diff --git a/CHANGELOG.md b/CHANGELOG.md
index 813750f4ec0136c705b858aeeced2dd6c3b75774..fd0d61ea57237a113b622cff13a58c34190df091 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -39,6 +39,7 @@ release.
- Added adjusted XYZ point coordinate sigmas to the points.csv jigsaw output file. Modified
ctest FunctionalTestJigsawApollo to validate this output. [#5710](https://github.com/DOI-USGS/ISIS3/issues/5710)
- Added OFFBODY and OFFBODYTRIM parameters to cam2cam. Added tests and updated documentation. [#3602] (https://github.com/DOI-USGS/ISIS3/issues/3602)
+- Added support for reading, writing, and viewing GeoTIFFs in ISIS. [#5618](https://github.com/DOI-USGS/ISIS3/pull/5618)
### Changed
diff --git a/environment.yml b/environment.yml
index d0441833c774349f01e723a48d13696443579a39..bdbf5cc5fd3867e56f8e64c54e5d665eb80a753d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,8 +5,8 @@ dependencies:
- ale =0.10.0,<1
- aom
- armadillo
- - boost >=1.78.0,<1.79
- - boost-cpp >=1.78.0,<1.79
+ - boost >=1.76.0,<1.82
+ - boost-cpp >=1.76.0,<1.82
- blas
- usgs-astrogeology::bullet
- bz2file
@@ -22,6 +22,7 @@ dependencies:
- ffmpeg
- geos >=3.12, <3.13
- geotiff
+ - gdal >=3.5 ,<3.9.0a0
- gmp
- graphviz
- conda-forge::gsl >=2.6, <2.7
@@ -34,10 +35,10 @@ dependencies:
- kalasiris
- krb5
- libgdal >=3.7,<3.8
- - libopencv >=4.7,<4.8
+ - libopencv >=4.5,<4.8
- libpng >=1.6.34,<1.7
- libprotobuf
- - libtiff >=4.5,<4.6
+ - libtiff >=4.5,<4.8
- libxml2
- make
- mesalib
@@ -47,17 +48,17 @@ dependencies:
- nlohmann_json=3.11.2
- ninja >=1.7.2,<1.8
- nn
- - opencv >=4.7,<4.8
+ - opencv >=4.5,<4.8
- openssl >=3.1.2,<3.2
- pcl >=1.13,<1.14
- plio
- protobuf
- - python >=3.10
- - python_abi >=3.10
+ - python >=3.9
+ - python_abi >=3.9
- pytest
- rclone
- qhull
- - qt-main>=5.15.8, <5.16
+ - qt-main>=5.15, <5.16
- qwt <6.3.0
- sqlite >=3.46.0,<3.47
- suitesparse <7.7.0
diff --git a/gtest b/gtest
index b10fad38c4026a29ea6561ab15fc4818170d1c10..f8d7d77c06936315286eb55f8de22cd23c188571 160000
--- a/gtest
+++ b/gtest
@@ -1 +1 @@
-Subproject commit b10fad38c4026a29ea6561ab15fc4818170d1c10
+Subproject commit f8d7d77c06936315286eb55f8de22cd23c188571
diff --git a/isis/CMakeLists.txt b/isis/CMakeLists.txt
index 8584042726be66daa8768e9d10e717504240f606..8bdf20b3015dfef06b97019e180c95557bd83724 100644
--- a/isis/CMakeLists.txt
+++ b/isis/CMakeLists.txt
@@ -267,6 +267,7 @@ find_package(CSM 3.0.3.3 REQUIRED)
find_package(CSPICE 65 REQUIRED)
find_package(Eigen REQUIRED)
find_package(Embree 3.13.0 REQUIRED)
+find_package(GDAL REQUIRED CONFIG)
find_package(GeoTIFF 2 REQUIRED)
SET(GSL_ROOT_DIR $ENV{CONDA_PREFIX})
find_package(GSL 2.2.1 REQUIRED)
@@ -353,7 +354,7 @@ foreach (_variableName ${_variableNames})
endforeach()
# add target based linkages to ALLLIBS variable
-list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree)
+list(APPEND ALLLIBS pantor::inja sensorutilities protobuf::libprotobuf embree GDAL::GDAL)
# Sometimes we add the same lib more than once (especially with LIBDIRS)
list(REMOVE_DUPLICATES ALLLIBDIRS)
diff --git a/isis/src/apollo/apps/apollopanstitcher/apollopanstitcher.cpp b/isis/src/apollo/apps/apollopanstitcher/apollopanstitcher.cpp
index 4a4ad3a4147b600a1377a792c4a2ddbfc5dcb3f7..de48692a9a8f14d05b71e90689f8838b15696df5 100644
--- a/isis/src/apollo/apps/apollopanstitcher/apollopanstitcher.cpp
+++ b/isis/src/apollo/apps/apollopanstitcher/apollopanstitcher.cpp
@@ -715,11 +715,11 @@ namespace Isis {
att.setFileFormat( panC[0]->format() );
att.setByteOrder( panC[0]->byteOrder() );
att.setPixelType( panC[0]->pixelType() );
- if (panC[0]->labelsAttached()) {
- att.setLabelAttachment(AttachedLabel);
+ if (panC[0]->labelsAttached() == Cube::AttachedLabel) {
+ att.setLabelAttachment(Cube::AttachedLabel);
}
else {
- att.setLabelAttachment(DetachedLabel);
+ att.setLabelAttachment(Cube::DetachedLabel);
}
//define an output cube
diff --git a/isis/src/base/apps/cathist/main.cpp b/isis/src/base/apps/cathist/main.cpp
index 4280d3ad27944938010082de83e76ef71f7ade74..ccdd311f9d08d413916c1cc17738ce63fe063045 100644
--- a/isis/src/base/apps/cathist/main.cpp
+++ b/isis/src/base/apps/cathist/main.cpp
@@ -26,9 +26,17 @@ void IsisMain() {
}
// Extract history from file
- Blob historyBlob("IsisCube", "History", fromfile.expanded());
- History hist(historyBlob);
- Pvl pvl = hist.ReturnHist();
+ Pvl pvl;
+ try {
+ Blob historyBlob("IsisCube", "History", fromfile.expanded());
+ History hist(historyBlob);
+ pvl = hist.ReturnHist();
+ }
+ catch (...) {
+ Cube cube(fromfile);
+ History hist = cube.readHistory();
+ pvl = hist.ReturnHist();
+ }
// Print full history
if(mode == "FULL") {
diff --git a/isis/src/base/apps/catlab/main.cpp b/isis/src/base/apps/catlab/main.cpp
index f48d3a0525c1ff5e9703b423b4e5a64b59c40a3c..a9595e30545b4227c1a7745696cb5bf82cecc8ef 100644
--- a/isis/src/base/apps/catlab/main.cpp
+++ b/isis/src/base/apps/catlab/main.cpp
@@ -17,7 +17,14 @@ void IsisMain() {
QString file = ui.GetCubeName("FROM");
// Extract label from file
- Pvl label(file);
+ Pvl label;
+ try {
+ label = Pvl(file);
+ }
+ catch (...) {
+ Cube cube(file);
+ label = *cube.label();
+ }
// Output to file if entered
if(ui.WasEntered("TO")) {
diff --git a/isis/src/base/apps/catoriglab/main.cpp b/isis/src/base/apps/catoriglab/main.cpp
index 6702a19274a0ebe2161b323d326c897c348ec3cb..2d14832746fcc832d9a3091088bbf80957de5bc2 100644
--- a/isis/src/base/apps/catoriglab/main.cpp
+++ b/isis/src/base/apps/catoriglab/main.cpp
@@ -22,9 +22,10 @@ void IsisMain() {
UserInterface &ui = Application::GetUserInterface();
QString file = ui.GetCubeName("FROM");
- Pvl fromLabel(file);
+ Cube fromCube(file);
+ Pvl fromLabel = *(fromCube.label());
if ( fromLabel.hasObject("OriginalLabel") ) {
- OriginalLabel origLab(file);
+ OriginalLabel origLab = fromCube.readOriginalLabel();
Pvl pvl = origLab.ReturnLabels();
if (ui.IsInteractive()) {
Application::GuiLog(pvl);
diff --git a/isis/src/base/apps/crop/crop.cpp b/isis/src/base/apps/crop/crop.cpp
index 6943e20c3a30e9ea5551197d810dc117dba361f6..b7d0f3a9703e60e6019c3386ed40a6c5b148e00f 100644
--- a/isis/src/base/apps/crop/crop.cpp
+++ b/isis/src/base/apps/crop/crop.cpp
@@ -140,7 +140,7 @@ namespace Isis {
}
// Read the table into a table object
- Table table(obj["Name"], from);
+ Table table = cube->readTable(obj["Name"]);
// We are not going to bother with line/sample associations; they apply
// only to the alpha cube at this time. I'm leaving this code here for the
diff --git a/isis/src/base/apps/noproj/noproj.cpp b/isis/src/base/apps/noproj/noproj.cpp
index 021792ec28beed901127f06cab09e52774d3b9a4..76a44d56abc6d6a8f90dcc5da5c027cbeb262139 100644
--- a/isis/src/base/apps/noproj/noproj.cpp
+++ b/isis/src/base/apps/noproj/noproj.cpp
@@ -191,7 +191,7 @@ namespace Isis {
CubeAttributeOutput cao;
// Can we do a regular label? Didn't work on 12-15-2006
- cao.setLabelAttachment(Isis::DetachedLabel);
+ cao.setLabelAttachment(Cube::DetachedLabel);
FileName matchCubeFile = FileName::createTempFile("$Temporary/match.cub");
QString matchCubeFileNoExt = matchCubeFile.path() + "/" + matchCubeFile.baseName();
diff --git a/isis/src/base/apps/shadow/ShadowFunctor.cpp b/isis/src/base/apps/shadow/ShadowFunctor.cpp
index 02447dbfae635bd6275a908e09614823e7cc3c2e..8bdf79e031a36f1c669541e2227e8dd678ee7a69 100644
--- a/isis/src/base/apps/shadow/ShadowFunctor.cpp
+++ b/isis/src/base/apps/shadow/ShadowFunctor.cpp
@@ -394,7 +394,7 @@ namespace Isis {
Portal portal(3, 3, m_inputDem->pixelType(), -0.5, -0.5);
- portal.SetPosition(sample, line, input.Band());
+ portal.SetPosition(sample + 1, line + 1, input.Band());
if (!portal.CopyOverlapFrom(input)) {
m_inputDem->read(portal);
diff --git a/isis/src/base/apps/spiceinit/spiceinit.cpp b/isis/src/base/apps/spiceinit/spiceinit.cpp
index cd9f23d493df7dbfc75ed8b7990e8521b1dffd93..611a0b96cc9d97ccb27588463619408231c33e34 100644
--- a/isis/src/base/apps/spiceinit/spiceinit.cpp
+++ b/isis/src/base/apps/spiceinit/spiceinit.cpp
@@ -263,7 +263,6 @@ namespace Isis {
}
}
icube->deleteGroup("CsmInfo");
-
p.WriteHistory(*icube);
p.EndProcess();
}
@@ -592,7 +591,6 @@ namespace Isis {
icube->putGroup(originalKernels);
return false;
}
-
return true;
}
diff --git a/isis/src/base/apps/tabledump/main.cpp b/isis/src/base/apps/tabledump/main.cpp
index 1880572f589fb4641d7db7f0c1322a3da2ce9424..898fc4ada18f9d1c6c8d3993e4392d76cfb18c95 100644
--- a/isis/src/base/apps/tabledump/main.cpp
+++ b/isis/src/base/apps/tabledump/main.cpp
@@ -27,7 +27,14 @@ void IsisMain() {
UserInterface &ui = Application::GetUserInterface();
FileName file = ui.GetCubeName("FROM");
QString tableName = ui.GetString("NAME");
- Table table(tableName, file.expanded());
