           >> m_positionAprioriSigma
-           >> positionInterpType;
-
-    delete m_id;
-    m_id = NULL;
-    m_id = new QUuid(id);
-
-    m_instrumentPointingSolveOption = (InstrumentPointingSolveOption)anglesSolveOption;
-    m_ckDegree = (int)ckDegree;
-    m_ckSolveDegree = (int)ckSolveDegree;
-    m_numberCamAngleCoefSolved = (int)numCamAngleCoefSolved;
-    m_pointingInterpolationType = (SpiceRotation::Source)anglesInterpType;
-    m_instrumentPositionSolveOption = (InstrumentPositionSolveOption)positionSolveOption;
-    m_spkDegree = (int)spkDegree;
-    m_spkSolveDegree = (int)spkSolveDegree;
-    m_numberCamPosCoefSolved = (int)numCamPosCoefSolved;
-    m_positionInterpolationType = (SpicePosition::Source)positionInterpType;
-
-    return stream;
-
-  }
-
-
-  /**
-   * Insertion operator.
-   *
-   * Overloads the insertion operator to write the state of a BundleObservationSolveSettings
-   * to a stream.
-   *
-   * @param stream QDataStream to write state to
-   * @param settings Reference to the BundleObservationSolveSettings to write
-   *
-   * @see BundleObservationSolveSettings::write(QDataStream &stream)
-   */
-  QDataStream &operator<<(QDataStream &stream, const BundleObservationSolveSettings &settings) {
-    return settings.write(stream);
-  }
-
-
-  /**
-   * Extraction operator.
-   *
-   * Overloads the extraction operator to read the state of a BundleObservationSolveSettings
-   * into this BundleObservationSolveSettings.
-   *
-   * @param stream QDataStream to read from
-   * @param settings Reference to the BundleObservationSolveSettings to read
-   */
-  QDataStream &operator>>(QDataStream &stream, BundleObservationSolveSettings &settings) {
-    return settings.read(stream);
-  }
-
-
-#if 0
-  /** 
-   *  H5 compound data type uses the offesets from the QDataStream returned by
-   *  the write(QDataStream &stream) method.
-   */
-  H5::CompType BundleObservationSolveSettings::compoundH5DataType() {
-
-    H5::CompType compoundDataType((size_t)   );
-
-    size_t offset = 0;
-
-    compoundDataType.insertMember("InstrumentId", offset, H5::PredType::C_S1);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("InstrumentPointingSolveOption", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("NumCamAngleCoefSolved", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("CkDegree", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("CkSolveDegree", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("SolveTwist", offset, H5::PredType::NATIVE_HBOOL);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("SolvePointingPolynomialOverExisting", offset, H5::PredType::NATIVE_HBOOL);
-
-    offset += sizeof(m_instrumentId);
-???    compoundDataType.insertMember("AnglesAprioriSigma", offset, H5::PredType::NATIVE_DOUBLE);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("PointingInterpolationType", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("InstrumentPositionSolveOption", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_instrumentId);
-    compoundDataType.insertMember("NumCamPosCoefSolved", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_numberCamPosCoefSolved);
-    compoundDataType.insertMember("SpkDegree", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_spkDegree);
-    compoundDataType.insertMember("SpkSolveDegree", offset, H5::PredType::NATIVE_INT);
-
-    offset += sizeof(m_spkSolveDegree);
-    compoundDataType.insertMember("SolvePositionOverHermiteSpline", offset, H5::PredType::NATIVE_HBOOL);
-
-    offset += sizeof(m_solvePositionOverHermiteSpline);
-???    compoundDataType.insertMember("PositionAprioriSigma", offset, H5::PredType::NATIVE_DOUBLE);
-
-    offset += sizeof(m_positionAprioriSigma);
-    compoundDataType.insertMember("PositionInterpolationType", offset, H5::PredType::NATIVE_INT);
-
-    return compoundDataType;
-
-  }
-#endif
 }
diff --git a/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.h b/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.h
index 91890de7108ea45f68090c2a37f7f7d07994e393..fd570fee7c28eea9e0724afe066b11fb7575e26c 100644
--- a/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.h
+++ b/isis/src/control/objs/BundleUtilities/BundleObservationSolveSettings.h
@@ -74,8 +74,9 @@ namespace Isis {
    *                           observationNumbers() members to associate multiple observation types
    *                           with these settings. Removed the setFromPvl() method. When re-
    *                           implemented, it should be put in jigsaw. References #4293.
-   *  
-   *  
+   *   @history 2017-04-24 Ian Humphrey - Removed pvlObject(). Fixes #4797.
+   *
+   *
    *   @todo Figure out why solve degree and num coefficients does not match solve option.
    *   @todo Determine whether xml stuff needs a Project pointer.
    *   @todo Determine which XmlStackedHandlerReader constructor is preferred.
@@ -85,18 +86,16 @@ class BundleObservationSolveSettings {
 
     public:
       BundleObservationSolveSettings();
-      BundleObservationSolveSettings(Project *project, 
+      BundleObservationSolveSettings(Project *project,
                                      XmlStackedHandlerReader *xmlReader);  // TODO: does xml stuff need project???
-      BundleObservationSolveSettings(FileName xmlFile, 
-                                     Project *project, 
+      BundleObservationSolveSettings(FileName xmlFile,
+                                     Project *project,
                                      XmlStackedHandlerReader *xmlReader);  // TODO: does xml stuff need project???
       BundleObservationSolveSettings(const BundleObservationSolveSettings &src);
       ~BundleObservationSolveSettings();
       BundleObservationSolveSettings &operator=(const BundleObservationSolveSettings &src);
       void initialize();
 
-      PvlObject pvlObject(QString name = "") const; // Default name is instrument ID.
-
       void setInstrumentId(QString instrumentId);
       QString instrumentId() const;
       void addObservationNumber(QString observationNumber);
@@ -118,13 +117,13 @@ class BundleObservationSolveSettings {
 
       static InstrumentPointingSolveOption stringToInstrumentPointingSolveOption(QString option);
       static QString instrumentPointingSolveOptionToString(InstrumentPointingSolveOption option);
-      void setInstrumentPointingSettings(InstrumentPointingSolveOption option, 
-                                         bool solveTwist, 
-                                         int ckDegree = 2, 
+      void setInstrumentPointingSettings(InstrumentPointingSolveOption option,
+                                         bool solveTwist,
+                                         int ckDegree = 2,
                                          int ckSolveDegree = 2,
-                                         bool solvePolynomialOverExisting = false, 
+                                         bool solvePolynomialOverExisting = false,
                                          double anglesAprioriSigma = -1.0,
-                                         double angularVelocityAprioriSigma = -1.0, 
+                                         double angularVelocityAprioriSigma = -1.0,
                                          double angularAccelerationAprioriSigma = -1.0);
       InstrumentPointingSolveOption instrumentPointingSolveOption() const;
       bool solveTwist() const;
@@ -166,9 +165,8 @@ class BundleObservationSolveSettings {
       SpicePosition::Source positionInterpolationType() const;
 
       // TODO: does xml stuff need project???
-      void save(QXmlStreamWriter &stream, const Project *project) const;  
-      QDataStream &write(QDataStream &stream) const;
-      QDataStream &read(QDataStream &stream);
+      void save(QXmlStreamWriter &stream, const Project *project) const;
+
 
     private:
       /**
@@ -183,16 +181,16 @@ class BundleObservationSolveSettings {
           // TODO: does xml stuff need project???
           XmlHandler(BundleObservationSolveSettings *settings, Project *project);
           ~XmlHandler();
-   
+
           virtual bool startElement(const QString &namespaceURI, const QString &localName,
                                     const QString &qName, const QXmlAttributes &atts);
           virtual bool characters(const QString &ch);
           virtual bool endElement(const QString &namespaceURI, const QString &localName,
                                   const QString &qName);
-   
+
         private:
           Q_DISABLE_COPY(XmlHandler);
-   
+
           BundleObservationSolveSettings *m_xmlHandlerObservationSettings;
           Project *m_xmlHandlerProject;  // TODO: does xml stuff need project???
           QString m_xmlHandlerCharacters;
@@ -217,12 +215,12 @@ class BundleObservationSolveSettings {
       int m_ckSolveDegree;                        /**< Degree of the camera angles polynomial being
                                                        fit to in the bundle adjustment. **/
       bool m_solveTwist;                          //!< Solve for "twist" angle.
-      bool m_solvePointingPolynomialOverExisting; /**< The polynomial will be fit over the existing 
+      bool m_solvePointingPolynomialOverExisting; /**< The polynomial will be fit over the existing
                                                        pointing polynomial.*/
       QList m_anglesAprioriSigma; /**< The image position a priori sigmas.The size of the
                                                list is equal to the number of coefficients in the
-                                               solution. An Isis::Null value implies no weighting 
-                                               will be applied.*/ 
+                                               solution. An Isis::Null value implies no weighting
+                                               will be applied.*/
       SpiceRotation::Source
           m_pointingInterpolationType;    /**< SpiceRotation interpolation type.
                                                Defined in SpiceRotation.cpp, these types are:
@@ -247,7 +245,7 @@ class BundleObservationSolveSettings {
       QList m_positionAprioriSigma; /**< The instrument pointing a priori sigmas. The
                                                   size of the list is equal to the number of
                                                   coefficients in the solution. An Isis:Null value
-                                                  implies no weighting will be applied.*/ 
+                                                  implies no weighting will be applied.*/
       SpicePosition::Source
           m_positionInterpolationType;      /**< SpicePosition interpolation types.
                                                  Defined in SpicePosition.cpp, these types are:
@@ -256,17 +254,13 @@ class BundleObservationSolveSettings {
                                                  3) HermiteCache: read from splined table,
                                                  4) PolyFunction: calced from nth degree polynomial,
                                                  5) PolyFunctionOverHermiteConstant: read from
-                                                    splined table and adding nth degree 
-                                                    polynomial.*/ 
+                                                    splined table and adding nth degree
+                                                    polynomial.*/
 
   };
   //!  Definition for BundleObservationSolveSettingsQsp, a QSharedPointer to a
   //!< BundleObservationSolveSettings object.
   typedef QSharedPointer BundleObservationSolveSettingsQsp;
-  
-  // Operators to read/write BundleResults to/from binary data.
-  QDataStream &operator<<(QDataStream &stream, const BundleObservationSolveSettings &settings);
-  QDataStream &operator>>(QDataStream &stream, BundleObservationSolveSettings &settings);
 };
 
 #endif // BundleObservationSolveSettings_h
diff --git a/isis/src/control/objs/BundleUtilities/BundleTargetBody.cpp b/isis/src/control/objs/BundleUtilities/BundleTargetBody.cpp
index 93df5f86987e3fe1caea9c88c942b78972f92896..e0affaff46ee0dfd279cbc878768d236ad6d38d9 100644
--- a/isis/src/control/objs/BundleUtilities/BundleTargetBody.cpp
+++ b/isis/src/control/objs/BundleUtilities/BundleTargetBody.cpp
@@ -152,7 +152,7 @@ namespace Isis {
   /**
    * @brief Sets the solve settings for the target body.
    * 
-   * @description Sets the solve settings for the target body's right ascension, declination,
+   * Sets the solve settings for the target body's right ascension, declination,
    * prime meridian, and radius based on the input values.
    * Parameter vectors, sigma vectors and the weight vector will be filled in the following order:
    * 
@@ -556,7 +556,7 @@ namespace Isis {
   /**
    * @brief Applies a vector of corrections to the parameters for the target body.
    * 
-   * @description Applies a vector of corrections to the internal parameters for the
+   * Applies a vector of corrections to the internal parameters for the
    * target body and records the corrections in the internal corrections vector.
    * The corrections vector should be ordered the same as the parameter vector descriped
    * in setSolveSettings.
@@ -802,7 +802,7 @@ namespace Isis {
   /**
    * @brief Returns the number of radius parameters being solved for.
    * 
-   * @description Returns the number of radius parameters being solved for
+   * Returns the number of radius parameters being solved for
    * which is based on the target radius solve method:
    * None -> 0
    * Mean -> 1
@@ -834,7 +834,7 @@ namespace Isis {
   /**
    * @brief Returns the coefficients of the right ascension polynomial.
    * 
-   * @description Returns The vector of right ascension polynomial coefficients ordered as:
+   * Returns The vector of right ascension polynomial coefficients ordered as:
    * 
    * angle,
    * velocity,
@@ -852,7 +852,7 @@ namespace Isis {
   /**
    * @brief Returns the coefficients of the declination polynomial.
    * 
-   * @description Returns The vector of declination polynomial coefficients ordered as:
+   * Returns The vector of declination polynomial coefficients ordered as:
    * 
    * angle,
    * velocity,
@@ -870,7 +870,7 @@ namespace Isis {
   /**
    * @brief Returns the coefficients of the prime meridian polynomial.
    * 
-   * @description Returns The vector of prime meridian polynomial coefficients ordered as:
+   * Returns The vector of prime meridian polynomial coefficients ordered as:
    * 
    * angle,
    * velocity,
@@ -888,7 +888,7 @@ namespace Isis {
   /**
    * @brief Returns the radius values.
    * 
-   * @description Returns the vector of radius values formatted as RadiusA, RadiusB, RadiusC.
+   * Returns the vector of radius values formatted as RadiusA, RadiusB, RadiusC.
    * 
    * @return @b vector The vector of radius values.
    * 
@@ -924,7 +924,7 @@ namespace Isis {
   /**
    * @brief Calculates and returns the weighted sum of the squares of the corrections.
    * 
-   * @description Calculates and returns the weighted sum of the squares of the corrections
+   * Calculates and returns the weighted sum of the squares of the corrections
    * computed by V(T)*P*V where:
    * V is the vector of corrections,
    * P is the weight matrix,
diff --git a/isis/src/control/objs/BundleUtilities/BundleUtilities.truth b/isis/src/control/objs/BundleUtilities/BundleUtilities.truth
index adf913fe0d5bab4de998a79e683a3d0dafb20702..d5a62b3853461203a91e148399e118ff5437dc9e 100644
--- a/isis/src/control/objs/BundleUtilities/BundleUtilities.truth
+++ b/isis/src/control/objs/BundleUtilities/BundleUtilities.truth
@@ -4,191 +4,179 @@ XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
 Testing BundleObservationSolveSettings...
 
 Printing PVL group with settings from the default constructor...
-Object = DefaultBundleObservationSolveSettings
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+    
+ 
+
 
 Testing copy constructor...
-Object = CopySettingsObject
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+    
+ 
+
 
 Testing assignment operator to set this equal to itself...
-Object = SelfAssignedSettingsObject
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+    
+ 
+
 
 Testing assignment operator to create a new settings object...
-Object = AssignedSettingsObject
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+    
+ 
+
 
 Testing mutator methods...
 setInstrument(), setInstrumentPointingSettings(), setInstrumentPositionSettings()
-Object = MyInstrumentId
-  InstrumentPointingSolveOption       = AnglesAndVelocity
-  NumberAngleCoefficientsSolved       = 2
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = (3.0, 4.0)
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = PositionOnly
-  NumberPositionCoefficientsSolved    = 1
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = Yes
-  PositionAprioriSigmas               = 800.0
-  InstrumentPositionInterpolationType = 4
-End_Object
-
-Testing pvlObject()...
-Object = SettingsFromPvlGroup-SolveForNone
-  InstrumentPointingSolveOption       = None
-  NumberAngleCoefficientsSolved       = N/A
-  CKDegree                            = N/A
-  CKSolveDegree                       = N/A
-  SolveTwist                          = N/A
-  SolvePointingPolynomialOverExisting = N/A
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = N/A
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
-
-Object = SettingsFromPvlGroup-SolveForAnglesPositions
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = PositionOnly
-  NumberPositionCoefficientsSolved    = 1
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = No
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = 3
-End_Object
-
-Object = SettingsFromPvlGroup-SolveForVelocities
-  InstrumentPointingSolveOption       = AnglesAndVelocity
-  NumberAngleCoefficientsSolved       = 2
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = (N/A, N/A)
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = PositionAndVelocity
-  NumberPositionCoefficientsSolved    = 2
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = No
-  PositionAprioriSigmas               = (N/A, N/A)
-  InstrumentPositionInterpolationType = 3
-End_Object
-
-Object = SettingsFromPvlGroup-SolveForAccelerations
-  InstrumentPointingSolveOption       = AnglesVelocityAndAcceleration
-  NumberAngleCoefficientsSolved       = 3
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = (N/A, N/A, N/A)
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = PositionVelocityAndAcceleration
-  NumberPositionCoefficientsSolved    = 3
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = No
-  PositionAprioriSigmas               = (N/A, N/A, N/A)
-  InstrumentPositionInterpolationType = 3
-End_Object
-
-Object = SettingsFromPvlGroup-SolveForAllCoefficients
-  InstrumentPointingSolveOption       = AllPolynomialCoefficients
-  NumberAngleCoefficientsSolved       = 6
-  CKDegree                            = 4
-  CKSolveDegree                       = 5
-  SolveTwist                          = No
-  SolvePointingPolynomialOverExisting = Yes
-  AngleAprioriSigmas                  = (1.0, N/A, 3.0)
-  InstrumentPointingInterpolationType = 4
-  InstrumentPositionSolveOption       = AllPolynomialCoefficients
-  NumberPositionCoefficientsSolved    = 8
-  SPKDegree                           = 6
-  SPKSolveDegree                      = 7
-  SolvePositionOverHermiteSpline      = Yes
-  PositionAprioriSigmas               = (8.0, 9.0, N/A)
-  InstrumentPositionInterpolationType = 4
-End_Object
+
+
+    
+    MyInstrumentId
+    
+        
+            3.0
+            4.0
+        
+    
+    
+        
+            800.0
+        
+    
+ 
+
+
+
+
+    
+    
+    
+        
+    
+    
+        
+    
+ 
+
+
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+            N/A
+        
+    
+ 
+
+
+
+
+    
+    
+    
+        
+            N/A
+            N/A
+        
+    
+    
+        
+            N/A
+            N/A
+        
+    
+ 
+
+
+
+
+    
+    
+    
+        
+            N/A
+            N/A
+            N/A
+        
+    
+    
+        
+            N/A
+            N/A
+            N/A
+        
+    
+ 
+
+
+
+
+    
+    MyInstrumentId
+    
+        
+            1.0
+            N/A
+            3.0
+        
+    
+    
+        
+            8.0
+            9.0
+            N/A
+        
+    
+ 
+
 
 Testing static unused enum-to-string and string-to-enum methods...
 "None"
@@ -202,139 +190,120 @@ Testing static unused enum-to-string and string-to-enum methods...
 "PositionVelocityAndAcceleration"
 "AllPolynomialCoefficients"
 
-Testing serialization...
-Object = SerializedSettings
-  InstrumentPointingSolveOption       = AllPolynomialCoefficients
-  NumberAngleCoefficientsSolved       = 6
-  CKDegree                            = 4
-  CKSolveDegree                       = 5
-  SolveTwist                          = No
-  SolvePointingPolynomialOverExisting = Yes
-  AngleAprioriSigmas                  = (1.0, N/A, 3.0)
-  InstrumentPointingInterpolationType = 4
-  InstrumentPositionSolveOption       = AllPolynomialCoefficients
-  NumberPositionCoefficientsSolved    = 8
-  SPKDegree                           = 6
-  SPKSolveDegree                      = 7
-  SolvePositionOverHermiteSpline      = Yes
-  PositionAprioriSigmas               = (8.0, 9.0, N/A)
-  InstrumentPositionInterpolationType = 4
-End_Object
-
 Testing XML: write XML from BundleObservationSolveSettings object...
 Testing XML: read XML to BundleObservationSolveSettings object...
-Object = FromXml-1
-  InstrumentPointingSolveOption       = None
-  NumberAngleCoefficientsSolved       = N/A
-  CKDegree                            = N/A
-  CKSolveDegree                       = N/A
-  SolveTwist                          = N/A
-  SolvePointingPolynomialOverExisting = N/A
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = N/A
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+    
+ 
+
 
 Testing XML: read XML to BundleObservationSolveSettings object...
-Object = FromXml-2
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = PositionOnly
-  NumberPositionCoefficientsSolved    = 1
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = No
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = 3
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+            N/A
+        
+    
+ 
+
 
 Testing XML: read XML to BundleObservationSolveSettings object...
-Object = FromXml-3
-  InstrumentPointingSolveOption       = AnglesAndVelocity
-  NumberAngleCoefficientsSolved       = 2
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = (N/A, N/A)
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = PositionAndVelocity
-  NumberPositionCoefficientsSolved    = 2
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = No
-  PositionAprioriSigmas               = (N/A, N/A)
-  InstrumentPositionInterpolationType = 3
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+            N/A
+        
+    
+    
+        
+            N/A
+            N/A
+        
+    
+ 
+
 
 Testing XML: read XML to BundleObservationSolveSettings object...
-Object = FromXml-4
-  InstrumentPointingSolveOption       = AnglesVelocityAndAcceleration
-  NumberAngleCoefficientsSolved       = 3
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = (N/A, N/A, N/A)
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = PositionVelocityAndAcceleration
-  NumberPositionCoefficientsSolved    = 3
-  SPKDegree                           = 2
-  SPKSolveDegree                      = 2
-  SolvePositionOverHermiteSpline      = No
-  PositionAprioriSigmas               = (N/A, N/A, N/A)
-  InstrumentPositionInterpolationType = 3
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+            N/A
+            N/A
+        
+    
+    
+        
+            N/A
+            N/A
+            N/A
+        
+    
+ 
+
 
 Testing XML: read XML to BundleObservationSolveSettings object...
-Object = FromXml
-  InstrumentPointingSolveOption       = AllPolynomialCoefficients
-  NumberAngleCoefficientsSolved       = 6
-  CKDegree                            = 4
-  CKSolveDegree                       = 5
-  SolveTwist                          = No
-  SolvePointingPolynomialOverExisting = Yes
-  AngleAprioriSigmas                  = (1.0, N/A, 3.0)
-  InstrumentPointingInterpolationType = 4
-  InstrumentPositionSolveOption       = AllPolynomialCoefficients
-  NumberPositionCoefficientsSolved    = 8
-  SPKDegree                           = 6
-  SPKSolveDegree                      = 7
-  SolvePositionOverHermiteSpline      = Yes
-  PositionAprioriSigmas               = (8.0, 9.0, N/A)
-  InstrumentPositionInterpolationType = 4
-End_Object
+
+
+    
+    MyInstrumentId
+    
+        
+            1.0
+            N/A
+            3.0
+        
+    
+    
+        
+            8.0
+            9.0
+            N/A
+        
+    
+ 
+
 
 Testing XML: read XML with no attributes or values to object...
-Object = DefaultSettingsFromEmptyXml
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+    
+ 
+
 
 Testing error throws...
 **ERROR** Unknown bundle instrument pointing solve option Nonsense.
@@ -372,23 +341,18 @@ Testing assignment operator to create a new object...
 Testing copy constructor...
 Testing mutators and accessors...
     Set/get solve settings using with CAMESOLVE=NONE...
-Object = NoCamAngles
-  InstrumentPointingSolveOption       = None
-  NumberAngleCoefficientsSolved       = N/A
-  CKDegree                            = N/A
-  CKSolveDegree                       = N/A
-  SolveTwist                          = N/A
-  SolvePointingPolynomialOverExisting = N/A
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = N/A
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+    
+    
+        
+    
+ 
+
 
     output bundle observation...
 0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,
@@ -408,23 +372,26 @@ DEC  (t0)       0.00000000           0.00000000          0.00000000
 TWI  (t0)       0.00000000           0.00000000          0.00000000               N/A               N/A
 
     Set solve settings using with TWIST=FALSE...
-Object = NoTwist
-  InstrumentPointingSolveOption       = AllPolynomialCoefficients
-  NumberAngleCoefficientsSolved       = 6
-  CKDegree                            = 4
-  CKSolveDegree                       = 5
-  SolveTwist                          = No
-  SolvePointingPolynomialOverExisting = Yes
-  AngleAprioriSigmas                  = (1.0, N/A, 3.0)
-  InstrumentPointingInterpolationType = 4
-  InstrumentPositionSolveOption       = AllPolynomialCoefficients
-  NumberPositionCoefficientsSolved    = 8
-  SPKDegree                           = 6
-  SPKSolveDegree                      = 7
-  SolvePositionOverHermiteSpline      = Yes
-  PositionAprioriSigmas               = (8.0, 9.0, N/A)
-  InstrumentPositionInterpolationType = 4
-End_Object
+
+
+    
+    MyInstrumentId
+    
+        
+            1.0
+            N/A
+            3.0
+        
+    
+    
+        
+            8.0
+            9.0
+            N/A
+        
+    
+ 
+
 
     output bundle observation...
 0.0,0.0,0.0,8.0,0.00000000,0.0,0.0,0.0,9.0,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,8.0,0.00000000,0.0,0.0,0.0,9.0,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,8.0,0.00000000,0.0,0.0,0.0,9.0,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,1.0,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,3.0,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,1.0,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,3.0,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,
@@ -516,23 +483,20 @@ TWI  (t0)       0.00000000           0.00000000          0.00000000
      (t5)       0.00000000           0.00000000          0.00000000               N/A               N/A
 
     Set solve settings using with CAMSOLVE=ALL and TWIST=TRUE...
-Object = SettingsFromBundleObservation
-  InstrumentPointingSolveOption       = AnglesOnly
-  NumberAngleCoefficientsSolved       = 1
-  CKDegree                            = 2
-  CKSolveDegree                       = 2
-  SolveTwist                          = Yes
-  SolvePointingPolynomialOverExisting = No
-  AngleAprioriSigmas                  = N/A
-  InstrumentPointingInterpolationType = 3
-  InstrumentPositionSolveOption       = None
-  NumberPositionCoefficientsSolved    = N/A
-  SPKDegree                           = N/A
-  SPKSolveDegree                      = N/A
-  SolvePositionOverHermiteSpline      = N/A
-  PositionAprioriSigmas               = N/A
-  InstrumentPositionInterpolationType = N/A
-End_Object
+
+
+    
+    
+    
+        
+            N/A
+        
+    
+    
+        
+    
+ 
+
 
 index =  "1"
 instrument id =  "InstrumentId2"
@@ -556,6 +520,7 @@ TWI  (t0)       0.00000000           0.00000000          0.00000000
 
 0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,N/A,N/A,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,0.0,0.0,0.0,FREE,0.00000000,
 init exterior orientiation successful?   "Yes"
+apply param corrections successful?
 **ERROR** Unable to apply parameter corrections to BundleObservation.
 **ERROR** Instrument rotation is NULL, but pointing solve option is AnglesOnly.
 
diff --git a/isis/src/control/objs/BundleUtilities/unitTest.cpp b/isis/src/control/objs/BundleUtilities/unitTest.cpp
index ec2a0f3d5d4e3c91dffc303e01fb22b9907e2a18..260cc5d848fc5b5ceab9689080b97f90297cb827 100755
--- a/isis/src/control/objs/BundleUtilities/unitTest.cpp
+++ b/isis/src/control/objs/BundleUtilities/unitTest.cpp
@@ -40,10 +40,11 @@ using namespace std;
 using namespace Isis;
 
 void printBundleMeasure(BundleMeasure &);
+void printXml(const BundleObservationSolveSettings &);
 
 /**
  * This class is used to test loading objects from xml files.
- * 
+ *
  * @author 2014 Jeannie Backer
  *
  * @internal
@@ -67,7 +68,7 @@ namespace Isis {
         QXmlInputSource xmlInputSource(&file);
         bool success = reader->parse(xmlInputSource);
         if (!success) {
-          throw IException(IException::Unknown, 
+          throw IException(IException::Unknown,
                            QString("Failed to parse xml file, [%1]").arg(xmlPath),
                             _FILEINFO_);
         }
@@ -94,6 +95,9 @@ namespace Isis {
  *   @history 2016-10-13 Ian Humphrey - Removed references to setFromPvl(), as
  *                           BundleObservationSolveSettings::setFromPvl() was moved to jigsaw as
  *                           setSettingsFromPvl(). References #4293.
+ *   @history 2016-12-01 Ian Humphrey - Added extra qDebug() stream so the "apply param
+ *                           corrections successful?" string will be in the unitTest output.
+ *   @history 2017-04-24 Ian Humphrey - Replaced pvlObject() with XML save(). Fixes #4797.
  */
 int main(int argc, char *argv[]) {
   Preference::Preferences(true);
@@ -109,25 +113,21 @@ int main(int argc, char *argv[]) {
     // default constructor
     qDebug() << "Printing PVL group with settings from the default constructor...";
     BundleObservationSolveSettings boss;
-    PvlObject pvl = boss.pvlObject("DefaultBundleObservationSolveSettings");
-    cout << pvl << endl << endl;
-    
+    printXml(boss);
+
     qDebug() << "Testing copy constructor...";
     BundleObservationSolveSettings copySettings(boss);
-    pvl = copySettings.pvlObject("CopySettingsObject");
-    cout << pvl << endl << endl;
-    
+    printXml(copySettings);
+
     qDebug() << "Testing assignment operator to set this equal to itself...";
     boss = boss;
-    pvl = boss.pvlObject("SelfAssignedSettingsObject");
-    cout << pvl << endl << endl;
-    
+    printXml(boss);
+
     qDebug() << "Testing assignment operator to create a new settings object...";
     BundleObservationSolveSettings assignmentOpSettings;
     assignmentOpSettings = boss;
-    pvl = assignmentOpSettings.pvlObject("AssignedSettingsObject");
-    cout << pvl << endl << endl;
-    
+    printXml(assignmentOpSettings);
+
     qDebug() << "Testing mutator methods...";
     qDebug() << "setInstrument(), setInstrumentPointingSettings(), setInstrumentPositionSettings()";
     boss.setInstrumentId("MyInstrumentId");
@@ -135,46 +135,39 @@ int main(int argc, char *argv[]) {
                                        false, 3.0, 4.0, 5.0);
     boss.setInstrumentPositionSettings(BundleObservationSolveSettings::PositionOnly, 6, 7,
                                        true, 800.0, 900.0, 1000.0);
-    pvl = boss.pvlObject();// using MyInstrumentId as PvlObject name
-    cout << pvl << endl << endl;
-    
-    qDebug() << "Testing pvlObject()...";
+    printXml(boss);
+
     BundleObservationSolveSettings solveNone;
     solveNone.setInstrumentPointingSettings(BundleObservationSolveSettings::NoPointingFactors,
                                                true);
     solveNone.setInstrumentPositionSettings(BundleObservationSolveSettings::NoPositionFactors);
-    pvl = solveNone.pvlObject("SettingsFromPvlGroup-SolveForNone");
-    cout << pvl << endl << endl;
+    printXml(solveNone);
 
     BundleObservationSolveSettings solveAnglesPositions;
     solveAnglesPositions.setInstrumentPointingSettings(BundleObservationSolveSettings::AnglesOnly,
                                                        true);
     solveAnglesPositions.setInstrumentPositionSettings(
         BundleObservationSolveSettings::PositionOnly);
-    pvl = solveAnglesPositions.pvlObject("SettingsFromPvlGroup-SolveForAnglesPositions");
-    cout << pvl << endl << endl;
+    printXml(solveAnglesPositions);
 
     BundleObservationSolveSettings solveVelocities;
     solveVelocities.setInstrumentPointingSettings(BundleObservationSolveSettings::AnglesVelocity,
                                                   true);
     solveVelocities.setInstrumentPositionSettings(BundleObservationSolveSettings::PositionVelocity);
-    pvl = solveVelocities.pvlObject("SettingsFromPvlGroup-SolveForVelocities");
-    cout << pvl << endl << endl;
+    printXml(solveVelocities);
 
     BundleObservationSolveSettings solveAccelerations;
     solveAccelerations.setInstrumentPointingSettings(
         BundleObservationSolveSettings::AnglesVelocityAcceleration, true);
     solveAccelerations.setInstrumentPositionSettings(
         BundleObservationSolveSettings::PositionVelocityAcceleration);
-    pvl = solveAccelerations.pvlObject("SettingsFromPvlGroup-SolveForAccelerations");
-    cout << pvl << endl << endl;
-    
+    printXml(solveAccelerations);
+
     boss.setInstrumentPointingSettings(BundleObservationSolveSettings::AllPointingCoefficients,
                                        false, 4, 5, true, 1.0, -1.0, 3.0);
     boss.setInstrumentPositionSettings(BundleObservationSolveSettings::AllPositionCoefficients,
                                        6, 7, true, 8.0, 9.0, -1.0);
-    pvl = boss.pvlObject("SettingsFromPvlGroup-SolveForAllCoefficients");
-    cout << pvl << endl << endl;
+    printXml(boss);
 
     qDebug() << "Testing static unused enum-to-string and string-to-enum methods...";
     qDebug() << BundleObservationSolveSettings::instrumentPointingSolveOptionToString(
@@ -209,31 +202,13 @@ int main(int argc, char *argv[]) {
                                                                       "AllPolynomialCoefficients"));
     qDebug() << "";
 
-    qDebug() << "Testing serialization...";
-    QByteArray byteArray;
-    QDataStream outputData(&byteArray, QIODevice::WriteOnly);
-    outputData << boss;
-    QDataStream inputData(byteArray);
-    BundleObservationSolveSettings newBoss;
-    inputData >> newBoss;
-    pvl = newBoss.pvlObject("SerializedSettings");
-    cout << pvl << endl;
-//    QFile file("BundleObservationSolveSettingsTest.dat");
-//    file.open(QIODevice::WriteOnly);
-//    QDataStream out(&file);
-//    out << boss;
-//    file.close();
-//    file.open(QIODevice::ReadOnly);
-//    QDataStream in(&file);
-//    in >> newBoss;
-    qDebug() << "";
 
     qDebug() << "Testing XML: write XML from BundleObservationSolveSettings object...";
-    // write xml 
+    // write xml
     FileName xmlFile("./BundleObservationSolveSettings.xml");
     QString xmlPath = xmlFile.expanded();
     QFile qXmlFile(xmlPath);
-  
+
     // For test coverage, we need to write/read BundleObservationSolveSettings objects
     // with 0,1,2,3 apriori sigmas and an empty xml
     if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
@@ -248,12 +223,11 @@ int main(int argc, char *argv[]) {
     solveNone.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
+    // read xml
     qDebug() << "Testing XML: read XML to BundleObservationSolveSettings object...";
     XmlStackedHandlerReader reader;
     XmlHandlerTester bsFromXml1(project, &reader, xmlFile);
-    pvl = bsFromXml1.pvlObject("FromXml-1");
-    cout << pvl << endl << endl;
+    printXml(bsFromXml1);
 
     if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
       throw IException(IException::Io,
@@ -265,11 +239,10 @@ int main(int argc, char *argv[]) {
     solveAnglesPositions.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
+    // read xml
     qDebug() << "Testing XML: read XML to BundleObservationSolveSettings object...";
     XmlHandlerTester bsFromXml2(project, &reader, xmlFile);
-    pvl = bsFromXml2.pvlObject("FromXml-2");
-    cout << pvl << endl << endl;
+    printXml(bsFromXml2);
 
     if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
       throw IException(IException::Io,
@@ -281,11 +254,10 @@ int main(int argc, char *argv[]) {
     solveVelocities.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
+    // read xml
     qDebug() << "Testing XML: read XML to BundleObservationSolveSettings object...";
     XmlHandlerTester bsFromXml3(project, &reader, xmlFile);
-    pvl = bsFromXml3.pvlObject("FromXml-3");
-    cout << pvl << endl << endl;
+    printXml(bsFromXml3);
 
     if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
       throw IException(IException::Io,
@@ -297,11 +269,10 @@ int main(int argc, char *argv[]) {
     solveAccelerations.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
+    // read xml
     qDebug() << "Testing XML: read XML to BundleObservationSolveSettings object...";
     XmlHandlerTester bsFromXml4(project, &reader, xmlFile);
-    pvl = bsFromXml4.pvlObject("FromXml-4");
-    cout << pvl << endl << endl;
+    printXml(bsFromXml4);
 
     if (!qXmlFile.open(QIODevice::WriteOnly|QIODevice::Text)) {
       throw IException(IException::Io,
@@ -313,19 +284,17 @@ int main(int argc, char *argv[]) {
     boss.save(writer, project);
     writer.writeEndDocument();
     qXmlFile.close();
-    // read xml    
+    // read xml
     qDebug() << "Testing XML: read XML to BundleObservationSolveSettings object...";
     XmlHandlerTester bossToFill(project, &reader, xmlFile);
 //    BundleObservationSolveSettings bossToFill(xmlFile, project, &reader);
-    pvl = bossToFill.pvlObject("FromXml");
-    cout << pvl << endl << endl;
+    printXml(bossToFill);
 
     // read xml with no attributes or values
     qDebug() << "Testing XML: read XML with no attributes or values to object...";
     FileName emptyXmlFile("./unitTest_NoElementValues.xml");
     XmlHandlerTester bsFromEmptyXml(project, &reader, emptyXmlFile);
-    pvl = bsFromEmptyXml.pvlObject("DefaultSettingsFromEmptyXml");
-    cout << pvl << endl << endl;
+    printXml(bsFromEmptyXml);
 
     //bool deleted = qXmlFile.remove();
     //if (!deleted) {
@@ -336,27 +305,27 @@ int main(int argc, char *argv[]) {
     qDebug() << "Testing error throws...";
     try {
       BundleObservationSolveSettings::stringToInstrumentPointingSolveOption("Nonsense");
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       BundleObservationSolveSettings::instrumentPointingSolveOptionToString(
           BundleObservationSolveSettings::InstrumentPointingSolveOption(-1));
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       BundleObservationSolveSettings::stringToInstrumentPositionSolveOption("Nonsense");
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
     try {
       BundleObservationSolveSettings::instrumentPositionSolveOptionToString(
           BundleObservationSolveSettings::InstrumentPositionSolveOption(-2));
-    } 
+    }
     catch (IException &e) {
       e.print();
     }
@@ -416,15 +385,15 @@ int main(int argc, char *argv[]) {
     BundleObservation bo;
     BundleTargetBodyQsp bundleTargetBody = BundleTargetBodyQsp(new BundleTargetBody);
     qDebug() << "Constructing BundleObservation object from BundleImage...";
-    BundleObservation bo2(bi2, 
-                          "ObservationNumber2", 
-                          "InstrumentId2", 
+    BundleObservation bo2(bi2,
+                          "ObservationNumber2",
+                          "InstrumentId2",
                           bundleTargetBody);
 
     BundleImageQsp nullImage;
-    BundleObservation nullBO(nullImage, 
-                             "NullObservationNumber", 
-                             "NullInstrumentId", 
+    BundleObservation nullBO(nullImage,
+                             "NullObservationNumber",
+                             "NullInstrumentId",
                              bundleTargetBody);
 
     qDebug() << "Testing assignment operator to set this equal to itself...";
@@ -438,8 +407,7 @@ int main(int argc, char *argv[]) {
     qDebug() << "    Set/get solve settings using with CAMESOLVE=NONE...";
     bo2.setSolveSettings(solveNone);
     BundleObservationSolveSettings bossFromBo = *bo2.solveSettings();
-    pvl = bossFromBo.pvlObject("NoCamAngles");
-    cout << pvl << endl << endl;
+    printXml(bossFromBo);
     qDebug() << "    output bundle observation...";
     qDebug().noquote() << bo2.formatBundleOutputString(true,true);
     qDebug().noquote() << bo2.formatBundleOutputString(false,true);
@@ -448,8 +416,7 @@ int main(int argc, char *argv[]) {
     qDebug() << "    Set solve settings using with TWIST=FALSE...";
     bo2.setSolveSettings(bossToFill);
     bossFromBo = *bo2.solveSettings();
-    pvl = bossFromBo.pvlObject("NoTwist");
-    cout << pvl << endl << endl;
+    printXml(bossFromBo);
     qDebug() << "    output bundle observation...";
     qDebug().noquote() << bo2.formatBundleOutputString(true,true);
     qDebug().noquote() << bo2.formatBundleOutputString(false,true);
@@ -458,13 +425,12 @@ int main(int argc, char *argv[]) {
 