+ Table table(tableName);
+ try {
+ table = Table(tableName, file.expanded());
+ }
+ catch (...) {
+ Cube fromCube(file);
+ table = fromCube.readTable(tableName);
+ }
// Set the character to separate the entries
QString delimit;
@@ -147,7 +154,14 @@ void helperButtonGetTableList() {
UserInterface &ui = Application::GetUserInterface();
QString currentFile = ui.GetCubeName("FROM");
- const Pvl label(FileName(currentFile).expanded());
+ Pvl label;
+ try {
+ label = Pvl(FileName(currentFile).expanded());
+ }
+ catch (...) {
+ Cube cube(FileName(currentFile).expanded());
+ label = *cube.label();
+ }
// Check to see if the "FILE" parameter has changed since last press
if (currentFile != g_previousFile) {
diff --git a/isis/src/base/objs/Blob/Blob.cpp b/isis/src/base/objs/Blob/Blob.cpp
index 42791b03d9bae8f23aaf49cd0ed1070aafb9fe29..5dfd0d38c02653259490fb4edd13cfbe9106fa72 100644
--- a/isis/src/base/objs/Blob/Blob.cpp
+++ b/isis/src/base/objs/Blob/Blob.cpp
@@ -9,6 +9,8 @@ find files of those names at the top level of this repository. **/
#include <cstring>
#include <fstream>
#include <sstream>
+#include <filesystem>
+#include <gdal_priv.h>
#include <QDebug>
@@ -17,7 +19,11 @@ find files of those names at the top level of this repository. **/
#include "Message.h"
#include "Pvl.h"
+namespace fs = std::filesystem;
+using json = nlohmann::json;
+using ordered_json = nlohmann::ordered_json;
using namespace std;
+
namespace Isis {
/**
* Constructs a Blob object using a name and type.
@@ -244,6 +250,33 @@ namespace Isis {
}
}
+ void Blob::ReadGdal(GDALDataset *dataset) {
+ try {
+ std::string key = QString(p_type + "_" + p_blobName).toStdString();
+ const char *jsonblobStr = dataset->GetMetadataItem(key.c_str(), "USGS");
+ if (jsonblobStr == nullptr) {
+ QString msg = "The key [" + QString::fromStdString(key) + "] does not exist on the geodata set.";
+ throw IException( IException::Io, msg, _FILEINFO_);
+ }
+ ordered_json jsonblob = ordered_json::parse(jsonblobStr);
+ std::string blobData = jsonblob[key]["Data"];
+ jsonblob[key].erase("Data");
+
+ Pvl pvl;
+ Pvl::readObject(pvl, jsonblob);
+
+ p_blobName = QString::fromStdString(jsonblob[key]["Name"]);
+ p_type = QString::fromStdString(jsonblob[key]["_container_name"]);
+
+ Find(pvl);
+ ReadData(blobData);
+ }
+ catch(exception &e) {
+ QString msg = "Failed to read blob [" + p_blobName + "]: " + e.what();
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+ }
+
/**
* This method reads Pvl values from a specified file.
*
@@ -255,7 +288,7 @@ namespace Isis {
void Blob::Read(const QString &file, const std::vector<PvlKeyword> keywords) {
// Expand the filename
QString temp(FileName(file).expanded());
-
+
// Get the pvl
Pvl pvl;
try {
@@ -351,7 +384,8 @@ namespace Isis {
void Blob::ReadData(std::istream &stream) {
// Read the binary data
if (p_buffer != NULL) delete [] p_buffer;
- p_buffer = new char[p_nbytes];
+ p_buffer = new char[p_nbytes + 1];
+ p_buffer[p_nbytes] = '\0';
streampos sbyte = p_startByte - 1;
stream.seekg(sbyte, std::ios::beg);
@@ -380,8 +414,16 @@ namespace Isis {
* @param nbytes The amount of data in the buffer
*/
void Blob::setData(const char *buffer, int nbytes) {
- char *buf = new char[nbytes];
- memcpy(buf, buffer, nbytes);
+ char *buf;
+ if (buffer[nbytes - 1] != '\0') {
+ buf = new char[nbytes + 1];
+ memcpy(buf, buffer, nbytes);
+ buf[nbytes] = '\0';
+ }
+ else {
+ buf = new char[nbytes];
+ memcpy(buf, buffer, nbytes);
+ }
takeData(buf, nbytes);
}
@@ -405,6 +447,46 @@ namespace Isis {
p_buffer = buffer;
}
+ void Blob::WriteGdal(GDALDataset *dataset) {
+ try {
+ WriteInit();
+ Pvl pvl;
+ pvl.addObject(p_blobPvl);
+ ostringstream os;
+ os << pvl << endl;
+ os.seekp(0, std::ios::end);
+
+ stringstream stream;
+ WriteData(stream);
+ PvlObject &blobObj = pvl.findObject(p_type);
+
+ blobObj["Bytes"] = toString(p_nbytes);
+ blobObj["StartByte"] = toString(1);
+ if(blobObj.hasKeyword("Data")) {
+ blobObj["Data"] = QString::fromStdString(stream.str());
+ }
+ else {
+ blobObj += PvlKeyword("Data", QString::fromStdString(stream.str()));
+ }
+
+ if(blobObj.hasKeyword("Name")) {
+ blobObj["Name"] = p_blobName;
+ }
+ else {
+ blobObj += PvlKeyword("Name", p_blobName);
+ }
+
+ // update metadata
+ string jsonblobstr = pvl.toJson().dump();
+ string key = this->Type().toStdString() + "_" + this->Name().toStdString();
+ dataset->SetMetadataItem(key.c_str(), jsonblobstr.c_str(), "USGS");
+ }
+ catch(exception &e) {
+ cout << "Failed to write blob [" + p_blobName + "]: " << e.what() << endl;
+ }
+ }
+
+
/**
* Write the blob data out to a file.
*
@@ -415,7 +497,7 @@ namespace Isis {
* @throws IException::Io - Error creating file
*/
void Blob::Write(const QString &file) {
- // Determine the size of the label and write it out
+ // Determine the size of the label and write it out
try {
WriteInit();
Pvl pvl;
@@ -456,6 +538,7 @@ namespace Isis {
}
}
+
/**
* Write the blob data out to a Pvl object.
* @param pvl The pvl object to update
@@ -464,10 +547,10 @@ namespace Isis {
* the name of the file
*/
void Blob::Write(Pvl &pvl, std::fstream &stm,
- const QString &detachedFileName, bool overwrite) {
+ const QString &detachedFileName, bool overwrite, bool inline_data) {
+
// Handle 64-bit I/O
WriteInit();
-
// Find out where they wanted to write the blob
streampos sbyte = stm.tellp();
sbyte += 1;
@@ -482,11 +565,9 @@ namespace Isis {
p_blobPvl += PvlKeyword("^" + p_type, detachedFileName);
}
-
p_blobPvl["StartByte"] = toString((BigInt)sbyte);
p_blobPvl["Bytes"] = toString(p_nbytes);
-
// See if the blob is already in the file
bool found = false;
if (overwrite) {
@@ -570,6 +651,55 @@ namespace Isis {
}
+ /**
+ * Writes blob data to a stream
+ *
+ * @param stream Output stream blob data will be written to
+ *
+ * @throws IException::Io - Error writing data to stream
+ */
+ void Blob::WriteData(std::stringstream &stream) {
+ stream << std::hex << std::setfill('0');
+ int copy = 0;
+ for (int i = 0; i < p_nbytes; ++i) {
+ memcpy(©, &(p_buffer[i]), 1);
+ stream << std::setw(2) << copy;
+ }
+
+ if (!stream.good()) {
+ QString msg = "Error writing data to " + p_type + " [" + p_blobName + "]";
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+ }
+
+
+ /**
+ * Writes blob data to a stream
+ *
+ * @param stream Output steam blob data will be written to
+ *
+ * @throws IException::Io - Error writing data to stream
+ */
+ void Blob::ReadData(string &hexdata) {
+ // Read the binary data
+ if (p_buffer != NULL) delete [] p_buffer;
+ p_buffer = new char[p_nbytes + 1];
+ p_buffer[p_nbytes] = '\0';
+
+ // Loop through the hex string and bytes, hex is two characters at a time
+ for (size_t i=0,j=0; i < p_nbytes; i++,j+=2) {
+ string byteString = hexdata.substr(j, 2);
+
+ char byteValue = static_cast<char>(
+ stoi(byteString, nullptr, 16));
+
+ // Add the byte to the byte array
+ p_buffer[i] = byteValue;
+ }
+ }
+
+
+
/**
* Checks pvl object and returns whether or not it is a Blob
*
diff --git a/isis/src/base/objs/Blob/Blob.h b/isis/src/base/objs/Blob/Blob.h
index 1abf7828e4fada4476670b54a980ee41e5fbc846..f431171d0327dffc880aa5d9e662e09e3e25b1c4 100644
--- a/isis/src/base/objs/Blob/Blob.h
+++ b/isis/src/base/objs/Blob/Blob.h
@@ -11,6 +11,8 @@ find files of those names at the top level of this repository. **/
#include <QList>
#include <QPair>
+#include "gdal_priv.h"
+
#include "PvlObject.h"
namespace Isis {
@@ -70,11 +72,13 @@ namespace Isis {
const std::vector<PvlKeyword> keywords = std::vector<PvlKeyword>());
virtual void Read(const Pvl &pvl, std::istream &is,
const std::vector<PvlKeyword> keywords = std::vector<PvlKeyword>());
+ void ReadData(std::string &hexdata);
void Write(const QString &file);
void Write(Pvl &pvl, std::fstream &stm,
- const QString &detachedFileName = "", bool overwrite=true);
-
+ const QString &detachedFileName = "", bool overwrite=true, bool inline_data=true);
+ void WriteGdal(GDALDataset *dataset);
+ void ReadGdal(GDALDataset *dataset);
char *getBuffer();
void setData(const char *buffer, int nbytes);
@@ -86,6 +90,7 @@ namespace Isis {
virtual void ReadData(std::istream &is);
virtual void WriteInit();
virtual void WriteData(std::fstream &os);
+ virtual void WriteData(std::stringstream &os);
PvlObject p_blobPvl; //!< Pvl Blob object
QString p_blobName; //!< Name of the Blob object
diff --git a/isis/src/base/objs/Blob/Blob.truth b/isis/src/base/objs/Blob/Blob.truth
deleted file mode 100644
index 0079631fb369a650f9284205b243f457be6bc6d1..0000000000000000000000000000000000000000
--- a/isis/src/base/objs/Blob/Blob.truth
+++ /dev/null
@@ -1,27 +0,0 @@
-Testing Blob(name, type) constructor and Write(filename) method...