 
 
-    
+
     qDebug() << "    Set solve settings using with CAMSOLVE=ALL and TWIST=TRUE...";
     bo3.setSolveSettings(bsFromEmptyXml);
 
     bossFromBo = *bo3.solveSettings();
-    pvl = bossFromBo.pvlObject("SettingsFromBundleObservation");
-    cout << pvl << endl << endl;
+    printXml(bossFromBo);
     bo3.setIndex(1);
     qDebug() << "index = " << toString(bo3.index());
     qDebug() << "instrument id = " << bo3.instrumentId();
@@ -499,7 +465,7 @@ int main(int argc, char *argv[]) {
       vectors.append("     ");
     }
     qDebug().noquote() << vectors;
-    
+
     // initializeBodyRotation (verify???)
     // bo3.initializeBodyRotation(); //Seg fault
 
@@ -507,13 +473,13 @@ int main(int argc, char *argv[]) {
     qDebug().noquote() << bo3.formatBundleOutputString(false,true);
     qDebug().noquote() << bo3.formatBundleOutputString(false);
     qDebug().noquote() << bo3.formatBundleOutputString(true,true);
-    qDebug() << "init exterior orientiation successful?  " 
+    qDebug() << "init exterior orientiation successful?  "
              << toString(bo3.initializeExteriorOrientation());
     //TODO: We should not have to catch an exception here, we need to use an observation
     //      with a better (i.e. non-null) Camera. See ticket #4249.
     try {
-      qDebug() << "apply param corrections successful?     " 
-               << toString(bo3.applyParameterCorrections(paramCor));
+      qDebug() << "apply param corrections successful?";
+      qDebug() << toString(bo3.applyParameterCorrections(paramCor));
     }
     catch (IException &e) {
       e.print();
@@ -522,9 +488,9 @@ int main(int argc, char *argv[]) {
     qDebug() << "";
 
     // spiceRotation and spicePosition (verify???)
-    //SpiceRotation *rotation = 
+    //SpiceRotation *rotation =
     bo3.spiceRotation();
-    //SpicePosition *position = 
+    //SpicePosition *position =
     bo3.spicePosition();
 
     qDebug() << "    add another image...";
@@ -545,7 +511,7 @@ int main(int argc, char *argv[]) {
       nullBO.applyParameterCorrections(paramCor);
     }
     catch (IException &e) {
-      e.print(); 
+      e.print();
     }
     try {
       bo3.applyParameterCorrections(paramCor);
@@ -579,7 +545,7 @@ int main(int argc, char *argv[]) {
                   bo.instId() != this.instId
                   bundleObservation != null
                   bundleSettings.numberSolveSettings() != 1
-      6) addNew - 
+      6) addNew -
                   map.contains(obsNumber)
                   bo.instId() != this.instId
                   bundleObservation == null
@@ -587,7 +553,7 @@ int main(int argc, char *argv[]) {
       8) getObsByCubeSerialNumber - map.contains(sn)
       9) getObsByCubeSerialNumber - map.contains(sn) == false
 
-    #endif               
+    #endif
     BundleObservationVector bov;
     BundleSettingsQsp bundleSettings = BundleSettingsQsp(new BundleSettings);
     // BundleObservation *obs1 = bov.addNew(bi2, "obs1", "InstrumentIdBOV", bundleSettings);
@@ -598,7 +564,7 @@ int main(int argc, char *argv[]) {
     qDebug() << "number of position parameters: " << toString(bov.numberPositionParameters());
     qDebug() << "number of pointing parameters: " << toString(bov.numberPointingParameters());
     qDebug() << "number of parameters: " << toString(bov.numberParameters());
-    
+
 #if 0
     BundleObservation obs1b = *bov.getObservationByCubeSerialNumber("obs1");
     qDebug() << "same observation?" << toString((obs1 == obs1b));
@@ -636,7 +602,7 @@ int main(int argc, char *argv[]) {
     qDebug() << "Set BundleControlPoint 1 to rejected - is rejected?"
         << toString(bcp1.isRejected());
     bcp1.setRejected(false);
-    qDebug() << "Set BundleControlPoint 1 to non-rejected - is rejected?" 
+    qDebug() << "Set BundleControlPoint 1 to non-rejected - is rejected?"
         << toString(bcp1.isRejected());
 
     qDebug() << "Number of rejected measures:" << bcp1.numberOfRejectedMeasures();
@@ -657,8 +623,8 @@ int main(int argc, char *argv[]) {
     qDebug() << "";
 
     qDebug() << "Modify FreePoint - setAdjustedSurfacePoint(0,0,10) and addMeasure()";
-    SurfacePoint sp1(Latitude(0.0, Angle::Degrees), 
-                     Longitude(0.0, Angle::Degrees), 
+    SurfacePoint sp1(Latitude(0.0, Angle::Degrees),
+                     Longitude(0.0, Angle::Degrees),
                      Distance(10.0, Distance::Meters));
     bcp1.setAdjustedSurfacePoint(sp1);
     // ??? this appears to do nothing! measure is added to the internal QVector of measures,
@@ -746,8 +712,8 @@ int main(int argc, char *argv[]) {
     ControlPoint *fixedPoint = new ControlPoint("FixedPoint");
     fixedPoint->SetType(ControlPoint::Fixed);
     BundleControlPoint *bcp3 = new BundleControlPoint(fixedPoint);
-    SurfacePoint sp2(Latitude(90.0, Angle::Degrees), 
-                     Longitude(180.0, Angle::Degrees), 
+    SurfacePoint sp2(Latitude(90.0, Angle::Degrees),
+                     Longitude(180.0, Angle::Degrees),
                      Distance(10.0, Distance::Meters));
     bcp3->setAdjustedSurfacePoint(sp2);
     qDebug().noquote() << bcp3->formatBundleOutputSummaryString(errorProp);
@@ -896,11 +862,11 @@ int main(int argc, char *argv[]) {
       e.print();
     }
     bundleMeasure.setParentObservation(BundleObservationQsp(new BundleObservation(bo2)));
-    // const BundleObservationSolveSettings *solveSettings = 
+    // const BundleObservationSolveSettings *solveSettings =
     bundleMeasure.observationSolveSettings();
-    // Camera *cam = 
+    // Camera *cam =
     bundleMeasure.camera();
-    // BundleObservation  *parentObs = 
+    // BundleObservation  *parentObs =
     bundleMeasure.parentBundleObservation();
     BundleControlPoint *parentBCP = bundleMeasure.parentControlPoint();
     qDebug() << "parent control point id" << parentBCP->id();
@@ -923,7 +889,7 @@ int main(int argc, char *argv[]) {
     printBundleMeasure(bundleMeasure);
     printBundleMeasure(bundleMeasureRejected);
     printBundleMeasure(bundleMeasureEq);
-      
+
     qDebug() << "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";
     qDebug() << "";
 
@@ -1325,7 +1291,7 @@ int main(int argc, char *argv[]) {
     // This causes the Angle(double, Angle::Radians) to throw an exception.
     try {
       LinearAlgebra::Vector hasSpecial(btb1.numberParameters());
-      hasSpecial[0] = Isis::Lrs; 
+      hasSpecial[0] = Isis::Lrs;
       btb1.applyParameterCorrections(hasSpecial);
     }
     catch (IException &e) {
@@ -1711,7 +1677,7 @@ int main(int argc, char *argv[]) {
     }
     qDebug() << "";
     qDebug() << "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX";
-  } 
+  }
   catch (IException &e) {
     e.print();
   }
@@ -1737,7 +1703,15 @@ int main(int argc, char *argv[]) {
    qDebug() << "computed focal x" << toString(m.focalPlaneComputedX());
    qDebug() << "computed focal y" << toString(m.focalPlaneComputedY());
    qDebug() << "observation index" << toString(m.observationIndex());
-   qDebug() << "";  
+   qDebug() << "";
 }
 
 
+void printXml(const BundleObservationSolveSettings &printable) {
+  QString output;
+  QXmlStreamWriter writer(&output);
+  writer.setAutoFormatting(true);
+  printable.save(writer, NULL);
+  output.remove(QRegExp("[^<]*"));
+  qDebug().noquote() << output << endl << endl;
+}
diff --git a/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.cpp b/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.cpp
index d61ccaf6b1748bc481cbb07338a09c619d756269..4066c8cae04cf961e1296f51e24b507b7f20001a 100644
--- a/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.cpp
+++ b/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.cpp
@@ -195,10 +195,10 @@ namespace Isis {
       double pSample, double pLine, const ControlMeasure *pMeasure, Cube *pCube,
       Camera *measureCamera, PvlGroup *pMeasureGrp) {
 
-    mdEmissionAngle  = 0;
-    mdIncidenceAngle = 0;
+    mdEmissionAngle  = Null;
+    mdIncidenceAngle = Null;
     mdDnValue        = 0;
-    mdResolution     = 0;
+    mdResolution     = Null;
     mdSampleResidual = 0;
     mdLineResidual   = 0;
     mdResidualMagnitude=0;
@@ -207,11 +207,12 @@ namespace Isis {
     m_pixelShift = 0;
 
     if (measureCamera != NULL) {
-      measureCamera->SetImage(pSample, pLine);
-
-      mdEmissionAngle     = measureCamera->EmissionAngle();
-      mdIncidenceAngle    = measureCamera->IncidenceAngle();
-      mdResolution        = measureCamera->PixelResolution();
+      bool success = measureCamera->SetImage(pSample, pLine);
+      if (success) {
+        mdEmissionAngle     = measureCamera->EmissionAngle();
+        mdIncidenceAngle    = measureCamera->IncidenceAngle();
+        mdResolution        = measureCamera->PixelResolution();
+      }
     }
 
     if (pMeasure != NULL) {
@@ -254,11 +255,16 @@ namespace Isis {
     }
 
     if(pMeasureGrp != NULL) {
-      if(mbCameraRequired) {
+      if(mbCameraRequired && (mdEmissionAngle != Null || mdIncidenceAngle != Null || mdResolution != Null)) {
         *pMeasureGrp += Isis::PvlKeyword("EmissionAngle",  toString(mdEmissionAngle));
         *pMeasureGrp += Isis::PvlKeyword("IncidenceAngle", toString(mdIncidenceAngle));
         *pMeasureGrp += Isis::PvlKeyword("Resolution",     toString(mdResolution));
       }
+      else {
+        *pMeasureGrp += Isis::PvlKeyword("EmissionAngle",  "Invalid Emission Angle");
+        *pMeasureGrp += Isis::PvlKeyword("IncidenceAngle", "Invalid Incidence Angle");
+        *pMeasureGrp += Isis::PvlKeyword("Resolution",     "Invalid Resolution");
+      }
       if(mbValidateDN) {
         *pMeasureGrp += Isis::PvlKeyword("DNValue", toString(mdDnValue));
       }
@@ -281,7 +287,7 @@ namespace Isis {
 
       if(!ValidIncidenceAngle(mdIncidenceAngle)) {
         results.addFailure(MeasureValidationResults::IncidenceAngle,
-            mdIncidenceAngle, mdMinIncidenceAngle, mdMaxEmissionAngle);
+            mdIncidenceAngle, mdMinIncidenceAngle, mdMaxIncidenceAngle);
       }
 
       if(!ValidResolution(mdResolution)) {
diff --git a/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.h b/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.h
index 60ca22aed6ed4e79f5ca0bc66a3c02e83daef1e9..9f2fdd5c1531f31a15a24dd8e74d1be2647b3621 100644
--- a/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.h
+++ b/isis/src/control/objs/ControlNetValidMeasure/ControlNetValidMeasure.h
@@ -74,6 +74,9 @@ namespace Isis {
     *                          Fixes #1436. 
     *  @history 2014-03-03 Janet Barrett - Initialize the mdDnValue variable in
     *                          the ValidStandardOptions method. Fixes #2040.
+    *  @history 2016-07-13 Adam Paquette - Updated ValidStandardOptions to only
+    *                          get the EmissionAngle, IncidenceAngle, and PixelResolution
+    *                          if an image was properly set.
     */
 
   class ControlNetValidMeasure {
diff --git a/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.cpp b/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.cpp
index 84265570ad36bce799bbb49745b8c4de88909710..5b0ec3bac75cf3bbf1c1d892a9a1de2b1be6bdbc 100644
--- a/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.cpp
+++ b/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.cpp
@@ -183,7 +183,8 @@ namespace Isis {
 
 
   /**
-  * @description This method reads the covariance matrix in from a file,
+  * @brief Read covariance matrix and compute correlation values
+  * This method reads the covariance matrix in from a file,
   * one SparseBlockColumnMatrix at a time.  It then stores the diagonal values from that column
   * and computes the correlation values. The resulting SparseBlockMatrix is written to a
   * new file, one SparseBlockColumnMatrix at a time.
@@ -270,7 +271,8 @@ namespace Isis {
 
 
   /**
-   * @description This method will open the correlation matrix file and read in the blocks that
+   * @brief Extract requested area from correlation matrix
+   * This method will open the correlation matrix file and read in the blocks that
    * apply to the requested area. It will populate m_visibleElements.
    *
    * @param x first coordinate of the location in the matrix that the user wants to see.
@@ -315,7 +317,8 @@ namespace Isis {
 
 
   /**
-   * @description This is used to make sure the covariance matrix exists.
+   * @brief Check if the correlation matrix has a covariance matrix
+   * This is used to make sure the covariance matrix exists.
    * If it doesn't this class is not valid. If this file exists, we can compute the
    * correlation matrix.
    *
@@ -409,7 +412,7 @@ namespace Isis {
 
 
   /**
-   * @description This method will read the matrix in from the file and hold on to the whole thing.
+   * @brief This method will read the matrix in from the file and hold on to the whole thing.
    * This will only be used when the matrix is small enough that this will be useful.
    *
    */
@@ -427,7 +430,8 @@ namespace Isis {
 
 
   /**
-   * @description This method will be used when the matrix is too big to display the whole thing.
+   * @brief Display only part of a matrix
+   * This method will be used when the matrix is too big to display the whole thing.
    * It will read in the block we want to see and the two blocks for the diagonals that belong to
    * the right images.
    */
@@ -445,7 +449,7 @@ namespace Isis {
 
 
   /**
-   * @description This method creates a Pvl group with the information necessary to recreate
+   * @brief This method creates a Pvl group with the information necessary to recreate
    * this correlation matrix.
    *
    * Object = CorrelationMatrixData
@@ -477,88 +481,4 @@ namespace Isis {
     
     return corrMatInfo;
   }
-
-
-  /**
-   * @brief Writes CorrelationMatrix data to the output stream and returns this stream
-   * to the user.
-   * @param stream  The input stream containing the data.
-   * @return @b QDataStream Returns the output stream.
-   */
-
-  QDataStream &CorrelationMatrix::write(QDataStream &stream) const {
-    // QMaps
-    stream << *m_imagesAndParameters;
-    // FileNames
-    stream << m_covarianceFileName->expanded() << m_correlationFileName->expanded();
-    // QLists
-    stream << *m_diagonals << *m_visibleBlocks;
-    return stream;
-  }
-
-
-  /**
-   * @brief Reads CorrelationMatrix data from the input stream and places the data
-   * in member variables.
-   * @param stream  The input input stream containing the data.
-   * @return @b QDataStream Returns the output data stream.
-   */
-    QDataStream &CorrelationMatrix::read(QDataStream &stream) {
-    // QMaps
-    QMap imagesAndParameters;
-    stream >> imagesAndParameters;
-    delete m_imagesAndParameters;
-    m_imagesAndParameters = NULL;
-    m_imagesAndParameters = new QMap(imagesAndParameters);
-
-    // FileNames
-    QString covarianceFileName;
-    stream >> covarianceFileName;
-    delete m_covarianceFileName;
-    m_covarianceFileName = NULL;
-    m_covarianceFileName  = new FileName(covarianceFileName);
-
-    QString correlationFileName;
-    stream >> correlationFileName;
-    delete m_correlationFileName;
-    m_correlationFileName = NULL;
-    m_correlationFileName = new FileName(correlationFileName);
-
-    // QLists
-    QList diagonals;
-    stream >> diagonals;
-    delete m_diagonals;
-    m_diagonals = NULL;
-    m_diagonals = new QList(diagonals);
-
-    QList visibleBlocks;
-    stream >> visibleBlocks;
-    delete m_visibleBlocks;
-    m_visibleBlocks = NULL;
-    m_visibleBlocks = new QList(visibleBlocks);
-
-    return stream;
-  }
-
-
-  /**
-   * @brief The operator <<  writes matrix data to a QDataStream.
-   * @param stream The output stream upon which the matrix data is written.
-   * @param matrix The CorrelationMatrix containing the data.
-   * @return @b QDataStream Returns the output stream containing the matrix data.
-   */
-  QDataStream &operator<<(QDataStream &stream, const CorrelationMatrix &matrix) {
-    return matrix.write(stream);
-  }
-
-
-  /**
-   * @brief The operator >> reads matrix data from a QDataStream.
-   * @param stream  The input stream containing the CorrelationMatrix data.
-   * @param matrix  The matrix which is going to be overwritten by the input stream.
-   * @return @b QDataStream Returns the output stream containing the matrix data.
-   */
-  QDataStream &operator>>(QDataStream &stream, CorrelationMatrix &matrix) {
-    return matrix.read(stream);
-  }
 }
diff --git a/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.h b/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.h
index 327f66231df8fb896e2d23070bfa3963f272f543..d7a55ad3c02ec4b2ca5fa5a2fa37a1f914a244b5 100644
--- a/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.h
+++ b/isis/src/control/objs/CorrelationMatrix/CorrelationMatrix.h
@@ -106,8 +106,6 @@ namespace Isis {
 
       PvlObject pvlObject();
 
-      QDataStream &write(QDataStream &stream) const;
-      QDataStream &read(QDataStream &stream);
 
     private:
       //! This map holds the images used to create this matrix and their associated parameters.
@@ -131,9 +129,7 @@ namespace Isis {
        */
       QList *m_visibleBlocks;
   };
-  // operators to read/write CorrelationMatrix to/from binary disk file
-  QDataStream &operator<<(QDataStream &stream, const CorrelationMatrix &matrix);
-  QDataStream &operator>>(QDataStream &stream, CorrelationMatrix &matrix);
+
 };
 
 Q_DECLARE_METATYPE(Isis::CorrelationMatrix);
diff --git a/isis/src/docsys/Object/Makefile b/isis/src/docsys/Object/Makefile
index d0948e7673eb43b64473f80cbe8b32ddecc36a81..82a930a88e80c49beecfe48a819adeda07c9d8d7 100644
--- a/isis/src/docsys/Object/Makefile
+++ b/isis/src/docsys/Object/Makefile
@@ -16,6 +16,7 @@ help:
 	echo "Isis Object Documentation Make System Commands"
 	echo "------------------------ "
 	echo "make docs      : Build Isis Object Documentation"
+	echo "                 SHOWDOCWARNINGS=1 will show doxygen warnings"
 	echo " "
 	echo "make wwwdocsrc : Sync Source to Public Web Server" 
 	echo "make devdocsrc : Sync Source to Development Web Server" 
@@ -32,160 +33,94 @@ docs: conf assetsDir
 documentation: 
 	echo "      Creating Object Documentation"
 	mkdir -p $(ISISROOT)/doc/Object
-	mkdir -p $(ISISROOT)/doc/Object/apps
 	mkdir -p $(ISISROOT)/doc/Object/Developer
 	mkdir -p $(ISISROOT)/doc/Object/Programmer
 	mkdir -p $(ISISROOT)/doc/documents/DocStyle/assets
-#dls 2006-10-04 -- took out -d on rsync that i'd added to make Sun happy
-# (Sun = hipeaks)... Linux (orkin) was complaining
-	rsync -qlHptr --delete --rsh=ssh *.html $(ISISROOT)/doc/Object/
 	rsync -qlHptr --delete --rsh=ssh build/isisDoxyDefs.doxydef $(ISISROOT)/doc/documents/DocStyle/assets/
 
 
 assetsDir:
 	echo "        ...copying assets"
+	mkdir -p $(ISISROOT)/doc/Object
 	rsync -qlHptr --delete --rsh=ssh assets $(ISISROOT)/doc/Object/ 
 
 conf:
-	echo "        ...building apps configuration"
-	mkdir -p build/apps
-	cat build/apps_tag.conf                                     >  build/apps_tag_temp.conf
-	echo "LATEX_CMD_NAME   = $(LATEX)"                          >> build/apps_tag_temp.conf
-	echo "OUTPUT_DIRECTORY = $(ISISROOT)/doc/Object/"           >> build/apps_tag_temp.conf
-	echo "STRIP_FROM_PATH  = $(ISISROOT)/"                      >> build/apps_tag_temp.conf
-	echo "INPUT            = $(ISISROOT)/src/ \\"               >> build/apps_tag_temp.conf
-	echo "                   build/isisAppsDoxyDefs.doxydef"    >> build/apps_tag_temp.conf
-	echo "HTML_HEADER      = build/IsisObjectHeaderApps.html"   >> build/apps_tag_temp.conf
-	echo "HTML_FOOTER      = build/IsisObjectFooter.html"       >> build/apps_tag_temp.conf
-	echo "HTML_OUTPUT      = apps"                              >> build/apps_tag_temp.conf
-	echo "HTML_STYLESHEET  = build/doxygen_apps.css"            >> build/apps_tag_temp.conf
-
-	if [[ "$(DOT_PATH)" != "" ]];                                          \
-	then                                                                   \
-	  echo "DOT_PATH  = /opt/local/bin" >> build/apps_tag_temp.conf;       \
-	fi
-
 	echo "        ...building Programmer configuration"
 	cat build/Programmer.conf                                        >  build/Programmer_temp.conf
 	echo "OUTPUT_DIRECTORY = $(ISISROOT)/doc/Object/"                >> build/Programmer_temp.conf
-	echo "FILE_PATTERNS    = *objs*.h \ "                            >> build/Programmer_temp.conf
-	echo "                   *objs*.cpp \ "                          >> build/Programmer_temp.conf
-	echo "                   *build/isisDoxyDefs.doxydef"            >> build/Programmer_temp.conf
 	echo "STRIP_FROM_PATH  = $(ISISROOT)/"                           >> build/Programmer_temp.conf
 	echo "INPUT            = build/isisDoxyDefs.doxydef $(ISISROOT)/src/ " >> build/Programmer_temp.conf
-	echo "HTML_HEADER      = build/IsisObjectHeaderProgrammers.html" >> build/Programmer_temp.conf
-	echo "HTML_FOOTER      = build/IsisObjectFooter.html"            >> build/Programmer_temp.conf
 	echo "HTML_OUTPUT      = Programmer"                             >> build/Programmer_temp.conf
-	echo "TAGFILES         = build/apps/apps_fix.tag"                >> build/Programmer_temp.conf
-	echo "HTML_STYLESHEET  = build/doxygen_prog.css"                 >> build/Programmer_temp.conf
-	echo "IMAGE_PATH       = "                                     >> build/Programmer_temp.conf
 
 	if [ "$(findstring LOUD,$(MODE))" = "LOUD" ]; \
 	then \
 	  echo "QUIET                  = NO"                         >> build/Programmer_temp.conf; \
-	  echo "WARNINGS               = YES"                        >> build/Programmer_temp.conf; \
-	  echo "WARN_IF_UNDOCUMENTED   = YES"                        >> build/Programmer_temp.conf; \
-	  echo "WARN_IF_DOC_ERROR      = YES"                        >> build/Programmer_temp.conf; \
-	  echo "WARN_NO_PARAMDOC       = YES"                        >> build/Programmer_temp.conf; \
-        else \
-	  echo "QUIET                  = YES"                        >> build/Programmer_temp.conf; \
-	  echo "WARNINGS               = YES"                        >> build/Programmer_temp.conf; \
-	  echo "WARN_IF_UNDOCUMENTED   = YES"                        >> build/Programmer_temp.conf; \
-	  echo "WARN_IF_DOC_ERROR      = YES"                        >> build/Programmer_temp.conf; \
-	  echo "WARN_NO_PARAMDOC       = YES"                        >> build/Programmer_temp.conf; \
 	fi
 
-	if [[ "$(DOT_PATH)" != "" ]];                                          \
-	then                                                                   \
-	  echo "DOT_PATH  = /opt/local/bin" >> build/Programmer_temp.conf;     \
+	if [[ "$(DOT_PATH)" != "" ]];                                      \
+	then                                                               \
+	  echo "DOT_PATH  = $(DOT_PATH)" >> build/Programmer_temp.conf;    \
 	fi
 
-	for dirname in "$(OBJECTASSETS)"; do \
-	  echo "$$dirname \\"                                          >> build/Programmer_temp.conf ; \
-	done
+	if [[ "$(SHOWDOCWARNINGS)" != "" ]];                               \
+	then                                                               \
+	  echo "WARN_LOGFILE = " >> build/Programmer_temp.conf;            \
+	fi
 
 	echo "        ...building Developer configuration"
 	cat build/Developer.conf                                    >  build/Developer_temp.conf
-	echo "LATEX_CMD_NAME   = $(LATEX)"                          >> build/Developer_temp.conf
 	echo "OUTPUT_DIRECTORY = $(ISISROOT)/doc/Object/"           >> build/Developer_temp.conf
 	echo "STRIP_FROM_PATH  = $(ISISROOT)/"                      >> build/Developer_temp.conf
 	echo "INPUT            = $(ISISROOT)/src/ \\"               >> build/Developer_temp.conf
 	echo "                   build/isisDoxyDefs.doxydef"        >> build/Developer_temp.conf
-	echo "HTML_HEADER      = build/IsisObjectHeader.html"       >> build/Developer_temp.conf
-	echo "HTML_FOOTER      = build/IsisObjectFooter.html"       >> build/Developer_temp.conf
 	echo "HTML_OUTPUT      = Developer"                         >> build/Developer_temp.conf
-	echo "TAGFILES         = build/apps/apps_fix.tag"           >> build/Developer_temp.conf
-	echo "HTML_STYLESHEET  = build/doxygen.css"                 >> build/Developer_temp.conf
-	echo "IMAGE_PATH       = "                                >> build/Developer_temp.conf
 	if [ "$(findstring LOUD,$(MODE))" = "LOUD" ]; \
 	then \
 	  echo "QUIET                  = NO"                         >> build/Developer_temp.conf; \
-	  echo "WARNINGS               = YES"                        >> build/Developer_temp.conf; \
-	  echo "WARN_IF_UNDOCUMENTED   = YES"                        >> build/Developer_temp.conf; \
-	  echo "WARN_IF_DOC_ERROR      = YES"                        >> build/Developer_temp.conf; \
-	  echo "WARN_NO_PARAMDOC       = YES"                        >> build/Developer_temp.conf; \
-        else \
-	  echo "QUIET                  = YES"                        >> build/Developer_temp.conf; \
-	  echo "WARNINGS               = NO"                         >> build/Developer_temp.conf; \
-	  echo "WARN_IF_UNDOCUMENTED   = NO"                         >> build/Developer_temp.conf; \
-	  echo "WARN_IF_DOC_ERROR      = NO"                         >> build/Developer_temp.conf; \
-	  echo "WARN_NO_PARAMDOC       = NO"                         >> build/Developer_temp.conf; \
 	fi
 
-	for dirname in "$(OBJECTASSETS)" ; do \
-	    echo "$$dirname \\"                                     >> build/Developer_temp.conf ; \
-	done
+	if [[ "$(DOT_PATH)" != "" ]];                                      \
+	then                                                               \
+	  echo "DOT_PATH  = $(DOT_PATH)" >> build/Developer_temp.conf;     \
+	fi
 
+	if [[ "$(SHOWDOCWARNINGS)" != "" ]];                               \
+	then                                                               \
+	  echo "WARN_LOGFILE = " >> build/Developer_temp.conf;             \
+	fi
 
-render: doApps doProg doDev
-doApps:
-	echo "        ...building apps documentation"
-	$(DOXYGEN) build/apps_tag_temp.conf
-#	cp build/apps/apps.tag $(ISISROOT)/doc/Object/apps/
-	$(XALAN) $(XALAN_OUTFILE_OPTION) build/apps/apps_fix.tag $(XALAN_INFILE_OPTION) build/apps/apps.tag $(XALAN_XSL_OPTION) build/IsisApplicationTagFix.xsl
-	cp build/apps/apps_fix.tag $(ISISROOT)/doc/Object/apps/
+
+
+render: doProg doDev
 
 doProg:
 	echo "        ...building Programmer documentation"
 	$(DOXYGEN) build/Programmer_temp.conf
-	cd $(ISISROOT)/doc/Object/Programmer ; cd $(ISISROOT)/src/docsys/Object/
 
 doDev:
 	echo "        ...building Developer documentation"
 	$(DOXYGEN) build/Developer_temp.conf
-	cd $(ISISROOT)/doc/Object/Developer ; cd $(ISISROOT)/src/docsys/Object/
 
+# The doProgTest target can be used to build documentation for an individual Object.
+# E.G. from isis/src/base/objs/Camera do
+#      ( cd ../../../docsys/Object ; make CURDIR=/scratch/m04585/isis/src/base/objs/Camera doProgTest )
 doProgTest:
-	echo "Building ProgTester configuration"
+	echo "Building ProgTester configuration in: $(CURDIR) ISISROOT is: $(ISISROOT)"
 	mkdir -p docbuild
 	cat $(ISISROOT)/src/docsys/Object/build//Programmer.conf         >  docbuild/ProgTester_temp.conf
-	echo "FILE_PATTERNS          = *.h \ "                           >> docbuild/ProgTester_temp.conf
-	echo "                         *.cpp \ "                         >> docbuild/ProgTester_temp.conf
-	echo "                         *build/isisDoxyDefs.doxydef"      >> docbuild/ProgTester_temp.conf
 	echo "OUTPUT_DIRECTORY = $(CURDIR)/"                             >> docbuild/ProgTester_temp.conf
 	echo "STRIP_FROM_PATH  = $(CURDIR)/"                             >> docbuild/ProgTester_temp.conf
 	echo "INPUT            = $(CURDIR)/ \\"                          >> docbuild/ProgTester_temp.conf
-	echo "                   $(ISISROOT)/src/docsys/Object/build/isisDoxyDefs.doxydef"            >> docbuild/ProgTester_temp.conf
-	echo "HTML_HEADER      = $(ISISROOT)/src/docsys/Object/build/IsisObjectHeaderProgTester.html" >> docbuild/ProgTester_temp.conf
-	echo "HTML_FOOTER      = $(ISISROOT)/src/docsys/Object/build/IsisObjectFooterProgTester.html" >> docbuild/ProgTester_temp.conf
+	echo "                   $(ISISROOT)/src/docsys/Object/build/isisDoxyDefs.doxydef"  >> docbuild/ProgTester_temp.conf
+	echo "HTML_HEADER      = $(ISISROOT)/src/docsys/Object/build/IsisObjectHeader.html" >> docbuild/ProgTester_temp.conf
+	echo "HTML_FOOTER      = $(ISISROOT)/src/docsys/Object/build/IsisObjectFooter.html" >> docbuild/ProgTester_temp.conf
 	echo "HTML_OUTPUT      = html"                                   >> docbuild/ProgTester_temp.conf
-	echo "TAGFILES         = "                                       >> docbuild/ProgTester_temp.conf
-	echo "HTML_STYLESHEET  = $(ISISROOT)/src/docsys/Object/build/doxygen.css"                     >> docbuild/ProgTester_temp.conf
-	echo "LATEX_CMD_NAME   = $(LATEX)"                               >> docbuild/ProgTester_temp.conf
-	if [ "$(findstring LOUD,$(MODE))" = "LOUD" ]; \
-	then \
-	  echo "QUIET                  = NO"                           >> build/ProgTester_temp.conf; \
-	  echo "WARNINGS               = YES"                          >> build/ProgTester_temp.conf; \
-	  echo "WARN_IF_UNDOCUMENTED   = YES"                          >> build/ProgTester_temp.conf; \
-	  echo "WARN_IF_DOC_ERROR      = YES"                          >> build/ProgTester_temp.conf; \
-	  echo "WARN_NO_PARAMDOC       = YES"                          >> build/ProgTester_temp.conf; \
-	else \
-	  echo "QUIET                  = YES"                          >> build/ProgTester_temp.conf; \
-	  echo "WARNINGS               = NO"                           >> build/ProgTester_temp.conf; \
-	  echo "WARN_IF_UNDOCUMENTED   = NO"                           >> build/ProgTester_temp.conf; \
-	  echo "WARN_IF_DOC_ERROR      = NO"                           >> build/ProgTester_temp.conf; \
-	  echo "WARN_NO_PARAMDOC       = NO"                           >> build/ProgTester_temp.conf; \
-	fi
+	echo "WARN_LOGFILE           = "                                 >> docbuild/ProgTester_temp.conf
+	echo "QUIET                  = YES"                              >> docbuild/ProgTester_temp.conf
+	echo "WARNINGS               = YES"                              >> docbuild/ProgTester_temp.conf
+	echo "WARN_IF_UNDOCUMENTED   = YES"                              >> docbuild/ProgTester_temp.conf
+	echo "WARN_IF_DOC_ERROR      = YES"                              >> docbuild/ProgTester_temp.conf
+	echo "WARN_NO_PARAMDOC       = YES"                              >> docbuild/ProgTester_temp.conf
 	$(DOXYGEN) docbuild/ProgTester_temp.conf
 	echo "View your documentation by opening the file html/index.html in a browser"
 #do the following on a clean, as well as whacking the html directory created in this dir by doxy
@@ -196,11 +131,11 @@ doProgTest:
 #----
 # CLEAN
 clean:
-	rm -f  build/apps_tag_temp.conf 
 	rm -f  build/Programmer_temp.conf
 	rm -f  build/Developer_temp.conf 
-	rm -rf build/apps
+	rm -rf docbuild
 	rm -f ../documents/DocStyle/assets/isisDoxyDefs.doxydef
+	rm -f doxyWarnDeveloper.txt doxyWarnProgrammer.txt
 
 cleandoc:
 	rm -r $(ISISROOT)/doc/Object
diff --git a/isis/src/docsys/Object/alpha.html b/isis/src/docsys/Object/alpha.html
deleted file mode 100644
index a7db0cdec2aeb5b97368b4d4cf3417ad4e33689d..0000000000000000000000000000000000000000
--- a/isis/src/docsys/Object/alpha.html
+++ /dev/null
@@ -1,50 +0,0 @@
-
-
-
-
-            USGS: Isis Object Table of Contents (Alphabetized)
-        
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-USGS
-
      
-
      
-        Isis 3.0 Object Documentation
      
-
      
-
      
-
-Oops! You have reached a deprecated page!
-The Isis Object Developers' Reference (the Isis API)
-has moved. If your browser does not redirect to the new location momentarily,
-follow this link to the Developers' Reference.
-
-
      
-
-
-
diff --git a/isis/src/docsys/Object/alpha_prog.html b/isis/src/docsys/Object/alpha_prog.html
deleted file mode 100644
index d755f982ae0cf3b27d1c8fadb7f716f8c91c30bb..0000000000000000000000000000000000000000
--- a/isis/src/docsys/Object/alpha_prog.html
+++ /dev/null
@@ -1,51 +0,0 @@
-
-
-
-
-            USGS: Isis Object Table of Contents (Alphabetized)
-        
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-USGS
-
      
-
      
-        Isis 3.0 Object Documentation
      
-
      
-
-
      
-
-Oops! You have reached a deprecated page!
-The Isis Object Programmers' Reference
-has moved. If your browser does not redirect to the new location momentarily,
-follow this link to the Programmers' Reference.
-
-
      