-Name = UnitTest
-Number of Bytes = 4
-StartByte = 150
-Type = Blob
-
-Testing Blob(name, type, file) constructor...
-Name = UNITtest
-Number of Bytes = 4
-StartByte = 150
-Type = Blob
-ABCD
-
-Testing writing into existing space...
-Testing Write(pvl, stream)...
-Name = UNITtest
-Number of Bytes = 3
-StartByte = 150
-Type = Blob
-
-Testing writing over existing space at the end of file...
-Testing Write(pvl, stream)...
-Name = UNITtest
-Number of Bytes = 4
-StartByte = 150
-Type = Blob
-
diff --git a/isis/src/base/objs/Blob/unitTest.cpp b/isis/src/base/objs/Blob/unitTest.cpp
deleted file mode 100644
index 56113ace38951da7f56ee740e5f85c13caca3b81..0000000000000000000000000000000000000000
--- a/isis/src/base/objs/Blob/unitTest.cpp
+++ /dev/null
@@ -1,100 +0,0 @@
-/** This is free and unencumbered software released into the public domain.
-The authors of ISIS do not claim copyright on the contents of this file.
-For more details about the LICENSE terms and the AUTHORS, you will
-find files of those names at the top level of this repository. **/
-
-/* SPDX-License-Identifier: CC0-1.0 */
-#include <iostream>
-#include "Blob.h"
-#include "IException.h"
-#include "IString.h"
-#include "Preference.h"
-
-using namespace Isis;
-using namespace std;
-
-class MyBlob : public Isis::Blob {
- public:
- MyBlob(const QString &name) : Isis::Blob(name, "Blob") {};
- MyBlob(const QString &name, const QString &file) : Isis::Blob(name, "Blob", file) {};
- void MyBuf(char *buf, int size) {
- p_buffer = new char[size];
- p_nbytes = size;
- memcpy(p_buffer, buf, size);
- };
- int StartByte() {
- return p_startByte;
- };
- void GetBuf(char *buf) {
- memcpy(buf, p_buffer, p_nbytes);
- }
-};
-
-int main(int argc, char *argv[]) {
- Isis::Preference::Preferences(true);
- try {
- cout << "Testing Blob(name, type) constructor and Write(filename) method..." << endl;
- MyBlob b("UnitTest");
- char buf[] = {"ABCD"};
- b.MyBuf(buf, 4);
- b.Write("junk");
- cout << "Name = " << b.Name() << endl;
- cout << "Number of Bytes = " << b.Size() << endl;
- cout << "StartByte = " << b.StartByte() << endl;
- cout << "Type = " << b.Type() << endl;
- cout << endl;
-
- cout << "Testing Blob(name, type, file) constructor..." << endl;
- MyBlob c("UNITtest", "junk");
- char buf2[5];
- c.GetBuf(buf2);
- buf2[4] = 0;
- cout << "Name = " << c.Name() << endl;
- cout << "Number of Bytes = " << c.Size() << endl;
- cout << "StartByte = " << c.StartByte() << endl;
- cout << "Type = " << c.Type() << endl;
- cout << buf2 << endl;
- cout << endl;
-
- // Test writing into existing space
- cout << "Testing writing into existing space..." << endl;
- cout << "Testing Write(pvl, stream)..." << endl;
- Isis::Pvl pvl("junk");
- fstream strm;
- strm.open("junk", std::ios::binary | std::ios::out);
- c.MyBuf(buf, 3);
- c.Write(pvl, strm);
- strm.seekp(0, std::ios::beg);
- strm << pvl;
- cout << "Name = " << c.Name() << endl;
- cout << "Number of Bytes = " << c.Size() << endl;
- cout << "StartByte = " << c.StartByte() << endl;
- cout << "Type = " << c.Type() << endl;
- cout << endl;
- strm.close();
-
- // Test writing over existing space at the end of file
- cout << "Testing writing over existing space at the end of file..." << endl;
- cout << "Testing Write(pvl, stream)..." << endl;
- Isis::Pvl pvl2("junk");
- fstream strm2;
- strm2.open("junk", std::ios::binary | std::ios::out);
- c.MyBuf(buf, 4);
- c.Write(pvl2, strm2);
- strm2.seekp(0, std::ios::beg);
- strm2 << pvl2;
- cout << "Name = " << c.Name() << endl;
- cout << "Number of Bytes = " << c.Size() << endl;
- cout << "StartByte = " << c.StartByte() << endl;
- cout << "Type = " << c.Type() << endl;
- cout << endl;
- strm2.close();
-
- remove("junk");
-
- }
- catch(Isis::IException &e) {
- e.print();
- }
-}
-
diff --git a/isis/src/base/objs/Brick/Brick.cpp b/isis/src/base/objs/Brick/Brick.cpp
index 630458f0d0a3f04cb681ac6b0b5f360abf419604..c0bb72a675087be5d5b9a0883682a1ce7e64d6e8 100644
--- a/isis/src/base/objs/Brick/Brick.cpp
+++ b/isis/src/base/objs/Brick/Brick.cpp
@@ -22,7 +22,27 @@ namespace Isis {
p_nsamps = nsamps;
p_nlines = nlines;
p_nbands = nbands;
- p_npixels = p_nsamps * p_nlines * p_nbands;
+ if(p_nsamps <= 0) {
+ std::string message = "Invalid value for sample dimensions (nsamps)";
+ throw IException(IException::Programmer, message, _FILEINFO_);
+ }
+ if(p_nlines <= 0) {
+ std::string message = "Invalid value for line dimensions (nlines)";
+ throw IException(IException::Programmer, message, _FILEINFO_);
+ }
+ if(p_nbands <= 0) {
+ std::string message = "Invalid value for band dimensions (nbands)";
+ throw IException(IException::Programmer, message, _FILEINFO_);
+ }
+ if (int(p_nsamps * p_scale) <= 0) {
+ std::string message = "Scaleing [" + std::to_string(p_nsamps) + "] by [" + std::to_string(p_scale) + "] resulted in 0 samples in the buffer";
+ throw IException(IException::Programmer, message, _FILEINFO_);
+ }
+ if (int(p_nlines * p_scale) <= 0) {
+ std::string message = "Scaleing [" + std::to_string(p_nlines) + "] by [" + std::to_string(p_scale) + "] resulted in 0 lines in the buffer";
+ throw IException(IException::Programmer, message, _FILEINFO_);
+ }
+ p_npixels = (int(p_nsamps * p_scale) * int(p_nlines * p_scale)) * p_nbands;
Allocate();
}
diff --git a/isis/src/base/objs/Brick/Brick.h b/isis/src/base/objs/Brick/Brick.h
index 29ce6c54ccdee36dd7952b6beed6078bbf6b9092..25494657e436fb9b6bd5690ca0e05d7e41416509 100644
--- a/isis/src/base/objs/Brick/Brick.h
+++ b/isis/src/base/objs/Brick/Brick.h
@@ -58,9 +58,9 @@ namespace Isis {
* bands first, then lines, then samples.
*/
Brick(const int nsamps, const int nlines, const int nbands,
- const Isis::PixelType type, bool reverse=false) :
+ const Isis::PixelType type, bool reverse=false, double scale=1.0) :
Isis::BufferManager(nsamps, nlines, nbands,
- nsamps, nlines, nbands, type, reverse) {
+ nsamps, nlines, nbands, type, reverse, scale) {
};
/**
@@ -78,10 +78,10 @@ namespace Isis {
*/
Brick(const Isis::Cube &cube, const int &bufNumSamples,
const int &bufNumLines, const int &bufNumBands,
- bool reverse=false) :
+ bool reverse=false, double scale=1.0) :
Isis::BufferManager(cube.sampleCount(), cube.lineCount(),
cube.bandCount(), bufNumSamples, bufNumLines,
- bufNumBands, cube.pixelType(), reverse) {
+ bufNumBands, cube.pixelType(), reverse, scale) {
};
/**
@@ -103,9 +103,9 @@ namespace Isis {
*/
Brick(int maxSamples, int maxLines, int maxBands, int bufNumSamples,
int bufNumLines, int bufNumBands, Isis::PixelType type,
- bool reverse=false) :
+ bool reverse=false, double scale=1.0) :
Isis::BufferManager(maxSamples, maxLines, maxBands, bufNumSamples,
- bufNumLines, bufNumBands, type, reverse) {
+ bufNumLines, bufNumBands, type, reverse, scale) {
};
public:
diff --git a/isis/src/base/objs/Buffer/Buffer.cpp b/isis/src/base/objs/Buffer/Buffer.cpp
index 0757c99bc306afba8fe0ecc3ef814b9df679a877..cf00d406e7ec638bd3d0de6180b1aa5ea61a532e 100644
--- a/isis/src/base/objs/Buffer/Buffer.cpp
+++ b/isis/src/base/objs/Buffer/Buffer.cpp
@@ -5,10 +5,11 @@ find files of those names at the top level of this repository. **/
/* SPDX-License-Identifier: CC0-1.0 */
-#include "PixelType.h"
#include "Buffer.h"
#include "IException.h"
#include "Message.h"
+#include "PixelType.h"
+#include "SpecialPixel.h"
#include <iostream>
@@ -24,7 +25,7 @@ namespace Isis {
*/
Buffer::Buffer() : p_sample(0), p_nsamps(0), p_line(0), p_nlines(0),
p_band(0), p_nbands(0), p_npixels(0), p_buf(0),
- p_pixelType(None), p_rawbuf(0) { }
+ p_pixelType(None), p_rawbuf(0), p_scale(1) { }
/**
@@ -39,9 +40,11 @@ namespace Isis {
* @throws Isis::iException::Programmer - Invalid value for a dimension
*/
Buffer::Buffer(const int nsamps, const int nlines,
- const int nbands, const Isis::PixelType type) :
+ const int nbands, const Isis::PixelType type,
+ const double scale) :
p_nsamps(nsamps), p_nlines(nlines),
- p_nbands(nbands), p_pixelType(type) {
+ p_nbands(nbands), p_pixelType(type),
+ p_scale(scale) {
p_sample = p_line = p_band = 0;
@@ -57,8 +60,20 @@ namespace Isis {
string message = "Invalid value for band dimensions (nbands)";
throw IException(IException::Programmer, message, _FILEINFO_);
}
+ if(p_scale <= 0 || scale > 1) {
+ string message = "Invalid value for scale (scale)";
+ throw IException(IException::Programmer, message, _FILEINFO_);
+ }
+ p_nsampsScaled = int(p_nsamps * p_scale);
+ if (p_nsampsScaled <= 0) {
+ p_nsampsScaled = 1;
+ }
+ p_nlinesScaled = int(p_nlines * p_scale);
+ if (p_nlinesScaled <= 0) {
+ p_nlinesScaled = 1;
+ }
- p_npixels = p_nsamps * p_nlines * p_nbands;
+ p_npixels = (p_nsampsScaled * p_nlinesScaled) * p_nbands;
Allocate();
}
@@ -111,6 +126,29 @@ namespace Isis {
SetBaseBand(start_band);
}
+ /**
+ * This method is used to print out a buffer
+ *
+ * @param os Output stream to write to
+ * @param buffer The buffer to write to the output stream
+ *
+ * @return The updated output stream
+ */
+ std::ostream &operator<<(std::ostream &os, Buffer &buffer) {
+ for(int i = 1; i < buffer.size() + 1; i++) {
+ os << buffer[i - 1];
+
+ if ((i % buffer.SampleDimensionScaled()) == 0) {
+ os << std::endl;
+ }
+ if ((i % (buffer.SampleDimensionScaled() * buffer.LineDimensionScaled())) == 0) {
+ os << std::endl;
+ }
+ }
+
+ return os;
+ }
+
/**
* Returns the sample position associated with a shape buffer index. The
@@ -212,9 +250,10 @@ namespace Isis {
}
// Got a valid reference location so compute the index and return
- int index = (i_band - p_band) * (p_nlines * p_nsamps) +
- (i_line - p_line) * (p_nsamps) +
- (i_samp - p_sample);
+ int bandOffset = (i_band - p_band) * (p_nsampsScaled * p_nlinesScaled);
+ int lineOffset = (int((i_line - p_line) * p_scale) % p_nlinesScaled) * p_nsampsScaled;
+ int sampleOffset = (int((i_samp - p_sample) * p_scale));
+ int index = bandOffset + lineOffset + sampleOffset;
return (index);
}
@@ -283,7 +322,45 @@ namespace Isis {
* @return The operation was successful (the buffers overlapped)
*/
bool Buffer::CopyOverlapFrom(const Buffer &in) {
- bool isSubareaOfIn = (p_npixels <= in.size());
+ bool isSubareaOfIn = true;
+
+ // If one rectangle is on left side of other
+ // if (l1.x > r2.x || l2.x > r1.x)
+ if (p_line > in.p_line + in.p_nlines ||
+ in.p_line > p_line + p_nlines)
+ isSubareaOfIn = false;
+
+ // If one rectangle is above other
+ // if (r1.y > l2.y || r2.y > l1.y)
+ if (p_sample + p_nsamps < in.p_sample ||
+ in.p_sample + in.p_nsamps < p_sample)
+ isSubareaOfIn = false;
+
+ if (isSubareaOfIn) {
+ int topLine = max(in.p_line, p_line);
+ int topSamp = max(in.p_sample, p_sample);
+
+ int bottomLine = min(in.p_line + in.p_nlines, p_line + p_nlines);
+ int bottomSamp = min(in.p_sample + in.p_nsamps, p_sample + p_nsamps);
+
+ int firstBand = max(in.p_band, p_band);
+ int lastBand = min(in.p_band + in.p_nbands, p_band + p_nbands);
+
+ for (int b = firstBand; b < lastBand; b++) {
+ for (int i = topLine; i < bottomLine; i++) {
+ for (int j = topSamp; j < bottomSamp; j++) {
+ try {
+ (*this)[Index(j, i, b)] = in[in.Index(j, i, b)];
+ }
+ catch(...) {
+ (*this)[Index(j, i, b)] = NULL8;
+ }
+ }
+ }
+ }
+ }
+
+ isSubareaOfIn = (p_npixels <= in.size());
isSubareaOfIn &= (p_sample >= in.p_sample);
isSubareaOfIn &= (p_line >= in.p_line);
isSubareaOfIn &= (p_band >= in.p_band);
@@ -301,12 +378,6 @@ namespace Isis {
isSubareaOfIn &= (endLine <= otherEndLine);
isSubareaOfIn &= (endBand <= otherEndBand);
- if (isSubareaOfIn) {
- for (int i = 0; i < size(); i++) {
- (*this)[i] = in[in.Index(Sample(i), Line(i), Band(i))];
- }
- }
-
return isSubareaOfIn;
}
@@ -322,10 +393,13 @@ namespace Isis {
p_nbands(rhs.p_nbands), p_pixelType(rhs.p_pixelType) {
p_sample = rhs.p_sample;
+ p_nsampsScaled = rhs.p_nsampsScaled;
p_line = rhs.p_line;
+ p_nlinesScaled = rhs.p_nlinesScaled;
p_band = rhs.p_band;
p_npixels = rhs.p_npixels;
+ p_scale = rhs.p_scale;
Allocate();
Copy(rhs);
@@ -364,5 +438,6 @@ namespace Isis {
QString message = Message::MemoryAllocationFailed();
throw IException(IException::Unknown, message, _FILEINFO_);
}
+ (*this) = NULL8;
}
}
diff --git a/isis/src/base/objs/Buffer/Buffer.h b/isis/src/base/objs/Buffer/Buffer.h
index f0e52986024ee31fec29a9d3837bdfe49232fc7c..90f2d0918cf855b3b6f7a1d7ac775baa08d09a95 100644
--- a/isis/src/base/objs/Buffer/Buffer.h
+++ b/isis/src/base/objs/Buffer/Buffer.h
@@ -54,7 +54,7 @@ namespace Isis {
public:
Buffer();
Buffer(const int nsamps, const int nlines, const int nbands,
- const Isis::PixelType type);
+ const Isis::PixelType type, const double scale = 1);
~Buffer();
@@ -80,6 +80,24 @@ namespace Isis {
return (p_nlines);
}
+ /**
+ * Returns the number of samples in the shape buffer
+ *
+ * @return int
+ */
+ inline int SampleDimensionScaled() const {
+ return (p_nsampsScaled);
+ }
+
+ /**
+ * Returns the number of lines in the shape buffer
+ *
+ * @return int
+ */
+ inline int LineDimensionScaled() const {
+ return (p_nlinesScaled);
+ }
+
/**
* Returns the number of bands in the shape buffer
*
@@ -89,6 +107,15 @@ namespace Isis {
return (p_nbands);
}
+ /**
+ * Returns the scale of the shape buffer
+ *
+ * @return double
+ */
+ inline double scale() const {
+ return (p_scale);
+ }
+
/**
* Returns the total number of pixels in the shape buffer
*
@@ -161,10 +188,12 @@ namespace Isis {
return p_pixelType;
};
- protected:
void SetBasePosition(const int start_sample, const int start_line,
const int start_band);
+ friend std::ostream &operator<<(std::ostream &os, Buffer &buffer);
+
+ protected:
/**
* This method is used to set the base sample position of the shape buffer.
*
@@ -197,20 +226,25 @@ namespace Isis {
int p_sample; //!< Starting sample to read/write
int p_nsamps; //!< Number of samples to read/write
+ int p_nsampsScaled;
int p_line; //!< Starting line to read/write
int p_nlines; //!< Number of lines to read/write
+ int p_nlinesScaled;
int p_band; //!< Starting band to read/write
int p_nbands; //!< Number of bands to read/write
- int p_npixels; //!< Number of pixels (nsamps * nlines * nbands)
+ int p_npixels; //!< Number of pixels (nsamps * nlines * scale ** 2) * bands
double *p_buf; /**< Shape buffer allocated to the size of npixels for
handling reads/writes*/
const Isis::PixelType p_pixelType; //!< The pixel type of the raw buffer
void *p_rawbuf; //!< The raw dm read from the disk
+ // Might need x and y scale
+ double p_scale; //!< Amount to scale the buffers lines and samples, defaults to 1
+
void Allocate();
/**
diff --git a/isis/src/base/objs/Buffer/Buffer.truth b/isis/src/base/objs/Buffer/Buffer.truth
deleted file mode 100644
index 29652d23140ebd0440fe021a25947b139a14fba6..0000000000000000000000000000000000000000
--- a/isis/src/base/objs/Buffer/Buffer.truth
+++ /dev/null
@@ -1,53 +0,0 @@
-Isis::Buffer Unit Test
-
-SampleDimension: 4
-LineDimension: 3
-BandDimension: 2
-Size: 24
-
-Sample(): 0
-Line(): 0
-Band(): 0
-Position: 0 0 0
-Index: 0
-
-at(0): 0
-at(10): 10
-at(23): 23
-b[0]: 0
-b[10]: 10
-b[23]: 23
-
-Sample(): 3
-Line(): 2
-Band(): 1
-Position: 3 2 1
-Index: 0
-
-Sample(16): 3
-Line(16): 3
-Band(16): 2
-Position: 3 3 2
-Index: 16
-
-Copy constructor: Worked
-SampleDimension: 4
-LineDimension: 3
-BandDimension: 2
-Size: 24
-a[0]: 0
-a[23]: 23
-
-PixelType = SignedInteger
-
-Null Buffer size: 0
-
-Test assignment operator for a constant...