-
-
-
diff --git a/isis/src/docsys/Object/assets/MathJax.js b/isis/src/docsys/Object/assets/MathJax.js
new file mode 100644
index 0000000000000000000000000000000000000000..45459f34c4c90a12da00d7ea685c0fdd843ff707
--- /dev/null
+++ b/isis/src/docsys/Object/assets/MathJax.js
@@ -0,0 +1,64 @@
+/* 
+ *  MathJax single file build "" 
+ *
+ *  created with MathJax-grunt-concatenator 
+ *
+ *  Copyright (c) 2016 The MathJax Consortium
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ */
+
+
+document.getElementById&&document.childNodes&&document.createElement&&(window.MathJax&&MathJax.Hub||(window.MathJax?window.MathJax={AuthorConfig:window.MathJax}:window.MathJax={},MathJax.version="2.7.1",MathJax.fileversion="2.7.1",MathJax.cdnVersion="2.7.1",MathJax.cdnFileVersions={},function(a){var b=window.MathJax;b||(b=window.MathJax={});var c=[],d=function(a){var b=a.constructor;b||(b=function(){});for(var c in a)"constructor"!==c&&a.hasOwnProperty(c)&&(b[c]=a[c]);return b},e=function(){return function(){return arguments.callee.Init.call(this,arguments)}};b.Object=d({constructor:e(),Subclass:function(a,b){var d=e();return d.SUPER=this,d.Init=this.Init,d.Subclass=this.Subclass,d.Augment=this.Augment,d.protoFunction=this.protoFunction,d.can=this.can,d.has=this.has,d.isa=this.isa,d.prototype=new this(c),d.prototype.constructor=d,d.Augment(a,b),d},Init:function(a){var b=this;return 1===a.length&&a[0]===c?b:(b instanceof a.callee||(b=new 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b=this.data.join("");if(b.length>1)return!1;var c=this.CoreParent();if(c&&c.isa(e.munderover)&&1===this.CoreText(c.data[c.base]).length){var f=c.data[c.over],g=c.data[c.under];f&&this===f.CoreMO()&&c.Get("accent")?b=d.FONTDATA.REMAPACCENT[b]||b:g&&this===g.CoreMO()&&c.Get("accentunder")&&(b=d.FONTDATA.REMAPACCENTUNDER[b]||b)}b=d.FONTDATA.DELIMITERS[b.charCodeAt(0)];var h=b&&b.dir==a.substr(0,1);return h||delete this.svg,this.forceStretch=h&&(this.Get("minsize",!0)||this.Get("maxsize",!0)),h},SVGstretchV:function(a,b){var c,e=this.svg||this.toSVG(),f=this.getValues("symmetric","maxsize","minsize"),g=d.TeX.axis_height*e.scale,h=this.SVGgetMu(e);return c=f.symmetric?2*Math.max(a-g,b+g):a+b,f.maxsize=d.length2em(f.maxsize,h,e.h+e.d),f.minsize=d.length2em(f.minsize,h,e.h+e.d),c=Math.max(f.minsize,Math.min(f.maxsize,c)),c!=f.minsize&&(c=[Math.max(c*d.TeX.delimiterfactor/1e3,c-d.TeX.delimitershortfall),c]),e=d.createDelimiter(this.data.join("").charCodeAt(0),c,e.scale),c=f.symmetric?(e.h+e.d)/2+g:(e.h+e.d)*a/(a+b),e.y=c-e.h,this.SVGhandleSpace(e),this.SVGhandleColor(e),delete this.svg.element,this.SVGsaveData(e),e.stretched=!0,e},SVGstretchH:function(a){var b=this.svg||this.toSVG(),c=this.SVGgetMu(b),f=this.getValues("maxsize","minsize","mathvariant","fontweight");return("bold"===f.fontweight||parseInt(f.fontweight)>=600)&&!this.Get("mathvariant",!0)&&(f.mathvariant=e.VARIANT.BOLD),f.maxsize=d.length2em(f.maxsize,c,b.w),f.minsize=d.length2em(f.minsize,c,b.w),a=Math.max(f.minsize,Math.min(f.maxsize,a)),b=d.createDelimiter(this.data.join("").charCodeAt(0),a,b.scale,f.mathvariant),this.SVGhandleSpace(b),this.SVGhandleColor(b),delete this.svg.element,this.SVGsaveData(b),b.stretched=!0,b}}),e.mn.Augment({SVGremapMinus:function(a){return a.replace(/^-/,"−")},toSVG:function(){this.SVGgetStyles();var a=this.SVGgetVariant(),b=this.SVG();this.SVGgetScale(b),this.SVGhandleSpace(b);for(var c=this.SVGremapMinus,d=0,e=this.data.length;db.w&&1===g.length&&!a.noIC&&(b.ic=b.r-b.w,b.w=b.r),this.SVGhandleColor(b),this.SVGsaveData(b),b}}),e.mtext.Augment({toSVG:function(){if(d.config.mtextFontInherit||"merror"===this.Parent().type){this.SVGgetStyles();var a=this.SVG(),b=this.SVGgetScale(a);this.SVGhandleSpace(a);var c=this.SVGgetVariant(),e={direction:this.Get("dir")};return c.bold&&(e["font-weight"]="bold"),c.italic&&(e["font-style"]="italic"),c=this.Get("mathvariant"),"monospace"===c?e.class="MJX-monospace":c.match(/sans-serif/)&&(e.class="MJX-sans-serif"),a.Add(j.TEXT(100*b/d.config.scale,this.data.join(""),e)),a.Clean(),this.SVGhandleColor(a),this.SVGsaveData(a),a}return this.SUPER(arguments).toSVG.call(this)}}),e.merror.Augment({toSVG:function(a,b){this.SVGgetStyles();var c=this.SVG(),e=d.length2em(this.styles.fontSize||1)/1e3;this.SVGhandleSpace(c);var f=1!==e?{transform:"scale("+d.Fixed(e)+")"}:{},g=j(f);if(g.Add(this.SVGchildSVG(0)),g.Clean(),1!==e){g.removeable=!1;for(var h=["w","h","d","l","r","D","H"],i=0,k=h.length;ic.H&&(c.H=c.h),c.d>c.D&&(c.D=c.d)}return this.SVGhandleColor(c),this.SVGsaveData(c),c},SVGlength2em:function(a,b,c,e,f){null==f&&(f=-d.BIGDIMEN);var g=String(b).match(/width|height|depth/),h=g?a[g[0].charAt(0)]:e?a[e]:0,i=d.length2em(b,c,h/this.mscale)*this.mscale;return e&&String(b).match(/^\s*[-+]/)?Math.max(f,a[e]+i):i}}),e.mrow.Augment({SVG:j.ROW,toSVG:function(a,b){this.SVGgetStyles();var c=this.SVG();this.SVGhandleSpace(c),null!=b&&(c.sh=a,c.sd=b);for(var d=0,e=this.data.length;dd.linebreakWidth||this.hasNewline())},SVGmultiline:function(a){e.mbase.SVGautoloadFile("multiline")},SVGstretchH:function(a){var b=this.SVG();this.SVGhandleSpace(b);for(var c=0,d=this.data.length;ch&&(g=(e.h+e.d-(h-k))/2),c=j.RECT(k,0,i.w),h=i.h+g+k,l=this.SVGaddRoot(a,e,l,e.h+e.d-h,b),a.Add(e,l,h-e.h),a.Add(c,l+e.w,h-c.h),a.Add(i,l+e.w,0),a.Clean(),a.h+=k,a.H+=k,this.SVGhandleColor(a),this.SVGsaveData(a),a},SVGaddRoot:function(a,b,c,d,e){return c}}),e.mroot.Augment({toSVG:e.msqrt.prototype.toSVG,SVGaddRoot:function(a,b,c,d,e){var f=(b.isMultiChar?.55:.65)*b.w;if(this.data[1]){var g=this.data[1].toSVG();g.x=0;var h=this.SVGrootHeight(b.h+b.d,e,g)-d,i=Math.min(g.w,g.r);c=Math.max(i,f),a.Add(g,c-i,h)}else f=c;return c-f},SVGrootHeight:function(a,b,c){return.45*(a-900*b)+600*b+Math.max(0,c.d-75)}}),e.mfenced.Augment({SVG:j.ROW,toSVG:function(){this.SVGgetStyles();var a=this.SVG();this.SVGhandleSpace(a),this.data.open&&a.Check(this.data.open),null!=this.data[0]&&a.Check(this.data[0]);for(var b=1,c=this.data.length;bp&&(p=m[k].w),!n[k]&&p>o&&(o=p));for(null==b&&null!=a?o=a:o==-d.BIGDIMEN&&(o=p),k=p=0,l=this.data.length;kp&&(p=m[k].w));var q,r,s,t,u,v,w,x=d.TeX.rule_thickness*this.mscale,y=0;for(f=m[this.base]||{w:0,h:0,d:0,H:0,D:0,l:0,r:0,y:0,scale:h},f.ic&&(y=1.3*f.ic+.05),k=0,l=this.data.length;kp&&(g.skew+=(p-i.w-q)/2))):(s=d.TeX.big_op_spacing1*h,t=d.TeX.big_op_spacing3*h,w=Math.max(s,t-Math.max(0,i.d))),w=Math.max(w,1500/d.em),q+=y/2,r=f.y+f.h+i.d+w,i.h+=u,i.h>i.H&&(i.H=i.h)):k==this.under&&(z?(w=3*x*h,u=0):(s=d.TeX.big_op_spacing2*h,t=d.TeX.big_op_spacing4*h,w=Math.max(s,t-i.h)),w=Math.max(w,1500/d.em),q-=y/2,r=f.y-(f.d+i.h+w),i.d+=u,i.d>i.D&&(i.D=i.d)),g.Add(i,q,r)}return g.Clean(),this.SVGhandleColor(g),this.SVGsaveData(g),g}}),e.msubsup.Augment({toSVG:function(a,b){this.SVGgetStyles();var c=this.SVG(),e=this.SVGgetScale(c);this.SVGhandleSpace(c);var f,g,h=this.SVGgetMu(c),i=c.Add(this.SVGdataStretched(this.base,a,b)),j=(this.data[this.sup]||this.data[this.sub]||this).SVGgetScale(),k=d.TeX.x_height*e,l=d.TeX.scriptspace*e;this.SVGnotEmpty(this.data[this.sup])&&(f=this.data[this.sup].toSVG(),f.w+=l,f.r=Math.max(f.w,f.r)),this.SVGnotEmpty(this.data[this.sub])&&(g=this.data[this.sub].toSVG(),g.w+=l,g.r=Math.max(g.w,g.r));var m,n=d.TeX.sup_drop*j,o=d.TeX.sub_drop*j,p=i.h+(i.y||0)-n,q=i.d-(i.y||0)+o,r=0;i.ic&&(i.w-=i.ic,r=1.3*i.ic+.05),!this.data[this.base]||"mi"!==this.data[this.base].type&&"mo"!==this.data[this.base].type||1!==this.data[this.base].data.join("").length||1!==i.scale||i.stretched||this.data[this.base].Get("largeop")||(p=q=0);var s=this.getValues("subscriptshift","superscriptshift");s.subscriptshift=""===s.subscriptshift?0:d.length2em(s.subscriptshift,h),s.superscriptshift=""===s.superscriptshift?0:d.length2em(s.superscriptshift,h);var t=i.w+i.x;if(f)if(g){q=Math.max(q,d.TeX.sub2*e);var u=d.TeX.rule_thickness*e;p-f.d-(g.h-q)<3*u&&(q=3*u-p+f.d+g.h,(n=.8*k-(p-f.d))>0&&(p+=n,q-=n)),c.Add(f,t+r,Math.max(p,s.superscriptshift)),c.Add(g,t,-Math.max(q,s.subscriptshift)),this.data[this.sup].SVGdata.dx=r,this.data[this.sup].SVGdata.dy=Math.max(p,s.superscriptshift),this.data[this.sub].SVGdata.dy=-Math.max(q,s.subscriptshift)}else values=this.getValues("displaystyle","texprimestyle"),m=d.TeX[values.displaystyle?"sup1":values.texprimestyle?"sup3":"sup2"],p=Math.max(p,m*e,f.d+.25*k,s.superscriptshift),c.Add(f,t+r,p),this.data[this.sup].SVGdata.dx=r,this.data[this.sup].SVGdata.dy=p;else g&&(q=Math.max(q,d.TeX.sub1*e,g.h-.8*k,s.subscriptshift),c.Add(g,t,-q),this.data[this.sub].SVGdata.dy=-q);return c.Clean(),this.SVGhandleColor(c),this.SVGsaveData(c),c}}),e.mmultiscripts.Augment({toSVG:e.mbase.SVGautoload}),e.mtable.Augment({toSVG:e.mbase.SVGautoload}),e["annotation-xml"].Augment({toSVG:e.mbase.SVGautoload}),e.math.Augment({SVG:j.Subclass({type:"svg",
+removeable:!1}),toSVG:function(a,c){var f=d.config;if(this.data[0]){this.SVGgetStyles(),e.mbase.prototype.displayAlign=b.config.displayAlign,e.mbase.prototype.displayIndent=b.config.displayIndent,String(b.config.displayIndent).match(/^0($|[a-z%])/i)&&(e.mbase.prototype.displayIndent="0");var g=j.G();g.Add(this.data[0].toSVG(),0,0,!0),g.Clean(),this.SVGhandleColor(g),d.Element(g.element,{stroke:"currentColor",fill:"currentColor","stroke-width":0,transform:"matrix(1 0 0 -1 0 0)"}),g.removeable=!1;var i=this.SVG();if(i.element.setAttribute("xmlns:xlink",h),f.useFontCache&&!f.useGlobalCache&&i.element.appendChild(j.GLYPH.defs),i.Add(g),i.Clean(),this.SVGsaveData(i),!a)return i.element=i.element.firstChild,i.element.removeAttribute("transform"),i.removable=!0,i;var k=Math.max(-i.l,0),l=Math.max(i.r-i.w,0),m=i.element.style,n=d.TeX.x_height/d.ex,o=(Math.ceil(i.H/n)+1)*n+d.HFUZZ,p=(Math.ceil(i.D/n)+1)*n+d.DFUZZ,q=k+i.w+l;i.element.setAttribute("width",d.Ex(q)),i.element.setAttribute("height",d.Ex(o+p)),m.verticalAlign=d.Ex(-p),k&&(m.marginLeft=d.Ex(-k)),l&&(m.marginRight=d.Ex(-l)),i.element.setAttribute("viewBox",d.Fixed(-k,1)+" "+d.Fixed(-o,1)+" "+d.Fixed(q,1)+" "+d.Fixed(o+p,1)),i.H>i.h&&(m.marginTop=d.Ex(i.h-o)),i.D>i.d&&(m.marginBottom=d.Ex(i.d-p),m.verticalAlign=d.Ex(-i.d)),Math.abs(q-d.cwidth)<10&&(m.maxWidth=d.Fixed(d.cwidth*d.em/1e3));var r=this.Get("alttext");if(r&&!i.element.getAttribute("aria-label")&&i.element.setAttribute("aria-label",r),i.element.getAttribute("role")||i.element.setAttribute("role","img"),i.element.setAttribute("focusable","false"),a.appendChild(i.element),i.element=null,!this.isMultiline&&"block"===this.Get("display")&&!i.hasIndent){var s=this.getValues("indentalignfirst","indentshiftfirst","indentalign","indentshift");s.indentalignfirst!==e.INDENTALIGN.INDENTALIGN&&(s.indentalign=s.indentalignfirst),s.indentalign===e.INDENTALIGN.AUTO&&(s.indentalign=this.displayAlign),s.indentshiftfirst!==e.INDENTSHIFT.INDENTSHIFT&&(s.indentshift=s.indentshiftfirst),"auto"===s.indentshift&&(s.indentshift="0");var t=d.length2em(s.indentshift,1,d.cwidth);if("0"!==this.displayIndent){var u=d.length2em(this.displayIndent,1,d.cwidth);t+=s.indentalign===e.INDENTALIGN.RIGHT?-u:u}c.style.textAlign=s.indentalign,t&&b.Insert(m,{left:{marginLeft:d.Ex(t)},right:{marginRight:d.Ex(-t),marginLeft:d.Ex(Math.max(0,t-q))},center:{marginLeft:d.Ex(t),marginRight:d.Ex(-t)}}[s.indentalign])}}return a}}),e.TeXAtom.Augment({toSVG:function(a,b){this.SVGgetStyles();var c=this.SVG();if(this.SVGhandleSpace(c),null!=this.data[0]){var 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@@ -247,16 +247,7 @@ xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Applica
       BThe binning number.
     
     
-
-
-
     
-
-
-
-
-
-
   
    
   
    
     
    Step 5: Flat-field correction:
    
@@ -271,21 +262,50 @@ xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Applica
     flat-field image.
   
    
   
    
-    
    Step 6: Convert units to I over F:
    
-    This converts the raw DN values to I/F (radiance) units.  The formula is as follows:
+    
    Step 6 (Optional): Convert output units to Radiance or I over F:
    
+    This step is optional, and the formula used depends on the value of the UNITS user parameter. 
+
+    If UNITS=RADIANCE, the following formula will be used to convert the raw DN values to radiance 
+    (W/m2/sr/µm):
+
+    

    
+     
    
+      
    R = Raw*RadianceStandard*RadianceScaleFactor
    
+      

    
+      
    
+      
+          
+     
+     
+          
+     
+     
+          
+     
+     
+          
+     
+     
+          
+     
+     
    VariableDescription
    RThe calibrated radiance (w/m2/sr/µm). 
    RawThe raw DN value. 
    RadianceStandardThe standard conversion factor from DNs to radiance. 
    RadianceScaleFactorAn adjustment factor for each filter.
    
+     
    
+
+    If UNITS = IOF, first the above formula will be used to convert from raw DNs to calibrated Radiance, and then
+    the following formula will be used to convert the raw DN values to I/F (radiance) units:
     

    
      
    
-      
    IoF = Raw*[pi*(Rs)2]/F
    
+      
    IoF = R*[pi*(Rs)2]/F
    
       

    
       
    
-          
+          
-          
+          
-          
+          
    
       
    
           VariableDescription
      
    
      
    RawThe raw DN value.IoFThe calibrated radiance in units of I over F.
      
    
      
    IoFThe IoF units of the raw DN value.RThe calibrated radiance (w/m2/sr/µm). 
      
    
      
    
          RsThe distance in Astronomical Units (AU) between the Sun
@@ -293,14 +313,15 @@ xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Applica
          
      
    
      
    FThe solar flux at the target body.FThe solar flux (w/m2/µm) at 1 AU. 
      
    
      
    
      
    
 
+    If UNITS=DN, no output conversion will be performed and the output units will be in raw DNs. 
   
    
-  
    
 
+ 
   
    
   
    Notes
    
   
      
@@ -450,14 +471,14 @@ xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Applica
   
      
 
 
-  
      
+ 
 
   
 
@@ -482,7 +503,35 @@ xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Applica
       a single-band ISIS cube to an OpenCV::OpenMat matrix and vice versa for the purpose
       of translating and scaling flat-field images so their dimensions match
       some AMICA images which have been cropped.  Fixes #3880.
-
+    
+    
+        Determined the LOSSY compression images must be scaled by a factor of 
+        16 to match the LOSSLESS mode for proper calibration. Added the UNIT 
+        option to specify output calibration units as DN, RADIANCE or I/F. This
+        parameter replaces the IOF parameter. Added option to allow user to
+        determine to apply PSF correction. Added CONFIG parameter that user
+        can provide a version of the calibration parameters to apply in amicacal.
+    
+    
+        Added the "APPLYSMEAR" option which will force the smear correction calibration
+        to be applied, and a new test for smear correction.
+        The default is for this option to not be applied except in the case where an image is
+        being processed for which on-board smear correction was not applied.  Also made the
+        applyPSF boolean parameter into a global variable for consistency with the applySmear
+        global variable.
+    
+    
+       Removed the "APPLYSMEAR" option as a user-specifiable parameter. The smear correction
+       will still be applied automatically when an image is being processed for which on-board smear 
+       correction was not applied (NSUB <= 1). Also updated application code for conformity with ISIS3
+       Coding Standards. Backward Compatibility Issue: The APPLYSMEAR parameter was removed. The smear
+       correction will automatically be applied to images with 1 sub-image. 
+    
+    
+       Removed the "PSF" correction option, since the PSF correction is not yet working. Related code has been commented-
+       out rather than removed entirely so that this work can potentially be resumed at a later date. 
+       Backward Compatibility Issue: The PSF parameter was removed, since it is not yet working. 
+       amicacal cannot apply a PSF correction anymore.
     
   
 
@@ -504,68 +553,115 @@ xsi:noNamespaceSchemaLocation="http://isis.astrogeology.usgs.gov/Schemas/Applica
       
         cube
         output
+        real
         
-          Non-PSF Corrected Output cube
+          Corrected Output cube
         
         
           This is the output file. The output cube will be a calibrated version 
-          of the input cube (without PSF correction).
+          of the input cube.
         
         
           *.cub
         
-            
-
-      
-
+        *.trn
+        $hayabusa/calibration/amica/amicaCalibration????.trn
+                  
+    
 
 
-    
     
+
+ 
+
       
         boolean
         True
         
           Set polarized pixels to ISIS::Null.
         
-	
+        
           Four position angle glass polarizers (of dimension 200 x 200 pixels each) 
           are attached to the upper left of the CCD chip.  This option sets those
           pixels to Null in the calibrated image by default.
-	
+	    
         
 
-      
-        boolean
-        True
+      
+        string
+        IOF 
         
-          Convert to I/F units.
+          Convert to specified output calibrated units.
         
         
-
         
+        
+          
+
+          
+
+            
+        
       
 
-	
+
+    
   
-  
 
diff --git a/isis/src/hayabusa/apps/amicacal/tsts/iof/Makefile b/isis/src/hayabusa/apps/amicacal/tsts/iof/Makefile
index f6301e3bf5ffd74c6159bcb2f7dfcd0b87e7041d..87af6af201e9e6a1272f4b59826f144a48d487c8 100644
--- a/isis/src/hayabusa/apps/amicacal/tsts/iof/Makefile
+++ b/isis/src/hayabusa/apps/amicacal/tsts/iof/Makefile
@@ -9,4 +9,4 @@ commands:
         $(APPNAME) \
         FROM=$(INPUT)/st_2459265790_w.cub \
         TO=$(OUTPUT)/corrected_noiof_st_2459265790_w.cub \
-        iof=no > /dev/null;
+        units=dn > /dev/null;
diff --git a/isis/src/hayabusa/apps/amicacal/tsts/smearCorrection/Makefile b/isis/src/hayabusa/apps/amicacal/tsts/smearCorrection/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..ad1af965f6d5dae6130e1218695891cb2bbdd593
--- /dev/null
+++ b/isis/src/hayabusa/apps/amicacal/tsts/smearCorrection/Makefile
@@ -0,0 +1,17 @@
+APPNAME = amicacal
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	# Test application of smear removal for SubImageCount = 1
+	$(APPNAME) \
+	FROM=$(INPUT)/st_2539482843_v.cub \
+	TO=$(OUTPUT)/smearCorrected_nsubimages1_st_2539482843_v.cub.cub \
+	nullpolarpix=no > /dev/null;
+
+	# Test NON-application of smear removal for SubImageCount = 2
+	$(APPNAME) \
+	FROM=$(INPUT)/st_2433548889_w.cub \
+	TO=$(OUTPUT)/notSmearCorrected_nsubimages2_st_2433548889_w.cub \
+	nullpolarpix=no >/dev/null;\
+
diff --git a/isis/src/hayabusa/apps/nirs2isis/ImportFits.cpp b/isis/src/hayabusa/apps/nirs2isis/ImportFits.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..0d4b24e025597a84286e71b532e2aa4618ce8090
--- /dev/null
+++ b/isis/src/hayabusa/apps/nirs2isis/ImportFits.cpp
@@ -0,0 +1,255 @@
+/**
+ * @file
+ * $Revision: 6715 $
+ * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are public
+ *   domain. See individual third-party library and package descriptions for
+ *   intellectual property information,user agreements, and related information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or implied,
+ *   is made by the USGS as to the accuracy and functioning of such software
+ *   and related material nor shall the fact of distribution constitute any such
+ *   warranty, and no responsibility is assumed by the USGS in connection
+ *   therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
+ *   the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+#include "ImportFits.h"
+
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+
+#include "FileName.h"
+#include "IException.h"
+#include "IString.h"
+#include "Pvl.h"
+#include "PvlObject.h"
+
+
+using namespace std;
+
+namespace Isis {
+
+
+  /** 
+   * Default constructor. This constructor initializes the FITS object
+   *
+   */
+  ImportFits::ImportFits() {
+    init();
+  }
+
+  /**
+   * @brief This constructor automatically loads the given label and table files.
+   *
+   * This constructor takes the name of the label file describing the PDS 
+   * table, the table data file name, and the name of the PDS table object.  
+   * It will extract the description of the columns and read the contents of the 
+   * table data file.
+   *
+   * If no table file is given or an empty QString is given for the table file, 
+   * the table location will be read from the label file.
+   *
+   * If no table name is given, the default name for the object is TABLE.
+   *
+   * This constructor may be used for ASCII or BINARY PDS tables.
+   *
+   * @param pdsLabFile Name of table label file
+   * @param pdsTableName The name of the table object in the PDS file.
+   */
+  ImportFits::ImportFits(const FileName &fitsFile,
+                                 const QString &fitsLabelName) {
+    init();
+    load(fitsFile.expanded(), fitsLabelName);
+  }
+
+  /**
+   * Destructs the ImportFits object.
+   */ 
+  ImportFits::~ImportFits() {
+  }
+
+  /** Return the number of samples in the FITS image */
+  int ImportFits::samples() const {
+    return (m_samples);
+  }
+
+  /** Return the number of lines in the FITS image */
+  int ImportFits::lines() const {
+    return (m_lines);
+  }
+
+  /** Return the number of bands in the FITS image */
+  int ImportFits::bands() const {
+    return (m_bands);
+  }
+
+  /** Returns the FITS label in a object name specified in the constructor */
+  PvlObject ImportFits::label() const {
+    return (m_label);
+  }
+
+
+  /**
+   * @brief Loads a PDS table label and (optional) data file
+   *
+   * This method will load a PDS table dataset using a label file describing the
+   * contents of the table data.  The caller can provide the table data file,
+   * otherwise, the location of the table data is extracted from the ^TABLE_NAME
+   * keyword in the provided labels.  The table data is then loaded.
+   *
+   * This method needs to be called if the default constructor is used. 
+   * Otherwise, it is invoked in the constructor that takes the label, table 
+   * file, and table name. This method may be used to overwrite the label and 
+   * table file used. When it is invoked, the current contents of the object are
+   * discarded.
+   *
+   * This method is used for ASCII or BINARY PDS tables.
+   *
+   * @param pdsLabFile Name of PDS table label file
+   * @param pdsTableFile Name of PDS table data file to be imported into Isis 
+   *                (optional)
+   */
+  void ImportFits::load(const QString &fitsfile,
+                       const QString &fitsLabelName) {
+
+    init();
+
+    //  Set up file state
+    m_file = fitsfile;
+
+      // Setup to read headers/labels
+    ifstream input;
+    input.open(m_file.expanded().toLatin1().data(), ios::in | ios::binary);
+
+  // Check stream open status
+    if ( !input.is_open() ) {
+      QString msg = "Cannot open input file [" + fitsfile + "]";
+      throw IException(IException::Io, msg, _FILEINFO_);
+    }
+  
+    //  Parse the labels
+    m_label = parseLabel(input, fitsLabelName);
+
+    //  Get data dimensions
+    int naxis = toInt(m_label["NAXIS"][0]);
+    if (naxis == 2) {
+      m_samples = toInt(m_label["NAXIS1"][0]);
+      m_lines = toInt(m_label["NAXIS2"][0]);
+      m_bands = 1;
+    }
+    else if (naxis == 3) {
+      m_samples = toInt(m_label["NAXIS1"][0]);
+      m_lines = toInt(m_label["NAXIS2"][0]);
+      m_bands = toInt(m_label["NAXIS3"][0]);
+    }
+    else {
+      QString msg = "NAXIS count of [" + m_label["NAXIS"][0] + 
+                    "] is not supported at this time"; 
+      throw IException(IException::User, msg, _FILEINFO_);
+    }
+
+    return;
+  }
+
+
+  /** 
+   * Initialize object variables 
+   *  
+   * This method is reentrant. 
+   *
+   */
+  void ImportFits::init() {
+    m_file = "";
+    m_lines = m_samples = m_bands = 0;
+    m_label = PvlObject("FitsLabel");
+    return;
+  }
+
+/**
+ * @brief Import a FITS label in to PvlGroup
+ * 
+ * @author 2013-11-07 kbecker 
+ * 
+ * @param input        Input stream to read label from
+ * @param fitLabelName Name of group to parse and store FITS label into
+ * 
+ * @return PvlObject Returns the FITS keywords in this object
+ */
+  PvlObject ImportFits::parseLabel(std::ifstream &input, 
+                                  const QString &fitLabelName) {
+
+    char reading[81];
+    IString line = "";
+    unsigned int place = 0;
+    PvlObject labels(fitLabelName);
+
+    // Load first line
+    input.seekg(0);
+    input.read(reading, 80);
+    reading[80] = '\0';
+    line = reading;
+    place += 80;
+
+    // Read in and place in PvlKeywords and a PvlObject
+    while(line.substr(0, 3) != "END") {
+      // Check for blank lines
+      if (line.substr(0, 1) != " " && line.substr(0, 1) != "/") {
+        // Name of keyword
+        PvlKeyword label(line.Token(" =").ToQt()); // Stop on spaces OR equal sign
+        // Remove up to beginning of data
+        line.TrimHead(" =");
+        line.TrimTail(" ");
+        if (label.name() == "COMMENT" || label.name() == "HISTORY") {
+          label += line.ToQt();
+        }
+        else {
+          // Check for a quoted value
+          if (line.substr(0,1) == "'") {
+            line.TrimHead("'");
+            label += line.Token("'").TrimHead(" ").TrimTail(" ").ToQt();
+            line.TrimHead(" '");
+          }
+          else {
+            // Access any remaining data without the trailing comment if there is one
+            IString value = line.Token("/");
+            // Clear to end of data
+            value.TrimTail(" ");
+            label += value.ToQt();
+            line.TrimHead(" ");
+          }
+          // If the line still has anything in it, treat it is as a comment.
+          if (line.size() > 0) {
+            line.TrimHead(" /");
+            label.addComment(line.ToQt());
+            // A possible format for units, other possiblites exist.
+            if (line != line.Token("[")) {
+              label.setUnits(line.Token("[").Token("]").ToQt());
+            }
+          }
+        }
+        labels += label;
+      }
+      // Load next line
+      input.seekg(place);
+      input.read(reading, 80);
+      reading[80] = '\0';
+      place += 80;
+      line = reading;
+    }
+
+    return (labels);
+  }
+
+}  //  namespace Isis
+
diff --git a/isis/src/hayabusa/apps/nirs2isis/ImportFits.h b/isis/src/hayabusa/apps/nirs2isis/ImportFits.h
new file mode 100644
index 0000000000000000000000000000000000000000..bb4850a3846249d7772ab7a815f4decb47695b29
--- /dev/null
+++ b/isis/src/hayabusa/apps/nirs2isis/ImportFits.h
@@ -0,0 +1,88 @@
+#ifndef ImportFits_h
+#define ImportFits_h
+/**
+ * @file
+ * $Revision: 5602 $
+ * $Date: 2013-11-27 11:40:00 -0700 (Wed, 27 Nov 2013) $
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are public
+ *   domain. See individual third-party library and package descriptions for
+ *   intellectual property information,user agreements, and related information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or implied,
+ *   is made by the USGS as to the accuracy and functioning of such software
+ *   and related material nor shall the fact of distribution constitute any such
+ *   warranty, and no responsibility is assumed by the USGS in connection
+ *   therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
+ *   the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+
+#include 
+
+#include 
+#include 
+#include 
+
+#include "FileName.h"
+#include "PvlObject.h"
+
+namespace Isis {
+
+  /**
+   * @brief Import a FITS file with a label description
+   *
+   * This class interrogates a \b simple file formatted with the Flexible Image
+   * Transport System (FITS) file and provides tools to converts it to an ISIS 
+   * image cube. 
+   * 
+   * Example of interrogation of a FITS file in an ImportFits object. 
+   * 
+   *   ImportFits fits(fitsfile, fitsLabelName);
+   *   Pvl label;
+   *   label.addGroup(fits.label());
+   * 
+   * 
+   * @ingroup Utility
+   *
+   * @author 2013-11-07 Kris Becker
+   *
+   * @internal 
+   */
+  class ImportFits {
+    public:
+      ImportFits();
+      ImportFits(const FileName &fitsfile, 
+                 const QString &fitsLabelName="FitsLabel");
+      ~ImportFits();
+  
+      int samples() const;
+      int lines() const;
+      int bands() const;
+
+      PvlObject label() const;
+  
+      void load(const QString &fitsfile, 
+                const QString &fitsLabelName = "FitsLabel");
+  
+    private:
+      void init();
+      PvlObject parseLabel(std::ifstream &in, const QString &fitLabelName);
+
+      // Private instance variables
+      FileName  m_file;       //!< FITS file name
+      int       m_lines;      //!< Number lines in image
+      int       m_samples;    //!< Number samples in image
+      int       m_bands;      //!< Number bands in image
+      PvlObject  m_label;      //!< FITS label converted to ISIS format
+
+  };
+
+}
+#endif
+
+
diff --git a/isis/src/hayabusa/apps/nirs2isis/Makefile b/isis/src/hayabusa/apps/nirs2isis/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..7578f0b21d038db6a5042c095cda9b34b6bb2570
--- /dev/null
+++ b/isis/src/hayabusa/apps/nirs2isis/Makefile
@@ -0,0 +1,7 @@
+ifeq ($(ISISROOT), $(BLANK))
+.SILENT:
+error:
+	echo "Please set ISISROOT";
+else
+	include $(ISISROOT)/make/isismake.apps
+endif
\ No newline at end of file
diff --git a/isis/src/hayabusa/apps/nirs2isis/nirs2isis.cpp b/isis/src/hayabusa/apps/nirs2isis/nirs2isis.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b16a0cd51de3825587323be679c207152663d9f2
--- /dev/null
+++ b/isis/src/hayabusa/apps/nirs2isis/nirs2isis.cpp
@@ -0,0 +1,182 @@
+#include "Isis.h"
+
+#include "Cube.h"
+#include "IException.h"
+#include "ImportFits.h"
+#include "iTime.h"
+#include "LineManager.h"
+#include "PixelType.h"
+#include "Preference.h"
+#include "ProcessByLine.h"
+#include "ProcessImportPds.h"
+#include "Pvl.h"
+#include "PvlGroup.h"
+#include "PvlKeyword.h"
+#include "PvlTranslationManager.h"
+#include "OriginalLabel.h"
+#include "UserInterface.h"
+
+#include 
+#include 
+
+using namespace std;
+using namespace Isis;
+
+void IsisMain() {
+
+  UserInterface &ui = Application::GetUserInterface();
+
+  ProcessImportPds processPDS;
+
+  FileName detachedLabel = ui.GetFileName("FROM");
+  Pvl label;
+  processPDS.SetPdsFile (detachedLabel.expanded(), "", label);
+
+  QString fitsImage = detachedLabel.path() + "/" + (QString) label.findKeyword("^COMBINED_SPECTRUM"); 
+  FileName fitsFile(fitsImage);
+  ImportFits fits(fitsFile, "FitsLabel");
+  label += fits.label();
+
+  QString axisCount;
+  QString axis1Length;
+  QString axis2Length;
+  try {
+    axisCount   = (QString) label.findKeyword ("NAXIS", PvlObject::Traverse);
+    axis1Length = (QString) label.findKeyword ("NAXIS1", PvlObject::Traverse);
+    axis2Length = (QString) label.findKeyword ("NAXIS2", PvlObject::Traverse);
+  }
+  catch (IException &e) {
+    QString msg = "Unable to read [NAXIS], [NAXIS1] or [NAXIS2] "
+                  "from FITS label in input [" + fitsImage + "].";
+    throw IException(e, IException::Io, msg, _FILEINFO_);
+  }
+  axisCount = axisCount.simplified().trimmed();
+  axis1Length = axis1Length.simplified().trimmed();
+  axis2Length = axis2Length.simplified().trimmed();
+  if ( !( axisCount   == "2"  &&
+          axis1Length == "64" &&
+          axis2Length == "2"     ) ) {
+    QString msg = "Input file [" + fitsImage +
+                  "] does not have the correct dimensions " +
+                  "for a Hayabusa NIRS FITS image.\n" +
+                  "Expected dimensions are [2] axes, [64 x 2]. " +
+                  "File dimensions are [" + axisCount + "] axes, [" +
+                  axis1Length + " x " + axis2Length + "].";
+    throw IException(IException::User, msg, _FILEINFO_);
+  }
+
+  processPDS.OmitOriginalLabel();
+
+  QString tempCubeName = detachedLabel.baseName() + ".temp.cub";
+  CubeAttributeOutput outputAtts = ui.GetOutputAttribute("TO");
+  outputAtts.setPixelType( Isis::Real);
+  Cube* tempCube = processPDS.SetOutputCube(tempCubeName, outputAtts);
+
+  // Convert the fits file into an ISIS cube
+  processPDS.StartProcess();
+
+  // Check the temp cube's dimensions
+  if ( (tempCube->sampleCount() != 64) ||
+       (tempCube->lineCount()   != 2 ) ||
+       (tempCube->bandCount()   != 1 )    ) {
+    QString msg = "Invalid temp cube dimensions. Dimensions "
+                  "must be 64 samples, by 2 lines, by 1 band.\n"
+                  "Temp cube dimensions are [" +
+                  toString( tempCube->sampleCount() ) +
+                  "] samples, by [" +
+                  toString( tempCube->lineCount() ) +
+                  "] lines, by [" +
+                  toString( tempCube->bandCount() ) +
+                  "] bands.";
+    throw IException(IException::Unknown, msg, _FILEINFO_);
+  }
+
+  // Write the image data to the output cubes
+
+  Cube* reflectanceCube = processPDS.SetOutputCube(ui.GetFileName("TO"),
+                                                   outputAtts,
+                                                   1, 1, 64);
+  Cube* stdevCube = processPDS.SetOutputCube(ui.GetFileName("TOSTDDEV"),
+                                             outputAtts,
+                                             1, 1, 64);
+
+  LineManager tempManager(*tempCube);
+  LineManager reflectanceManager(*reflectanceCube);
+  LineManager stdevManager(*reflectanceCube);
+
+  // The first line is reflectance values in reverse order
+  tempManager.SetLine(1);
+  tempCube->read(tempManager);
+  for (int sample = 0; sample < tempCube->sampleCount(); sample++) {
+    reflectanceManager.SetLine(1, 64 - sample);
+    reflectanceManager[0] = tempManager[sample];
+    reflectanceCube->write(reflectanceManager);
+  }
+
+  // The second line is standard deviation values in reverse order
+  tempManager.SetLine(2);
+  tempCube->read(tempManager);
+  for (int sample = 0; sample < tempCube->sampleCount(); sample++) {
+    stdevManager.SetLine(1, 64 - sample);
+    stdevManager[0] = tempManager[sample];
+    stdevCube->write(stdevManager);
+  }
+
+  PvlGroup dataDir(Preference::Preferences().findGroup("DataDirectory", Pvl::Traverse));
+  QString transDir = (QString) dataDir["hayabusa"] + "/translations/";
+  QString instrumentTrans = transDir + "nirsInstrument.trn";
+  QString archiveTrans = transDir + "nirsArchive.trn";
+
+  Pvl newLabel;
+
+  Isis::PvlTranslationManager instXlater(label, instrumentTrans);
+  instXlater.Auto(newLabel);
+
+  Isis::PvlTranslationManager archXlater(label, archiveTrans);
+  archXlater.Auto(newLabel);
+
+  // Create the bandbin group
+  // The following equation is from:
+  // Abe et al., 2004. Characteristics and current status of near infrared
+  // spectrometer for Hayabusa mission. Lunar & Planet. Sci. XXXV, 1724.
+  PvlGroup bandBinGroup("BandBin");
+  PvlKeyword filterNumber("FilterNumber");
+  PvlKeyword center("Center");
+  for (int i = 1; i <= 64; i++) {
+    filterNumber += toString( i );
+    center += toString( 2.27144 - 0.02356 * (65 - i) );
+  }
+  bandBinGroup += filterNumber;
+  bandBinGroup += center;
+
+  // Create the Kernels group
+  PvlGroup kerns("Kernels");
+  kerns += PvlKeyword("NaifFrameCode","-130200");
+
+  //  Create YearDoy keyword in Archive group
+  iTime stime(newLabel.findGroup("Instrument", Pvl::Traverse)["StartTime"][0]);
+  PvlKeyword yeardoy("YearDoy", toString(stime.Year()*1000 + stime.DayOfYear()));
+  (void) newLabel.findGroup("Archive", Pvl::Traverse).addKeyword(yeardoy);
+
+  // Add the instrument, band bin, archive, mission data, and kernels
+  // groups to the output cube labels
+  reflectanceCube->putGroup( newLabel.findGroup("Instrument", Pvl::Traverse) );
+  reflectanceCube->putGroup( bandBinGroup );
+  reflectanceCube->putGroup( newLabel.findGroup("Archive", Pvl::Traverse) );
+  reflectanceCube->putGroup( newLabel.findGroup("MissionData", Pvl::Traverse) );
+  reflectanceCube->putGroup( kerns );
+  stdevCube->putGroup( newLabel.findGroup("Instrument", Pvl::Traverse) );
+  stdevCube->putGroup( bandBinGroup );
+  stdevCube->putGroup( newLabel.findGroup("Archive", Pvl::Traverse) );
+  stdevCube->putGroup( newLabel.findGroup("MissionData", Pvl::Traverse) );
+  stdevCube->putGroup( kerns );
+
+  // Attach the original fits label and detached label
+  OriginalLabel originalFits(label);
+  reflectanceCube->write(originalFits);
+  stdevCube->write(originalFits);
+
+  // Clean up
+  processPDS.EndProcess();
+  QFile(tempCubeName).remove();
+}
diff --git a/isis/src/hayabusa/apps/nirs2isis/nirs2isis.xml b/isis/src/hayabusa/apps/nirs2isis/nirs2isis.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ff75e1082e217e41ddf7ee99b5b111b3be45a571
--- /dev/null
+++ b/isis/src/hayabusa/apps/nirs2isis/nirs2isis.xml
@@ -0,0 +1,87 @@
+
+
+
+
+  
+    Import Hayabusa NIRS FITS files into ISIS format
+  
+  
+    This program will import a PDS formatted Hayabusa Near-Infrared
+    Spectrometer (NIRS) image into ISIS cube format. The image data must be in
+    a FITS format (.fit or .fits). An accompanying label file must also be
+    provided (.lbl).
+  
+
+  
+    
+      Original version
+    
+    
+      Changed category from "Import and Export" to "Hayabusa".
+      Updated documentation after review.
+    
+  
+
+  
+    
+      nirs2isis
+    
+  
+
+  
+    Hayabusa
+  
+
+  
+    
+      
+        filename
+        input
+        
+          The image label file
+        
+        
+          The detached label file for the image. The application will use the
+          FITS image file associated with the label file. The FITS header will
+          be combined with the label file to produce complete labels for the
+          output cubes.
+        
+        
+          *.lbl *.LBL
+        
+      
+
+      
+        cube
+        output
+        
+          The output reflectance cube.
+        
+        
+          The output cube containing averaged reflectance values for the
+          entire observation. A temporary cube will be created using the output
+          cube's base name followed by ".temp.cub". This temporary file will be
+          removed when the program finishes.
+        
+        
+          *.cub
+        
+      
+
+      
+        cube
+        output
+        
+          The output standard deviation cube.
+        
+        
+          The output cube containing the standard deviation of reflectance
+          values for the entire observation.
+        
+        
+          *.cub
+        
+      
+    
+  
+
diff --git a/isis/src/hayabusa/apps/nirs2isis/tsts/Makefile b/isis/src/hayabusa/apps/nirs2isis/tsts/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..46d84c74c297304e943452a44e06b111f179a92b
--- /dev/null
+++ b/isis/src/hayabusa/apps/nirs2isis/tsts/Makefile
@@ -0,0 +1,4 @@
+BLANKS = "%-6s"    
+LENGTH = "%-40s"
+
+include $(ISISROOT)/make/isismake.tststree
diff --git a/isis/src/hayabusa/apps/nirs2isis/tsts/default/Makefile b/isis/src/hayabusa/apps/nirs2isis/tsts/default/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..8cd737a8f996b603e9fc634be8b36d50a18605e2
--- /dev/null
+++ b/isis/src/hayabusa/apps/nirs2isis/tsts/default/Makefile
@@ -0,0 +1,21 @@
+APPNAME = nirs2isis
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	$(APPNAME) from=$(INPUT)/2392975548_lvl3_0.lbl \
+	to=$(OUTPUT)/2392975548_lvl3_0.refl.cub \
+	tostddev=$(OUTPUT)/2392975548_lvl3_0.stdev.cub \
+	> /dev/null;
+	catlab from=$(OUTPUT)/2392975548_lvl3_0.refl.cub \
+	to=$(OUTPUT)/2392975548_lvl3_0.refl.pvl \
+	> /dev/null;
+	catlab from=$(OUTPUT)/2392975548_lvl3_0.stdev.cub \
+	to=$(OUTPUT)/2392975548_lvl3_0.stdev.pvl \
+	> /dev/null;
+	catoriglab from=$(OUTPUT)/2392975548_lvl3_0.refl.cub \
+	to=$(OUTPUT)/2392975548_lvl3_0.refl.orig.pvl \
+	> /dev/null;
+	catoriglab from=$(OUTPUT)/2392975548_lvl3_0.stdev.cub \
+	to=$(OUTPUT)/2392975548_lvl3_0.stdev.orig.pvl \
+	> /dev/null;
diff --git a/isis/src/hayabusa/objs/AmicaCamera/Camera.plugin b/isis/src/hayabusa/objs/AmicaCamera/Camera.plugin
deleted file mode 100644
index c48833360fa700d921210497ddde15f9fcf6f60a..0000000000000000000000000000000000000000
--- a/isis/src/hayabusa/objs/AmicaCamera/Camera.plugin
+++ /dev/null
@@ -1,6 +0,0 @@
-Group = Hayabusa/Amica
-  Version = 1
-  Library = AmicaCamera
-  Routine = AmicaCameraPlugin
-EndGroup
- 
diff --git a/isis/src/hayabusa/objs/HayabusaAmicaCamera/Camera.plugin b/isis/src/hayabusa/objs/HayabusaAmicaCamera/Camera.plugin
new file mode 100644
index 0000000000000000000000000000000000000000..5c0f9ea83edce2e4de96fcdbe371816fbd8353d2
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaAmicaCamera/Camera.plugin
@@ -0,0 +1,6 @@
+Group = Hayabusa/Amica
+  Version = 1
+  Library = HayabusaAmicaCamera
+  Routine = HayabusaAmicaCameraPlugin
+EndGroup
+ 
diff --git a/isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.cpp b/isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.cpp
similarity index 70%
rename from isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.cpp
rename to isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.cpp
index 456260396d3ea4e140433f880c433b16246d0a3b..ab5d34c246294f01200fb818a9c024201b6fd709 100644
--- a/isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.cpp
+++ b/isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.cpp
@@ -18,7 +18,7 @@
  *   http://www.usgs.gov/privacy.html.
  */
 
-#include "AmicaCamera.h"
+#include "HayabusaAmicaCamera.h"
 
 #include 
 
@@ -35,13 +35,13 @@ using namespace std;
 
 namespace Isis {
   /**
-   * Constructs a Hayabusa AmicaCamera object using the image labels.
+   * Constructs a Hayabusa HayabusaAmicaCamera object using the image labels.
    *
    * @param lab Pvl label from a Hayabusa AMICA image.
    *
    * @internal
    */
-  AmicaCamera::AmicaCamera(Cube &cube) : FramingCamera(cube) {
+  HayabusaAmicaCamera::HayabusaAmicaCamera(Cube &cube) : FramingCamera(cube) {
     m_instrumentNameLong = "Amica";
     m_instrumentNameShort = "Amica";
     m_spacecraftNameLong = "Hayabusa";
@@ -79,10 +79,20 @@ namespace Isis {
 
     focalMap->SetDetectorOrigin(bSamples, bLines);
 
-    // Setup detector map
+    // Setup detector map. FirstSample is zero-based indexing, Detector is one-based.
     CameraDetectorMap *detMap =  new CameraDetectorMap(this);
     detMap->SetStartingDetectorSample((int) inst["FirstSample"] + 1);
-    detMap->SetStartingDetectorLine((int) inst["FirstLine"] + 1);
+
+    // We flip the image over the horizontal axis on ingestion to
+    // match fits viewers. So for cubes that are for subframes, first/last line
+    // values in the label are flipped about the detector's x-axis. We need to
+    // compensate to set the detector's first line. FirstLine is zero-based
+    // indexing and there are 1024 lines on the detector so the Detector last
+    // line index is 1023.
+    int actualFirstLine = 1023 - ((int) inst["LastLine"]);
+
+    //The detector line indexing is one-based. 
+    detMap->SetStartingDetectorLine(actualFirstLine + 1);
 
     // Handle summing
     int binning = inst["Binning"];
@@ -102,6 +112,14 @@ namespace Isis {
     NaifStatus::CheckErrors();
   }
 
+
+  /** 
+   * Destructor 
+   */ 
+  HayabusaAmicaCamera::~HayabusaAmicaCamera() {
+  }
+
+
   /**
    * Returns the shutter open and close times. The user should pass in the
    * ExposureDuration keyword value, converted from milliseconds to seconds, and
@@ -124,23 +142,56 @@ namespace Isis {
    * @internal
    *   @history 2011-05-03 Jeannie Walldren - Original version.
    */
-  pair AmicaCamera::ShutterOpenCloseTimes(double time,
+  pair HayabusaAmicaCamera::ShutterOpenCloseTimes(double time,
                                                         double exposureDuration) {
     return FramingCamera::ShutterOpenCloseTimes(time, exposureDuration);
   }
+
+
+  /**
+   * CK frame ID -  - Instrument Code from spacit run on CK
+   *
+   * @return @b int The appropriate instrument code for the "Camera-matrix"
+   *         Kernel Frame ID
+   */
+  int HayabusaAmicaCamera::CkFrameId() const { 
+    return (-130000); 
+  }
+
+
+  /**
+   * CK Reference ID - J2000
+   *
+   * @return @b int The appropriate instrument code for the "Camera-matrix"
+   *         Kernel Reference ID
+   */
+  int HayabusaAmicaCamera::CkReferenceId() const { 
+    return (1); 
+  }
+
+
+  /**
+   * SPK Reference ID - J2000
+   *
+   * @return @b int The appropriate instrument code for the Spacecraft
+   *         Kernel Reference ID
+   */
+  int HayabusaAmicaCamera::SpkReferenceId() const { 
+    return (1); 
+  }
 }
 
 
 /**
- * This is the function that is called in order to instantiate an AmicaCamera
+ * This is the function that is called in order to instantiate an HayabusaAmicaCamera
  * object.
  *
  * @param lab Cube labels
  *
- * @return Isis::Camera* AmicaCamera
+ * @return Isis::Camera* HayabusaAmicaCamera
  * @internal
  *   @history 2013-11-27 Kris Becker - Original Version
  */
-extern "C" Isis::Camera *AmicaCameraPlugin(Isis::Cube &cube) {
-  return new Isis::AmicaCamera(cube);
+extern "C" Isis::Camera *HayabusaAmicaCameraPlugin(Isis::Cube &cube) {
+  return new Isis::HayabusaAmicaCamera(cube);
 }
diff --git a/isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.h b/isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.h
similarity index 73%
rename from isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.h
rename to isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.h
index a4f53290c926e45f8659d9914717a898b039f0e2..6c67df6a2c5b8a3c6b5dadfc92e2e53696659bc8 100644
--- a/isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.h
+++ b/isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.h
@@ -1,5 +1,5 @@
-#ifndef AmicaCamera_h
-#define AmicaCamera_h
+#ifndef HayabusaAmicaCamera_h
+#define HayabusaAmicaCamera_h
 /**
  * @file
  *
@@ -47,38 +47,23 @@ namespace Isis {
    *   @history 2016-09-14 Kelvin Rodriguez - Enforced the order in which BORESIGHT_LINE and
    *                           BORESIGHT_SAMPLE are added to the PVL. Part of porting to
    *                           OSX 10.11 
+   *   @history 2017-01-03 Jeannie Backer - Renamed from AmicaCamera to HayabusaAmicaCamera.
+   *   @history 2017-01-03 Jeannie Backer - Fixed bug in constructor. When setting the detector
+   *                           start line, the camera model was not taking into account the image
+   *                           flip on ingestion. Added subframe example to test. Fixes #.
    */
-  class AmicaCamera : public FramingCamera {
+  class HayabusaAmicaCamera : public FramingCamera {
     public:
-      AmicaCamera(Cube &cube);
-      /** Destructor  */
-      ~AmicaCamera() { }
-      virtual std::pair  ShutterOpenCloseTimes(double time,
-                                                             double exposureDuration);
+      HayabusaAmicaCamera(Cube &cube);
 
-      /**
-       * CK frame ID -  - Instrument Code from spacit run on CK
-       *
-       * @return @b int The appropriate instrument code for the "Camera-matrix"
-       *         Kernel Frame ID
-       */
-      virtual int CkFrameId() const { return (-130000); }
+      ~HayabusaAmicaCamera();
 
-      /**
-       * CK Reference ID - J2000
-       *
-       * @return @b int The appropriate instrument code for the "Camera-matrix"
-       *         Kernel Reference ID
-       */
-      virtual int CkReferenceId() const { return (1); }
+      virtual std::pair  ShutterOpenCloseTimes(double time,
+                                                             double exposureDuration);
 
-      /**
-       * SPK Reference ID - J2000
-       *
-       * @return @b int The appropriate instrument code for the Spacecraft
-       *         Kernel Reference ID
-       */
-      virtual int SpkReferenceId() const { return (1); }
+      virtual int CkFrameId() const;
+      virtual int CkReferenceId() const;
+      virtual int SpkReferenceId() const;
   };
 };
 #endif
diff --git a/isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.truth b/isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.truth
new file mode 100644
index 0000000000000000000000000000000000000000..aeed791189307c59264624e67e4aa13dde9497cc
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaAmicaCamera/HayabusaAmicaCamera.truth
@@ -0,0 +1,84 @@
+Unit Test for HayabusaAmicaCamera...
+
+----------------------------------------------
+Test for full frame image...
+FileName:  "st_2530292409_v.cub"
+CK Frame:  -130102
+
+Kernel IDs: 
+CK Frame ID      =  -130000
+CK Reference ID  =  1
+SPK Target ID    =  -130
+SPK Reference ID =  1
+
+Spacecraft Name Long:   "Hayabusa"
+Spacecraft Name Short:  "Hayabusa"
+Instrument Name Long:   "Amica"
+Instrument Name Short:  "Amica"
+
+Shutter open  =  "184747466.18263"
+Shutter close =  "184747466.1826735"
+
+For upper left corner ...
+DeltaSample =  0
+DeltaLine   =  0
+
+For upper right corner ...
+DeltaSample =  0
+DeltaLine   =  0
+
+For lower left corner ...
+DeltaSample =  0
+DeltaLine   =  0
+
+For lower right corner ...
+DeltaSample =  0
+DeltaLine   =  0
+
+For center pixel position ...
+Latitude OK
+Longitude OK
+DeltaSample =  0
+DeltaLine   =  0
+
+----------------------------------------------
+Test for subframe image...
+FileName:  "st_2391934788_v.cub"
+CK Frame:  -130102
+
+Kernel IDs: 
+CK Frame ID      =  -130000
+CK Reference ID  =  1
+SPK Target ID    =  -130
+SPK Reference ID =  1
+
+Spacecraft Name Long:   "Hayabusa"
+Spacecraft Name Short:  "Hayabusa"
+Instrument Name Long:   "Amica"
+Instrument Name Short:  "Amica"
+
+Shutter open  =  "180453955.8918987"
+Shutter close =  "180453955.8919857"
+
+For upper left corner ...
+DeltaSample = No Intersection
+DeltaLine   = No Intersection
+
+For upper right corner ...
+DeltaSample = No Intersection
+DeltaLine   = No Intersection
+
+For lower left corner ...
+DeltaSample = No Intersection
+DeltaLine   = No Intersection
+
+For lower right corner ...
+DeltaSample = No Intersection
+DeltaLine   = No Intersection
+
+For center pixel position ...
+Latitude OK
+Longitude OK
+DeltaSample =  0
+DeltaLine   =  0
+
diff --git a/isis/src/hayabusa/objs/HayabusaAmicaCamera/Makefile b/isis/src/hayabusa/objs/HayabusaAmicaCamera/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..f122bc88227c5c7ebd108dea5d339d1d2e074d82
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaAmicaCamera/Makefile
@@ -0,0 +1,7 @@
+ifeq ($(ISISROOT), $(BLANK))
+.SILENT:
+error:
+	echo "Please set ISISROOT";
+else
+	include $(ISISROOT)/make/isismake.objs
+endif
\ No newline at end of file
diff --git a/isis/src/hayabusa/objs/AmicaCamera/assets/amicaAddendumXXX.ti b/isis/src/hayabusa/objs/HayabusaAmicaCamera/assets/amicaAddendumXXX.ti
similarity index 100%
rename from isis/src/hayabusa/objs/AmicaCamera/assets/amicaAddendumXXX.ti
rename to isis/src/hayabusa/objs/HayabusaAmicaCamera/assets/amicaAddendumXXX.ti
diff --git a/isis/src/hayabusa/objs/HayabusaAmicaCamera/unitTest.cpp b/isis/src/hayabusa/objs/HayabusaAmicaCamera/unitTest.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..59dbd58cf7c62fa614cbf5097ea6d2615991ed7a
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaAmicaCamera/unitTest.cpp
@@ -0,0 +1,174 @@
+/**
+ * @file
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are public
+ *   domain. See individual third-party library and package descriptions for 
+ *   intellectual property information,user agreements, and related information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or implied,
+ *   is made by the USGS as to the accuracy and functioning of such software 
+ *   and related material nor shall the fact of distribution constitute any such 
+ *   warranty, and no responsibility is assumed by the USGS in connection 
+ *   therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see 
+ *   the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+#include 
+
+#include 
+#include 
+
+#include "HayabusaAmicaCamera.h"
+#include "Camera.h"
+#include "CameraFactory.h"
+#include "IException.h"
+#include "iTime.h"
+#include "Preference.h"
+#include "Pvl.h"
+#include "PvlGroup.h"
+
+using namespace std;
+using namespace Isis;
+
+void testCamera(Cube &c, double knownLat, double knownLon);
+void testLineSamp(Camera *cam, double sample, double line);
+
+/**
+ * Unit Test for the Hayabusa AMICA camera.
+ *
+ * @author  2013-11-27 Kris Becker
+ *
+ * @internal
+ *   @history 2013-11-27 Kris Becker - Original version
+ *   @history 2017-01-03 Jeannie Backer - Added subframe example. 100% test
+ *            coverage.
+ */
+int main(void) {
+  Preference::Preferences(true);
+
+  qDebug() << "Unit Test for HayabusaAmicaCamera...";
+  try {
+    // These should be lat/lon at center of image. To obtain these numbers for a new cube/camera,
+    // set both the known lat and known lon to zero and copy the unit test output "Latitude off by: "
+    // and "Longitude off by: " values directly into these variables.
+    qDebug() << "";
+    qDebug() << "----------------------------------------------";
+    qDebug() << "Test for full frame image...";
+    double knownLat = 7.1916683215196819;
+    double knownLon = 38.6275886424948496;
+    Cube c("$hayabusa/testData/st_2530292409_v.cub", "r");
+    testCamera(c, knownLat, knownLon);
+
+    qDebug() << "----------------------------------------------";
+    qDebug() << "Test for subframe image...";
+    knownLat = -0.5692959687806523;
+    knownLon = 210.4073369962932816;
+    Cube c2("$hayabusa/testData/st_2391934788_v.cub", "r");
+    testCamera(c2, knownLat, knownLon);
+  }
+  catch(IException &e) {
+    e.print();
+  }
+
+}
+
+
+void testCamera(Cube &c, double knownLat, double knownLon) {
+  HayabusaAmicaCamera *cam = (HayabusaAmicaCamera *) CameraFactory::Create(c);
+  qDebug() << "FileName: " << FileName(c.fileName()).name();
+  qDebug() << "CK Frame: " << cam->instrumentRotation()->Frame();
+  qDebug() << "";
+
+  // Test kernel IDs
+  qDebug() << "Kernel IDs: ";
+  qDebug() << "CK Frame ID      = " << cam->CkFrameId();
+  qDebug() << "CK Reference ID  = " << cam->CkReferenceId();
+  qDebug() << "SPK Target ID    = " << cam->SpkTargetId();
+  qDebug() << "SPK Reference ID = " << cam->SpkReferenceId();
+  qDebug() << "";
+  
+  // Test name methods
+  qDebug() << "Spacecraft Name Long:  " << cam->spacecraftNameLong();
+  qDebug() << "Spacecraft Name Short: " << cam->spacecraftNameShort();
+  qDebug() << "Instrument Name Long:  " << cam->instrumentNameLong();
+  qDebug() << "Instrument Name Short: " << cam->instrumentNameShort();
+  qDebug() << "";
+
+  // Test Shutter Open/Close 
+  const PvlGroup &inst = c.label()->findGroup("Instrument", Pvl::Traverse);
+  double exposureDuration = ((double) inst["ExposureDuration"])/1000;
+  QString stime = inst["StartTime"];
+  double et; // StartTime keyword is the center exposure time
+  str2et_c(stime.toLatin1().data(), &et);
+  pair  shuttertimes = cam->ShutterOpenCloseTimes(et, exposureDuration);
+  qDebug() << "Shutter open  = " << toString(shuttertimes.first.Et(), 16);
+  qDebug() << "Shutter close = " << toString(shuttertimes.second.Et(), 16);
+  qDebug() << "";
+
+  // Test all four corners to make sure the conversions are right
+  qDebug() << "For upper left corner ...";
+  testLineSamp(cam, 1.0, 1.0);
+
+  qDebug() << "For upper right corner ...";
+  testLineSamp(cam, cam->Samples(), 1.0);
+
+  qDebug() << "For lower left corner ...";
+  testLineSamp(cam, 1.0, cam->Lines());
+
+  qDebug() << "For lower right corner ...";
+  testLineSamp(cam, cam->Samples(), cam->Lines());
+
+  qDebug() << "For center pixel position ...";
+
+  if(!cam->SetImage((cam->Samples()/2.0), (cam->Lines()/2.0))) {
+    throw IException(IException::Unknown, "ERROR setting image to known position.", _FILEINFO_);
+  }
+
+  if(abs(cam->UniversalLatitude() - knownLat) < 1E-10) {
+    qDebug() << "Latitude OK";
+  }
+  else {
+    qDebug() << "Latitude off by:  " << toString(cam->UniversalLatitude() - knownLat, 16);
+  }
+
+  if(abs(cam->UniversalLongitude() - knownLon) < 1E-10) {
+    qDebug() << "Longitude OK";
+  }
+  else {
+    qDebug() << "Longitude off by: " << toString(cam->UniversalLongitude() - knownLon, 16);
+  }
+
+  testLineSamp( cam, (cam->Samples()/2.0), (cam->Lines()/2.0) );
+}
+
+
+void testLineSamp(Camera *cam, double sample, double line) {
+  bool success = cam->SetImage(sample, line);
+
+  if(success) {
+    success = cam->SetUniversalGround(cam->UniversalLatitude(), cam->UniversalLongitude());
+  }
+
+  if(success) {
+    double deltaSamp = sample - cam->Sample();
+    double deltaLine = line - cam->Line();
+//    qDebug() << "DeltaSample = " << deltaSamp;
+//    qDebug() << "DeltaLine   = " << deltaLine;
+//    qDebug() << "";
+    if(fabs(deltaSamp) < 0.001) deltaSamp = 0;
+    if(fabs(deltaLine) < 0.001) deltaLine = 0;
+    qDebug() << "DeltaSample = " << deltaSamp;
+    qDebug() << "DeltaLine   = " << deltaLine;
+    qDebug() << "";
+  }
+  else {
+    qDebug() << "DeltaSample = No Intersection";
+    qDebug() << "DeltaLine   = No Intersection";
+    qDebug() << "";
+  }
+}
+
diff --git a/isis/src/hayabusa/objs/HayabusaNirsCamera/Camera.plugin b/isis/src/hayabusa/objs/HayabusaNirsCamera/Camera.plugin
new file mode 100644
index 0000000000000000000000000000000000000000..5d0fc51dd60d1b88ed0123695feeb55d7a0d386a
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/Camera.plugin
@@ -0,0 +1,6 @@
+Group = Hayabusa/Nirs
+  Version = 1
+  Library = HayabusaNirsCamera
+  Routine = HayabusaNirsCameraPlugin
+EndGroup
+ 
diff --git a/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.cpp b/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..643f90f57d1e1b46a11e258fb194b375b8295f3b
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.cpp
@@ -0,0 +1,185 @@
+/**
+ * @file
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are public
+ *   domain. See individual third-party library and package descriptions for
+ *   intellectual property information,user agreements, and related information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or implied,
+ *   is made by the USGS as to the accuracy and functioning of such software
+ *   and related material nor shall the fact of distribution constitute any such
+ *   warranty, and no responsibility is assumed by the USGS in connection
+ *   therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
+ *   the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+
+#include "HayabusaNirsCamera.h"
+
+#include 
+
+#include "CameraDistortionMap.h"
+#include "CameraFocalPlaneMap.h"
+#include "CameraGroundMap.h"
+#include "CameraSkyMap.h"
+#include "IString.h"
+#include "iTime.h"
+#include "NaifStatus.h"
+#include "NirsDetectorMap.h"
+
+using namespace std;
+
+namespace Isis {
+  /**
+   * Constructs a HayabusaNirsCamera object using the image labels.
+   *
+   * @param lab Pvl label from a Hayabusa NIRS image.
+   *
+   * @internal
+   */
+  HayabusaNirsCamera::HayabusaNirsCamera(Cube &cube) : FramingCamera(cube) {
+    m_instrumentNameLong = "Near InfraRed Spectrometer";
+    m_instrumentNameShort = "NIRS";
+    m_spacecraftNameLong = "Hayabusa";
+    m_spacecraftNameShort = "Hayabusa";
+
+    NaifStatus::CheckErrors();
+    Pvl &lab = *cube.label();
+
+    // Get focal length and pixel pitch from IAK
+    SetFocalLength();
+    SetFocalLength(FocalLength() * 1000.0);  // Convert from meters to mm
+    SetPixelPitch();
+
+    // Get the start time in et
+    PvlGroup &inst = lab.findGroup("Instrument", Pvl::Traverse);
+
+    // get the start and stop times
+    QString startTime = inst["SpacecraftClockStartCount"];
+    QString stopTime = inst["SpacecraftClockStopCount"];
+    iTime etStart = getClockTime(startTime);
+    iTime etStop = getClockTime(stopTime);
+
+    double exposureDuration = etStop - etStart;
+    iTime centerTime  = etStart + (exposureDuration / 2.0);
+
+    // Setup focal plane map
+    CameraFocalPlaneMap *focalMap = new CameraFocalPlaneMap(this, naifIkCode());
+    
+    // lines and samples added to the pvl in the order you
+    // call getDouble()
+    double bLines = Spice::getDouble("INS" + toString(naifIkCode()) + "_BORESIGHT_LINE");
+    double bSamples = Spice::getDouble("INS" + toString(naifIkCode()) + "_BORESIGHT_SAMPLE");
+
+    focalMap->SetDetectorOrigin(bSamples, bLines);
+
+    // Setup detector map
+    CameraDetectorMap *detMap = new NirsDetectorMap(exposureDuration, this);
+    detMap->SetStartingDetectorSample(0);
+    detMap->SetStartingDetectorLine(0);
+
+    // Setup distortion map
+    new CameraDistortionMap(this);
+
+    // Setup the ground and sky map
+    new CameraGroundMap(this);
+    new CameraSkyMap(this);
+
+    setTime(centerTime);
+    LoadCache();
+    NaifStatus::CheckErrors();
+  }
+
+
+  /**
+   * Destroys a HayabusaNirsCamera object
+   */
+  HayabusaNirsCamera::~HayabusaNirsCamera() {
+    
+  }
+
+
+  /**
+   * Returns the shutter open and close times. The user should pass in the
+   * ExposureDuration keyword value, converted from milliseconds to seconds, and
+   * the StartTime keyword value, converted to ephemeris time. The StartTime
+   * keyword value from the labels represents the time at the start of the
+   * observation, as noted in the Clementine EDR image SIS. This method uses the
+   * FramingCamera class implementation, returning the given time value as the
+   * shutter open and the sum of the time value and exposure duration as the
+   * shutter close.
+   *
+   * @param exposureDuration ExposureDuration keyword value from the labels,
+   *                         converted to seconds.
+   * @param time The StartTime keyword value from the labels, converted to
+   *             ephemeris time.
+   *
+   * @return @b pair < @b iTime, @b iTime > The first value is the shutter
+   *         open time and the second is the shutter close time.
+   *
+   * @author 2011-05-03 Jeannie Walldren
+   * @internal
+   *   @history 2011-05-03 Jeannie Walldren - Original version.
+   */
+  pair HayabusaNirsCamera::ShutterOpenCloseTimes(double time,
+                                                               double exposureDuration) {
+    return FramingCamera::ShutterOpenCloseTimes(time, exposureDuration);
+  }
+
+
+  /**
+   * @brief Returns the pixel ifov offsets from center of pixel.
+   * 
+   * Returns the pixel ifov offset from the center of pixel for 8 points along
+   * each edge of the fov. The Camera implementation only uses the four
+   * corners.  Because the FOV of each pixel is so large, this uses 8 points on
+   * each edge for a total of 28 points.
+   * 
+   * @return @b QList A list of offset values to add to the look vector.
+   */
+   QList HayabusaNirsCamera::PixelIfovOffsets() {
+
+     QList offsets;
+
+     //  Create 8 pts on each edge of pixel
+     int npts = 8;
+
+     //  Top edge of pixel
+     for (double x = -PixelPitch() / 2.0; x <= PixelPitch() / 2.0; x += PixelPitch() / (npts-1)) {
+       offsets.append(QPointF(x, -PixelPitch() / 2.0));
+     }
+     //  Right edge of pixel
+     for (double y = -PixelPitch() / 2.0; y <= PixelPitch() / 2.0; y += PixelPitch() / (npts-1)) {
+       offsets.append(QPointF(PixelPitch() / 2.0, y));
+     }
+     //  Bottom edge of pixel
+     for (double x = PixelPitch() / 2.0; x >= -PixelPitch() / 2.0; x -= PixelPitch() / (npts-1)) {
+       offsets.append(QPointF(x, PixelPitch() / 2.0));
+     }
+     //  Left edge of pixel
+     for (double y = PixelPitch() / 2.0; y >= -PixelPitch() / 2.0; y -= PixelPitch() / (npts-1)) {
+       offsets.append(QPointF(-PixelPitch() / 2.0, y));
+     }
+
+     return offsets;
+   }
+}
+
+
+/**
+ * This is the function that is called in order to instantiate a HayabusaNirsCamera
+ * object.
+ *
+ * @param lab Cube labels
+ *
+ * @return Isis::Camera* HayabusaNirsCamera
+ * @internal
+ *   @history 2013-11-27 Kris Becker - Original Version
+ */
+extern "C" Isis::Camera *HayabusaNirsCameraPlugin(Isis::Cube &cube) {
+  return new Isis::HayabusaNirsCamera(cube);
+}
diff --git a/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.h b/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.h
new file mode 100644
index 0000000000000000000000000000000000000000..2ccaf6cbb36e92691e645930e295714a6b828795
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.h
@@ -0,0 +1,73 @@
+#ifndef HayabusaNirsCamera_h
+#define HayabusaNirsCamera_h
+/**
+ * @file
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are public
+ *   domain. See individual third-party library and package descriptions for
+ *   intellectual property information,user agreements, and related information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or implied,
+ *   is made by the USGS as to the accuracy and functioning of such software
+ *   and related material nor shall the fact of distribution constitute any such
+ *   warranty, and no responsibility is assumed by the USGS in connection
+ *   therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
+ *   the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+
+#include "FramingCamera.h"
+
+namespace Isis {
+  /**
+   * This is the camera model for the Hayabusa NIRS camera.
+   *
+   * @ingroup SpiceInstrumentsAndCameras
+   * @ingroup Hayabusa
+   *
+   * @author 2016-12-30 Jesse Mapel
+   *
+   * @internal
+   *   @history 2016-12-30 Jesse Mapel - Original version.
+   *                           Modified from AmicaCamera. Fixes #4576.
+   */
+  class HayabusaNirsCamera : public FramingCamera {
+    public:
+      HayabusaNirsCamera(Cube &cube);
+      ~HayabusaNirsCamera();
+
+      /**
+       * CK frame ID - Instrument Code from spacit run on CK
+       *
+       * @return @b int The appropriate instrument code for the "Camera-matrix"
+       *         Kernel Frame ID
+       */
+      virtual int CkFrameId() const { return (-130000); }
+
+      /**
+       * CK Reference ID - J2000
+       *
+       * @return @b int The appropriate instrument code for the "Camera-matrix"
+       *         Kernel Reference ID
+       */
+      virtual int CkReferenceId() const { return (1); }
+
+      /**
+       * SPK Reference ID - J2000
+       *
+       * @return @b int The appropriate instrument code for the Spacecraft
+       *         Kernel Reference ID
+       */
+      virtual int SpkReferenceId() const { return (1); }
+
+      virtual std::pair ShutterOpenCloseTimes(double time,
+                                                            double exposureDuration);
+
+      virtual QList PixelIfovOffsets();
+  };
+};
+#endif
diff --git a/isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.truth b/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.truth
similarity index 54%
rename from isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.truth
rename to isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.truth
index 2271acfd62edefcb39da845482fccf8d07bd4503..9a10329b06c6babe53bff3cf228fb094634a3cf7 100644
--- a/isis/src/hayabusa/objs/AmicaCamera/AmicaCamera.truth
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/HayabusaNirsCamera.truth
@@ -1,6 +1,6 @@
-Unit Test for AmicaCamera...
-FileName: st_2530292409_v.cub
-CK Frame: -130102
+Unit Test for HayabusaNirsCamera...
+FileName: 2392975548_lvl3_0.refl.cub
+CK Frame: -130200
 
 Kernel IDs: 
 CK Frame ID = -130000
@@ -10,19 +10,16 @@ SPK Reference ID = 1
 
 Spacecraft Name Long: Hayabusa
 Spacecraft Name Short: Hayabusa
-Instrument Name Long: Amica
-Instrument Name Short: Amica
-
-Shutter open = 184747466.182630032
-Shutter close = 184747466.182673544
+Instrument Name Long: Near InfraRed Spectrometer
+Instrument Name Short: NIRS
 
 For upper left corner ...
-DeltaSample = 0.000000000
-DeltaLine = 0.000000000
+DeltaSample = ERROR
+DeltaLine = ERROR
 
 For upper right corner ...
-DeltaSample = 0.000000000
-DeltaLine = 0.000000000
+DeltaSample = ERROR
+DeltaLine = ERROR
 
 For lower left corner ...
 DeltaSample = 0.000000000
@@ -35,6 +32,3 @@ DeltaLine = 0.000000000
 For center pixel position ...
 Latitude OK
 Longitude OK
-DeltaSample = 0.000000000
-DeltaLine = 0.000000000
-
diff --git a/isis/src/hayabusa/objs/HayabusaNirsCamera/Makefile b/isis/src/hayabusa/objs/HayabusaNirsCamera/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..f122bc88227c5c7ebd108dea5d339d1d2e074d82
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/Makefile
@@ -0,0 +1,7 @@
+ifeq ($(ISISROOT), $(BLANK))
+.SILENT:
+error:
+	echo "Please set ISISROOT";
+else
+	include $(ISISROOT)/make/isismake.objs
+endif
\ No newline at end of file
diff --git a/isis/src/hayabusa/objs/HayabusaNirsCamera/NirsDetectorMap.cpp b/isis/src/hayabusa/objs/HayabusaNirsCamera/NirsDetectorMap.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a3f791fa4f734b3069b93dea34079f6d94c89541
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/NirsDetectorMap.cpp
@@ -0,0 +1,71 @@
+/**
+ * @file
+ * $Revision: 1.2 $
+ * $Date: 2009/04/08 02:32:55 $
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are
+ *   public domain. See individual third-party library and package descriptions
+ *   for intellectual property information, user agreements, and related
+ *   information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or
+ *   implied, is made by the USGS as to the accuracy and functioning of such
+ *   software and related material nor shall the fact of distribution
+ *   constitute any such warranty, and no responsibility is assumed by the
+ *   USGS in connection therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html
+ *   in a browser or see the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+#include "NirsDetectorMap.h"
+
+namespace Isis {
+
+  /**
+   * Constructs a NirsDetectorMap object.
+   * 
+   * @param exposureDuration The time for the observations.
+   * @param parent The parent camera that uses the detector map.
+   */
+  NirsDetectorMap::NirsDetectorMap(double exposureDuration, Camera *parent = 0):
+                                   CameraDetectorMap(parent) {
+    m_exposureDuration = exposureDuration;
+  }
+
+
+  /**
+   * Destroys a NirsDetectorMap object.
+   */
+  NirsDetectorMap::~NirsDetectorMap() {
+    
+  }
+
+
+  /**
+   * Sets the exposure duration
+   * 
+   * @param exposureDuration The time for the observations.
+   */
+  void NirsDetectorMap::setExposureDuration(double exposureDuration) {
+    m_exposureDuration = exposureDuration;
+  }
+
+
+  /**
+   * Returns the exposure duration for a given pixel.
+   * 
+   * @param sample The sample location of the pixel.
+   * @param line The line location of the pixel.
+   * @param band The band location of the pixel.
+   * 
+   * @return @b double The exposure duration for the pixel in seconds.
+   */
+  double NirsDetectorMap::exposureDuration(const double sample,
+                                           const double line,
+                                           const int band) const {
+    return m_exposureDuration;
+  }
+}
\ No newline at end of file
diff --git a/isis/src/hayabusa/objs/HayabusaNirsCamera/NirsDetectorMap.h b/isis/src/hayabusa/objs/HayabusaNirsCamera/NirsDetectorMap.h
new file mode 100644
index 0000000000000000000000000000000000000000..ed2aef2149d85b37aea6e8e5cac90b6aa9e17d47
--- /dev/null
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/NirsDetectorMap.h
@@ -0,0 +1,55 @@
+#ifndef NirsDetectorMap_h
+#define NirsDetectorMap_h
+/**
+ * @file
+ *
+ *   Unless noted otherwise, the portions of Isis written by the USGS are public
+ *   domain. See individual third-party library and package descriptions for
+ *   intellectual property information,user agreements, and related information.
+ *
+ *   Although Isis has been used by the USGS, no warranty, expressed or implied,
+ *   is made by the USGS as to the accuracy and functioning of such software
+ *   and related material nor shall the fact of distribution constitute any such
+ *   warranty, and no responsibility is assumed by the USGS in connection
+ *   therewith.
+ *
+ *   For additional information, launch
+ *   $ISISROOT/doc//documents/Disclaimers/Disclaimers.html in a browser or see
+ *   the Privacy & Disclaimers page on the Isis website,
+ *   http://isis.astrogeology.usgs.gov, and the USGS privacy and disclaimers on
+ *   http://www.usgs.gov/privacy.html.
+ */
+
+#include "CameraDetectorMap.h"
+
+namespace Isis {
+  /**
+   * @brief The detector map class for the Hayabusa NIRS camera.
+   * 
+   * The detector map class to allow for exposure duration storage and retrieval
+   * in the Hayabusa NIRS camera.
+   *
+   * @ingroup SpiceInstrumentsAndCameras
+   * @ingroup Hayabusa
+   *
+   * @author 2017-01-04 Jesse Mapel
+   *
+   * @internal
+   *   @history 2017-01-04 Jesse Mapel - Original version. Fixes #4576.
+   */
+  class NirsDetectorMap : public CameraDetectorMap {
+    public:
+      NirsDetectorMap(double exposureDuration, Camera *parent);
+
+      ~NirsDetectorMap();
+
+      void setExposureDuration(double exposureDuration);
+
+      virtual double exposureDuration(const double sample,
+                                      const double line,
+                                      const int band) const;
+    protected:
+      double m_exposureDuration; //!< The total time for the observation
+  };
+};
+#endif
\ No newline at end of file
diff --git a/isis/src/hayabusa/objs/AmicaCamera/unitTest.cpp b/isis/src/hayabusa/objs/HayabusaNirsCamera/unitTest.cpp
similarity index 78%
rename from isis/src/hayabusa/objs/AmicaCamera/unitTest.cpp
rename to isis/src/hayabusa/objs/HayabusaNirsCamera/unitTest.cpp
index aeb70523cec026f13c3a53bc2241bd202713ad1c..64530ab4b15dd75d90d515a07ce34b5a7b78d0a5 100644
--- a/isis/src/hayabusa/objs/AmicaCamera/unitTest.cpp
+++ b/isis/src/hayabusa/objs/HayabusaNirsCamera/unitTest.cpp
@@ -20,7 +20,7 @@
 #include 
 #include 
 