-d.size(): 8
-d[0]: 999
-d[2]: 999
-d[n]: 999
-
-**PROGRAMMER ERROR** Array subscript [-1] is out of array bounds.
-**PROGRAMMER ERROR** Array subscript [24] is out of array bounds.
-**PROGRAMMER ERROR** Input and output buffers are not the same pixel type.
diff --git a/isis/src/base/objs/Buffer/unitTest.cpp b/isis/src/base/objs/Buffer/unitTest.cpp
deleted file mode 100644
index 2babf6da8e240686cd49b5221e465bc631650d23..0000000000000000000000000000000000000000
--- a/isis/src/base/objs/Buffer/unitTest.cpp
+++ /dev/null
@@ -1,134 +0,0 @@
-/** This is free and unencumbered software released into the public domain.
-The authors of ISIS do not claim copyright on the contents of this file.
-For more details about the LICENSE terms and the AUTHORS, you will
-find files of those names at the top level of this repository. **/
-
-/* SPDX-License-Identifier: CC0-1.0 */
-#include <iostream>
-#include "Buffer.h"
-#include "IException.h"
-#include "Preference.h"
-
-using namespace std;
-using namespace Isis;
-
-class Test : public Buffer {
- public:
- Test(int s, int l, int b) : Isis::Buffer(s, l, b, Isis::SignedInteger) {};
- ~Test() {};
- void print();
-};
-
-void Test::print() {
- SetBasePosition(3, 2, 1);
- cout << "Sample(): " << Sample() << endl;
- cout << "Line(): " << Line() << endl;
- cout << "Band(): " << Band() << endl;
-
- int samp, line, band;
- Position(0, samp, line, band);
- cout << "Position: " << samp << " " << line << " " << band
- << endl;
- cout << "Index: " << Index(samp, line, band) << endl << endl;
-
- cout << "Sample(16): " << Sample(16) << endl;
- cout << "Line(16): " << Line(16) << endl;
- cout << "Band(16): " << Band(16) << endl;
-
- Position(16, samp, line, band);
- cout << "Position: " << samp << " " << line << " " << band
- << endl;
- cout << "Index: " << Index(samp, line, band) << endl << endl;
-}
-
-int main(int argc, char *argv[]) {
- Isis::Preference::Preferences(true);
- cout << "Isis::Buffer Unit Test" << endl << endl;
-
- Test b(4, 3, 2);
- for(int i = 0; i < b.size(); i++) {
- b[i] = i;
- }
-
- cout << "SampleDimension: " << b.SampleDimension() << endl;
- cout << "LineDimension: " << b.LineDimension() << endl;
- cout << "BandDimension: " << b.BandDimension() << endl;
- cout << "Size: " << b.size() << endl << endl;
-
- cout << "Sample(): " << b.Sample() << endl;
- cout << "Line(): " << b.Line() << endl;
- cout << "Band(): " << b.Band() << endl;
-
- int samp, line, band;
- b.Position(0, samp, line, band);
- cout << "Position: " << samp << " " << line << " " << band
- << endl;
- cout << "Index: " << b.Index(samp, line, band) << endl << endl;
-
- cout << "at(0): " << b.at(0) << endl;
- cout << "at(10): " << b.at(10) << endl;
- cout << "at(23): " << b.at(23) << endl;
- cout << "b[0]: " << b[0] << endl;
- cout << "b[10]: " << b[10] << endl;
- cout << "b[23]: " << b[23] << endl << endl;
-
- b.print();
-
- Test a = b;
- if(a.DoubleBuffer() != b.DoubleBuffer()) {
- cout << "Copy constructor: Worked" << endl;
- }
- else {
- cout << "Copy constructor: Failed" << endl;
- }
- cout << "SampleDimension: " << a.SampleDimension() << endl;
- cout << "LineDimension: " << a.LineDimension() << endl;
- cout << "BandDimension: " << a.BandDimension() << endl;
- cout << "Size: " << a.size() << endl ;
- cout << "a[0]: " << a[0] << endl;
- cout << "a[23]: " << a[23] << endl << endl;
-
- cout << "PixelType = " << Isis::PixelTypeName(a.PixelType()) << endl;
- cout << endl;
-
- // Test new default constructor. Enclose in braces so destructor is tested
- {
- Buffer nullbuf;
- cout << "Null Buffer size: " << nullbuf.size() << endl << endl;
- }
-
- // Test assignment operator
- cout << "Test assignment operator for a constant...\n";
- Buffer d(2, 2, 2, Double);
- d = 999.0;
- cout << "d.size(): " << d.size() << endl;
- cout << "d[0]: " << d[0] << endl;
- cout << "d[2]: " << d[2] << endl;
- cout << "d[n]: " << d[d.size()-1] << endl << endl;
-
- try {
- a.at(-1);
- }
- catch(Isis::IException &e) {
- e.print();
- }
-
- try {
- a.at(24);
- }
- catch(Isis::IException &e) {
- e.print();
- }
-
- try {
- Buffer a2(2, 2, 2, Isis::SignedWord);
- Buffer b2(2, 2, 2, Isis::SignedByte);
-
- a2.Copy(b2);
- }
- catch(Isis::IException &e) {
- e.print();
- }
-
- return 0;
-}
diff --git a/isis/src/base/objs/BufferManager/BufferManager.cpp b/isis/src/base/objs/BufferManager/BufferManager.cpp
index 7b2ff2fb24cfa3e48035f8943312c6d5f816bddc..3da87df37f6d79e877b4b49f7b970148746ff7f3 100644
--- a/isis/src/base/objs/BufferManager/BufferManager.cpp
+++ b/isis/src/base/objs/BufferManager/BufferManager.cpp
@@ -44,8 +44,9 @@ namespace Isis {
BufferManager::BufferManager(int maxsamps, int maxlines,
int maxbands, int bufsamps,
int buflines, int bufbands,
- Isis::PixelType type, bool reverse) :
- Isis::Buffer(bufsamps, buflines, bufbands, type),
+ Isis::PixelType type, bool reverse,
+ double scale) :
+ Isis::Buffer(bufsamps, buflines, bufbands, type, scale),
p_maxSamps(maxsamps), p_maxLines(maxlines),
p_maxBands(maxbands) {
SetIncrements(bufsamps, buflines, bufbands);
diff --git a/isis/src/base/objs/BufferManager/BufferManager.h b/isis/src/base/objs/BufferManager/BufferManager.h
index b034f146e2e0a1f03fd4712106a10aaeb9268e2e..746599704c463efddb59bf339ab94bbf28a58f96 100644
--- a/isis/src/base/objs/BufferManager/BufferManager.h
+++ b/isis/src/base/objs/BufferManager/BufferManager.h
@@ -56,7 +56,8 @@ namespace Isis {
BufferManager();
BufferManager(int maxsamps, int maxlines, int maxbands,
int bufsamps, int buflines, int bufbands,
- Isis::PixelType type, bool reverse = false);
+ Isis::PixelType type, bool reverse = false,
+ double scale = 1.0);
BufferManager(const BufferManager &other);
//! Destroys the BufferManager object
diff --git a/isis/src/base/objs/Cube/Cube.cpp b/isis/src/base/objs/Cube/Cube.cpp
index c4206bf0c15ca4b9c2ff1223e98a6e5980a23088..9c842ba8773cf5e77b9eb19bd2af555d136766b0 100644
--- a/isis/src/base/objs/Cube/Cube.cpp
+++ b/isis/src/base/objs/Cube/Cube.cpp
@@ -25,6 +25,7 @@ find files of those names at the top level of this repository. **/
#include "CubeStretch.h"
#include "Endian.h"
#include "FileName.h"
+#include "GdalIoHandler.h"
#include "History.h"
#include "ImageHistogram.h"
#include "ImagePolygon.h"
@@ -42,12 +43,13 @@ find files of those names at the top level of this repository. **/
#include "TProjection.h"
#include "Longitude.h"
-
using namespace std;
namespace Isis {
//! Constructs a Cube object.
Cube::Cube() {
+ GDALAllRegister();
+ CPLSetErrorHandler(CPLQuietErrorHandler);
construct();
}
@@ -60,6 +62,8 @@ namespace Isis {
* "r" or read-write "rw".
*/
Cube::Cube(const FileName &fileName, QString access) {
+ GDALAllRegister();
+ CPLSetErrorHandler(CPLQuietErrorHandler);
construct();
open(fileName.toString(), access);
}
@@ -74,6 +78,8 @@ namespace Isis {
* "r" or read-write "rw".
*/
void Cube::fromLabel(const FileName &fileName, Pvl &label, QString access) {
+ GDALAllRegister();
+ CPLSetErrorHandler(CPLQuietErrorHandler);
initCoreFromLabel(label);
create(fileName.expanded());
@@ -97,6 +103,8 @@ namespace Isis {
* "r" or read-write "rw".
*/
void Cube::fromIsd(const FileName &fileName, Pvl &label, nlohmann::json &isd, QString access) {
+ GDALAllRegister();
+ CPLSetErrorHandler(CPLQuietErrorHandler);
fromLabel(fileName, label, access);
PvlGroup &instGrp = label.findGroup("Instrument", Pvl::Traverse);
@@ -220,8 +228,18 @@ namespace Isis {
throw IException(IException::Programmer, msg, _FILEINFO_);
}
- if ((m_labelFile->openMode() & QIODevice::ReadWrite) != QIODevice::ReadWrite)
- readOnly = true;
+ if (m_labelFile) {
+ if ((m_labelFile->openMode() & QIODevice::ReadWrite) != QIODevice::ReadWrite)
+ readOnly = true;
+ }
+ else if (m_geodataSet) {
+ if (m_geodataSet->GetAccess() == GA_ReadOnly)
+ readOnly = true;
+ }
+ else {
+ QString msg = "No source files open";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
return readOnly;
}
@@ -247,7 +265,7 @@ namespace Isis {
*
* @returns True for attached labels, false for detached
*/
- bool Cube::labelsAttached() const {
+ Cube::LabelAttachment Cube::labelsAttached() const {
return m_attached;
}
@@ -284,15 +302,15 @@ namespace Isis {
Cube *result = new Cube;
+ result->setLabelsAttached(newFileAttributes.labelAttachment());
- if (newFileAttributes.labelAttachment() != ExternalLabel) {
+ if (result->labelsAttached() != ExternalLabel) {
result->setDimensions(sampleCount(), lineCount(), bandCount());
result->setByteOrder(newFileAttributes.byteOrder());
result->setFormat(newFileAttributes.fileFormat());
- if (newFileAttributes.labelAttachment() == DetachedLabel) {
- result->setLabelsAttached(false);
- }
+ // if (newFileAttributes.labelAttachment() == DetachedLabel) {
+ // }
if (newFileAttributes.propagatePixelType()) {
result->setPixelType(pixelType());
@@ -413,7 +431,7 @@ namespace Isis {
* is forced). Environment variables in the filename will be
* automatically expanded as well.
*/
- void Cube::create(const QString &cubeFileName) {
+ void Cube::create(const QString &imageFileName) {
// Already opened?
if (isOpen()) {
string msg = "You already have a cube opened";
@@ -430,11 +448,11 @@ namespace Isis {
if (m_pixelType == None) {
throw IException(IException::Unknown,
QString("Cannot create the cube [%1] with a pixel type set to None")
- .arg(cubeFileName),
+ .arg(imageFileName),
_FILEINFO_);
}
- if (m_storesDnData) {
+ if (labelsAttached() == LabelAttachment::AttachedLabel) {
// Make sure the cube is not going to exceed the maximum size preference
BigInt size = (BigInt)m_samples * m_lines *
(BigInt)m_bands * (BigInt)SizeOf(m_pixelType);
@@ -450,7 +468,7 @@ namespace Isis {
if (size > maxSizePreference) {
QString msg;
- msg += "The cube you are attempting to create [" + cubeFileName + "] is ["
+ msg += "The cube you are attempting to create [" + imageFileName + "] is ["
+ toString(size) + "GB]. This is larger than the current allowed "
"size of [" + toString(maxSizePreference) + "GB]. The cube "
"dimensions were (S,L,B) [" + toString(m_samples) + ", " +
@@ -465,59 +483,106 @@ namespace Isis {
}
// Expand output name
- FileName cubFile(cubeFileName);
+ FileName imageFile(imageFileName);
PvlObject isiscube("IsisCube");
PvlObject core("Core");
- if (m_storesDnData) {
- cubFile = cubFile.addExtension("cub");
+ // Create the size of the core
+ PvlGroup dims("Dimensions");
+ dims += PvlKeyword("Samples", toString(m_samples));
+ dims += PvlKeyword("Lines", toString(m_lines));
+ dims += PvlKeyword("Bands", toString(m_bands));
+
+ // Create the pixel type
+ PvlGroup ptype("Pixels");
+ ptype += PvlKeyword("Type", PixelTypeName(m_pixelType));
+
+ // And the byte ordering
+ ptype += PvlKeyword("ByteOrder", ByteOrderName(m_byteOrder));
+ ptype += PvlKeyword("Base", toString(m_base));
+ ptype += PvlKeyword("Multiplier", toString(m_multiplier));
+
+ if (labelsAttached() != LabelAttachment::ExternalLabel) {
+ if (format() != Format::GTiff) {
+ imageFile = imageFile.addExtension("cub");
+ }
+ else if (format() == Format::GTiff) {
+ imageFile = imageFile.addExtension("tiff");
+ }
+ else {
+ QString msg = "Unknown format type [" + toString(format()) + "]";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
+
+ m_dataFileName = new FileName(imageFile);
// See if we have attached or detached labels
- if (m_attached) {
+ if (labelsAttached() == LabelAttachment::AttachedLabel) {
// StartByte is 1-based (why!!) so we need to do + 1
core += PvlKeyword("StartByte", toString(m_labelBytes + 1));
- m_labelFileName = new FileName(cubFile);
- m_dataFileName = new FileName(cubFile);
+ m_labelFileName = new FileName(imageFile);
m_labelFile = new QFile(m_labelFileName->expanded());
}
- else {
+ else if (labelsAttached() == LabelAttachment::DetachedLabel) {
core += PvlKeyword("StartByte", toString(1));
- core += PvlKeyword("^Core", cubFile.name());
- m_dataFileName = new FileName(cubFile);
+ core += PvlKeyword("^Core", imageFile.name());
m_dataFile = new QFile(realDataFileName().expanded());
- FileName labelFileName(cubFile);
+ FileName labelFileName(imageFile);
labelFileName = labelFileName.setExtension("lbl");
m_labelFileName = new FileName(labelFileName);
m_labelFile = new QFile(m_labelFileName->expanded());
}
-
- // Create the size of the core
- PvlGroup dims("Dimensions");
- dims += PvlKeyword("Samples", toString(m_samples));
- dims += PvlKeyword("Lines", toString(m_lines));
- dims += PvlKeyword("Bands", toString(m_bands));
+ else {
+ QString msg = "Label type [" + LabelAttachmentName(labelsAttached()) + "] not supported";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
core.addGroup(dims);
-
- // Create the pixel type
- PvlGroup ptype("Pixels");
- ptype += PvlKeyword("Type", PixelTypeName(m_pixelType));
-
- // And the byte ordering
- ptype += PvlKeyword("ByteOrder", ByteOrderName(m_byteOrder));
- ptype += PvlKeyword("Base", toString(m_base));
- ptype += PvlKeyword("Multiplier", toString(m_multiplier));
core.addGroup(ptype);
}
- else {
- cubFile = cubFile.addExtension("ecub");
+ else if (labelsAttached() == LabelAttachment::ExternalLabel) {
+ if (!m_dataFileName) {
+ if (format() == Bsq || format() == Tile) {
+ imageFile = imageFile.addExtension("cub");
+
+ Pvl dnLabel;
+ PvlObject isiscube("IsisCube");
+ PvlObject dnCore(core);
+ PvlKeyword fileFormat("Format", toString(format()));
+
+ dnCore.addKeyword(fileFormat);
+ dnCore.addGroup(dims);
+ dnCore.addGroup(ptype);
- core += PvlKeyword("^DnFile", m_dataFileName->original());
-// m_dataFileName = new FileName(cubFile);
- m_dataFile = new QFile(realDataFileName().expanded());
+ isiscube.addObject(dnCore);
+ dnLabel.addObject(isiscube);
- m_labelFileName = new FileName(cubFile);
- m_labelFile = new QFile(cubFile.expanded());
+ Cube dnCube;
+ dnCube.fromLabel(imageFile, dnLabel, "rw");
+ dnCube.close();
+
+ m_dataFileName = new FileName(imageFile);
+ }
+ else if (format() == Format::GTiff) {
+ imageFile = imageFile.setExtension("tiff");
+ m_dataFileName = new FileName(imageFile);
+ }
+
+ imageFile = imageFile.setExtension("ecub");
+ FileName labelFileName(imageFile);
+ m_labelFileName = new FileName(labelFileName);
+ m_labelFile = new QFile(m_labelFileName->expanded());
+ }
+
+ core += PvlKeyword("^DnFile", m_dataFileName->name());
+ m_dataFile = new QFile(m_dataFileName->expanded());
+
+ m_labelFileName = new FileName(imageFile);
+ m_labelFile = new QFile(m_labelFileName->expanded());
+ }
+ else {
+ QString msg = "Label type [" + LabelAttachmentName(labelsAttached()) + "] not supported";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
}
isiscube.addObject(core);
@@ -545,15 +610,15 @@ namespace Isis {
cleanUp(false);
throw IException(IException::Io, msg, _FILEINFO_);
}
-
+
if (m_dataFile) {
- if (m_storesDnData && !m_dataFile->open(QIODevice::Truncate | QIODevice::ReadWrite)) {
+ if (labelsAttached() != ExternalLabel && !m_dataFile->open(QIODevice::Truncate | QIODevice::ReadWrite)) {
QString msg = "Failed to create [" + m_dataFile->fileName() + "]. ";
msg += "Verify the output path exists and you have permission to write to the path.";
cleanUp(false);
throw IException(IException::Io, msg, _FILEINFO_);
}
- else if (!m_storesDnData && !m_dataFile->open(QIODevice::ReadOnly)) {
+ else if (labelsAttached() == ExternalLabel && !m_dataFile->open(QIODevice::ReadWrite)) {
QString msg = "Failed to open [" + m_dataFile->fileName() + "] for reading. ";
msg += "Verify the output path exists and you have permission to read from the path.";
cleanUp(false);
@@ -561,24 +626,103 @@ namespace Isis {
}
}
- bool dataAlreadyOnDisk = m_storesDnData ? false : true;
+ bool dataAlreadyOnDisk = (labelsAttached() == ExternalLabel);
- if (m_format == Bsq) {
- m_ioHandler = new CubeBsqHandler(dataFile(), m_virtualBandList, realDataFileLabel(),
- dataAlreadyOnDisk);
- }
- else {
- m_ioHandler = new CubeTileHandler(dataFile(), m_virtualBandList, realDataFileLabel(),
+ if (format() != GTiff) {
+ if (format() == Bsq) {
+ m_ioHandler = new CubeBsqHandler(dataFile(), m_virtualBandList, realDataFileLabel(),
dataAlreadyOnDisk);
+ }
+ else if(format() == Tile) {
+ m_ioHandler = new CubeTileHandler(dataFile(), m_virtualBandList, realDataFileLabel(),
+ dataAlreadyOnDisk);
+ }
+
+ if (!dataAlreadyOnDisk) {
+ m_ioHandler->updateLabels(*m_label);
+ }
}
+ else if(format() == Format::GTiff) {
+ char **papszOptions = NULL;
+ papszOptions = CSLSetNameValue(papszOptions, "COMPRESS", "DEFLATE");
+ papszOptions = CSLSetNameValue(papszOptions, "PREDICTOR", "2");
+ QString datafile = m_dataFileName->expanded();
+ QString format = "GTiff";