-#include "AmicaCamera.h"
+#include "HayabusaNirsCamera.h"
 #include "Camera.h"
 #include "CameraFactory.h"
 #include "IException.h"
@@ -37,16 +37,16 @@ void TestLineSamp(Camera *cam, double samp, double line);
 int main(void) {
   Preference::Preferences(true);
 
-  cout << "Unit Test for AmicaCamera..." << endl;
+  cout << "Unit Test for HayabusaNirsCamera..." << endl;
   try {
     // These should be lat/lon at center of image. To obtain these numbers for a new cube/camera,
     // set both the known lat and known lon to zero and copy the unit test output "Latitude off by: "
     // and "Longitude off by: " values directly into these variables.
-    double knownLat = 7.1916683215196819;
-    double knownLon = 38.6275886424948496;
+    double knownLat = 36.1707660310976067;
+    double knownLon = 345.6570666219602685;
 
-    Cube c("$hayabusa/testData/st_2530292409_v.cub", "r");
-    AmicaCamera *cam = (AmicaCamera *) CameraFactory::Create(c);
+    Cube c("$hayabusa/testData/2392975548_lvl3_0.refl.cub", "r");
+    HayabusaNirsCamera *cam = (HayabusaNirsCamera *) CameraFactory::Create(c);
     cout << "FileName: " << FileName(c.fileName()).name() << endl;
     cout << "CK Frame: " << cam->instrumentRotation()->Frame() << endl << endl;
     cout.setf(std::ios::fixed);
@@ -65,31 +65,21 @@ int main(void) {
     cout << "Instrument Name Long: " << cam->instrumentNameLong() << endl;
     cout << "Instrument Name Short: " << cam->instrumentNameShort() << endl << endl;
 
-    // Test Shutter Open/Close 
-    const PvlGroup &inst = c.label()->findGroup("Instrument", Pvl::Traverse);
-    double exposureDuration = ((double) inst["ExposureDuration"])/1000;
-    QString stime = inst["StartTime"];
-    double et; // StartTime keyword is the center exposure time
-    str2et_c(stime.toLatin1().data(), &et);
-    pair  shuttertimes = cam->ShutterOpenCloseTimes(et, exposureDuration);
-    cout << "Shutter open = " << shuttertimes.first.Et() << endl;
-    cout << "Shutter close = " << shuttertimes.second.Et() << endl << endl;
-
     // Test all four corners to make sure the conversions are right
     cout << "For upper left corner ..." << endl;
-    TestLineSamp(cam, 1.0, 1.0);
+    TestLineSamp(cam, 0.5, 0.5);
 
     cout << "For upper right corner ..." << endl;
-    TestLineSamp(cam, cam->Samples(), 1.0);
+    TestLineSamp(cam, 1.5, 0.5);
 
     cout << "For lower left corner ..." << endl;
-    TestLineSamp(cam, 1.0, cam->Lines());
+    TestLineSamp(cam, 0.5, 1.5);
 
     cout << "For lower right corner ..." << endl;
-    TestLineSamp(cam, cam->Samples(), cam->Lines());
+    TestLineSamp(cam, 1.5, 1.5);
 
-    double samp = cam->Samples() / 2;
-    double line = cam->Lines() / 2;
+    double samp = 1;
+    double line = 1;
     cout << "For center pixel position ..." << endl;
 
     if(!cam->SetImage(samp, line)) {
@@ -110,8 +100,6 @@ int main(void) {
     else {
       cout << setprecision(16) << "Longitude off by: " << cam->UniversalLongitude() - knownLon << endl;
     }
-
-    TestLineSamp(cam, samp, line);
   }
   catch(IException &e) {
     e.print();
diff --git a/isis/src/hayabusa/tsts/Makefile b/isis/src/hayabusa/tsts/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..016388fc898d8c89f380cae1fd08942c29611582
--- /dev/null
+++ b/isis/src/hayabusa/tsts/Makefile
@@ -0,0 +1,4 @@
+BLANKS = "%-6s"    
+LENGTH = "%-42s"
+
+include $(ISISROOT)/make/isismake.tststree
diff --git a/isis/src/hayabusa/tsts/fullframe/Makefile b/isis/src/hayabusa/tsts/fullframe/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..b2803875aefdd7790fabc4b7c1e99d7d5d76a681
--- /dev/null
+++ b/isis/src/hayabusa/tsts/fullframe/Makefile
@@ -0,0 +1,66 @@
+# 2017-01-03 Jeannie Backer - Make sure that proper spice is added to labels.
+#
+# This test uses a full frame cube to verify that the cube has the proper labels after 
+# 1. spiceinit with dsk
+# 2. sumspice, updating times
+# 3. spiceinit
+# 4. sumspice, updating spice
+ 
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	amica2isis $(TSTARGS) from=$(INPUT)/st_2393680156_v.lbl \
+	                      to=$(OUTPUT)/st_2393680156_v.cub \
+	                      > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                  to=$(OUTPUT)/st_2393680156_v_label.pvl \
+	                  > /dev/null;
+	spiceinit $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                     ckpredict=true \
+	                     spkpredict=true \
+	                     shape=user \
+	                     model='$$hayabusa/kernels/dsk/hay_a_amica_5_itokawashape_v1_0_512q.bds' \
+	                     > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                  to=$(OUTPUT)/st_2393680156_v_label_init.pvl \
+	                  > /dev/null;
+	campt $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                 to=$(OUTPUT)/st_2393680156_v_campt_init.pvl \
+	                 > /dev/null;
+	sumspice $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                    sumfile=$(INPUT)/N2391934788.SUM \
+	                    update=times \
+	                    > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                  to=$(OUTPUT)/st_2393680156_v_label_init_timeupdate.pvl \
+	                  > /dev/null;
+	spiceinit $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                     ckpredict=true \
+	                     spkpredict=true \
+	                     shape=user \
+	                     model='$$hayabusa/kernels/dsk/hay_a_amica_5_itokawashape_v1_0_512q.bds' \
+	                     > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                  to=$(OUTPUT)/st_2393680156_v_label_init_timeupdate_init.pvl \
+	                  > /dev/null;
+	campt $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                 to=$(OUTPUT)/st_2393680156_v_campt_init_timeupdate_init.pvl \
+					 sample=450 \
+					 line=512 \
+	                 > /dev/null;
+	sumspice $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                    sumfile=$(INPUT)/N2391934788.SUM \
+	                    update=spice \
+	                    > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                  to=$(OUTPUT)/st_2393680156_v_label_init_timeupdate_init_spiceupdate.pvl \
+	                  > /dev/null;
+	campt $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                 to=$(OUTPUT)/st_2393680156_v_campt_init_timeupdate_init_spiceupdate.pvl \
+					 sample=450 \
+					 line=512 \
+	                 > /dev/null;
+	$(ECHO) "Output of getsn..." > $(OUTPUT)/st_2393680156_v--getsnOutput.txt
+	getsn $(TSTARGS) from=$(OUTPUT)/st_2393680156_v.cub \
+	                 >> $(OUTPUT)/st_2393680156_v--getsnOutput.txt
+	                 > /dev/null;
diff --git a/isis/src/hayabusa/tsts/subframe/Makefile b/isis/src/hayabusa/tsts/subframe/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..6c96813d803b0b761f2b4995c12b866ececa20a7
--- /dev/null
+++ b/isis/src/hayabusa/tsts/subframe/Makefile
@@ -0,0 +1,62 @@
+# 2017-01-03 Jeannie Backer - Make sure that proper spice is added to labels.
+#
+# This test uses a subframe cube to verify that the cube has the proper labels after 
+# 1. spiceinit with dsk
+# 2. sumspice, updating times
+# 3. spiceinit
+# 4. sumspice, updating spice
+ 
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	amica2isis $(TSTARGS) from=$(INPUT)/st_2391934788_v.lbl \
+	                      to=$(OUTPUT)/st_2391934788_v.cub \
+	                      > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                  to=$(OUTPUT)/st_2391934788_v_label.pvl \
+	                  > /dev/null;
+	spiceinit $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                     ckpredict=true \
+	                     spkpredict=true \
+	                     shape=user \
+	                     model='$$hayabusa/kernels/dsk/hay_a_amica_5_itokawashape_v1_0_512q.bds' \
+	                     > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                  to=$(OUTPUT)/st_2391934788_v_label_init.pvl \
+	                  > /dev/null;
+	campt $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                 to=$(OUTPUT)/st_2391934788_v_campt_init.pvl \
+	                 > /dev/null;
+	sumspice $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                    sumfile=$(INPUT)/N2391934788.SUM \
+	                    update=times \
+	                    > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                  to=$(OUTPUT)/st_2391934788_v_label_init_timeupdate.pvl \
+	                  > /dev/null;
+	spiceinit $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                     ckpredict=true \
+	                     spkpredict=true \
+	                     shape=user \
+	                     model='$$hayabusa/kernels/dsk/hay_a_amica_5_itokawashape_v1_0_512q.bds' \
+	                     > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                  to=$(OUTPUT)/st_2391934788_v_label_init_timeupdate_init.pvl \
+	                  > /dev/null;
+	campt $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                 to=$(OUTPUT)/st_2391934788_v_campt_init_timeupdate_init.pvl \
+	                 > /dev/null;
+	sumspice $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                    sumfile=$(INPUT)/N2391934788.SUM \
+	                    update=spice \
+	                    > /dev/null;
+	catlab $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                  to=$(OUTPUT)/st_2391934788_v_label_init_timeupdate_init_spiceupdate.pvl \
+	                  > /dev/null;
+	campt $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                 to=$(OUTPUT)/st_2391934788_v_campt_init_timeupdate_init_spiceupdate.pvl \
+	                 > /dev/null;
+	$(ECHO) "Output of getsn..." > $(OUTPUT)/st_2391934788_v--getsnOutput.txt
+	getsn $(TSTARGS) from=$(OUTPUT)/st_2391934788_v.cub \
+	                 >> $(OUTPUT)/st_2391934788_v--getsnOutput.txt
+	                 > /dev/null;
diff --git a/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.cpp b/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.cpp
index d8d12367207200099dc2e75f85bbacc28a3a72ef..99ba4d231c3dd225c1cacbbc9e298f25aa55bf40 100644
--- a/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.cpp
+++ b/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.cpp
@@ -22,10 +22,17 @@
  */
 #include "CNetSuiteMainWindow.h"
 
+#include 
+#include 
+#include 
+#include 
+#include 
 #include 
 #include 
 #include 
+#include 
 #include 
+#include 
 
 #include "AbstractProjectItemView.h"
 #include "Directory.h"
@@ -84,7 +91,7 @@ namespace Isis {
 
     QStringList args = QCoreApplication::arguments();
 /**
-    if (args.count() == 2) {    
+    if (args.count() == 2) {
       qDebug() << args.last();
       m_directory->project()->open(args.last());
     }
@@ -174,18 +181,20 @@ namespace Isis {
     centralWidget->setTabsMovable(true);
     centralWidget->setTabsClosable(true);
 
-    // ken testing
-    setActiveView(projectTreeView);
-    // ken testing
-
     if (args.count() == 2) {
       m_directory->project()->open(args.last());
     }
+
+    // ken testing  If this is used, we will not need to call updateMenuActions() or updateToolBar()
+    // above.  They are both called from setActiveView.
+    //  setActiveView(projectTreeView);
+    // ken testing
   }
 
 
   /**
-   * 
+   * This is connected from Directory's newWidgetAvailable signal and called when re-attaching a
+   * view which was detached from the MDI main window.
    *
    * @param[in] newWidget (QWidget *)
    */
@@ -201,6 +210,8 @@ namespace Isis {
       if ( QMdiArea *mdiArea = qobject_cast( centralWidget() ) ) {
         mdiArea->addSubWindow(newWidget);
         newWidget->show();
+        mdiArea->setActiveSubWindow(qobject_cast(newWidget));
+        setActiveView(qobject_cast(newWidget));
       }
     }
   }
@@ -234,59 +245,71 @@ namespace Isis {
   void CNetSuiteMainWindow::updateMenuActions() {
 
     m_fileMenu->clear();
+    // Get Directory FileMenu actions
     foreach ( QAction *action, m_directory->fileMenuActions() ) {
       m_fileMenu->addAction(action);
     }
     m_fileMenu->addSeparator();
+    // Get FileMenu actions for the active view (eg. CubeDnView, Footprint2DView)
     if (m_activeView) {
       foreach ( QAction *action, m_activeView->fileMenuActions() ) {
         m_fileMenu->addAction(action);
       }
     }
     m_fileMenu->addSeparator();
+    // Get FileMenu actions from the CNetsuiteMainWindow, Exit is the only action
     foreach ( QAction *action, m_fileMenuActions ) {
       m_fileMenu->addAction(action);
     }
 
     m_projectMenu->clear();
+    //  Get Project menu actions from Directory
     foreach ( QAction *action, m_directory->projectMenuActions() ) {
       m_projectMenu->addAction(action);
     }
     m_projectMenu->addSeparator();
+    //  Get Project menu actions from the active view
     if (m_activeView) {
       foreach ( QAction *action, m_activeView->projectMenuActions() ) {
         m_projectMenu->addAction(action);
       }
     }
     m_projectMenu->addSeparator();
+    //  Get Project menu actions from CNetSuiteMainWindow
     foreach ( QAction *action, m_projectMenuActions ) {
       m_projectMenu->addAction(action);
     }
 
     m_editMenu->clear();
+    // Get Edit menu actions from Directory
     foreach ( QAction *action, m_directory->editMenuActions() ) {
       m_editMenu->addAction(action);
     }
     m_editMenu->addSeparator();
+    // Get Edit menu actions from active view
     if (m_activeView) {
       foreach ( QAction *action, m_activeView->editMenuActions() ) {
         m_editMenu->addAction(action);
       }
     }
     m_editMenu->addSeparator();
+    // Get Edit menu actions from CNetSuiteMainWindow
     foreach ( QAction *action, m_editMenuActions ) {
       m_editMenu->addAction(action);
     }
 
     m_viewMenu->clear();
+    // Get View menu actions from Directory
     foreach ( QAction *action, m_directory->viewMenuActions() ) {
       m_viewMenu->addAction(action);
     }
     m_viewMenu->addSeparator();
+    // Get View menu actions from CNetSuiteMainWindow
     foreach ( QAction *action, m_viewMenuActions ) {
       m_viewMenu->addAction(action);
     }
     m_viewMenu->addSeparator();
+    // Get View menu actions from active view
     if (m_activeView) {
       foreach ( QAction *action, m_activeView->viewMenuActions() ) {
         m_viewMenu->addAction(action);
@@ -294,31 +317,37 @@ namespace Isis {
     }
 
     m_settingsMenu->clear();
+    // Get Settings menu actions from Directory
     foreach ( QAction *action, m_directory->settingsMenuActions() ) {
       m_settingsMenu->addAction(action);
     }
     m_settingsMenu->addSeparator();
+    // Get Settings menu actions from active view
     if (m_activeView) {
       foreach ( QAction *action, m_activeView->settingsMenuActions() ) {
         m_settingsMenu->addAction(action);
       }
     }
     m_settingsMenu->addSeparator();
+    // Get Settings menu actions from CNetSuiteMainWindow
     foreach ( QAction *action, m_settingsMenuActions ) {
       m_settingsMenu->addAction(action);
     }
 
     m_helpMenu->clear();
+    // Get Help menu actions from Directory
     foreach ( QAction *action, m_directory->helpMenuActions() ) {
       m_helpMenu->addAction(action);
     }
     m_helpMenu->addSeparator();
+    // Get Help menu actions from active view
     if (m_activeView) {
       foreach ( QAction *action, m_activeView->helpMenuActions() ) {
         m_helpMenu->addAction(action);
       }
     }
     m_helpMenu->addSeparator();
+    // Get Help menu actions from CNetSuiteMainWindow
     foreach ( QAction *action, m_helpMenuActions ) {
       m_helpMenu->addAction(action);
     }
@@ -408,7 +437,7 @@ namespace Isis {
         return true;
       }
     }
- 
+
     return QMainWindow::eventFilter(watched, event);
   }
 
@@ -499,6 +528,11 @@ namespace Isis {
     m_projectMenu = menuBar()->addMenu(tr("&Project"));
     m_projectMenu->setObjectName("projectMenu");
 
+    // Allow tool tips to be displayed for the project menu's actions (e.g. "Bundle Adjustment")
+    // This is a work around for Qt's what this text not working on disabled actions
+    // (even though the Qt documentation says it should work on disabled QAction's).
+    m_projectMenu->setToolTipsVisible(true);
+
     m_editMenu = menuBar()->addMenu(tr("&Edit"));
     m_editMenu->setObjectName("editMenu");
 
@@ -517,14 +551,14 @@ namespace Isis {
    * Write the window positioning and state information out to a
    * config file. This allows us to restore the settings when we
    * create another main window (the next time this program is run).
-   * 
+   *
    * The state will be saved according to the currently loaded project and its name.
    *
    * When no project is loaded (i.e. the default "Project" is open), the config file used is
    * $HOME/.Isis/$APPNAME/$APPNAME_Project.config.
    * When a project, ProjectName, is loaded, the config file used is
    * $HOME/.Isis/$APPNAME/$APPNAME_ProjectName.config.
-   * 
+   *
    * @param[in] project Pointer to the project that is currently loaded (default is "Project")
    *
    * @internal
@@ -532,8 +566,8 @@ namespace Isis {
    *                           References #4358.
    */
   void CNetSuiteMainWindow::writeSettings(const Project *project) const {
-    // Ensure that we are not using a NULL pointer   
-    if (!project) { 
+    // Ensure that we are not using a NULL pointer
+    if (!project) {
       QString msg = "Cannot write settings with a NULL Project pointer.";
       throw IException(IException::Programmer, msg, _FILEINFO_);
     }
diff --git a/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.h b/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.h
index fca97fec8d6d4b6866a60f351e8a1879e9544f36..13936cbce6fa046c3e0ac2adf319c5b9c2fe627d 100644
--- a/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.h
+++ b/isis/src/local/apps/cnetsuite/CNetSuiteMainWindow.h
@@ -79,6 +79,12 @@ namespace Isis {
    *                           The m_permToolBar, m_activeToolBar, and m_toolPad now have object
    *                           names set, so the saveState() call within writeSettings() now works.
    *                           Fixes #4358.
+   *   @history 2016-12-09 Tracie Sucharski - One of the previous 2 changes caused a problem with
+   *                           view toolbars not to be restored.  Added setActiveSubWindow and
+   *                           show to the ::addView method.  Fixes #4546.
+   *   @history 2017-04-17 Ian Humphrey - Updated createMenus() to set tool tips (hover text)
+   *                           visible so the JigsawWorkOrder tool tip can be displayed to user
+   *                           (which indicates why it is disabled by default). Fixes #4749.
    */
   class CNetSuiteMainWindow : public QMainWindow {
       Q_OBJECT
diff --git a/isis/src/lro/apps/lromakeflat/Makefile b/isis/src/lro/apps/lromakeflat/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..7578f0b21d038db6a5042c095cda9b34b6bb2570
--- /dev/null
+++ b/isis/src/lro/apps/lromakeflat/Makefile
@@ -0,0 +1,7 @@
+ifeq ($(ISISROOT), $(BLANK))
+.SILENT:
+error:
+	echo "Please set ISISROOT";
+else
+	include $(ISISROOT)/make/isismake.apps
+endif
\ No newline at end of file
diff --git a/isis/src/lro/apps/lromakeflat/lromakeflat.cpp b/isis/src/lro/apps/lromakeflat/lromakeflat.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7c8062ef26afbc133dfb5fdf9f25cdd7339bbfeb
--- /dev/null
+++ b/isis/src/lro/apps/lromakeflat/lromakeflat.cpp
@@ -0,0 +1,505 @@
+/**
+ * @Brief This application creates three flatfield (Sensitivity Non-Uniformity Matrix) cubes used for calibration
+ *
+ * This application creates three flatfield (Sensitivity Non-Uniformity Matrix) cubes used for calibration.
+ * The cubes consist of median, mean, and standard deviation values per pixel. Process varies for the three 
+ * cameras this application can be used for but general pixel stacking column approach is the same. The 
+ * three camera types are line-scan, push-frame, and framing. Invalid pixel values are changed to Isis::Null. 
+ *
+ * The application uses a two step process.
+ *
+ * Step #1 - STACKING PIXELS INTO PIXEL COLUMNS
+ *
+ * The first part of the process is to stack cube pixels at their respective pixel locations.
+ *
+ * These stacked pixels are processed to produce the median, mean, and standard deviation values for the 
+ * pixel location, and to toss out invalid pixel values.  Normalization can also be done at this time if 
+ * images were not normalized prior. The mean is used to normalize images. 
+ *
+ * Step #2 - PROCESSING STACKED PIXEL COLUMNS AND TRANSFERRING TO SNU
+ *
+ * Once pixels have been stacked into pixel columns mean and median averages, and standard devation for that 
+ * pixel location is saved to the SNU matrix (flatfield cubes).
+ *
+ * Mean
+ *  -The summed pixels are divided by the number of pixels.
+ * Standard Deviation 
+ *  -The mean average is used to calculate the standard deviation. 
+ * Median
+ *  -The pixel column is sorted and the median is obtained.
+ *
+ * @author Victor Silva - 2016-08-17
+ *
+ * @internal
+ *   @history 2016-08-17 Victor Silva - New app for lroc adapted from makeflat app
+ *
+ */
+#include "Isis.h"
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+
+#include "FileList.h"
+#include "Histogram.h"
+#include "IException.h"
+#include "LineManager.h"
+#include "PvlGroup.h"
+
+using namespace std;
+using namespace Isis;
+
+// Container for two-dimensional matrix of doubles
+typedef vector < vector > Matrix2d;
+
+// This method returns stats for a vector of doubles and excludes special pixels
+void getVectorStats( vector (&inVec), double (&mean), double (&median), double (&stdev) );
+
+// Get normalization values for frames in list of cubes if so desired
+void getCubeListNormalization( Matrix2d (&matrix), int (cubeWidth), int (frameHeight), long (frameLineCount), long (iLineCount) );
+
+// Logs excluded files and frames
+void exclude( int listIndex, string reason );
+
+// Logs excluded files and frames
+void exclude( int listIndex, int frame, string reason );
+
+// Global variables
+int static g_sampleCount;
+int static g_numStdevs;
+QString static g_msg;
+Progress static g_prog;
+FileList static g_list;
+
+// This will keep track of excluded cubes from the cube list. The int is the index in the list (zero-based)
+map < int, string > g_excludedCubes;
+
+// Holds excluded frames.  (zero-based)
+map < pair, string> g_excludedFrames;
+
+// Holds exclusion details used for logging
+vector < PvlObject > g_excludedDetails;
+
+/**
+   * @brief Main method
+   *
+   * Computes flatfield image for linescan, pushbroom, and framing
+   * Cameras
+   * 
+   * @throws IException::User "Only single band images accepted"
+   * @throws IException::User "User selected lines value exceeds number of lines in cube"
+   * @throws IException::Programmer "Could not write to output cube"
+   *
+   * @author 2016-08-17 Victor Silva
+   *
+   * @internal
+   *   @history 2016-08-17 Victor Silva - New app for lroc adapted from makeflat app
+   *                         
+   */
+void IsisMain() {
+
+  // Set attributes
+  UserInterface &ui(Application::GetUserInterface());
+  g_list = FileName(ui.GetFileName("FROMLIST"));
+  g_numStdevs = abs(ui.GetDouble("STDEVTOL"));
+
+  // Input cube attributes
+  bool normalize = false;
+  long iLineCount, oLineCount; // sample count is the same for both input/output cubes
+  int cubeWidthPixels = 0, frameHeightLines = 0, framesPerCube, frameLineCount;
+
+  // Setup Sensitivity Non-uniformity Matrix cubes (flatfielding matrix) and line managers
+  Cube *oStdevCube = NULL, *oMedianCube = NULL, *oMeanCube = NULL; 
+  LineManager *oStdevlineMgr = NULL, *oMeanLineMgr = NULL, *oMedianLineMgr = NULL;
+
+  // Get some info from first cube in list
+  Cube firstCube;
+  firstCube.open(g_list[0].toString());
+  g_sampleCount = firstCube.sampleCount();
+  iLineCount = firstCube.lineCount();
+
+  if (firstCube.bandCount() != 1) {
+    string err = "Only single band images accepted. \n";
+    throw IException(IException::User, err, _FILEINFO_);
+  }
+
+  firstCube.close();
+  // to normalize or not
+  if (ui.GetString("NORMALIZATION") == "YES") {
+      normalize = true;
+      frameHeightLines = abs(ui.GetInteger("HEIGHT_LINES"));
+      cubeWidthPixels = abs(ui.GetInteger("WIDTH_PIXELS"));
+  }
+  // User selection of camera type will set addt'l attributes
+  if (ui.GetString("IMAGETYPE") == "FRAMING") {
+    frameLineCount = oLineCount = iLineCount;
+  }
+  else if (ui.GetString("IMAGETYPE") == "LINESCAN") {
+    oLineCount = 1;
+    frameLineCount = abs(ui.GetInteger("NUMLINES"));
+    if (iLineCount != frameLineCount) {
+      string err = "User selected lines value (" + IString(frameLineCount) + 
+         ") exceeds number of lines in cube (" + IString(iLineCount) + ". \n";
+      throw IException(IException::User, err, _FILEINFO_);
+    }
+  }
+  else {
+    oLineCount = frameLineCount = abs(ui.GetInteger("FRAMELETHEIGHT"));
+  }
+  // Number of frames in each cube
+  framesPerCube = (iLineCount / frameLineCount); //integer division
+  // 3d matrix of type pair to hold mean and stdev for normalization
+  Matrix2d normMatrix;
+  normMatrix.resize(g_list.size(), vector (framesPerCube, 1.0));
+  // Get normalization values from list of cubes if user selects normalization
+  if (normalize) {
+    getCubeListNormalization(normMatrix, cubeWidthPixels, frameHeightLines, frameLineCount, iLineCount);
+  }
+  // Create empty snu-flatfield output cubes and line managers
+  oStdevCube = new Cube();
+  oMedianCube = new Cube();
+  oMeanCube = new Cube();
+  // Set cube dimensions
+  oStdevCube->setDimensions(g_sampleCount, oLineCount, 1);
+  oMedianCube->setDimensions(g_sampleCount, oLineCount, 1);
+  oMeanCube->setDimensions(g_sampleCount, oLineCount, 1);
+  // Set name of cubes
+  oStdevCube->create(FileName(ui.GetFileName("TO")).expanded() + ".stdev.cub");
+  oMedianCube->create(FileName(ui.GetFileName("TO")).expanded() + ".median.cub");
+  oMeanCube->create(FileName(ui.GetFileName("TO")).expanded() + ".mean.cub");
+  // create new line manager
+  oStdevlineMgr = new LineManager(*oStdevCube);
+  oMedianLineMgr = new LineManager(*oMedianCube);
+  oMeanLineMgr = new LineManager(*oMeanCube);
+  // Set status msg
+  g_msg = "Stacking pixels into columns and processing them.";
+  g_prog.SetText(g_msg);
+  g_prog.SetMaximumSteps(oLineCount + 1);
+  // Stack pixels at each pixel location into pixel columns
+  for (long oLine = 1; oLine <= oLineCount; oLine++) {
+    g_prog.CheckStatus();
+    // 2d matrix to hold pixel columns
+    Matrix2d pixelMatrix;
+    pixelMatrix.resize(g_sampleCount, vector(g_list.size() * framesPerCube, Isis::Null));
+    for (int listIndex = 0; listIndex < g_list.size(); listIndex++) {
+      Cube tmp2;
+      tmp2.open(g_list[listIndex].toString());
+      // Only run for cubes with one band
+      if (tmp2.bandCount() != 1) {
+        string err = "Warning: This cube has too many bands(" + IString(tmp2.bandCount()) + 
+          " and will be excluded). Only single band images accepted. \n";
+        cerr << err << endl;
+        exclude(listIndex, err);
+        // Go directly to next cube. Do not stop at GO. Do not collect $200.
+        continue;
+      }
+      // Reset frame for every cube in list
+      int frame = 0;
+      // Cube line has to match oLine as we are slicing the cubes one line at a time to stack pixels 
+      for (long cubeLine = oLine; cubeLine <= iLineCount; cubeLine = cubeLine + frameLineCount) {
+        LineManager cubeMgr(tmp2);
+        cubeMgr.SetLine(cubeLine);
+        tmp2.read(cubeMgr);
+        double pixelVal;
+        // Iterate through columns
+        for (int column = 0; column < g_sampleCount; column++) {
+          pixelVal = cubeMgr[column];
+          int frameIndex = listIndex * framesPerCube + frame;
+          // If frame avg is zero, will cause div/zero error. Set pixel to 0? nil?  
+          (normMatrix[listIndex][frame])? pixelVal = (pixelVal/(normMatrix[listIndex][frame])):pixelVal = Isis::Null;
+          pixelMatrix[column][frameIndex] = pixelVal;
+        }
+        // Next frame
+        frame++;
+      }
+      tmp2.close();
+    }
+    // Process stacked pixel columns and write to snu-flatfield output cubes
+    // Set ouput cubeLine manager line to cube line
+    oStdevlineMgr->SetLine(oLine);
+    oMedianLineMgr->SetLine(oLine);
+    oMeanLineMgr->SetLine(oLine);
+    // Set values as we iterate through columns
+    for (int column = 0; column < g_sampleCount; column++) {
+      double columnMean, columnMedian, columnStdev;
+      getVectorStats(pixelMatrix[column], columnMean, columnMedian, columnStdev);
+      (*oStdevlineMgr)[column] = columnStdev;
+      (*oMedianLineMgr)[column] = columnMedian;
+      (*oMeanLineMgr)[column] = columnMean;
+    }
+    try {
+      // Write the stats saved at the pixel location to the snu matrix cubes
+      oStdevCube->write(*oStdevlineMgr);
+      oMeanCube->write(*oMeanLineMgr);
+      oMedianCube->write(*oMedianLineMgr);
+    }
+    catch (IException e) {
+      //cout << "It's no use at this point. Just go. Leave me here. I'll only slow you down.";
+      string err = "Could not write to output cube " + IString(FileName(ui.GetFileName("TO")).expanded()) + ".\n";
+      throw IException(IException::Programmer, err, _FILEINFO_);
+    }
+    pixelMatrix.clear();
+  }
+  // Clean-up
+  normMatrix.clear();
+  if (oStdevlineMgr ){
+    delete oStdevlineMgr;
+    oStdevlineMgr = NULL;
+  }
+  if(oMeanLineMgr){
+    delete oMeanLineMgr;
+    oMeanLineMgr = NULL;
+  }
+  if(oMedianLineMgr){
+    delete oMedianLineMgr;
+    oMedianLineMgr = NULL;
+  }
+  if(oStdevCube) {
+    oStdevCube->close();
+    delete oStdevCube;
+    oStdevCube = NULL;
+  }
+  if(oMeanCube) {
+    oMeanCube->close();
+    delete oMeanCube;
+    oMeanCube = NULL;
+  }
+  if(oMedianCube) {
+    oMedianCube->close();
+    delete oMedianCube;
+    oMedianCube = NULL;
+  }
+  // If user wanted an exclusion file created, create it pues.
+  if(ui.WasEntered("EXCLUDE")) {
+    Pvl excludeFile;
+    for(unsigned int i = 0; i < g_excludedDetails.size(); i++) {
+      excludeFile.addObject(g_excludedDetails[i]);
+    }
+    excludeFile.write(FileName(ui.GetFileName("EXCLUDE")).expanded());
+  }
+} // end of main
+
+
+/**
+ * @brief This function gets normalization values for a list of cubes
+ *
+ * It uses the user specified area of the image to be used for normalizing all
+ * the values at each pixel location. The user enters a height and width
+ * percentage of the frame.
+ *
+ * @param matrix  3D matrix that holds cube frame information such as stdev/normAvg
+ * @param int cubeWidth size of cube in samples
+ * @param int frameHeight size of frame in rows
+ * @param long frameLineCount number of lines to make a frame
+ * @param long iLineCount number of lines total in cube
+ * 
+ * @throws IException::User "This selection will yield less than 1 pixel (width). This is not enough to normalize."
+ * @throws IException::User "This percentage will yield less than 1 line. This is not enough to normalize."
+ *
+ * @author 2016-08-17 Victor Silva
+ *
+ * @internal
+ *   @history 2016-08-17 Victor Silva - New app for lroc adapted from makeflat app
+ *   
+ */
+void getCubeListNormalization(Matrix2d &matrix, int cubeWidth, int frameHeight, long frameLineCount, long iLineCount) {
+
+  for(int listIndex = 0; listIndex < g_list.size(); listIndex++) {
+    // open cubes in list unless they have already been excluded
+    if( g_excludedCubes.find(listIndex) != g_excludedCubes.end() ) {
+      continue;
+    }
+    Cube tmp;
+    tmp.open(g_list[listIndex].toString());
+    PvlGroup normResults("NormalizationResults");
+    g_msg = "Getting frame mean avg " + toString((int) listIndex + 1) + "/";
+    g_msg += toString((int) g_list.size()) + " (" + g_list[listIndex].name() + ")";
+    g_prog.SetText(g_msg);
+    g_prog.SetMaximumSteps(g_list.size());
+    g_prog.CheckStatus();
+    // width:
+    int startSample = 0, endSample = g_sampleCount;
+    if (cubeWidth){
+      if(cubeWidth <= g_sampleCount) {
+        startSample = (g_sampleCount - cubeWidth) / 2;
+        endSample = (g_sampleCount - 1) - startSample;
+      }
+      else {
+        string err = "This selection will yield less than 1 pixel (width). This is not enough to normalize. \n";
+        throw IException(IException::User, err, _FILEINFO_);
+      }
+    }
+    // height:
+    long startLine, endLine;
+    int lineShift = 0;
+    (frameHeight == 0) ? frameHeight = frameLineCount : lineShift = (frameLineCount - frameHeight)/ 2;
+    for(long cubeLine = 1; cubeLine <= iLineCount; cubeLine = cubeLine + frameLineCount) {
+      startLine = cubeLine + lineShift;
+      endLine = startLine + frameHeight;
+
+      if( (startLine < 0)||(endLine - startLine) < 0) {
+        string err = "This percentage will yield less than 1 line. This is not enough to normalize. \n";
+        throw IException(IException::User, err, _FILEINFO_);
+      }
+      Histogram hist = Histogram(tmp, 1, &g_prog, startSample, startLine, endSample, endLine, 0, true);
+      int frame = cubeLine/frameLineCount;
+      double normalizationAverage = hist.Average();
+      matrix[listIndex][frame] = normalizationAverage;
+      normResults += PvlKeyword("FileName", g_list[listIndex].toString());
+      normResults += PvlKeyword("Frame", toString(frame));
+      normResults += PvlKeyword("Frame_MeanAverage", toString(normalizationAverage));
+      Application::Log(normResults);
+    }
+    tmp.close();
+  }
+}
+
+
+/**
+ * @brief This function returns the median, mean, and standard deviation for a vector 
+ *        of valid pixels
+ *
+ * It will return Isis::Null if it doesn't find any valid pixels. The function builds 
+ * a vector of valid pixels. It also calculates the mean and standard deviation of the 
+ * vector. The function also sorts the vector and finds the median. If there are an even
+ * number of valid pixels, it will average (mean) the two middle pixels and return
+ * that average as the median. It does not return the median pixel but rather its
+ * value or average value of the two middle pixels.
+ *
+ * @param inVec   Vector of pixel values (double)
+ * @param mean    Value of vector mean (double)
+ * @param median  Value of vector median (double)
+ * @param stdev   Value of vector stdev (double)
+ *
+ * @author 2016-08-17 Victor Silva
+ *
+ * @internal
+ *   @history 2016-08-17 Victor Silva - New app for lroc adapted from makeflat app
+ */
+void getVectorStats(vector &inVec, double &mean, double &median, double &stdev) {
+  // Set defaults
+  int medianIndex = 0, v_size = 0;
+  double sum = 0.0, devSum = 0.0;
+  median = Isis::Null;
+  mean = Isis::Null;
+  stdev = Isis::Null;
+  // Check for empty initial vector
+  if(!(inVec.empty())) {
+    vector  v1;
+    v_size = int(inVec.size());
+    // strip invalid pixels
+    for (int i = 0; i < v_size; i++) {
+      if (!(IsNullPixel(inVec[i]) || IsSpecial(inVec[i]))){
+        v1.push_back(inVec[i]);
+        sum += inVec[i];
+      }
+    }
+    // check to see if we got any valid pixels
+    if (!(v1.empty())) {
+      v_size = int(v1.size());
+      // First pass - toss out outliers
+      double tempMean = sum / v_size;
+      for (int i = 0; i < v_size; i++) {
+        devSum += pow((v1[i] - tempMean), 2);
+      }
+      double tempStdev = sqrt(devSum / (v_size));
+      // Reset for second pass
+      devSum = 0;
+      sum = 0;
+      vector  v2;
+      for(int i = 0; i < v_size; i++ ){
+        if( (abs(tempMean - v1[i])) <= (tempStdev * g_numStdevs) ){  
+          v2.push_back(v1[i]);
+          sum += v1[i];
+        }
+      }
+      // Second pass - get stats
+      if (!(v2.empty())) {
+        v_size = int(v2.size());
+        // mean
+        mean = sum / v_size;
+        // stdev process
+        for ( int i = 0; i < v_size; i++ ) {
+          devSum += pow((v2[i] - mean), 2);
+        }
+        stdev= sqrt(devSum / (v_size));
+        // median
+        bool even = ((v_size % 2) == 0);
+        sort(v2.begin(), v2.end());
+        medianIndex = (v_size - 1) / 2;
+        if (even) {
+          median = double(((v2[medianIndex]) + (v2[medianIndex + 1])) / 2.0000);
+        }
+        else {
+          median = double(v2[medianIndex]);
+        }
+        v2.clear();
+      } 
+      v1.clear();
+    } 
+  } 
+}
+
+
+/**
+ * @brief This function excludes cubes and logs them
+ * Adds excluded cube files to containers that are used when creating the
+ * exclusion file. It also logs the exclusions to the application log window.
+ *
+ * @param listIndex  Location in list for a cube (zero-indexed)
+ * @param reason     Exclusion reason
+ *
+ * @author 2016-08-17 Victor Silva
+ *
+ * @internal
+ *   @history 2016-08-17 Victor Silva - New app for lroc adapted from makeflat app
+ */
+void exclude(int listIndex, string reason) {
+  if(g_excludedCubes.find(listIndex) == g_excludedCubes.end()) {
+    g_excludedCubes.insert(pair(listIndex, reason));
+    PvlObject exclusion("Excluded_Items");
+    PvlGroup excludedFiles("Excluded_Files");
+    excludedFiles += PvlKeyword("FileName", g_list[listIndex].toString());
+    excludedFiles += PvlKeyword("Reason", QString::fromStdString(reason));
+    Application::Log(excludedFiles);
+    exclusion.addGroup(excludedFiles);
+    g_excludedDetails.push_back(exclusion);
+  }
+}
+
+
+/**
+ * @brief This function excluded frames and logs them
+ * Adds excluded frames in the cube files to containers that are used when
+ * creating the exclusion file. It also logs the exclusions to the application
+ * log window.
+ *
+ * param listIndex          Location in list for a cube (zero-indexed)
+ * param frame              Location in cube for frame (zero-indexed)
+ * param reason             Exclusion reason
+ *
+ * @author 2016-08-17 Victor Silva
+ *
+ * @internal
+ *   @history 2016-08-17 Victor Silva - New app for lroc adapted from makeflat app
+ */
+void exclude(int listIndex, int frame, string reason){
+  if(g_excludedFrames.find(pair(listIndex,frame)) == g_excludedFrames.end()) {
+    g_excludedFrames.insert(pair < pair < int, int > , string > (pair(listIndex, frame), reason));
+    PvlObject exclusion("Excluded_Items");
+    PvlGroup excludedFiles("Excluded_Frames");
+    excludedFiles += PvlKeyword("Frame_from_cube", g_list[listIndex].toString());
+    excludedFiles += PvlKeyword("Frame_number", toString(frame));
+    excludedFiles += PvlKeyword("Exclusion_reason", QString::fromStdString(reason));
+    Application::Log(excludedFiles);
+    exclusion.addGroup(excludedFiles);
+    g_excludedDetails.push_back(exclusion);
+  }
+}
+
diff --git a/isis/src/lro/apps/lromakeflat/lromakeflat.xml b/isis/src/lro/apps/lromakeflat/lromakeflat.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3dfdae87a803524f1b7ad88a7c9742392f14df0f
--- /dev/null
+++ b/isis/src/lro/apps/lromakeflat/lromakeflat.xml
@@ -0,0 +1,265 @@
+
+
+
+
+  
+    Create a flat-field image for line-scan, push-frame, and framing instruments
+  
+
+  
+    
      
+      This program creates flat-field images for line scan, push frame, and framing instruments. 
+      All input cubes should have the same number of samples; any images in the list that do not
+      have the same number of samples as the first image will not be used.  The names of the cube 
+      files used to create the flat-field image must be entered using an ASCII file (FROMLIST) with 
+      one filename per line (any line beginning with a '#' or '//' is treated as a comment).  The 
+      specific equation for each camera type is below.
+    
      
+    
        
+      
      • Line Scan
        • 
+        
        
+          A frame is a NUMLINES line section of data. The equation for the final single line, single
+          band, flat field file is:
+         
        
+          Mean Calculation:
+         
        
+         Sum( Sum(FrameColumn) / Average(Frame) * ValidPixels(FrameColumn) ) / 
+         TotalColumnValidPixels
+         
        
+          Median Calculation:
+         
        
+          Median(PixelColumn(ValidPixel / Average(Frame)))
+        
        
+          
+      
      • Push Frame
        • 
+        
        
+          Mean Calculation:
+          
        
+          The equation for the final single framelet, single band flat field file is:
         Average(
+          PixelInFramelet1, PixelInFramelet2, PixelInFramelet3, ... )
+          
        
+          Median Calculation:
+          
        
+          Median(PixelColumn(ValidPixel / Average(Frame)))
+        
        
+      
      • Framing
        • 
+        
        
+          Mean Calculation:
+          
        
+          The equation for the final single framelet, single band flat field file is:
         Average(
+          PixelInCube1, PixelInCube2, PixelInCube3, ... )
+          
        
+          Median Calculation:
+          
        
+          Median(PixelColumn(ValidPixel / Average(Frame)))
+        
        
+    
      
+    
      
+      Warning: This program creates potentially large temporary files
+    
      
+  
+
+  
+    
+      Original version, Adapted from Isis3 version of makeflat.
+    
+  
+
+  
+    Math and Statistics
+    Radiometric and Photometric Correction
+  
+
+  
+    
+      
+        filename
+        input
+        
+          List of input cubes
+        
+        
+          Use this parameter to select the file which contains a list of
+          cube filenames to be used to create the flat file.
+        
+        
+          *.lis
+        
+     
+
+      
+        cube
+        real
+        output
+        
+          Output name prepended to flat field output cubes
+        
+        
+         Output prefix of the flat field cube's name
+        
+      
+
+      
+        filename
+        None
+        output
+        
+          Output PVL-formatted file of all excluded files and sections of data
+        
+        
+         Output PVL-formatted file of all excluded files and sections of data.
+        
+      
+    
+    
+      
+        string
+        LINESCAN
+        
+          This is the type of camera which took the image.
+        
+        
+          The type of camera that captured the input image.
+        
+        
+          
+          
+          
+        
+      
+      
+        integer
+        
+          This is the number of lines to consider when doing statistics
+        
+        
+          A single line often does not have enough data in it to perform good tolerance
+          calculations. The tolerance calculations will be performed on this many lines as
+          a time, and if found to be invalid, this many lines will be excluded from the output
+          flat file calculations at a time.
+        
+      
+      
+        integer
+        
+          This is the height of each framelet in the image.
+        
+        
+          Push frame images consist of framelets. The framelet size needs to be
+          known in order to make a flat field file for a push frame camera.
+        
+      
+    
+
+    
+      
+        string
+        NO
+        
+          Include Normalization Step
+        
+        
+          If this pre-processing step was not done prior, Makeflat will normalize each pixel by the frame's mean in
+          order to normalize to 1. You can select image dimensions (height and width in pixels) to use when calculating frame mean.
+        
+        
+          
+          
+        
+      
+      
+        double
+        2
+        
+          This is the number of standard deviations to use as outlier boundary.
+        
+        
+          Any pixel column averages beyond this boundary will be excluded. The default value is
+          +- 1 standard deviation. Any pixel column average within this range will be included.
+        
+      
+    
+    
+      
+        integer
+        0
+        
+          Width in Pixels from center of image to use for normalization
+        
+        
+          If value is left at zero, pixels will be normalized using entire width frame of image.
+        
+      
+      
+        integer
+        0
+        
+          Height in Lines from center of image to use for normalization
+        
+        
+          If LINESCAN, height will always equal 1. If value is left at zero and is not LINESCAN,
+          pixels will be normalized using entire frame height of image.
+        
+      
+    
+  
+
diff --git a/isis/src/lro/apps/lromakeflat/tsts/Makefile b/isis/src/lro/apps/lromakeflat/tsts/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..46d84c74c297304e943452a44e06b111f179a92b
--- /dev/null
+++ b/isis/src/lro/apps/lromakeflat/tsts/Makefile
@@ -0,0 +1,4 @@
+BLANKS = "%-6s"    
+LENGTH = "%-40s"
+
+include $(ISISROOT)/make/isismake.tststree
diff --git a/isis/src/lro/apps/lromakeflat/tsts/framing/Makefile b/isis/src/lro/apps/lromakeflat/tsts/framing/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..51aab3627386071ef40630b550ab5d424ca53ead
--- /dev/null
+++ b/isis/src/lro/apps/lromakeflat/tsts/framing/Makefile
@@ -0,0 +1,11 @@
+APPNAME = lromakeflat
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	ls $(INPUT)/*.cub > $(OUTPUT)/framing.lis
+	$(APPNAME) fromlist=$(OUTPUT)/framing.lis \
+	  to=$(OUTPUT)/framing \
+	  imagetype=framing stdevtol=3 \
+	  > /dev/null;
+	rm $(OUTPUT)/framing.lis
diff --git a/isis/src/lro/apps/lromakeflat/tsts/linescan/Makefile b/isis/src/lro/apps/lromakeflat/tsts/linescan/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..90b6d191f0f1bc6240616ee3ebd88e3eaa1f100a
--- /dev/null
+++ b/isis/src/lro/apps/lromakeflat/tsts/linescan/Makefile
@@ -0,0 +1,11 @@
+APPNAME = lromakeflat
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	ls $(INPUT)/*.cub > $(OUTPUT)/linescan.lis
+	$(APPNAME) fromlist=$(OUTPUT)/linescan.lis \
+	  to=$(OUTPUT)/linescan numlines=1\
+	  imagetype=linescan stdevtol=3 \
+	  > /dev/null;
+	rm $(OUTPUT)/linescan.lis
diff --git a/isis/src/lro/apps/lromakeflat/tsts/pushframe/Makefile b/isis/src/lro/apps/lromakeflat/tsts/pushframe/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..b6a7fb00480258d4739f2ae1ada3440345493443
--- /dev/null
+++ b/isis/src/lro/apps/lromakeflat/tsts/pushframe/Makefile
@@ -0,0 +1,11 @@
+APPNAME = lromakeflat
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	ls $(INPUT)/*.cub > $(OUTPUT)/pushframe.lis
+	$(APPNAME) fromlist=$(OUTPUT)/pushframe.lis \
+	  to=$(OUTPUT)/pushframe frameletheight=3\
+	  imagetype=pushframe stdevtol=3 \
+	  > /dev/null;
+	rm $(OUTPUT)/pushframe.lis
diff --git a/isis/src/lro/apps/lronac2isis/lronac2isis.cpp b/isis/src/lro/apps/lronac2isis/lronac2isis.cpp
index 7bcc8446aff6146d04a1daf15607d1d431b2a47f..466cbbf5758236a45ccf6d0f2ea42d09b912cc58 100644
--- a/isis/src/lro/apps/lronac2isis/lronac2isis.cpp
+++ b/isis/src/lro/apps/lronac2isis/lronac2isis.cpp
@@ -75,7 +75,9 @@ void IsisMain() {
   }
   catch(IException &e) {
     QString msg = "The PDS header is missing important keyword(s).";
-    throw IException(IException::Io, msg, _FILEINFO_);
+    IException finalException(IException::Io, msg, _FILEINFO_);
+    finalException.append(e);
+    throw finalException;
   }
 
   id = id.simplified().trimmed();
diff --git a/isis/src/lro/apps/lronac2isis/lronac2isis.xml b/isis/src/lro/apps/lronac2isis/lronac2isis.xml
index 76d2baae2cbc26ee771515d03ccda3bf97b0821c..b6375234f6ee1f9da90873dcdedf75d17d6e0f6d 100644
--- a/isis/src/lro/apps/lronac2isis/lronac2isis.xml
+++ b/isis/src/lro/apps/lronac2isis/lronac2isis.xml
@@ -15,6 +15,13 @@
         
             Original Version
         
+      	
+      	    Updated error messages to stack when necessary.
+      	
+        
+            Corrected error message stacking in lronac2isis, was not correctly dealt with on
+            2016-07-11
+        
     
 
     
diff --git a/isis/src/lro/apps/lronac2isis/tsts/nac-fail/Makefile b/isis/src/lro/apps/lronac2isis/tsts/nac-fail/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..4f1ed795ce3d684efa138e7ba9ae2e81233b7188
--- /dev/null
+++ b/isis/src/lro/apps/lronac2isis/tsts/nac-fail/Makefile
@@ -0,0 +1,12 @@
+APPNAME = lronac2isis
+FILE=nacl00015d79Edit
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+#    TEST A: Check that lronac2isis is returning the correct error messages
+	if [ `$(APPNAME) from=$(INPUT)/$(FILE).img \
+	  to=$(OUTPUT)/$(FILE).cub > /dev/null \
+	  2>> $(OUTPUT)/error_message_temp.txt > /dev/null` ]; \
+	  then true; \
+	fi;
\ No newline at end of file
diff --git a/isis/src/lro/apps/lronac2pds/md5.cpp b/isis/src/lro/apps/lronac2pds/md5.cpp
index aacf031673ef0a8aa243225c3effdecb7e40c2fd..cfc7e30bf3e392489bc6524e4d3b6e40887b91b1 100644
--- a/isis/src/lro/apps/lronac2pds/md5.cpp
+++ b/isis/src/lro/apps/lronac2pds/md5.cpp
@@ -1,34 +1,34 @@
 /*
- * 	This is the C++ implementation of the MD5 Message-Digest
- * 	Algorithm desrcipted in RFC 1321.
- * 	I translated the C code from this RFC to C++.
- * 	There is no warranty.
+ *      This is the C++ implementation of the MD5 Message-Digest
+ *      Algorithm desrcipted in RFC 1321.
+ *      I translated the C code from this RFC to C++.
+ *      There is no warranty.
  *
- * 	Feb. 12. 2005
- * 	Benjamin Gr�delbach
+ *      Feb. 12. 2005
+ *      Benjamin Gr�delbach
  */
 
 /*
- *	Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
- *	rights reserved.
+ *      Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
+ *      rights reserved.
  *
- *	License to copy and use this software is granted provided that it
- *	is identified as the "RSA Data Security, Inc. MD5 Message-Digest
- *	Algorithm" in all material mentioning or referencing this software
- *	or this function.
+ *      License to copy and use this software is granted provided that it
+ *      is identified as the "RSA Data Security, Inc. MD5 Message-Digest
+ *      Algorithm" in all material mentioning or referencing this software
+ *      or this function.
  *
- *	License is also granted to make and use derivative works provided
- *	that such works are identified as "derived from the RSA Data
- *	Security, Inc. MD5 Message-Digest Algorithm" in all material
- *	mentioning or referencing the derived work.
+ *      License is also granted to make and use derivative works provided
+ *      that such works are identified as "derived from the RSA Data
+ *      Security, Inc. MD5 Message-Digest Algorithm" in all material
+ *      mentioning or referencing the derived work.
  *
- *	RSA Data Security, Inc. makes no representations concerning either
- *	the merchantability of this software or the suitability of this
- *	software for any particular purpose. It is provided "as is"
- *	without express or implied warranty of any kind.
+ *      RSA Data Security, Inc. makes no representations concerning either
+ *      the merchantability of this software or the suitability of this
+ *      software for any particular purpose. It is provided "as is"
+ *      without express or implied warranty of any kind.
  *
- *	These notices must be retained in any copies of any part of this
- *	documentation and/or software.
+ *      These notices must be retained in any copies of any part of this
+ *      documentation and/or software.
  */
 
 //md5 class include
@@ -104,9 +104,9 @@ void MD5::MD5Init(MD5_CTX *context) {
 }
 
 /*
-	 MD5 block update operation. Continues an MD5 message-digest
-	 operation, processing another message block, and updating the
-	 context.
+         MD5 block update operation. Continues an MD5 message-digest
+         operation, processing another message block, and updating the
+         context.
 */
 void MD5::MD5Update(MD5_CTX *context, uint8_t *input, uint32_t inputLen) {
   uint32_t i, index, partLen;
diff --git a/isis/src/lro/apps/lronacpho/LROCEmpirical.cpp b/isis/src/lro/apps/lronacpho/LROCEmpirical.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c8b7a5c46875247bf5af9f192a4fe05407cd0b9f
--- /dev/null
+++ b/isis/src/lro/apps/lronacpho/LROCEmpirical.cpp
@@ -0,0 +1,343 @@
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include 
+#include "Camera.h"
+#include "DbProfile.h"
+#include "LROCEmpirical.h"
+#include "PvlObject.h"
+
+using namespace std;
+
+namespace Isis {
+
+ /**
+  * Create an LROCEmpirical photometric object
+  * 
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 - Code adapted from lrowacpho written by Kris Becker
+  */
+  LROCEmpirical::LROCEmpirical(PvlObject &pvl, Cube &cube, bool useCamera) :
+                 PhotometricFunction(pvl, cube, useCamera) {
+    init(pvl, cube);
+  }
+
+
+  /**
+   * Destructor
+   */
+  LROCEmpirical::~LROCEmpirical() {};
+
+
+  /**
+   * @brief Initialize class from input PVL and Cube files
+   *
+   * This method is typically called at the class instantiation
+   * time but is reentrant. It reads the parameter PVL file and 
+   * extracts Photometric model and Normalization models from it.
+   * The cube is needed to match all potential profiles for each
+   * band.
+   *
+   * @param pvl Input PVL parameter files
+   * @param cube Input cube file to correct
+   * 
+   * @throws IException::User "Errors in the input PVL file."
+   * @throws IException::User "Band with wavelength Center does not have
+   *                           PhotometricModel Algorithm group/profile."
+   *
+   * @author Victor Silva 2016-08-15
+   *
+   * @internal
+   *   @history 2016-08-15 Victor Silva - Adapted from the lrowacpho application
+   *                           written by Kris Becker.
+   */
+  void LROCEmpirical::init( PvlObject &pvl, Cube &cube ) {
+
+    //  Make it reentrant
+    m_profiles.clear();
+    m_bandpho.clear();
+
+    //  Interate over all Photometric groups
+    m_normProf = DbProfile(pvl.findObject("NormalizationModel").findGroup("Algorithm", Pvl::Traverse));
+    m_iRef = toDouble(ConfKey(m_normProf, "IncRef", toString(30.0)));
+    m_eRef = toDouble(ConfKey(m_normProf, "EmaRef", toString(0.0)));
+    m_gRef = toDouble(ConfKey(m_normProf, "PhaRef", toString(m_iRef)));
+
+    PvlObject &phoObj = pvl.findObject("PhotometricModel");
+    DbProfile phoProf = DbProfile(phoObj);
+    PvlObject::PvlGroupIterator algo = phoObj.beginGroup();
+
+    while (algo != phoObj.endGroup()) {
+
+      if (algo->name().toLower() == "algorithm") {
+        m_profiles.push_back(DbProfile(phoProf, DbProfile(*algo)));
+      }
+      ++algo;
+    }
+
+    Pvl *label = cube.label();
+    PvlKeyword center = label->findGroup("BandBin", Pvl::Traverse)["Center"];
+    QString errs("");
+
+    for (int i = 0; i < cube.bandCount(); i++) {
+      Parameters parms = findParameters(toDouble(center[i]));
+      if (parms.IsValid()) {
+        parms.band = i + 1;
+        parms.phoStd = photometry(parms, m_iRef, m_eRef, m_gRef);
+        m_bandpho.push_back(parms);
+      }
+      else { // Appropriate photometric parameters not found
+        ostringstream mess;
+        mess << "Band [" << i + 1 << "] with wavelength Center = [" << center[i] << 
+        "] does not have PhotometricModel Algorithm group/profile";
+        IException e(IException::User, mess.str(), _FILEINFO_);
+        errs += e.toString() + "\n";
+      }
+    }
+
+    // Check for errors and throw them all at the same time
+    if (!errs.isEmpty()) {
+      errs += " --> Errors in the input PVL file [" + pvl.fileName() + "]";
+      throw IException(IException::User, errs, _FILEINFO_);
+    }
+
+    return;
+  }
+
+
+  /**
+   * @brief Method to get photometric property given angles
+   *
+   * This method computes photometric property at the given cube location after 
+   * proper parameter container is found for the specific band.
+   * 
+   * @param i    Incidence angle in degrees
+   * @param e    Emission angle in degrees
+   * @param g    Phase angle in degrees
+   * @param band cube band to be tested
+   *
+   * 
+   * @throws IException::Programmer "Provided band out of range."
+   *
+   * @return @b double The photometric property
+   *
+   * @author 2016-08-15 Victor Silva
+   *
+   * @internal
+   *   @history 2016-08-15 Victor Silva - Adapted code from lrowacpho application
+   *                         written by Kris Becker
+   */
+  double LROCEmpirical::photometry( double i, double e, double g, int band ) const {
+
+    if ((band <= 0) || (band > (int) m_bandpho.size())) {
+      std::string mess = "Provided band " + IString(band) + " out of range.";
+      throw IException(IException::Programmer, mess, _FILEINFO_);
+    }
+
+    double ph = photometry(m_bandpho[band - 1], i, e, g);
+    return (m_bandpho[band - 1].phoStd / ph);
+  }
+
+
+  /**
+   * @brief Performs actual photometric correction calculations
+   *
+   * This routine computes photometric correction using parameters for the 
+   * LROC Emperical equation.
+   *
+   * @param parms Container of band-specific exponential parameters
+   * @param i     Incidence angle in degrees
+   * @param e     Emission angle in degrees
+   * @param g     Phase angle in degrees
+   *
+   * @return @b double Photometric correction parameter
+   *
+   * @author 2016-08-15 Victor Silva
+   *
+   * @internal
+   *   @history 2016-08-15 Victor Silva - Adapted code from lrowacpho application
+   *                         written by Kris Becker
+   *
+   */
+  double LROCEmpirical::photometry( const Parameters &parms, double i, double e, double g ) const {
+    //  Ensure problematic values are adjusted
+    if (i == 0.0) {
+      i = 10.E-12;
+    }
+    if (e == 0.0) {
+      e = 10.E-12;
+    }
+
+    // Convert to radians
+    i *= rpd_c();
+    e *= rpd_c();
+    g *= parms.phaUnit; //  Apply unit normalizer
+
+    // Compute Lommel-Seeliger components
+    double mu = cos(e);
+    double mu0 = cos(i);
+    double alpha = g;
+    double rcal =  exp(parms.a0 + parms.a1 * alpha + parms.a2 * mu +  parms.a3 * mu0);
+
+    return (rcal);
+  }
+
+
+  /**
+   * @brief Return parameters used for all bands
+   * 
+   * Method creates keyword vector of band-specific parameters
+   * used in the photometric correction.
+   *
+   * @param pvl Output PVL container for keywords written
+   *
+   * @author 2016-08-15 Victor Silva 
+   *
+   * @internal
+   *   @history 2016-08-15 Victor Silva - Adapted code from lrowacpho application
+   *                         written by Kris Becker
+   */
+  void LROCEmpirical::report( PvlContainer &pvl ) {
+
+    pvl.addComment("I/F = F(mu, mu0,phase)");
+    pvl.addComment(" where:");
+    pvl.addComment("  mu0 = cos(incidence)");
+    pvl.addComment("  mu = cos(emission)");
+    pvl.addComment("  F(mu, mu0, phase) = exp(A0 + A1 * phase + A2 * mu + A3 * mu0 ");
+
+    pvl += PvlKeyword("Algorithm", "LROC_Empirical");
+    pvl += PvlKeyword("IncRef", toString(m_iRef), "degrees");
+    pvl += PvlKeyword("EmaRef", toString(m_eRef), "degrees");
+    pvl += PvlKeyword("Algorithm", "LROC_Empirical");
+    pvl += PvlKeyword("IncRef", toString(m_iRef), "degrees");
+    pvl += PvlKeyword("EmaRef", toString(m_eRef), "degrees");
+    pvl += PvlKeyword("EmaRef", toString(m_eRef), "degrees");
+    pvl += PvlKeyword("Algorithm", "LROC_Empirical");
+    pvl += PvlKeyword("IncRef", toString(m_iRef), "degrees");
+    pvl += PvlKeyword("EmaRef", toString(m_eRef), "degrees");
+    pvl += PvlKeyword("PhaRef", toString(m_gRef), "degrees");
+
+    PvlKeyword units("FunctionUnits");
+    PvlKeyword phostd("PhotometricStandard");
+    PvlKeyword bbc("BandBinCenter");
+    PvlKeyword bbct("BandBinCenterTolerance");
+    PvlKeyword bbn("BandNumber");
+    PvlKeyword a0("A0");
+    PvlKeyword a1("A1");
+    PvlKeyword a2("A2");
+    PvlKeyword a3("A3");
+
+    for (unsigned int i = 0; i < m_bandpho.size(); i++) {
+      Parameters &p = m_bandpho[i];
+      units.addValue(p.units);
+      phostd.addValue(toString(p.phoStd));
+      bbc.addValue(toString(p.wavelength));
+      bbct.addValue(toString(p.tolerance));
+      bbn.addValue(toString(p.band));
+      a0.addValue(toString(p.a0));
+      a1.addValue(toString(p.a1));
+      a2.addValue(toString(p.a2));
+      a3.addValue(toString(p.a3));
+    }
+
+    pvl += units;
+    pvl += phostd;
+    pvl += bbc;
+    pvl += bbct;
+    pvl += bbn;
+    pvl += a0;
+    pvl += a1;
+    pvl += a2;
+    pvl += a3;
+
+    return;
+  }
+
+
+  /**
+   * @brief Determine LROC Empirical parameters given a wavewlength
+   *
+   * This method determines the set of LROCEmpirical parameters to
+   * use for a given wavelength. It iterates through all band profiles
+   * as read from the PVL file and computes the difference between 
+   * wavelength parameter and the BandBinCenter keyword. The absolute 
+   * value of this value is checke against the BandBinCenterTolerance 
+   * parameter and if it is less than or equal to it, a Parameter 
+   * container is returned. 
+   *
+   * @param wavelength The wavelength to find parameters for
+   *
+   * @return @b LROEmpirical::parameters The parameters used for the specified
+   *                                     wavelength. If a BandBinCenter is not
+   *                                     found for the wavelength then a
+   *                                     default parameters object is returned.
+   *
+   * @author 2016-08-15 Victor Silva 
+   * 
+   * @internal
+   *   @history 2016-08-15 Victor Silva - Adapted from the lrowacpho application
+   *                           written by Kris Becker.
+   */
+  LROCEmpirical::Parameters LROCEmpirical::findParameters( const double wavelength ) const {
+
+    for (unsigned int i = 0; i < m_profiles.size(); i++) {
+      const DbProfile &profile = m_profiles[i];
+
+      if (profile.exists("BandBinCenter")) {
+        double p_center = toDouble(ConfKey(profile, "BandBinCenter", toString(Null)));
+        double tolerance = toDouble(ConfKey(profile, "BandBinCenterTolerance", toString(1.0E-6)));
+
+        if (fabs(wavelength - p_center) <= fabs(tolerance)) {
+          Parameters pars = extract(profile);
+          pars.iProfile = i;
+          pars.wavelength = wavelength;
+          pars.tolerance = tolerance;
+          return (pars);
+        }
+      }
+    }
+    // Not found if we reach here
+    return (Parameters());
+  }
+
+
+
+  /*
+   * @brief Extracts necessary LROCEmprical parameters from profile
+   *
+   * Given a profile read from the input PVL file, this method extracts
+   * needed parameters (from keywords) in the PVL profile and creates
+   * a container of the converted values
+   *
+   * @param profile The profile to extract parameters for
+   *
+   * @return @b LROCEmpirical::parameters
+   *
+   * @author Victor Silva 2016-08-15
+   *
+   * @internal
+   *   @history 2016-08-15 Victor Silva - Adapted from the lrowacpho application
+                              written by Kris Becker.
+   */
+  LROCEmpirical::Parameters LROCEmpirical::extract( const DbProfile &profile) const {
+    Parameters pars;
+    pars.a1 = toDouble(ConfKey(profile, "A1", toString(0.0)));
+    pars.a2 = toDouble(ConfKey(profile, "A2", toString(0.0)));
+    pars.a3 = toDouble(ConfKey(profile, "A3", toString(0.0)));
+    pars.wavelength = toDouble(ConfKey(profile, "BandBinCenter", toString(Null)));
+    pars.tolerance = toDouble(ConfKey(profile, "BandBinCenterTolerance", toString(Null)));
+    //  Determine equation units - defaults to Radians
+    pars.units = ConfKey(profile, "Units", QString("Radians"));
+    pars.phaUnit = (pars.units.toLower() == "degrees") ? 1.0 : rpd_c();
+
+    return (pars);
+  }
+}
diff --git a/isis/src/lro/apps/lronacpho/LROCEmpirical.h b/isis/src/lro/apps/lronacpho/LROCEmpirical.h
new file mode 100644
index 0000000000000000000000000000000000000000..5ce915fb895988d12976828c6dfc3649b3a49f1c
--- /dev/null
+++ b/isis/src/lro/apps/lronacpho/LROCEmpirical.h
@@ -0,0 +1,77 @@
+#ifndef LROCEmpirical_h
+#define LROCEmpirical_h
+
+#include 
+#include 
+#include 
+#include 
+
+#include "Camera.h"
+#include "DbProfile.h"
+#include "IString.h"
+#include "PhotometricFunction.h"
+#include "SpecialPixel.h"
+
+namespace Isis {
+
+  class PvlObject;
+  class Camera;
+
+  /**
+   * @brief An implementation of photometric equation used for LRO NAC Cameras
+   *
+   * This class implements the LROC Empirical photometric equation used for the LRO NAC
+   * Cameras.
+   *
+   * @author 2016-08-15 Victor Silva
+   *
+   * @internal
+   *   @history 2016-08-15 - Code adapted from lrowacpho written by Kris Becker
+   *
+   */
+  class LROCEmpirical : public PhotometricFunction {
+    public:
+      LROCEmpirical (PvlObject &pvl, Cube &cube, bool useCamera);
+      virtual ~LROCEmpirical () ;
+
+      double photometry(double i, double e, double g, int band = 1) const;
+      void report( PvlContainer &pvl );
+
+    private:
+      /**
+       * Container for band photometric correction parameters
+       *
+       * @author 2016-08-15 Victor Silva
+       * 
+       * @internal
+       *   @history 2016-08-05 - Code adapted from lrowacpho written by Kris Becker
+       */
+      struct Parameters {
+        Parameters() : a0(0.0), a1(0.0), a2(0.0), a3(0.0),
+                       wavelength(0.0), tolerance(0.0),
+                       units("Degrees"), phaUnit(1.0), band(0), phoStd(0.0),
+                       iProfile(-1) { }
+        ~Parameters() { }
+        bool IsValid() const { return (iProfile != -1);}
+        double a0, a1, a2, a3; // m_profiles; // m_bandpho; //
+#include 
+#include 
+
+#include "Angle.h"
+#include "Camera.h"
+#include "DbProfile.h"
+#include "PhotometricFunction.h"
+#include "PvlObject.h"
+
+using namespace std;
+
+namespace Isis {
+ /**
+  * Construct Photometric function from Pvl and Cube file
+  * 
+  * @param pvl photometric parameter files
+  * @param cube Input cube file
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  PhotometricFunction::PhotometricFunction( PvlObject &pvl, Cube &cube , bool useCamera ) {
+    if (useCamera) {
+      m_camera = cube.camera();
+    }
+  }
+
+
+  /**
+   * Destructor
+   */
+  PhotometricFunction::~PhotometricFunction() {}
+
+
+  /**
+   * Set the camera used to compute photometric angles.
+   * 
+   * @param cam A pointer to the camera to be used
+   */
+  void PhotometricFunction::setCamera(Camera *cam) {
+    m_camera = cam;
+  }
+
+
+  /**
+   * Finds the name of the algorithm defined in a PVL object.
+   * 
+   * @param pvl The pvl to find the algorithm name in.
+   * 
+   * @return @b QString The algorithm name from the PVL object.
+   */
+  QString PhotometricFunction::algorithmName( const PvlObject &pvl ) {
+    return pvl.findObject("PhotometricModel").findGroup("Algorithm", Pvl::Traverse).findKeyword("Name")[0];
+  }
+
+
+ /**
+  * Computes Photometric function from cube attributes
+  * 
+  * @param line line number in cube
+  * @param sample sample number in cube
+  * @param band band number in cube
+  * @param useDem boolean to use provided Dem
+  * 
+  * @return @b double photometry calculations
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Victor Silva - Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  double PhotometricFunction::compute( const double &line, const double &sample, int band, bool useDem) {
+    // Update band if necessary
+    if (m_camera->Band() != band) {
+       m_camera->SetBand(band);
+    }
+    // Return null if not able to set image
+    if (!m_camera->SetImage(sample, line)) {
+      return (Null);
+    }
+    // calculate photometric angles
+    double i = m_camera->IncidenceAngle();
+    double e = m_camera->EmissionAngle();
+    double g = m_camera->PhaseAngle();
+    bool success = true;
+
+    if (useDem) {
+      Angle phase, incidence, emission;
+      m_camera->LocalPhotometricAngles(phase, incidence, emission, success);
+
+      if (success) {
+        g = phase.degrees();
+        i = incidence.degrees();
+        e = emission.degrees();
+      }
+    }
+
+    if ( !success || i < minimumIncidenceAngle() || i > maximumIncidenceAngle() || e < minimumEmissionAngle() || e
+                        > maximumEmissionAngle() || g < minimumPhaseAngle() || g > maximumPhaseAngle()) {
+      return (Null);
+    }
+
+    return photometry(i, e, g, band);
+  }
+
+
+ /**
+  * Mutator function to set minimum incidence angle
+  *
+  * @param double The new minimum incidence angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  void PhotometricFunction::setMinimumIncidenceAngle(double angle) {
+    m_minimumIncidenceAngle = angle;
+  }
+
+
+ /**
+  * Mutator function to set maximum incidence angle
+  *
+  * @param double the new maximum incidence angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  void PhotometricFunction::setMaximumIncidenceAngle(double angle) {
+    m_maximumIncidenceAngle = angle;
+  }
+
+
+ /**
+  * Mutator function to set minimum emission angle
+  *
+  * @param double The new minimum emission angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  void PhotometricFunction::setMinimumEmissionAngle(double angle) {
+    m_minimumEmissionAngle = angle;
+  }
+
+
+ /**
+  * Mutator function to set maximum emission angle
+  *
+  * @param double The new maximum emission angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  void PhotometricFunction::setMaximumEmissionAngle(double angle) {
+    m_maximumEmissionAngle = angle;
+  }
+
+
+ /**
+  * Mutator function to set minimum phase angle
+  *
+  * @param double The new minimum phase angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  void PhotometricFunction::setMinimumPhaseAngle(double angle) {
+    m_minimumPhaseAngle = angle;
+  }
+
+
+ /**
+  * Mutator function to set maximum phase angle
+  *
+  * @param double The new maximum phase angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  void PhotometricFunction::setMaximumPhaseAngle(double angle) {
+    m_maximumPhaseAngle = angle;
+  }
+
+
+ /**
+  * Accessor method to access minimum incidence angle
+  * 
+  * @return @b double The minimum incidence angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  double PhotometricFunction::minimumIncidenceAngle() {
+    return m_minimumIncidenceAngle;
+  }
+
+
+ /**
+  * Accessor method to access maximum incidence angle
+  * 
+  * @return @b double The maximum incidence angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  double PhotometricFunction::maximumIncidenceAngle() {
+    return m_maximumIncidenceAngle;
+  }
+
+
+ /**
+  * Accessor method to access minimum emission angle
+  * 
+  * @return @b double The minimum emission angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  double PhotometricFunction::minimumEmissionAngle() {
+    return m_minimumEmissionAngle;
+  }
+
+
+ /**
+  * Accessor method to access maximum emission angle
+  * 
+  * @return @b double The maximum emission angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  double PhotometricFunction::maximumEmissionAngle() {
+    return m_maximumEmissionAngle;
+  }
+
+
+ /**
+  * Accessor method to access minimum phase angle
+  * 
+  * @return @b double The minimum phase angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  double PhotometricFunction::minimumPhaseAngle() {
+    return m_minimumPhaseAngle;
+  }
+
+
+ /**
+  * Accessor method to access maximum phase angle
+  * 
+  * @return @b double The maximum phase angle
+  *
+  * @author 2016-08-15 Victor Silva
+  *
+  * @internal
+  *   @history 2016-08-15 Code adapted from lrowacpho written by Kris Becker
+  *
+  **/
+  double PhotometricFunction::maximumPhaseAngle() {
+    return m_maximumPhaseAngle;
+  }
+
+}
diff --git a/isis/src/lro/apps/lronacpho/PhotometricFunction.h b/isis/src/lro/apps/lronacpho/PhotometricFunction.h
new file mode 100644
index 0000000000000000000000000000000000000000..bd071a74b39fe6f240a81174b69150bf3f420fc7
--- /dev/null
+++ b/isis/src/lro/apps/lronacpho/PhotometricFunction.h
@@ -0,0 +1,136 @@
+#ifndef PhotometricFunction_h
+#define PhotometricFunction_h
+
+#include "IString.h"
+#include "Camera.h"
+#include "DbProfile.h"
+#include "SpecialPixel.h"
+
+#include 
+#include 
+#include 
+
+namespace Isis {
+
+  /**
+   * @brief Implement templatized MIN fumnction 
+   *
+   * Returns mininum value of both inputs of a specific type
+   *
+   * @param A first constant value of a type for comparison
+   * @param B second constant value of a type for comparison
+   * 
+   * @return @b T type value 
+   *
+   */
+  template inline T MIN( const T &A, const T &B ) {
+    if (A < B) {
+      return (A);
+    }
+    else {
+      return (B);
+    }
+  }
+
+  /** 
+   * @brief Implement templatized MAX fumnction 
+   *
+   * Returns maximum value of both inputs of a specifific type
+   *
+   * @param A first constant value of a type for comparison
+   * @param B second constant value of a type for comparison
+   *
+   * @return @b T type value 
+   *
+   */
+  template inline T MAX( const T &A, const T &B ) {
+    if (A > B) {
+      return (A);
+    }
+    else {
+      return (B);
+    }
+  }
+
+  class PvlObject;
+  class Camera;
+
+  /**
+   * @brief An abstract implementation of the photometric function
+   *
+   * This abstract class implements the a generic Photometric function.
+   * Child classes are expected to implement the photometry and report methods.
+   *
+   * @author 2016-08-15 Victor Silva
+   *
+   * @internal
+   *   @history 2016-08-15 - Code adapted from lrowacpho written by Kris Becker
+   */
+
+  class PhotometricFunction {
+
+    public:
+      PhotometricFunction(PvlObject &pvl, Cube &cube, bool useCamera);
+      virtual ~PhotometricFunction();
+
+      void setCamera(Camera *cam);
+      static QString algorithmName( const PvlObject &pvl );
+      virtual double compute( const double &line, const double &sample, int band = 1, bool useDem = false);
+      virtual double photometry( double i, double e, double g, int band = 1 ) const = 0;
+      virtual void report( PvlContainer &pvl ) = 0;
+      virtual void setMinimumIncidenceAngle( double angle );
+      virtual void setMaximumIncidenceAngle( double angle );
+      virtual void setMinimumEmissionAngle( double angle );
+      virtual void setMaximumEmissionAngle( double angle );
+      virtual void setMinimumPhaseAngle( double angle );
+      virtual void setMaximumPhaseAngle( double angle );
+      virtual double minimumIncidenceAngle();
+      virtual double maximumIncidenceAngle();
+      virtual double minimumEmissionAngle();
+      virtual double maximumEmissionAngle();
+      virtual double minimumPhaseAngle();
+      virtual double maximumPhaseAngle();
+
+
+    protected:
+
+      Camera *m_camera;               //
+      T ConfKey( const DbProfile &conf, const QString &keyname, const T &defval, int index = 0 ) const {
+        if (!conf.exists(keyname)) {
+          return (defval);
+        }
+        if (conf.count(keyname) < index) {
+          return (defval);
+        }
+         return conf.value(keyname, index);
+      }
+  };
+};
+#endif
diff --git a/isis/src/lro/apps/lronacpho/lronacpho.cpp b/isis/src/lro/apps/lronacpho/lronacpho.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..68bd934630193d6a03d05c60cc1d137b507cb8cd
--- /dev/null
+++ b/isis/src/lro/apps/lronacpho/lronacpho.cpp
@@ -0,0 +1,184 @@
+#include "Isis.h"
+
+#include 
+
+#include "Cube.h"
+#include "IException.h"
+#include "LROCEmpirical.h"
+#include "PhotometricFunction.h"
+#include "ProcessByLine.h"
+#include "Pvl.h"
+#include "PvlGroup.h"
+
+
+using namespace std;
+using namespace Isis;
+
+PhotometricFunction *g_pho;
+static bool g_useDEM;
+
+void phoCal (Buffer &in, Buffer &out);
+void phoCalWithBackplane (std::vector &in, std::vector &out );
+/**
+ *
+ * @brief Photometric application for the LRO NAC cameras
+ *
+ * This application provides featurs that allow multiband cubes for LRO NAC cameras 
+ *   to be photometrically corrected
+ *   
+ * @author 2016-09-16 Victor Silva   
+ *      
+ * @internal
+ *   @history 2016-09-19 Victor silva - Adapted from lrowacpho written by Kris Becker
+ * 
+ */
+void IsisMain (){
+  // Isis Processing by line
+  ProcessByLine p;
+  // Set up input cube and get camera info
+  Cube *iCube = p.SetInputCube("FROM");
+  // Set up output cube
+  Cube *oCube = p.SetOutputCube("TO");
+  // Set up the user interface
+  UserInterface &ui = Application::GetUserInterface();
+  // Backplane option
+  bool useBackplane = false;
+
+  if (ui.WasEntered("BACKPLANE")) {
+    CubeAttributeInput backplaneCai = ui.GetInputAttribute("BACKPLANE");
+
+    Cube bpCube;
+    bpCube.open(ui.GetFileName("BACKPLANE"));
+    int bpBands = bpCube.bandCount();
+    bpCube.close();
+
+    int bpCaiBands = backplaneCai.bands().size();
+
+    if (bpBands < 3 || (bpCaiBands != 3 && bpBands > 3)) {
+      string msg = "Invalid Backplane: The backplane must be exactly 3 bands";
+      throw IException(IException::User, msg, _FILEINFO_);
+    }
+
+    if (iCube->bandCount() != 1) {
+      string msg = "Invalid Image: The backplane option can only be used with a single image band at a time.";
+      throw IException(IException::User, msg, _FILEINFO_);
+    }
+
+    CubeAttributeInput cai;
+    bpCaiBands == 3 ? cai.setAttributes("+" + backplaneCai.bands()[0]) : cai.setAttributes("+1" ) ;
+    p.SetInputCube(ui.GetFileName("BACKPLANE"), cai);
+    bpCaiBands == 3 ? cai.setAttributes("+" + backplaneCai.bands()[1]) : cai.setAttributes("+2" ) ;
+    p.SetInputCube(ui.GetFileName("BACKPLANE"), cai);
+    bpCaiBands == 3 ? cai.setAttributes("+" + backplaneCai.bands()[2]) : cai.setAttributes("+3" ) ;
+    p.SetInputCube(ui.GetFileName("BACKPLANE"), cai);
+
+    useBackplane = true;
+  }
+
+  // Get parameters file
+  Pvl params(ui.GetFileName("PHOPAR"));
+  IString algoName =   PhotometricFunction::algorithmName(params);
+  algoName.UpCase();
+
+  // Use generic NAC algorithm
+  if (algoName == "LROC_EMPIRICAL") {
+    g_pho = new LROCEmpirical(params, *iCube, !useBackplane);
+  }
+  else {
+    string msg = " Algorithm Name [" + algoName + "] not recognized. ";
+    msg += "Compatible Algorithms are:\n LROC_Empirical";
+    throw IException(IException::User, msg, _FILEINFO_);
+  }
+
+  // Set user selected max and mins
+  g_pho->setMinimumPhaseAngle(ui.GetDouble("MINPHASE"));
+  g_pho->setMaximumPhaseAngle(ui.GetDouble("MAXPHASE"));
+  g_pho->setMinimumEmissionAngle(ui.GetDouble("MINEMISSION"));
+  g_pho->setMaximumEmissionAngle(ui.GetDouble("MAXEMISSION"));
+  g_pho->setMinimumIncidenceAngle(ui.GetDouble("MININCIDENCE"));
+  g_pho->setMaximumIncidenceAngle(ui.GetDouble("MAXINCIDENCE"));
+
+  // Set use of DEM to calculate photometric angles
+  g_useDEM = ui.GetBoolean("USEDEM");
+
+   // Begin processing by line
+  if(useBackplane) {
+    p.StartProcess(phoCalWithBackplane);
+  }
+  else {
+    p.StartProcess(phoCal);
+  }
+  // Start all the PVL
+  PvlGroup photo("Photometry");
+  g_pho->report(photo);
+  oCube->putGroup(photo);
+  Application::Log(photo);
+  p.EndProcess();
+  delete g_pho;
+}//end IsisMain
+
+/**
+ * @brief Apply LROC Empirical photometric correction
+ *
+ * Process function dispatched for each line to apply the LROC Empirical photometric
+ * correction function.
+ *
+ * @author 2016-09-19 Victor Silva
+ *
+ * @internal
+ *   @history 2016-09-19 Victor silva - Adapted from lrowacpho written by Kris Becker
+ *
+ * @param in Buffer containing input data
+ * @param out Buffer of photometrically corrected data
+ */
+void phoCal(Buffer &in, Buffer &out){
+  // Iterate through pixels
+  for(int i = 0; i < in.size(); i++){
+    // Ignore special pixels
+    if(IsSpecial(in[i])){
+      out[i] = in[i];
+    }
+    else{
+      // Get correction and test for validity
+      double ph = g_pho->compute(in.Line(i), in.Sample(i), in.Band(i), g_useDEM);
+      out[i] = ( IsSpecial(ph) ? Null : (in[i] * ph) );
+    }
+  }
+  return;
+}//end phoCal
+
+/**
+ * @brief Apply LROC Empirical photometric correction with backplane
+ *
+ * Short function dispatched for each line to apply the LROC Empirical photometric
+ * correction function.
+ *
+ * @author 2016-09-19 Victor Silva
+ *
+ * @internal
+ *   @history 2016-09-19 Victor silva - Adapted from lrowacpho written by Kris Becker
+ *
+ * @param in Buffer containing input data
+ * @param out Buffer of photometrically corrected data
+ */
+void phoCalWithBackplane ( std::vector &in, std::vector &out ) {
+
+  Buffer &image = *in[0];
+  Buffer &phase = *in[1];
+  Buffer &emission = *in[2];
+  Buffer &incidence = *in[3];
+  Buffer &calibrated = *out[0];
+
+  for (int i = 0; i < image.size(); i++) {
+    //  Don't correct special pixels
+    if (IsSpecial(image[i])) {
+      calibrated[i] = image[i];
+    }
+    else {
+    // Get correction and test for validity
+      double ph = g_pho->photometry(incidence[i], emission[i], phase[i], image.Band(i));
+      calibrated[i] = (IsSpecial(ph) ? Null : image[i] * ph);
+    }
+  }
+  return;
+}
diff --git a/isis/src/lro/apps/lronacpho/lronacpho.xml b/isis/src/lro/apps/lronacpho/lronacpho.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a3bd28c4af51a4ded4bdeaf49c5475386aa7a712
--- /dev/null
+++ b/isis/src/lro/apps/lronacpho/lronacpho.xml
@@ -0,0 +1,273 @@
+
+
+
+
+  
+    Apply general LROC NAC photometric correction to multiband cubes
+  
+
+  
+    
      