+ createGdal(datafile, format, papszOptions);
+
+ m_geodataSet = GDALDataset::FromHandle(GDALOpen(datafile.toStdString().c_str(), GA_Update));
+ if (!m_geodataSet) {
+ QString msg = "Failed opening GDALDataset from [" + m_dataFileName->name() + "]";
+ cleanUp(false);
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
- if (m_storesDnData)
+ m_ioHandler = new GdalIoHandler(gdalDataset(), m_virtualBandList, IsisPixelToGdal(pixelType()));
m_ioHandler->updateLabels(*m_label);
+ }
+ else {
+ QString msg = "Format [" + toString(format()) + "] not supported";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
// Write the labels
writeLabels();
}
+ void Cube::createGdal(QString &dataFileName, QString &driverName, char **papszOptions) {
+ GDALAllRegister();
+ CPLSetErrorHandler(CPLQuietErrorHandler);
+ GDALDriver* driver = GetGDALDriverManager()->GetDriverByName(driverName.toStdString().c_str());
+ if (driver) {
+ double noDataValue;
+ switch (pixelType()) {
+ case UnsignedByte:
+ noDataValue = (double) NULL1;
+ break;
+ case SignedByte:
+ noDataValue = (double) NULLS1;
+ break;
+ case UnsignedWord:
+ noDataValue = (double) NULLU2;
+ break;
+ case SignedWord:
+ noDataValue = (double) NULL2;
+ break;
+ case UnsignedInteger:
+ noDataValue = (double) NULLUI4;
+ break;
+ case SignedInteger:
+ noDataValue = (double) NULLI4;
+ break;
+ case Real:
+ noDataValue = (double) NULL4;
+ break;
+
+ default:
+ noDataValue = NULL8;
+ break;
+ }
+ GDALDataset *dataset = driver->Create(dataFileName.toStdString().c_str(), sampleCount(), lineCount(), bandCount(), IsisPixelToGdal(pixelType()), papszOptions);
+ if (!dataset) {
+ QString msg = "Could not create file [" + dataFileName + "] from [" + driverName + "] Driver.";
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+ for (int i = 1; i <= bandCount(); i++) {
+ GDALRasterBand *band = dataset->GetRasterBand(i);
+ band->SetScale(multiplier());
+ band->SetOffset(base());
+ band->SetNoDataValue(noDataValue);
+ band->Fill(noDataValue);
+ }
+ GDALClose(dataset);
+ CSLDestroy( papszOptions );
+ }
+ else {
+ QString msg = "No Driver found for name [" + driverName + "]";
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+ }
+
/**
* This method will create an isis cube for writing. The programmer should
@@ -606,7 +750,7 @@ namespace Isis {
setByteOrder(att.byteOrder());
setFormat(att.fileFormat());
- setLabelsAttached(att.labelAttachment() == AttachedLabel);
+ setLabelsAttached(att.labelAttachment());
if (!att.propagatePixelType())
setPixelType(att.pixelType());
setMinMax(att.minimum(), att.maximum());
@@ -615,11 +759,20 @@ namespace Isis {
create(cubeFileName);
}
+ void Cube::checkAccess(QString access) {
+ if (!(access == "r" || access == "rw")) {
+ QString msg = "Unknown value for access [" + access + "]. Expected 'r' "
+ " or 'rw'";
+ cleanUp(false);
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
+ }
+
/**
- * This method will open an existing isis cube for reading or
- * reading/writing. Any input cube attributes following the file
- * name will be applied.
+ * This method will try to open a file as either a cube or
+ * geotiff in either read or read/write. Any input cube
+ * attributes following the file name will be applied.
*
* @param[in] cubeFileName Name of the cube file to open. Environment
* variables in the filename will be automatically expanded.
@@ -634,7 +787,7 @@ namespace Isis {
throw IException(IException::Programmer, msg, _FILEINFO_);
}
- initLabelFromFile(cubeFileName, (access == "rw"));
+ checkAccess(access);
try {
Isis::CubeAttributeInput att(cubeFileName);
@@ -647,6 +800,49 @@ namespace Isis {
// there is an exception parsing and adding an attribute
}
+ QString msg = "Failed to open [" + cubeFileName + "]";
+ IException exceptions(IException::Io, msg, _FILEINFO_);
+ if (!isOpen()) {
+ try {
+ openCube(cubeFileName, access);
+ }
+ catch (IException &e) {
+ cleanUp(false);
+ exceptions.append(e);
+ }
+ }
+
+ if (!isOpen()) {
+ try {
+ openGdal(cubeFileName, access);
+ }
+ catch(IException &e) {
+ cleanUp(false);
+ exceptions.append(e);
+ }
+ }
+
+ if (!isOpen()) {
+ throw exceptions;
+ }
+
+ applyVirtualBandsToLabel();
+ }
+
+ /**
+ * This method will open an existing isis cube for reading or
+ * reading/writing.
+ *
+ * @param[in] cubeFileName Name of the cube file to open. Environment
+ * variables in the filename will be automatically expanded.
+ * @param[in] access (Default value of "r") Defines how the cube will be
+ * accessed. Either read-only "r" or read-write "rw".
+ */
+ void Cube::openCube(const QString &cubeFileName, QString access) {
+ checkAccess(access);
+
+ initLabelFromFile(cubeFileName, (access == "rw"));
+
// Figure out the name of the data file
try {
PvlObject &core = m_label->findObject("IsisCube").findObject("Core");
@@ -660,11 +856,13 @@ namespace Isis {
else {
m_dataFileName = new FileName(temp);
}
+ setLabelsAttached(LabelAttachment::DetachedLabel);
- m_attached = false;
- m_storesDnData = true;
+ FileName realDataFile = realDataFileName();
+ delete m_dataFileName;
+ m_dataFileName = new FileName(realDataFile.expanded());
- m_dataFile = new QFile(realDataFileName().expanded());
+ m_dataFile = new QFile(m_dataFileName->expanded());
}
// External cube files (ecub), ecub contains all labels and SPICE blobs, history
else if (core.hasKeyword("^DnFile")) {
@@ -676,103 +874,242 @@ namespace Isis {
else {
m_dataFileName = new FileName(dataFileName);
}
+ setLabelsAttached(LabelAttachment::ExternalLabel);
- m_attached = true;
- m_storesDnData = false;
- *m_dataFileName = FileName(realDataFileName().expanded());
- m_dataFile = new QFile(realDataFileName().expanded());
+ FileName realDataFile = realDataFileName();
+ delete m_dataFileName;
+ m_dataFileName = new FileName(realDataFile.expanded());
+
+ m_dataFile = new QFile(m_dataFileName->expanded());
}
// Typical cube containing labels, SPICE, history and dn data
else {
+ setLabelsAttached(LabelAttachment::AttachedLabel);
m_dataFileName = new FileName(*m_labelFileName);
- m_attached = true;
- m_storesDnData = true;
}
}
catch (IException &e) {
cleanUp(false);
- throw;
+ throw e;
}
- if (access == "r") {
- if (!m_labelFile->open(QIODevice::ReadOnly)) {
- QString msg = "Failed to open [" + m_labelFile->fileName() + "] with "
- "read only access";
- cleanUp(false);
- throw IException(IException::Io, msg, _FILEINFO_);
- }
-
- if (m_dataFile) {
- if (!m_dataFile->open(QIODevice::ReadOnly)) {
- QString msg = "Failed to open [" + m_dataFile->fileName() + "] with "
- "read only access";
- cleanUp(false);
- throw IException(IException::Io, msg, _FILEINFO_);
- }
- }
+ QIODevice::OpenModeFlag qtAccess = QIODevice::ReadOnly;
+ GDALAccess eAccess = GA_ReadOnly;
+ if (access == "rw") {
+ qtAccess = QIODevice::ReadWrite;
+ eAccess = GA_Update;
}
- else if (access == "rw") {
- if (!m_labelFile->open(QIODevice::ReadWrite)) {
+ if (!m_labelFile->open(qtAccess)) {
QString msg = "Failed to open [" + m_labelFile->fileName() + "] with "
- "read/write access";
+ "access [" + access + "]";
cleanUp(false);
throw IException(IException::Io, msg, _FILEINFO_);
}
if (m_dataFile) {
- if (m_storesDnData && !m_dataFile->open(QIODevice::ReadWrite)) {
- QString msg = "Failed to open [" + m_dataFile->fileName() + "] with "
- "read/write access";
- cleanUp(false);
- throw IException(IException::Io, msg, _FILEINFO_);
- }
- else if (!m_storesDnData && !m_dataFile->open(QIODevice::ReadOnly)) {
- QString msg = "Failed to open [" + m_dataFile->fileName() + "] with "
- "read access";
- cleanUp(false);
- throw IException(IException::Io, msg, _FILEINFO_);
+ if (!m_dataFile->open(qtAccess)) {
+ QString msg = "Failed to open [" + m_dataFile->fileName() + "] with "
+ "access [" + access + "]";
+ cleanUp(false);
+ throw IException(IException::Io, msg, _FILEINFO_);
}
- }
- }
- else {
- QString msg = "Unknown value for access [" + access + "]. Expected 'r' "
- " or 'rw'";
- cleanUp(false);
- throw IException(IException::Programmer, msg, _FILEINFO_);
}
initCoreFromLabel(*m_label);
// Determine the number of bytes in the label
- if (m_attached) {
+ if (labelsAttached() != LabelAttachment::DetachedLabel) {
m_labelBytes = m_label->findObject("Label")["Bytes"];
}
else {
m_labelBytes = labelSize(true);
}
- QPair<bool, Pvl *> dataLabel = qMakePair(false, m_label);
- if (!m_storesDnData) {
- dataLabel = qMakePair(true, new Pvl(m_dataFileName->expanded()));
- }
-
// Now examine the format to see which type of handler to create
if (m_format == Bsq) {
m_ioHandler = new CubeBsqHandler(dataFile(), m_virtualBandList,
realDataFileLabel(), true);
}
- else {
+ else if (m_format == Tile) {
m_ioHandler = new CubeTileHandler(dataFile(), m_virtualBandList,
realDataFileLabel(), true);
}
+ else if (m_format == GTiff) {
+ m_dataFile->close();
+ m_geodataSet = GDALDataset::FromHandle(GDALOpen(m_dataFileName->expanded().toStdString().c_str(), eAccess));
+ if (!m_geodataSet) {
+ QString msg = "Opening GDALDataset from [" + m_dataFileName->name() + "] failed with access [" + eAccess +"]";
+ cleanUp(false);
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+ m_ioHandler = new GdalIoHandler(gdalDataset(), m_virtualBandList, IsisPixelToGdal(pixelType()));
+ }
+ else {
+ QString msg = "Unknown format [" + toString(m_format) + "]";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
+ }
+
+ /**
+ * This method will open an existing geotiff for reading or
+ * reading/writing.