+      LROC Empirical implements a photometric correction  
+   
      
+    
      +      I/F = F(mu, mu0,phase)
+              where
+                  mu0 = cos(incidence)
+                  mu = cos(emission)
+                  F(mu, mu0, phase) = e(A0 + A1 * phase + A2 * mu + A3 * mu0) 
+    
      
+    
      
+      The equation described accounts for scattering dependance on incidence, 
+      emission, and phase angles.  Lunar Reflectance approximately follows this function 
+      and has been tested with repeat coverage at different illumination
+      geometries. The exponential equation has been derived from over 760,000 NAC
+      image tiles. More information can be found at:
+    
      
+    
      
+      http://www.hou.usra.edu/meetings/lpsc2014/pdf/2826.pdf
+    
      
+    
      
+      This application provides features that allow LROC NAC image cubes to be 
+      photometrically corrected with a properly formatted PVL input file much 
+      like that of the ISIS program photomet. This application restricts 
+      much of the options available to the more sophisticated photomet 
+      application.  Below is an example input parameter file for this 
+      application:
+    
      
+  
      +      Object = NormalizationModel
+        Group = Algorithm
+          Name = LROC_Empirical
+          PhotoModel = LROC_Empirical
+          Incref=30.0
+          Emaref=0.0
+          Pharef=30.0
+        EndGroup
+      EndObject
+
+      Object = PhotometricModel
+        Units = Degrees
+        Group = Algorithm
+          Name = LROC_Empirical
+          FilterName = "Broadband"
+          BandBinCenter = 600.0
+          A0 = -2.9811422
+          A1 = -0.0112862
+          A2 = -0.8084603
+          A3 = 1.3248888
+        EndGroup
+      EndObject
+  
      
+    
      
+      The Normalization object is the PhotometricModel evaluated at the given Incref,
+      Emaref and Pharef angles. The value of the Name parameter is ignored here.   
+      The Incref, Emaref, and Pharef are the incidence, emission and phase angles 
+      to be  used as the photometric standard. It will be used to normalize the photometric 
+      correction parameter to these angles. The equation used to create the 
+      photometrically corrected I/F dn is:
+    
      
+      
      +          odn = idn * (phostd  / ph)
+         
+              where phostd is the photometry model evaluated at the given Incref, 
+              Emaref and Pharef angles. ph is the photometric correction for the 
+              incidence, emission and phase at each pixel
+      
      
+  
      
+      The "Center" parameter in the above equality comes from the Center keyword 
+      in the BandBin group of the input cube file specified in the FROM 
+      parameter.  This keyword must exist in the input cube or an error is 
+      generated and the program aborts.   BandBinCenter and 
+      BandBinCenterTolerance are contained in each Algorithm group.  Only 
+      BandBinCenter is required.  If BandBinCenterTolerance is not present in an 
+      Algorithm group a value of 1.0E-6 is used.  All input bands in the FROM 
+      file must be matched to at least one of the Algorithm parameters otherwise 
+      an error is generated and the application is aborted.
+    
      
+    
      
+      The parameter Units is provided to specify if the phase angle is in 
+      units of degrees or radians.  It does not have to exist in any group or 
+      even in the top Object section.  If it does not exist, "Radians" is the 
+      default.
+    
      
+    
      
+      An additional feature of the PVL structure is that any keyword that exists 
+      in the Object section of the PhotometricModel Object is propagated to each 
+      Algorithm group when it  is read in unless the keyword already exists in 
+      the Algorithm group.  If a keyword exists in both the PhotometricModel 
+      object and an Algorithm group, the keyword in the Algorithm group has 
+      precedence.
+    
      
+    
      
+      Additional consequences of the photometric correction processing is any 
+      incidence angle greater than 90 degrees is set to the ISIS special Null 
+      pixel value.  And, of course, any ISIS special pixel encountered on input 
+      is propagated to the output TO file without modification.
+    
      
+        
+
+  
+    
+      Version adapted from Kris Becker's LROWACPHO application from 2010
+    
+  
+
+  
+    Lunar Reconnaissance Orbiter
+  
+
+  
+    
+      
+        cube
+        input
+        
+          Input cube
+        
+        
+          Use this parameter to select the input file name.
+        
+        
+          *.cub
+        
+      
+
+      
+        cube
+        real
+        output
+        
+          Output cube
+        
+        
+          This file will contain the photometrically corrected image data after 
+          being corrected by with LROC_Empirical algorithm.
+        
+      
+      
+      
+        cube
+        real
+        input
+        
+          Backplane Cube
+        
+        
+          This file will contain the backplane data. It must have "Phase Angle", "Emission Angle",
+          and "Incidence Angle" as the first three bands.
+        
+        
+            Calculate the photometry on the fly
+        
+      
+
+      
+        filename
+        input
+        
+          PVL file
+        
+        
+          This file will contain the parameters A0-A3 to use when 
+          applying the LROC Empirical photometric correction.  See the main program 
+          documentation for a full description.
+        
+         *.pvl
+      
+    
+    
+    
+      
+        double
+        0.0
+        Minimum phase angle to trim
+        
+          Pixels which have a phase angle less than this value will be
+          trimmed.
+        
+        0.0
+        180.0
+        MAXPHASE
+      
+      
+        double
+        180.0
+        Maximum phase angle to trim
+        
+          Pixels which have a phase angle greater than this value will be
+          trimmed.
+        
+        0.0
+        180.0
+        MINPHASE
+      
+
+      
+        double
+        0.0
+        Minimum emission angle to trim
+        
+          Pixels which have an emission angle less than this value will be
+          trimmed.
+        
+        0.0
+        90.0
+        MAXEMISSION
+      
+      
+        90.0
+        double
+        Maximum emission angle to trim
+        
+          Pixels which have a emission angle greater than this value will be
+          trimmed.
+        
+        0.0
+        90.0
+        MINEMISSION
+      
+
+      
+        double
+        0.0
+        Minimum incidence angle to trim
+        
+          Pixels which have an incidence angle less than this value will be
+          trimmed.
+        
+        0.0
+        180.0
+        MAXINCIDENCE
+      
+      
+        double
+        90.0
+        Maximum incidence angle to trim
+        
+          Pixels which have a incidence angle greater than this value will be
+          trimmed.
+        
+        0.0
+        180.0
+        MININCIDENCE
+      
+    
+    
+    
+      
+        boolean
+        False
+        
+          Use DEM instead of ellipsoid for photometric angle calculations
+        
+        
+          Phase, Emission, and Incidence angles can be calculated from the
+          ellipsoid (default) or from the DEM.  The difference is that using the
+          DEM the surface roughness is taken into account.
+        
+      
+    
+    
+  
+      
diff --git a/isis/src/lro/apps/lronacpho/tsts/Makefile b/isis/src/lro/apps/lronacpho/tsts/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..46d84c74c297304e943452a44e06b111f179a92b
--- /dev/null
+++ b/isis/src/lro/apps/lronacpho/tsts/Makefile
@@ -0,0 +1,4 @@
+BLANKS = "%-6s"    
+LENGTH = "%-40s"
+
+include $(ISISROOT)/make/isismake.tststree
diff --git a/isis/src/lro/apps/lronacpho/tsts/default/Makefile b/isis/src/lro/apps/lronacpho/tsts/default/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..f2cfd7917debdae542343cf24519e84b66fcf14c
--- /dev/null
+++ b/isis/src/lro/apps/lronacpho/tsts/default/Makefile
@@ -0,0 +1,9 @@
+APPNAME = lronacpho
+
+include $(ISISROOT)/make/isismake.tsts
+
+commands:
+	$(APPNAME) usedem=false \
+	  phopar=${INPUT}/LROC_Empirical_2014.pvl \
+	  from=$(INPUT)/M143947267L.cal.echo.crop.cub \
+	  to=$(OUTPUT)/M143947267L.cal.echo.crop.nodtmpho.test.cub > /dev/null;
diff --git a/isis/src/lro/apps/lrowac2isis/lrowac2isis.cpp b/isis/src/lro/apps/lrowac2isis/lrowac2isis.cpp
index e4843ca3b0d2cb8c44e0c84ab7f7c1911dda0f8f..c45691fdbae6870090da07291a37969045869ec3 100644
--- a/isis/src/lro/apps/lrowac2isis/lrowac2isis.cpp
+++ b/isis/src/lro/apps/lrowac2isis/lrowac2isis.cpp
@@ -485,7 +485,7 @@ void TranslateLabels(Pvl &pdsLab, Pvl &isis3VisEven, Pvl &isis3VisOdd,
 
   // color offset doesn't apply to BW mode (single band cubes)
   if(colorOffset && viseven && viseven->bandCount() == 1) {
-    genericInstrument.push_back(PvlKeyword("ColorOffset", 0));
+    genericInstrument.push_back(PvlKeyword("ColorOffset", QString::number(0)));
   }
   else {
     genericInstrument.push_back(PvlKeyword("ColorOffset", toString(colorOffset)));
diff --git a/isis/src/lro/apps/lrowac2pds/lrowac2pds.xml b/isis/src/lro/apps/lrowac2pds/lrowac2pds.xml
index 8775baa78d1c1de0f342672b1587d19e130c585e..9c628eeaed484b0dcdc204f1cdcc86152a240c50 100644
--- a/isis/src/lro/apps/lrowac2pds/lrowac2pds.xml
+++ b/isis/src/lro/apps/lrowac2pds/lrowac2pds.xml
@@ -2,10 +2,11 @@
 
 
   
-    Import LRO WAC EDR images into Isis cube format
+    Convert from cube to PDS IMG format
   
 
   
+    Program to convert LROC WAC calibrated cube to PDS IMG formatted file, with LROC specific label, as part of the WAC CDR product pipeline.
   
 
   
@@ -15,6 +16,9 @@
     
       Added a fix to allow for N-length product IDs. Fixes #1349.
     
+    
+      Update to documentation for consistentsy and clarity. Fixes #3913.
+    
   
 
   
@@ -24,30 +28,30 @@
   
     
       
-        filename
+        cube
         input
         
-          Input PDS formatted LRO WAC EDR image file.
+          Input cube to be converted
         
         
-          Use this parameter to select the LRO WAC EDR image filename.
+          The cube to be converted to PDS IMG format.
         
         
-          *.img *.IMG
+          *.cub
         
       
 
       
-         cube
+         filename
          output
          
-           Output Isis cube
+           Output PDS image
          
          
-           Use this parameter to select the base output filename.
+           The resulting PDS IMG file.
          
          
-           *.cub
+           *.img
          
        
       
@@ -57,7 +61,7 @@
           string
           Group to modify
           
-            The user input ID string
+            The user provided version ID string, used to uniquely identifty CDR products.
           
           "N/A"
         
diff --git a/isis/src/lro/apps/lrowac2pds/md5.cpp b/isis/src/lro/apps/lrowac2pds/md5.cpp
index aacf031673ef0a8aa243225c3effdecb7e40c2fd..cfc7e30bf3e392489bc6524e4d3b6e40887b91b1 100644
--- a/isis/src/lro/apps/lrowac2pds/md5.cpp
+++ b/isis/src/lro/apps/lrowac2pds/md5.cpp
@@ -1,34 +1,34 @@
 /*
- * 	This is the C++ implementation of the MD5 Message-Digest
- * 	Algorithm desrcipted in RFC 1321.
- * 	I translated the C code from this RFC to C++.
- * 	There is no warranty.
+ *      This is the C++ implementation of the MD5 Message-Digest
+ *      Algorithm desrcipted in RFC 1321.
+ *      I translated the C code from this RFC to C++.
+ *      There is no warranty.
  *
- * 	Feb. 12. 2005
- * 	Benjamin Gr�delbach
+ *      Feb. 12. 2005
+ *      Benjamin Gr�delbach
  */
 
 /*
- *	Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
- *	rights reserved.
+ *      Copyright (C) 1991-2, RSA Data Security, Inc. Created 1991. All
+ *      rights reserved.
  *
- *	License to copy and use this software is granted provided that it
- *	is identified as the "RSA Data Security, Inc. MD5 Message-Digest
- *	Algorithm" in all material mentioning or referencing this software
- *	or this function.
+ *      License to copy and use this software is granted provided that it
+ *      is identified as the "RSA Data Security, Inc. MD5 Message-Digest
+ *      Algorithm" in all material mentioning or referencing this software
+ *      or this function.
  *
- *	License is also granted to make and use derivative works provided
- *	that such works are identified as "derived from the RSA Data
- *	Security, Inc. MD5 Message-Digest Algorithm" in all material
- *	mentioning or referencing the derived work.
+ *      License is also granted to make and use derivative works provided
+ *      that such works are identified as "derived from the RSA Data
+ *      Security, Inc. MD5 Message-Digest Algorithm" in all material
+ *      mentioning or referencing the derived work.
  *
- *	RSA Data Security, Inc. makes no representations concerning either
- *	the merchantability of this software or the suitability of this
- *	software for any particular purpose. It is provided "as is"
- *	without express or implied warranty of any kind.
+ *      RSA Data Security, Inc. makes no representations concerning either
+ *      the merchantability of this software or the suitability of this
+ *      software for any particular purpose. It is provided "as is"
+ *      without express or implied warranty of any kind.
  *
- *	These notices must be retained in any copies of any part of this
- *	documentation and/or software.
+ *      These notices must be retained in any copies of any part of this
+ *      documentation and/or software.
  */
 
 //md5 class include
@@ -104,9 +104,9 @@ void MD5::MD5Init(MD5_CTX *context) {
 }
 
 /*
-	 MD5 block update operation. Continues an MD5 message-digest
-	 operation, processing another message block, and updating the
-	 context.
+         MD5 block update operation. Continues an MD5 message-digest
+         operation, processing another message block, and updating the
+         context.
 */
 void MD5::MD5Update(MD5_CTX *context, uint8_t *input, uint32_t inputLen) {
   uint32_t i, index, partLen;
diff --git a/isis/src/lro/apps/lrowac2pds/md5.h b/isis/src/lro/apps/lrowac2pds/md5.h
index 1f43c11062806fe94e97e8a6adffe75ff821930b..0a22fe5a1cbd741c04e2c94fec4ec74961e91f0e 100644
--- a/isis/src/lro/apps/lrowac2pds/md5.h
+++ b/isis/src/lro/apps/lrowac2pds/md5.h
@@ -1,11 +1,11 @@
 /*
- *	This is the C++ implementation of the MD5 Message-Digest
- *	Algorithm desrcipted in RFC 1321.
- *	I translated the C code from this RFC to C++.
- *	There is no warranty.
+ *      This is the C++ implementation of the MD5 Message-Digest
+ *      Algorithm desrcipted in RFC 1321.
+ *      I translated the C code from this RFC to C++.
+ *      There is no warranty.
  *
- *	Feb. 12. 2005
- *	Benjamin Gr�delbach
+ *      Feb. 12. 2005
+ *      Benjamin Gr�delbach
  */
 
 /*
@@ -49,9 +49,9 @@ typedef uint8_t *POINTER;
  * MD5 context.
  */
 typedef struct {
-  uint32_t state[4];   	      /* state (ABCD) */
-  uint32_t count[2]; 	      /* number of bits, modulo 2^64 (lsb first) */
-  uint8_t buffer[64];	      /* input buffer */
+  uint32_t state[4];          /* state (ABCD) */
+  uint32_t count[2];          /* number of bits, modulo 2^64 (lsb first) */
+  uint8_t buffer[64];         /* input buffer */
 } MD5_CTX;
 
 /*
diff --git a/isis/src/lro/apps/lrowaccal/lrowaccal.cpp b/isis/src/lro/apps/lrowaccal/lrowaccal.cpp
index c9e17817dbc5c9a48d04d3b680d128bab0d93eac..6e3faf2078e337bcfd41b50a3e80c3592e068e81 100644
--- a/isis/src/lro/apps/lrowaccal/lrowaccal.cpp
+++ b/isis/src/lro/apps/lrowaccal/lrowaccal.cpp
@@ -4,17 +4,20 @@
 
 #include 
 #include 
+#include 
 
 #include "Brick.h"
 #include "Camera.h"
 #include "Constants.h"
 #include "Cube.h"
 #include "CubeAttribute.h"
+#include "iTime.h"
 #include "Message.h"
+#include "Preference.h"
 #include "ProcessByBrick.h"
+#include "PvlGroup.h"
 #include "SpecialPixel.h"
 #include "Statistics.h"
-#include "iTime.h"
 
 using namespace Isis;
 using namespace std;
@@ -33,6 +36,7 @@ void ResetGlobals ();
 void Calibrate ( Buffer &in, Buffer &out );
 void CopyCubeIntoBuffer ( QString &fileString, Buffer* &data);
 double min ( double a, double b );
+QString GetCalibrationDirectory(QString calibrationType);
 
 void GetDark(QString fileString, double temp, double time, Buffer* &data1, Buffer* &data2, double & temp1, double & temp2, QString & file1, QString & file2);
 void GetMask(QString &fileString, double temp, Buffer* &data);
@@ -133,7 +137,7 @@ void IsisMain () {
       darkFiles.resize(2);
       double temp = (double) inst["MiddleTemperatureFpa"];
       double time = iTime(inst["StartTime"][0]).Et();
-      QString darkFile = "$lro/calibration/wac_darks/WAC_" + instModeId;
+      QString darkFile = GetCalibrationDirectory("wac_darks") + "WAC_" + instModeId;
       if (instModeId == "BW")
         darkFile += "_" + filter + "_Mode" + mode;
       darkFile += "_Offset" + offset + "_*C_*T_Dark.????.cub";
@@ -157,7 +161,7 @@ void IsisMain () {
 
   if (g_flatfield) {
     if (flatFile.toLower() == "default" || flatFile.length() == 0) {
-      flatFile = "$lro/calibration/wac_flats/WAC_" + instModeId;
+      flatFile = GetCalibrationDirectory("wac_flats") + "WAC_" + instModeId;
       if (instModeId == "BW")
         flatFile += "_" + filter + "_Mode" + mode;
       flatFile += "_Flatfield.????.cub";
@@ -177,7 +181,7 @@ void IsisMain () {
     Isis::PvlKeyword &bands = icube->label()->findGroup("BandBin", Pvl::Traverse).findKeyword("FilterNumber");
 
     if (radFile.toLower() == "default" || radFile.length() == 0)
-      radFile = "$lro/calibration/WAC_RadiometricResponsivity.????.pvl";
+      radFile = GetCalibrationDirectory("") + "WAC_RadiometricResponsivity.????.pvl";
 
     FileName radFileName(radFile);
     if (radFileName.isVersioned())
@@ -233,7 +237,7 @@ void IsisMain () {
 
   if (g_specpix) {
     if (specpixFile.toLower() == "default" || specpixFile.length() == 0) {
-      specpixFile = "$lro/calibration/wac_masks/WAC_" + instModeId;
+      specpixFile = GetCalibrationDirectory("wac_masks") + "WAC_" + instModeId;
       double temp = (double) inst["MiddleTemperatureFpa"];
       if (instModeId == "BW")
         specpixFile += "_" + filter + "_Mode" + mode;
@@ -244,9 +248,10 @@ void IsisMain () {
       CopyCubeIntoBuffer(specpixFile, g_specpixCube);
   }
 
+  PvlKeyword temperaturePvl("TemperatureFile");
   if (g_temprature) {
     if (tempFile.toLower() == "default" || tempFile.length() == 0)
-      tempFile = "$lro/calibration/WAC_TempratureConstants.????.pvl";
+      tempFile = GetCalibrationDirectory("") + "WAC_TempratureConstants.????.pvl"; 
 
     FileName tempFileName(tempFile);
     if (tempFileName.isVersioned())
@@ -258,6 +263,7 @@ void IsisMain () {
 
     Isis::PvlKeyword &bands = icube->label()->findGroup("BandBin", Pvl::Traverse).findKeyword("FilterNumber");
     Pvl tempPvl(tempFileName.expanded());
+    temperaturePvl.addValue(tempFileName.expanded());
     for (int b = 0; b < bands.size(); b++){
         g_TempratureConstants[g_bands[b]][0]=toDouble(tempPvl[bands[b]][0]);
         g_TempratureConstants[g_bands[b]][1]=toDouble(tempPvl[bands[b]][1]);
@@ -284,6 +290,9 @@ void IsisMain () {
 
   // Add an output group with the appropriate information
   PvlGroup calgrp("Radiometry");
+  if (g_temprature) {
+    calgrp += PvlKeyword("TemperatureFile",  temperaturePvl);
+  }
   if (g_dark) {
     PvlKeyword darks("DarkFiles");
     darks.addValue(darkFiles[0]);
@@ -594,7 +603,7 @@ struct DarkComp {
  * If there is only one tempurature, it will pick the 2 closest times at that tempurature.
  *
  *
- * @param fileString String pattern defining dark files to search (ie. $lro/calibration/wac_darks/WAC_COLOR_Offset68_*C_*T_Dark.????.cub)
+ * @param fileString String pattern defining dark files to search (ie. lro/calibration/wac_darks/WAC_COLOR_Offset68_*C_*T_Dark.????.cub)
  * @param temp Tempurature of WAC being calibrated
  * @param time Time of WAC being calibrated
  * @param data1 Buffer to hold dark file 1 cub data
@@ -749,3 +758,25 @@ void GetMask(QString &fileString, double temp, Buffer* &data) {
   CopyCubeIntoBuffer ( fileString, data );
 }
 
+/**
+ * This method returns a QString containing the path of an
+ * LRO calibration directory
+ *
+ * @param calibrationType The type of calibration data
+ * 
+ * @return @b QString Path of the calibration directory
+ *
+ * @internal
+ *   @history 2008-11-05 Jeannie Walldren - Original version
+ *   @history 2016-08-16 Victor Silva - Added option for base calibration directory
+ */
+QString GetCalibrationDirectory(QString calibrationType) {
+  // Get the directory where the CISS calibration directories are.
+  PvlGroup &dataDir = Preference::Preferences().findGroup("DataDirectory");
+  QString missionDir = (QString) dataDir["LRO"];
+  if(calibrationType != "") {
+    calibrationType += "/";
+  }
+
+  return missionDir + "/calibration/" + calibrationType;
+}
diff --git a/isis/src/lro/apps/mrf2isis/tsts/level2/Makefile b/isis/src/lro/apps/mrf2isis/tsts/level2/Makefile
index 2e2d9e1718f2a0dde3fab56004870c83e3837477..681a191117d2a9d9854eabdb43f68f1c31562cf0 100644
--- a/isis/src/lro/apps/mrf2isis/tsts/level2/Makefile
+++ b/isis/src/lro/apps/mrf2isis/tsts/level2/Makefile
@@ -7,3 +7,5 @@ commands:
 	to=$(OUTPUT)/FSL_CDR_LV2_00200_1Q.cub > /dev/null;
 	$(APPNAME) from=$(INPUT)/LSL_CDR_LV2_00300_1Q.LBL \
 	to=$(OUTPUT)/LSL_CDR_LV2_00300_1Q.cub > /dev/null;
+	catlab FROM=$(OUTPUT)/FSL_CDR_LV2_00200_1Q.cub to=$(OUTPUT)/FSL_CDR_LV2_00200_1Q.pvl > /dev/null;
+	catlab FROM=$(OUTPUT)/LSL_CDR_LV2_00300_1Q.cub to=$(OUTPUT)/LSL_CDR_LV2_00300_1Q.pvl > /dev/null;
diff --git a/isis/src/mer/apps/mical/mical.cpp b/isis/src/mer/apps/mical/mical.cpp
index f56a59401ad9f13eb2561fbae132c88eca257d57..fc270ad902d98b89894bee0c7bd7e7da55d8cd25 100644
--- a/isis/src/mer/apps/mical/mical.cpp
+++ b/isis/src/mer/apps/mical/mical.cpp
@@ -155,7 +155,7 @@ void IsisMain() {
   // output values to reflect no correction.
   if(!ui.GetBoolean("AACORRECTION")) {
     gbl::useActiveAreaValue = 0;
-    calgrp += PvlKeyword("ActiveAreaValue", 0);
+    calgrp += PvlKeyword("ActiveAreaValue", QString::number(0));
     calgrp += PvlKeyword("ActiveAreaImage", "NoCorrection");
   }
   else {
diff --git a/isis/src/mer/apps/mical/mical.xml b/isis/src/mer/apps/mical/mical.xml
index 307ac6e6bf6551f08f450f82a0d06f8f2b8c5a16..a9a57bbe98c355a6548a1779b2881187cc65f927 100644
--- a/isis/src/mer/apps/mical/mical.xml
+++ b/isis/src/mer/apps/mical/mical.xml
@@ -3,7 +3,7 @@
 
 
   
-     Radiometrically calibrates a Mars Exploration Rover (MER) 
+     Radiometrically calibrates a Mars Exploration Rover (MER)
      Microscopic Imager(MI) image
   
 
@@ -11,29 +11,29 @@
   
      
     mical performs radiometric corrections to images acquired by the MER
     MI camera.  MI images taken during science operations have 1024 samples
-    and 1024 lines and are single bands.  The pre calibration images are signed 
-    word or 16 bit images.  Subareas can be aquired but this was rarely done during 
+    and 1024 lines and are single bands.  The pre calibration images are signed
+    word or 16 bit images.  Subareas can be aquired but this was rarely done during
     the mission.
      
 
     mical has a number of parameters required to process MER MI image
     data.  Most of these parameters are read from an ISIS parameter defaults
-    file located in the mer directory specified in the IsisPreference file.  
+    file located in the mer directory specified in the IsisPreference file.
     This file has the form:
-     
          
+     
             $mer/calibration/mical.ker.xxx
-    
+
       where "xxx" is a positive number.
-     
        
+     
      
     mical will search for the parameter file with the highest number and
     load all its defaults needed to process MI images.  Note that the
     caller may explicity provide an alternative ISIS parameter defaults
     file name in the "CALKERNEL" input parameter if they have their own
     set of defaults that applies to MI data.  See an existing calibration
     file for details on how to configure this file.
-  
        
+  
      
 
      
     The level of calibration output can be selected.  by choosing one of the
-    output options, the user can choose to dark current correct, dark current and 
+    output options, the user can choose to dark current correct, dark current and
     flat field, or dark current, flat field and output in I/F values.
   
      
 
@@ -43,10 +43,10 @@
       r = dn - (rpi + rpv) + (zei * zev) + (aai * aav)
     
    
 
-    Where: 
+    Where:
             r is the aver signal being generated at the focal plane
             dn is the input pixel value
-            rpi is the referance pixel dn 
+            rpi is the referance pixel dn
             rpv is the referance pixel correction value
             zei is the zero exposure pixel dn
             zev is the zero exposure correction value
@@ -55,7 +55,7 @@
 
      The user can choose to not correct for the reference pixel, zero exposure
      or active area  by selecting or deselecting the RPCORRECTION, ZECORECTION,
-     or AACORRECTION checkbox.  The program will also determain if these 
+     or AACORRECTION checkbox.  The program will also determain if these
      corrections should be applied.  If the ShutteEffectCorrectionFlag is set to "TRUE"
      in the image labels, the reference pixel, and zero exposure will not be applied.
    
 
@@ -70,7 +70,7 @@
        f is a flat field pixel
    
 
        if the "ShutteEffectCorrectionFlag is false and the exposure duration is greater
-       them zero and less them 1000 and the image is mot equal to 1024 samples, a 
+       them zero and less them 1000 and the image is mot equal to 1024 samples, a
        image smear correction is applied.
 
    
 
@@ -83,6 +83,10 @@
     
       Original version
     
+    
+      Changed pvl.DIFF of input for all app tests to ignore file names. Allows test to pass when not
+      using default data area. Fixes #4738.
+    
   
 
   
@@ -141,7 +145,7 @@
             where "xxx" is a positive number.
    the kernel with the highest version (xxx) will be used. - See an existing calibration + See an existing calibration file for details on how to configure this file.     @@ -165,16 +169,16 @@ Referance Pixel image (ERP) - At times, a referance pixel image was aquired when image data was - taken. If a referance pixel image was acquired, it can be used in the - calibration. A referance pixel image uses the designation "ERP" rather + At times, a referance pixel image was aquired when image data was + taken. If a referance pixel image was acquired, it can be used in the + calibration. A referance pixel image uses the designation "ERP" rather then "EFF" in the file name. *.cub *.CUB Use Model Value -     +     cube input @@ -182,8 +186,8 @@ The flat field image used in correction - User can enter a flat field image that will be used in the correction. - If no value is entered, then the file listed in the calibration kernel + User can enter a flat field image that will be used in the correction. + If no value is entered, then the file listed in the calibration kernel will be used. @@ -199,11 +203,11 @@ The calibration stage to process - This parameter allows the user to control what calibration step will - be applied to the input image. if "DARK" is selected, then only a - dark current correction is preformed. If "FLAT" is selected, the - image is corrected for dark current and a flat field correction is - applied. if "IOF" is chosen then the final outut will in refiectance + This parameter allows the user to control what calibration step will + be applied to the input image. if "DARK" is selected, then only a + dark current correction is preformed. If "FLAT" is selected, the + image is corrected for dark current and a flat field correction is + applied. if "IOF" is chosen then the final outut will in refiectance values. @@ -223,7 +227,7 @@ Dark Current and Flat Field correction - The output will be a dark current corrected and flat field + The output will be a dark current corrected and flat field corrected. This is the "CFD" image in the PDS archive. @@ -232,8 +236,8 @@ Convert Dark current and Flat Field corrected image to I/F values - The output file will be a flat field corrected image that has been - converted to refiectance. This is the "IFF" file in the PDS + The output file will be a flat field corrected image that has been + converted to refiectance. This is the "IFF" file in the PDS archive. @@ -249,7 +253,7 @@ A user defined CCD temperature that will be used in calculations that use - the CCD temperature. If entered, this value will be used rather then the + the CCD temperature. If entered, this value will be used rather then the temperature in the image labels. Temperature from Labels @@ -262,8 +266,8 @@ A user defined PCB temperature that will be used in calculations that use - the PCB temperature. If entered, this value will be used rather then the - temperature in the image labels. + the PCB temperature. If entered, this value will be used rather then the + temperature in the image labels. Temperature from labels @@ -274,9 +278,9 @@ Correct for Referance Pixel - If this option is selected, the reference pixel correction will be applied. + If this option is selected, the reference pixel correction will be applied. if the ShutteEffectCorrectionFlag is set to TRUE then the reference pixel - correction is not applied, even if this parameter is set to true. The + correction is not applied, even if this parameter is set to true. The default is true which will apply the correction. TRUE @@ -288,9 +292,9 @@ Correct for Zero Exposure - If this option is selected, the zero exposure correction will be applied. + If this option is selected, the zero exposure correction will be applied. if the ShutteEffectCorrectionFlag is set to TRUE then the zero exposure - correction is not applied, even if this parameter is set to true. The + correction is not applied, even if this parameter is set to true. The default is true which will apply the correction. TRUE @@ -302,7 +306,7 @@ Correct for Active Area - If this option is selected, the active area. correction will be applied. + If this option is selected, the active area. correction will be applied. The default is true which will apply the correction. TRUE @@ -310,4 +314,3 @@     - diff --git a/isis/src/messenger/apps/mdis2isis/mdis2isis.cpp b/isis/src/messenger/apps/mdis2isis/mdis2isis.cpp index fcf053afe2f41c7670dc3c3eb1fed01f57c183d9..26a299cee8a84b448dc1624abd3c47aad0942616 100644 --- a/isis/src/messenger/apps/mdis2isis/mdis2isis.cpp +++ b/isis/src/messenger/apps/mdis2isis/mdis2isis.cpp @@ -1,4 +1,4 @@ -// $Id$ +// $Id: mdis2isis.cpp 5059 2013-03-11 16:37:00Z slambright@GS.DOI.NET $ #include "Isis.h" #include diff --git a/isis/src/messenger/apps/mdis2isis/mdis2isis.xml b/isis/src/messenger/apps/mdis2isis/mdis2isis.xml index 37c9d5b7d5d210219bb61be3d36d2a2ba2589377..58f7a05d3873dc0339b5bc5a3db34205330f645e 100644 --- a/isis/src/messenger/apps/mdis2isis/mdis2isis.xml +++ b/isis/src/messenger/apps/mdis2isis/mdis2isis.xml @@ -1,5 +1,5 @@ - + diff --git a/isis/src/messenger/apps/mdis2pds/mdis2pds.cpp b/isis/src/messenger/apps/mdis2pds/mdis2pds.cpp index eeabefbf63974473bb53c473bb5723bf78385a95..b6ff843a37531af73401d7dac1c8e689e737c0c7 100644 --- a/isis/src/messenger/apps/mdis2pds/mdis2pds.cpp +++ b/isis/src/messenger/apps/mdis2pds/mdis2pds.cpp @@ -89,7 +89,7 @@ inline void fixLabels(PvlObject &obj) { void IsisMain() { const QString mdis2pdsProgram = "mdis2pds"; const QString mdis2pdsVersion = "1.1"; - const QString mdis2pdsRevision = "$Revision$"; + const QString mdis2pdsRevision = "$Revision: 6715 $"; const QString mdis2pdsRuntime = Application::DateTime(); UserInterface &ui = Application::GetUserInterface(); diff --git a/isis/src/messenger/apps/mdis2pds/mdis2pds.xml b/isis/src/messenger/apps/mdis2pds/mdis2pds.xml index e439edd1b2e0cfef7c4629ea7064603b7d94515c..265d802511421d83681fda2fae1512e74efd59a8 100644 --- a/isis/src/messenger/apps/mdis2pds/mdis2pds.xml +++ b/isis/src/messenger/apps/mdis2pds/mdis2pds.xml @@ -1,5 +1,5 @@ - + diff --git a/isis/src/messenger/apps/mdiscal/DarkModelPixel.h b/isis/src/messenger/apps/mdiscal/DarkModelPixel.h index 2c76abeafd22f0319e835c2c892d036551dde10b..0906c4ee3af496d8f079a97679330f5401bfd9e6 100644 --- a/isis/src/messenger/apps/mdiscal/DarkModelPixel.h +++ b/isis/src/messenger/apps/mdiscal/DarkModelPixel.h @@ -2,8 +2,8 @@ #define DarkModelPixel_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6403 $ + * $Date: 2015-10-23 12:32:20 -0700 (Fri, 23 Oct 2015) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/messenger/apps/mdiscal/MdisCalUtils.h b/isis/src/messenger/apps/mdiscal/MdisCalUtils.h index b5333d9d5f457cf53d3da58b22be06ab942ac18e..b8a6e38ff76acbdf587a41f0b324173c4612dd85 100644 --- a/isis/src/messenger/apps/mdiscal/MdisCalUtils.h +++ b/isis/src/messenger/apps/mdiscal/MdisCalUtils.h @@ -2,8 +2,8 @@ #define MdisCalUtils_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/messenger/apps/mdiscal/mdiscal.cpp b/isis/src/messenger/apps/mdiscal/mdiscal.cpp index feec78c856da1df22bcd88640d560ef4a2276217..5f20636d17ebe9d47058ec2c84d62baa2b194aee 100644 --- a/isis/src/messenger/apps/mdiscal/mdiscal.cpp +++ b/isis/src/messenger/apps/mdiscal/mdiscal.cpp @@ -1,4 +1,4 @@ -// $Id$ +// $Id: mdiscal.cpp 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ #include "Isis.h" #include @@ -79,7 +79,7 @@ void IsisMain() { const QString mdiscalProgram = "mdiscal"; // 2015-09-02 Jeannie Backer - Increased cdr version to 6 since we added a new parameter, ECFACTOR const QString mdiscalVersion = "1.6"; - const QString mdiscalRevision = "$Revision$"; + const QString mdiscalRevision = "$Revision: 6715 $"; QString mdiscalRuntime = Application::DateTime(); // Specify the version of the CDR generated diff --git a/isis/src/messenger/apps/mdiscal/mdiscal.xml b/isis/src/messenger/apps/mdiscal/mdiscal.xml index 215239debd13d3073f4f406961cc19278ee0b3de..a362546c84ff560d01d642c2cddf69d44cb8dffc 100644 --- a/isis/src/messenger/apps/mdiscal/mdiscal.xml +++ b/isis/src/messenger/apps/mdiscal/mdiscal.xml @@ -1,5 +1,5 @@ - + diff --git a/isis/src/messenger/apps/mdisddr/mdisddr.cpp b/isis/src/messenger/apps/mdisddr/mdisddr.cpp index 5f49648aa76c72ece4425d7276d201641e1558ad..8d1ae8bff1d484606e21e312a7ed68be76dbd0c1 100644 --- a/isis/src/messenger/apps/mdisddr/mdisddr.cpp +++ b/isis/src/messenger/apps/mdisddr/mdisddr.cpp @@ -103,7 +103,7 @@ inline void writeBand(ProcessExportPds &process, ofstream &out, void IsisMain() { const QString mdisddrProgram = "mdisddr"; const QString mdisddrVersion = "1.0"; - const QString mdisddrRevision = "$Revision$"; + const QString mdisddrRevision = "$Revision: 6715 $"; const QString mdisddrRuntime = Application::DateTime(); const QString dataSetID = "MESS-E/V/H-MDIS-6-DDR-GEOMDATA-V1.0"; diff --git a/isis/src/messenger/apps/mdisddr/mdisddr.xml b/isis/src/messenger/apps/mdisddr/mdisddr.xml index 0c8db539bee30df0c5fcf78c10f8c8ac49216174..7814d2e3cffc6c13031729ce9177372342150608 100644 --- a/isis/src/messenger/apps/mdisddr/mdisddr.xml +++ b/isis/src/messenger/apps/mdisddr/mdisddr.xml @@ -1,5 +1,5 @@ - + diff --git a/isis/src/messenger/objs/MdisCamera/MdisCamera.cpp b/isis/src/messenger/objs/MdisCamera/MdisCamera.cpp index 0fa2318fa9699dca37a0c8b682d0b8fc8684a9d5..7f1707351fc67bcb7da38c93ccadc29f429d8129 100644 --- a/isis/src/messenger/objs/MdisCamera/MdisCamera.cpp +++ b/isis/src/messenger/objs/MdisCamera/MdisCamera.cpp @@ -1,7 +1,7 @@ /** * @file - * $Revision$ - * $Date$ + * $Revision: 6403 $ + * $Date: 2015-10-23 12:32:20 -0700 (Fri, 23 Oct 2015) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/messenger/objs/MdisCamera/MdisCamera.h b/isis/src/messenger/objs/MdisCamera/MdisCamera.h index 374cb21edec17a091caa40ad7b0f5052134fd0c7..3f326df9a31819e9f7897bfd061238b8553a5cb7 100644 --- a/isis/src/messenger/objs/MdisCamera/MdisCamera.h +++ b/isis/src/messenger/objs/MdisCamera/MdisCamera.h @@ -2,8 +2,8 @@ #define MdisCamera_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 6403 $ + * $Date: 2015-10-23 12:32:20 -0700 (Fri, 23 Oct 2015) $ * * Unless noted otherwise, the portions of Isis written by the USGS are public * domain. See individual third-party library and package descriptions for diff --git a/isis/src/messenger/objs/MdisCamera/MdisCamera.truth b/isis/src/messenger/objs/MdisCamera/MdisCamera.truth index f35ae61707f608a8ca2e11dca7a3f63eb73d708d..a90b6780f4ef5ceaf61eacc0de101674177fb21c 100644 --- a/isis/src/messenger/objs/MdisCamera/MdisCamera.truth +++ b/isis/src/messenger/objs/MdisCamera/MdisCamera.truth @@ -10,7 +10,7 @@ SPK Reference ID = 1 Shutter open = 234355674.731676608 Shutter close = 234355674.953676611 -Focal Length = 78.552880818 +Focal Length = 78.559574972 For upper left corner ... DeltaSample = 0.000000000 diff --git a/isis/src/messenger/objs/MdisCamera/unitTest.cpp b/isis/src/messenger/objs/MdisCamera/unitTest.cpp index 39dd2512bebca74583c8709752bb1a01df7aa026..7dcd319bb15d6718db84a4342be42e55d64a647f 100644 --- a/isis/src/messenger/objs/MdisCamera/unitTest.cpp +++ b/isis/src/messenger/objs/MdisCamera/unitTest.cpp @@ -47,8 +47,8 @@ int main(void) { // double knownLon = 225.0221110457575264; // Version 1 values // double knownLat = -0.1923383009013995; // double knownLon = 225.0671436738516888; - double knownLat = -0.1987371828743253; - double knownLon = 225.0531249933427489; + double knownLat = -0.1799382527687776; + double knownLon = 225.0254441224830941; Cube c("$messenger/testData/EW0089570936I.cub", "r"); MdisCamera *cam = (MdisCamera *) CameraFactory::Create(c); diff --git a/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp b/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp index 7ef7c14ccffebd19afff815296a0425b8ca2dbba..74e0f9955e2a8202d6460414d9a1ebcd07ac06b7 100644 --- a/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp +++ b/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp @@ -75,7 +75,28 @@ void IsisMain() { * if (index($detector_id,"MEX_HRSC_SRC") < 0 && * $processing_level_id < 3) */ - bool hasPrefix = (label["DETECTOR_ID"][0] != "MEX_HRSC_SRC" && (int)label["PROCESSING_LEVEL_ID"] < 3); + + bool isSrcFile = (label["DETECTOR_ID"][0] != "MEX_HRSC_SRC"); + bool mapProjRdr = ((int)label["PROCESSING_LEVEL_ID"] >= 3); + + try { + if (!isSrcFile) { + QString msg = "File [" + ui.GetFileName("FROM"); + msg += "] is SRC data and cannot be read."; + throw IException(IException::User, msg, _FILEINFO_); + } + + if (mapProjRdr) { + QString msg = "File [" + ui.GetFileName("FROM"); + msg += "] is map projected and cannot be read."; + throw IException(IException::User, msg, _FILEINFO_); + } + } + + catch (IException e) { + QString msg = "File cannot be read by hrsc2isis, use pds2isis."; + throw IException(e, IException::User, msg, _FILEINFO_); + } TableField ephTimeField("EphemerisTime", TableField::Double); TableField expTimeField("ExposureTime", TableField::Double); @@ -88,76 +109,65 @@ void IsisMain() { Table timesTable("LineScanTimes", timesRecord); - if(hasPrefix) { - p.SetDataPrefixBytes((int)label.findObject("IMAGE")["LINE_PREFIX_BYTES"]); - p.SaveDataPrefix(); - - p.Progress()->SetText("Reading Prefix Data"); - p.StartProcess(IgnoreData); - - // The prefix data is always in LSB format, regardless of the overall file format - EndianSwapper swapper("LSB"); - - std::vector ephemerisTimes; - std::vector exposureTimes; - std::vector< std::vector > prefix = p.DataPrefix(); - - for(int line = 0; line < p.Lines(); line++) { - double ephTime = swapper.Double((double *)prefix[0][line]); - double expTime = swapper.Float((float *)(prefix[0][line] + 8)) / 1000.0; - - if(line > 0) { - /** - * We know how many skipped lines with this equation. We take the - * difference in the current line and the last line's time, which will - * ideally be equal to the last line's exposure duration. We divide this by - * the last line's exposure duration, and the result is the 1-based count of - * how many exposures there were between the last line and the current line. - * We subtract one in order to remove the known exposure, and the remaining should - * be the 1-based count of how many lines were skipped. Add 0.5 to round up. - */ - int skippedLines = (int)((ephTime - ephemerisTimes.back()) / exposureTimes.back() - 1.0 + 0.5); - - for(int i = 0; i < skippedLines; i++) { - ephemerisTimes.push_back(ephemerisTimes.back() + exposureTimes.back()); - exposureTimes.push_back(exposureTimes.back()); - lineInFile.push_back(false); - } + p.SetDataPrefixBytes((int)label.findObject("IMAGE")["LINE_PREFIX_BYTES"]); + p.SaveDataPrefix(); + + p.Progress()->SetText("Reading Prefix Data"); + p.StartProcess(IgnoreData); + + // The prefix data is always in LSB format, regardless of the overall file format + EndianSwapper swapper("LSB"); + + std::vector ephemerisTimes; + std::vector exposureTimes; + std::vector< std::vector > prefix = p.DataPrefix(); + + for(int line = 0; line < p.Lines(); line++) { + double ephTime = swapper.Double((double *)prefix[0][line]); + double expTime = swapper.Float((float *)(prefix[0][line] + 8)) / 1000.0; + + if(line > 0) { + /** + * We know how many skipped lines with this equation. We take the + * difference in the current line and the last line's time, which will + * ideally be equal to the last line's exposure duration. We divide this by + * the last line's exposure duration, and the result is the 1-based count of + * how many exposures there were between the last line and the current line. + * We subtract one in order to remove the known exposure, and the remaining should + * be the 1-based count of how many lines were skipped. Add 0.5 to round up. + */ + int skippedLines = (int)((ephTime - ephemerisTimes.back()) / exposureTimes.back() - 1.0 + 0.5); + + for(int i = 0; i < skippedLines; i++) { + ephemerisTimes.push_back(ephemerisTimes.back() + exposureTimes.back()); + exposureTimes.push_back(exposureTimes.back()); + lineInFile.push_back(false); } - - ephemerisTimes.push_back(ephTime); - exposureTimes.push_back(expTime); - lineInFile.push_back(true); } - double lastExp = 0.0; - for(unsigned int i = 0; i < ephemerisTimes.size(); i++) { - if(lastExp != exposureTimes[i]) { - lastExp = exposureTimes[i]; - timesRecord[0] = ephemerisTimes[i]; - timesRecord[1] = exposureTimes[i]; - timesRecord[2] = (int)i + 1; - timesTable += timesRecord; - } - } - - outCube->setDimensions(p.Samples(), lineInFile.size(), p.Bands()); + ephemerisTimes.push_back(ephTime); + exposureTimes.push_back(expTime); + lineInFile.push_back(true); } - else { - //Checks if in file is rdr - FileName inFile = ui.GetFileName("FROM"); - QString msg = "[" + inFile.name() + "] appears to be an rdr file."; - msg += " Use pds2isis."; - throw IException(IException::User, msg, _FILEINFO_); + + double lastExp = 0.0; + for(unsigned int i = 0; i < ephemerisTimes.size(); i++) { + if(lastExp != exposureTimes[i]) { + lastExp = exposureTimes[i]; + timesRecord[0] = ephemerisTimes[i]; + timesRecord[1] = exposureTimes[i]; + timesRecord[2] = (int)i + 1; + timesTable += timesRecord; + } } + outCube->setDimensions(p.Samples(), lineInFile.size(), p.Bands()); + p.Progress()->SetText("Importing"); outCube->create(ui.GetFileName("TO")); p.StartProcess(WriteOutput); - if(hasPrefix) { - outCube->write(timesTable); - } + outCube->write(timesTable); // Get as many of the other labels as we can Pvl otherLabels; diff --git a/isis/src/mex/apps/hrsc2isis/hrsc2isis.xml b/isis/src/mex/apps/hrsc2isis/hrsc2isis.xml index 209e8832dad9e34528044b46c1c9585bd997424c..dad2d188bec25b52aea3c6658a3c6e7daeb12dcd 100644 --- a/isis/src/mex/apps/hrsc2isis/hrsc2isis.xml +++ b/isis/src/mex/apps/hrsc2isis/hrsc2isis.xml @@ -36,6 +36,10 @@ into only having entries on time changes, and the times no longer have a 'Z' at the end of them once imported. + + Updated the error messages thrown when hrsc2isis trys to ingest an image that is not an HRSC + image, and when hrsc2isis trys to ingest a map projected image. Fixes #4259. + diff --git a/isis/src/mex/apps/hrsc2isis/tsts/default/Makefile b/isis/src/mex/apps/hrsc2isis/tsts/default/Makefile index 87e320e6c1484adfde2a22001e7b519384f70239..2c56d55b61717f9b4be110d07a1ff514d041931a 100644 --- a/isis/src/mex/apps/hrsc2isis/tsts/default/Makefile +++ b/isis/src/mex/apps/hrsc2isis/tsts/default/Makefile @@ -8,6 +8,8 @@ commands: catlab FROM=$(OUTPUT)/h0279_0000_re2.cub to=$(OUTPUT)/h0279_0000_re2.pvl > /dev/null; if [ `$(APPNAME) FROM=$(INPUT)/h1580_0008_sr3.img \ TO=$(OUTPUT)/junk.cub \ - >& $(OUTPUT)/error.txt` ]; \ + >& $(OUTPUT)/error_message_temp.txt` ]; \ then true; \ fi; + $(SED) 's+\[/.*/input/+\[input/+' $(OUTPUT)/error_message_temp.txt > $(OUTPUT)/error.txt; + $(RM) $(OUTPUT)/error_message_temp.txt; diff --git a/isis/src/mex/apps/hrsc2isis/tsts/projection/Makefile b/isis/src/mex/apps/hrsc2isis/tsts/projection/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..104e315fd17be533f8677b859ff314508516a4a1 --- /dev/null +++ b/isis/src/mex/apps/hrsc2isis/tsts/projection/Makefile @@ -0,0 +1,14 @@ +APPNAME = hrsc2isis + +include $(ISISROOT)/make/isismake.tsts + +commands:# TEST A: Check that a projected HRSC image fails to be read + echo -e "Test hrsc2isis with a map projected image:" > $(OUTPUT)/error_message_temp.txt; + if [ `$(APPNAME) \ + FROM=$(INPUT)/h6541_0000_ir4.img \ + TO=$(OUTPUT)/temp.cub \ + 2>> $(OUTPUT)/error_message_temp.txt > /dev/null` ]; \ + then true; \ + fi; + $(SED) 's+\[/.*/input/+\[input/+' $(OUTPUT)/error_message_temp.txt > $(OUTPUT)/error_message.txt; + $(RM) $(OUTPUT)/error_message_temp.txt; diff --git a/isis/src/mex/apps/hrsc2isis/tsts/srcImage/Makefile b/isis/src/mex/apps/hrsc2isis/tsts/srcImage/Makefile new file mode 100644 index 0000000000000000000000000000000000000000..cddfcf70f59050a16babd435d41614102c626546 --- /dev/null +++ b/isis/src/mex/apps/hrsc2isis/tsts/srcImage/Makefile @@ -0,0 +1,14 @@ +APPNAME =hrsc2isis + +include $(ISISROOT)/make/isismake.tsts + +commands:# TEST A: Check that a projected HRSC image fails to be read + echo -e "Test hrsc2isis with an image that has SRC data:" > $(OUTPUT)/error_message_temp.txt; + if [ `$(APPNAME) \ + FROM=$(INPUT)/h2862_0006_sr2.img \ + TO=$(OUTPUT)/temp.cub \ + 2>> $(OUTPUT)/error_message_temp.txt > /dev/null` ]; \ + then true; \ + fi; + $(SED) 's+\[/.*/input/+\[input/+' $(OUTPUT)/error_message_temp.txt > $(OUTPUT)/error_message.txt; + $(RM) $(OUTPUT)/error_message_temp.txt; diff --git a/isis/src/mro/apps/hical/GainChannelNormalize.h b/isis/src/mro/apps/hical/GainChannelNormalize.h index 93059ee18ee07115c72264f9b743c2eace272bdc..05300ce6920ca13a521d6b201a5d83ee04a0becd 100644 --- a/isis/src/mro/apps/hical/GainChannelNormalize.h +++ b/isis/src/mro/apps/hical/GainChannelNormalize.h @@ -2,9 +2,9 @@ #define GainChannelNormalize_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: GainChannelNormalize.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/GainFlatField.h b/isis/src/mro/apps/hical/GainFlatField.h index 6bd25700cbacd5b1736d6e50c16746e6bda533b4..b85b753a9ba9e0737558d10b30f47752679a55bc 100644 --- a/isis/src/mro/apps/hical/GainFlatField.h +++ b/isis/src/mro/apps/hical/GainFlatField.h @@ -2,9 +2,9 @@ #define GainFlatField_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: GainFlatField.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/GainLineDrift.h b/isis/src/mro/apps/hical/GainLineDrift.h index 2093426276e4fc4504deea2300e9c648942bc544..efe34efcf44995ddeaebe61b3726b8583006953e 100644 --- a/isis/src/mro/apps/hical/GainLineDrift.h +++ b/isis/src/mro/apps/hical/GainLineDrift.h @@ -2,9 +2,9 @@ #define GainLineDrift_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: GainLineDrift.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/GainNonLinearity.h b/isis/src/mro/apps/hical/GainNonLinearity.h index 27b4f4edfb70199b63a7c2b356714383d1a8978b..a8f9c9af193228cd234e425a609f7c628ca38b40 100644 --- a/isis/src/mro/apps/hical/GainNonLinearity.h +++ b/isis/src/mro/apps/hical/GainNonLinearity.h @@ -2,9 +2,9 @@ #define GainNonLinearity_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: GainNonLinearity.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/GainTemperature.h b/isis/src/mro/apps/hical/GainTemperature.h index 6044ca895c9cabfc28b000e0532f846404764c23..ab34917df29ff4eded0ed9f70dd73aa75cb8dea5 100644 --- a/isis/src/mro/apps/hical/GainTemperature.h +++ b/isis/src/mro/apps/hical/GainTemperature.h @@ -2,9 +2,9 @@ #define GainTemperature_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 7131 $ + * $Date: 2016-09-26 18:18:07 -0700 (Mon, 26 Sep 2016) $ + * $Id: GainTemperature.h 7131 2016-09-27 01:18:07Z jwbacker@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/GainUnitConversion.h b/isis/src/mro/apps/hical/GainUnitConversion.h index 40970db3739db55d05328046b329cc3dada10dd2..82e747d146f9456c1066927975a346ecf052c1c8 100644 --- a/isis/src/mro/apps/hical/GainUnitConversion.h +++ b/isis/src/mro/apps/hical/GainUnitConversion.h @@ -2,9 +2,9 @@ #define GainUnitConversion_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: GainUnitConversion.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/HiBlob.h b/isis/src/mro/apps/hical/HiBlob.h index bf19492944a92e235a0c7b4dd262f62806062637..1231e8db09bc38d5f42169f45cb57f92bf907c5c 100644 --- a/isis/src/mro/apps/hical/HiBlob.h +++ b/isis/src/mro/apps/hical/HiBlob.h @@ -2,8 +2,8 @@ #define HiBlob_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/HiCalConf.cpp b/isis/src/mro/apps/hical/HiCalConf.cpp index 75be349137d155758f0d1dfd6604fa99c96be26f..aeff43a601d4b361cccbc3434c43a7306279921e 100644 --- a/isis/src/mro/apps/hical/HiCalConf.cpp +++ b/isis/src/mro/apps/hical/HiCalConf.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ + * $Id: HiCalConf.cpp 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/HiCalConf.h b/isis/src/mro/apps/hical/HiCalConf.h index fe881960d80d7b7dd189030f66fc5eac738c30e5..ae548cd5ec8b997230058fe1a006262cf3df3786 100644 --- a/isis/src/mro/apps/hical/HiCalConf.h +++ b/isis/src/mro/apps/hical/HiCalConf.h @@ -2,9 +2,9 @@ #define HiCalConf_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 7131 $ + * $Date: 2016-09-26 18:18:07 -0700 (Mon, 26 Sep 2016) $ + * $Id: HiCalConf.h 7131 2016-09-27 01:18:07Z jwbacker@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/HiCalData.h b/isis/src/mro/apps/hical/HiCalData.h index b59b5316fa10ca548b1ef515b8fc9592511137fd..4bddae4145398b7b9b73265ca0954ba28ba33851 100644 --- a/isis/src/mro/apps/hical/HiCalData.h +++ b/isis/src/mro/apps/hical/HiCalData.h @@ -2,9 +2,9 @@ #define HiCalData_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4941 $ + * $Date: 2013-01-03 13:02:20 -0700 (Thu, 03 Jan 2013) $ + * $Id: HiCalData.h 4941 2013-01-03 20:02:20Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/HiCalTypes.h b/isis/src/mro/apps/hical/HiCalTypes.h index 04e17cbc2a2a8e211f8f99fc2f7f6271d4943679..5104da0193e9918fe85724d1adf799c28c0a7fb5 100644 --- a/isis/src/mro/apps/hical/HiCalTypes.h +++ b/isis/src/mro/apps/hical/HiCalTypes.h @@ -2,8 +2,8 @@ #define HiCalTypes_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 5059 $ + * $Date: 2013-03-11 09:37:00 -0700 (Mon, 11 Mar 2013) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/HiCalUtil.h b/isis/src/mro/apps/hical/HiCalUtil.h index 313496f1475ba20dee236076995ea887b9890775..35b311ffb46f014ed05dc0e893032c1004bd159f 100644 --- a/isis/src/mro/apps/hical/HiCalUtil.h +++ b/isis/src/mro/apps/hical/HiCalUtil.h @@ -2,8 +2,8 @@ #define HiCalUtil_h /** * @file - * $Revision$ - * $Date$ + * $Revision: 5059 $ + * $Date: 2013-03-11 09:37:00 -0700 (Mon, 11 Mar 2013) $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/LoadCSV.cpp b/isis/src/mro/apps/hical/LoadCSV.cpp index 7cf17a5f44f9b92c2f0704a21e67ca8ed076855b..efa6243a9fa308e56032acf61bae2edf80650e65 100644 --- a/isis/src/mro/apps/hical/LoadCSV.cpp +++ b/isis/src/mro/apps/hical/LoadCSV.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ + * $Id: LoadCSV.cpp 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/LoadCSV.h b/isis/src/mro/apps/hical/LoadCSV.h index 188a3dab8aaad507e935532db87b2ba1cdbd310c..58e3e06049c217740873fa06d0eae699b35d677d 100644 --- a/isis/src/mro/apps/hical/LoadCSV.h +++ b/isis/src/mro/apps/hical/LoadCSV.h @@ -3,8 +3,8 @@ /** * @file * $Revision - * $Date$ - * $Id$ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: LoadCSV.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/LowPassFilter.h b/isis/src/mro/apps/hical/LowPassFilter.h index 4cad520ecde66eba6eaf4174a533d11af2af01d4..1526633c559a054b5b60ebce8eaca8ec54e4d04e 100644 --- a/isis/src/mro/apps/hical/LowPassFilter.h +++ b/isis/src/mro/apps/hical/LowPassFilter.h @@ -2,9 +2,9 @@ #define LowPassFilter_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: LowPassFilter.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/Module.h b/isis/src/mro/apps/hical/Module.h index 61ecd9aab40dabf745223cd22392c303751a820b..63ec37255c919289619f0300214dad3806d1f21f 100644 --- a/isis/src/mro/apps/hical/Module.h +++ b/isis/src/mro/apps/hical/Module.h @@ -2,9 +2,9 @@ #define Module_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 6715 $ + * $Date: 2016-04-28 10:58:43 -0700 (Thu, 28 Apr 2016) $ + * $Id: Module.h 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/NonLinearLSQ.cpp b/isis/src/mro/apps/hical/NonLinearLSQ.cpp index df929d738c2cbc52360fa6469a62a3f8185082c7..a116a079969130636613c862c9211a7a97c85409 100644 --- a/isis/src/mro/apps/hical/NonLinearLSQ.cpp +++ b/isis/src/mro/apps/hical/NonLinearLSQ.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 7140 $ + * $Date: 2016-09-27 15:40:47 -0700 (Tue, 27 Sep 2016) $ + * $Id: NonLinearLSQ.cpp 7140 2016-09-27 22:40:47Z jwbacker@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/NonLinearLSQ.h b/isis/src/mro/apps/hical/NonLinearLSQ.h index 14c016bef847df55828e2cb6961aa8888660563d..35356bd2560a0fab1a1647c2f8bb4e8f494ebb22 100644 --- a/isis/src/mro/apps/hical/NonLinearLSQ.h +++ b/isis/src/mro/apps/hical/NonLinearLSQ.h @@ -2,9 +2,9 @@ #define NonLinearLSQ_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: NonLinearLSQ.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/SplineFill.h b/isis/src/mro/apps/hical/SplineFill.h index c2a3242ce1245980d453c4e78285603499acc4c2..219d93dec61fdc7de73123e8c3b33b7f7ac45be3 100644 --- a/isis/src/mro/apps/hical/SplineFill.h +++ b/isis/src/mro/apps/hical/SplineFill.h @@ -2,9 +2,9 @@ #define SplineFill_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: SplineFill.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/ZeroBufferFit.cpp b/isis/src/mro/apps/hical/ZeroBufferFit.cpp index c0e8f038bc60df9a484bf01cdae9a491e04983e5..617faa66025dcd0fd56b99acbe69895de05d3a34 100644 --- a/isis/src/mro/apps/hical/ZeroBufferFit.cpp +++ b/isis/src/mro/apps/hical/ZeroBufferFit.cpp @@ -1,8 +1,8 @@ /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: ZeroBufferFit.cpp 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/ZeroBufferFit.h b/isis/src/mro/apps/hical/ZeroBufferFit.h index 9b76345c9d7d0d6de7382b9ee1a34306d38d97c3..6ced32a613cb871cdb1f2dd45d8faeaee356bfa5 100644 --- a/isis/src/mro/apps/hical/ZeroBufferFit.h +++ b/isis/src/mro/apps/hical/ZeroBufferFit.h @@ -2,9 +2,9 @@ #define ZeroBufferFit_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: ZeroBufferFit.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/ZeroBufferSmooth.h b/isis/src/mro/apps/hical/ZeroBufferSmooth.h index 5ee9f50dc26ebcbad5b81965f7b7d33ba7a023b8..6b80e4e27d0217a8f855cfe97323121489251bd7 100644 --- a/isis/src/mro/apps/hical/ZeroBufferSmooth.h +++ b/isis/src/mro/apps/hical/ZeroBufferSmooth.h @@ -2,9 +2,9 @@ #define ZeroBufferSmooth_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: ZeroBufferSmooth.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/ZeroDark.h b/isis/src/mro/apps/hical/ZeroDark.h index 7d9049f7cfac8a0fe229cda773b41506bd11cf39..85999079e49af97bb2820a93ac7c97a5446eb552 100644 --- a/isis/src/mro/apps/hical/ZeroDark.h +++ b/isis/src/mro/apps/hical/ZeroDark.h @@ -2,9 +2,9 @@ #define ZeroDark_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 4928 $ + * $Date: 2012-12-21 10:44:12 -0700 (Fri, 21 Dec 2012) $ + * $Id: ZeroDark.h 4928 2012-12-21 17:44:12Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/ZeroReverse.h b/isis/src/mro/apps/hical/ZeroReverse.h index 7fe974a8ab4b80007b787bef4715d6b5f9eb58d9..0de92da974195ad0998248d472da093a1ce6ad10 100644 --- a/isis/src/mro/apps/hical/ZeroReverse.h +++ b/isis/src/mro/apps/hical/ZeroReverse.h @@ -2,9 +2,9 @@ #define ZeroReverse_h /** * @file - * $Revision$ - * $Date$ - * $Id$ + * $Revision: 5059 $ + * $Date: 2013-03-11 09:37:00 -0700 (Mon, 11 Mar 2013) $ + * $Id: ZeroReverse.h 5059 2013-03-11 16:37:00Z slambright@GS.DOI.NET $ * * Unless noted otherwise, the portions of Isis written by the USGS are * public domain. See individual third-party library and package descriptions diff --git a/isis/src/mro/apps/hical/hical.cpp b/isis/src/mro/apps/hical/hical.cpp index d622da40eff2140e653ea9be5fe500cc3285fe52..70eeb27e1501fa8bccedb1652998b7b93545cd60 100644 --- a/isis/src/mro/apps/hical/hical.cpp +++ b/isis/src/mro/apps/hical/hical.cpp @@ -1,4 +1,4 @@ -// $Id$ +// $Id: hical.cpp 6715 2016-04-28 17:58:43Z tsucharski@GS.DOI.NET $ #include "Isis.h" #include @@ -109,7 +109,7 @@ void IsisMain(){ const QString hical_program = "hical"; const QString hical_version = "5.0"; - const QString hical_revision = "$Revision$"; + const QString hical_revision = "$Revision: 6715 $"; const QString hical_runtime = Application::DateTime(); UserInterface &ui = Application::GetUserInterface(); diff --git a/isis/src/mro/apps/hical/hical.xml b/isis/src/mro/apps/hical/hical.xml index e5e16f85606c8531d5bba0c06688fbfa228de274..ad9c6f3b084819fb4b3e4e67920a5b96777a32ab 100644 --- a/isis/src/mro/apps/hical/hical.xml +++ b/isis/src/mro/apps/hical/hical.xml @@ -1,5 +1,5 @@ - + diff --git a/isis/src/mro/apps/hicalproc/hicalproc.cpp b/isis/src/mro/apps/hicalproc/hicalproc.cpp index fa7c6f8ba8df9d23f301e12b25885df6854df695..205c8ac0323da015ec66836d267645af2b76c517 100644 --- a/isis/src/mro/apps/hicalproc/hicalproc.cpp +++ b/isis/src/mro/apps/hicalproc/hicalproc.cpp @@ -273,7 +273,7 @@ void IsisMain() { p5.AddToPipeline("hinoise"); p5.Application("hinoise").SetInputParameter ("FROM", false); p5.Application("hinoise").SetOutputParameter("TO", "hinoise"); - p5.Application("hinoise").AddConstParameter ("REMOVE", QString(bRemoveTempFiles)); + p5.Application("hinoise").AddConstParameter ("REMOVE", QString::number(bRemoveTempFiles)); // Values got from HiCal configuration file // Lowpass options diff --git a/isis/src/mro/apps/hideal2pds/hideal2pds.cpp b/isis/src/mro/apps/hideal2pds/hideal2pds.cpp index d2320362e7291ebaa375c76c00ed594364b72044..22db29ff2b9240ce17d2d12e8e17f67b2612002d 100644 --- a/isis/src/mro/apps/hideal2pds/hideal2pds.cpp +++ b/isis/src/mro/apps/hideal2pds/hideal2pds.cpp @@ -491,7 +491,7 @@ void updatePdsLabelRootObject(PvlObject *isisCubeLab, Pvl &pdsLabel, // mosaic input cube. // Add NaifKeywords Object values to the ROOT object - QString radiiName = "BODY" + QString(cam->naifBodyCode()) + "_RADII"; + QString radiiName = "BODY" + QString::number(cam->naifBodyCode()) + "_RADII"; PvlObject naifKeywordGroup = cam->getStoredNaifKeywords(); if (naifKeywordGroup.hasKeyword(radiiName)) { diff --git a/isis/src/mro/apps/hidestripe/hidestripe.cpp b/isis/src/mro/apps/hidestripe/hidestripe.cpp index ddc3d3bcfac11c9a2b251c88304de15ff8dadf27..2357d357496deb4715f2abda63f7d51dcb96b7ce 100644 --- a/isis/src/mro/apps/hidestripe/hidestripe.cpp +++ b/isis/src/mro/apps/hidestripe/hidestripe.cpp @@ -92,8 +92,8 @@ void IsisMain() { //Phases must be able to stretch across the entire cube if(totalSamples != phases[3]) { - QString required_samples(phases[3]); - QString bin_QString(binning_mode); + QString required_samples(QString::number(phases[3])); + QString bin_QString(QString::number(binning_mode)); QString msg = "image must have exactly "; msg += required_samples; msg += " samples per line for binning mode "; diff --git a/isis/src/mro/apps/hisharpen/hisharpen.cpp b/isis/src/mro/apps/hisharpen/hisharpen.cpp index 41f92841e218992401f96b4c8589e98e5dbb74bb..40a7bdb00f874a586f1b48232fffc9b3be2e5081 100644 --- a/isis/src/mro/apps/hisharpen/hisharpen.cpp +++ b/isis/src/mro/apps/hisharpen/hisharpen.cpp @@ -151,8 +151,8 @@ void CreatePsf(Pipeline &p) { if(fromCube.lineCount() != fromCube.sampleCount()) { QString message = "This program only works on square cubes, the number of samples [" + - QString(fromCube.sampleCount()) + "] must match the number of lines [" + - QString(fromCube.lineCount()) + "]"; + QString::number(fromCube.sampleCount()) + "] must match the number of lines [" + + QString::number(fromCube.lineCount()) + "]"; throw IException(IException::User, message, _FILEINFO_); } @@ -180,14 +180,14 @@ void CreatePsf(Pipeline &p) { psfCube.open(psfFile); if(psfCube.lineCount() > fromCube.lineCount()) { - QString message = "The input cube dimensions must be at least [" + QString(psfCube.lineCount()); + QString message = "The input cube dimensions must be at least [" + QString::number(psfCube.lineCount()); message += "] pixels in the line and sample dimensions"; throw IException(IException::User, message, _FILEINFO_); } if(!IsPowerOf2(fromCube.lineCount())) { QString message = "The input cube dimensions must be a power of 2 (found [" + - QString(fromCube.lineCount()) + "])"; + QString::number(fromCube.lineCount()) + "])"; throw IException(IException::User, message, _FILEINFO_); } diff --git a/isis/src/mro/apps/marcical/marcical.cpp b/isis/src/mro/apps/marcical/marcical.cpp index e83e6594385ca3535aae320f4ccd08afe80fc57d..e3fe98ef9188964fb9c181a09c4830f20cdbecfa 100644 --- a/isis/src/mro/apps/marcical/marcical.cpp +++ b/isis/src/mro/apps/marcical/marcical.cpp @@ -239,7 +239,7 @@ void IsisMain() { // Check our coefficient file if(calibrationData.objects() != 7) { QString msg = "Calibration file [" + calFile.expanded() + "] must contain data for 7 filters in ascending order;"; - msg += " only [" + QString(calibrationData.objects()) + "] objects were found"; + msg += " only [" + QString::number(calibrationData.objects()) + "] objects were found"; throw IException(IException::Programmer, msg, _FILEINFO_); } diff --git a/isis/src/near/apps/msi2isis/msi2isis.xml b/isis/src/near/apps/msi2isis/msi2isis.xml index 9ce5243cadef51f1fe14852edd0bbb3a25f29402..00073ec54bb6df287d102405ce4b8e8e1f65068d 100644 --- a/isis/src/near/apps/msi2isis/msi2isis.xml +++ b/isis/src/near/apps/msi2isis/msi2isis.xml @@ -12,7 +12,7 @@ The raw image must be in FITS (Flexible Image Transport) format and have a PDS label file that points to the location of the FITS image. You must input either the label file or the FITS file for the "TO" input - parameter. Please note if the FITS file is given, the label file must + parameter. Projected images are not supported. Please note if the FITS file is given, the label file must exist in the same directory or the program will throw an error. This program will verify that the input files are valid by checking the @@ -28,8 +28,8 @@ The output cube- successfully imported into ISIS3 goes through the following processes:
      -
    • Convert the raw FITS image data to an ISIS3 Cube.
      • -
    • Save the labels from the input PDS label file to the output ISIS3 Cube. Note that FITS labels are not transferred.
      • +
    • Convert the raw FITS image data to an ISIS3 cube.
      • +
    • Save the labels from the input PDS label file to the output ISIS3 cube. Note that FITS labels are not transferred.
    • Enlarge the image from 537 samples x 244 lines to 537 x 412 using the user-specified interpolation algorithm. Defaults to cubic convolution.
    • Flip the image vertically, i.e. across the horizontal axis.
    • Trim 33 pixels from the top, bottom, left and right sides. These @@ -105,8 +105,8 @@ Type of interpolation for enlarge process This is the type of interpolation to be performed on the input when - the image is enlarged from 537 samples by 244 lines to - 537 samples by 412 lines. + the image is enlarged from 537 samples x 244 lines to + 537 samples x 412 lines.