+ *
+ * @param[in] cubeFileName Name of the file to open. Environment
+ * variables in the filename will be automatically expanded.
+ * @param[in] access (Default value of "r") Defines how the cube will be
+ * accessed. Either read-only "r" or read-write "rw".
+ */
+ void Cube::openGdal(const QString &cubeFileName, QString access) {
+ checkAccess(access);
+
+ m_labelFileName = new FileName(cubeFileName);
+
+ setLabelsAttached(LabelAttachment::AttachedLabel);
+ m_dataFileName = new FileName(*m_labelFileName);
+
+ initCoreFromGdal(m_labelFileName->expanded());
+ GDALDataset *dataset = GDALDataset::FromHandle(GDALOpen(m_dataFileName->expanded().toStdString().c_str(), GA_ReadOnly));
+ if (!dataset) {
+ QString msg = "Failed opening GDALDataset from [" + m_dataFileName->name() + "]";
+ cleanUp(false);
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
- if (dataLabel.first) {
- delete dataLabel.second;
- dataLabel.second = NULL;
+ CPLStringList metadata = CPLStringList(dataset->GetMetadata("USGS"), false);
+
+ m_label = new Pvl();
+ if (metadata) {
+ for (int i = 0; i < metadata.size(); i++) {
+ const char *metadataItem = CPLParseNameValue(metadata[i], nullptr);
+ nlohmann::ordered_json metadataAsJson = nlohmann::ordered_json::parse(metadataItem);
+ Pvl pvl;
+ Pvl::readObject(pvl, metadataAsJson);
+ for (int i = 0; i < pvl.objects(); i++) {
+ m_label->addObject(pvl.object(i));
+ }
+ for (int i = 0; i < pvl.groups(); i++) {
+ m_label->addGroup(pvl.group(i));
+ }
+ }
}
+ else {
+ // Setup the PVL
+ PvlObject isiscube("IsisCube");
+ PvlObject core("Core");
- applyVirtualBandsToLabel();
+ // Create the size of the core
+ PvlGroup dims("Dimensions");
+ dims += PvlKeyword("Samples", toString(m_samples));
+ dims += PvlKeyword("Lines", toString(m_lines));
+ dims += PvlKeyword("Bands", toString(m_bands));
+
+ // Create the pixel type
+ PvlGroup ptype("Pixels");
+ ptype += PvlKeyword("Type", PixelTypeName(m_pixelType));
+
+ // And the byte ordering
+ ptype += PvlKeyword("ByteOrder", ByteOrderName(m_byteOrder));
+ ptype += PvlKeyword("Base", toString(m_base));
+ ptype += PvlKeyword("Multiplier", toString(m_multiplier));
+
+ core += PvlKeyword("StartByte", toString(m_labelBytes + 1));
+
+ core.addGroup(dims);
+ core.addGroup(ptype);
+
+ isiscube.addObject(core);
+
+ if (dataset->GetSpatialRef()) {
+ char ** projStr = new char*[1];
+ const OGRSpatialReference &oSRS = *dataset->GetSpatialRef();
+ oSRS.exportToProj4(projStr);
+ QString qProjStr = QString::fromStdString(std::string(projStr[0]) + " +type=crs");
+ delete[] projStr[0];
+ delete[] projStr;
+
+ char ** projJsonStr = new char*[1];
+ oSRS.exportToPROJJSON(projJsonStr, nullptr);
+ nlohmann::json projJson = nlohmann::json::parse(projJsonStr[0]);
+ CPLFree(projJsonStr);
+
+ PvlGroup mappingGroup("Mapping");
+ mappingGroup.addKeyword(PvlKeyword("ProjectionName", "IProj"));
+ mappingGroup.addKeyword(PvlKeyword("EquatorialRadius", toString(oSRS.GetSemiMajor()), "meters"));
+ mappingGroup.addKeyword(PvlKeyword("PolarRadius", toString(oSRS.GetSemiMinor()), "meters"));
+
+ if (projJson.contains("base_crs")) {
+ projJson = projJson["base_crs"];
+ }
+
+ std::string direction = projJson["coordinate_system"]["axis"][1]["direction"];
+ if (direction == "east") {
+ mappingGroup.addKeyword(PvlKeyword("LongitudeDirection", "PositiveEast"));
+ }
+ else if (direction == "west") {
+ mappingGroup.addKeyword(PvlKeyword("LongitudeDirection", "PositiveWest"));
+ }
+ else {
+ QString msg = "Unknown direction [" + QString::fromStdString(direction) + "]";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
+ mappingGroup.addKeyword(PvlKeyword("LongitudeDomain", "180"));
+ mappingGroup.addKeyword(PvlKeyword("LatitudeType", "Planetocentric"));
+ mappingGroup.addKeyword(PvlKeyword("ProjStr", qProjStr));
+
+ // Read the GeoTransform and get the elements we care about
+ double *padfTransform = new double[6];
+ dataset->GetGeoTransform(padfTransform);
+ if (abs(padfTransform[1]) != abs(padfTransform[5])) {
+ delete[] padfTransform;
+ QString msg = "Vertical and horizontal resolution do not match";
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+
+ double dfScale;
+ double dfRes;
+ double upperLeftX;
+ double upperLeftY;
+ dfRes = padfTransform[1] * oSRS.GetLinearUnits();
+ upperLeftX = padfTransform[0];
+ upperLeftY = padfTransform[3];
+ if (oSRS.IsProjected()) {
+ const double dfDegToMeter = oSRS.GetSemiMajor() * M_PI / 180.0;
+ dfScale = dfDegToMeter / dfRes;
+ mappingGroup.addKeyword(PvlKeyword("PixelResolution", toString(dfRes), "meters/pixel"));
+ }
+ else if (oSRS.IsGeographic()) {
+ dfScale = 1.0 / dfRes;
+ mappingGroup.addKeyword(PvlKeyword("PixelResolution", toString(dfRes), "degrees/pixel"));
+ }
+ else {
+ QString msg = "Gdal spatial reference is not Geographic or Projected";
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+ mappingGroup.addKeyword(PvlKeyword("Scale", toString(dfScale), "pixels/degree"));
+ mappingGroup.addKeyword(PvlKeyword("UpperLeftCornerX", toString(upperLeftX)));
+ mappingGroup.addKeyword(PvlKeyword("UpperLeftCornerY", toString(upperLeftY)));
+ delete[] padfTransform;
+
+ isiscube.addGroup(mappingGroup);
+ }
+ m_label->addObject(isiscube);
+ }
+ GDALClose(dataset);
+
+ GDALAccess eAccess = GA_ReadOnly;
+ if (access == "rw") {
+ eAccess = GA_Update;
+ }
+ m_geodataSet = GDALDataset::FromHandle(GDALOpen(m_dataFileName->expanded().toStdString().c_str(), eAccess));
+ if (!m_geodataSet) {
+ QString msg = "Opening GDALDataset from [" + m_dataFileName->name() + "] failed with access [" + eAccess +"]";
+ cleanUp(false);
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+
+ m_ioHandler = new GdalIoHandler(gdalDataset(), m_virtualBandList, IsisPixelToGdal(pixelType()));
+ m_ioHandler->updateLabels(*m_label);
}
@@ -827,9 +1164,14 @@ namespace Isis {
if (m_tempCube)
cubeFile = *m_tempCube;
- QMutexLocker locker(m_mutex);
- QMutexLocker locker2(m_ioHandler->dataFileMutex());
- blob.Read(cubeFile.toString(), *label(), keywords);
+ if (format() == Format::GTiff && labelsAttached() == LabelAttachment::AttachedLabel) {
+ blob.ReadGdal(gdalDataset());
+ }
+ else {
+ QMutexLocker locker(m_mutex);
+ QMutexLocker locker2(m_ioHandler->dataFileMutex());
+ blob.Read(cubeFile.toString(), *label(), keywords);
+ }
}
@@ -987,13 +1329,19 @@ namespace Isis {
throw IException(IException::Programmer, msg, _FILEINFO_);
}
+ if (m_format == Format::GTiff && labelsAttached() == LabelAttachment::AttachedLabel) {
+ // write new type of blob
+ blob.WriteGdal(gdalDataset());
+ return; // nothing else to do
+ }
+
if (!m_labelFile->isWritable()) {
string msg = "The cube must be opened in read/write mode, not readOnly";
throw IException(IException::Programmer, msg, _FILEINFO_);
}
// Write an attached blob
- if (m_attached) {
+ if (labelsAttached() != LabelAttachment::DetachedLabel) {
QMutexLocker locker(m_mutex);
QMutexLocker locker2(m_ioHandler->dataFileMutex());
@@ -1008,9 +1356,7 @@ namespace Isis {
// maxbyte = position after the cube DN data and labels
streampos maxbyte = (streampos) m_labelBytes;
- if (m_storesDnData) {
- maxbyte += (streampos) m_ioHandler->getDataSize();
- }
+ maxbyte += (streampos) m_ioHandler->getDataSize();
// If EOF is too early, allocate space up to where we want the blob
if (endByte < maxbyte) {
@@ -1021,7 +1367,7 @@ namespace Isis {
blob.Write(*m_label, stream, "", overwrite);
}
- // Write a detached blob
+ // Write a detached
else {
FileName blobFileName = fileName();
blobFileName = blobFileName.removeExtension();
@@ -1140,11 +1486,11 @@ namespace Isis {
throw IException(IException::Programmer, msg, _FILEINFO_);
}
- if (!m_storesDnData) {
- QString msg = "The cube [" + QFileInfo(fileName()).fileName() +
- "] does not support storing DN data because it is using an external file for DNs";
- throw IException(IException::Unknown, msg, _FILEINFO_);
- }
+ // if (labelsAttached() == ExternalLabel) {
+ // QString msg = "The cube [" + QFileInfo(fileName()).fileName() +
+ // "] does not support storing DN data because it is using an external file for DNs";
+ // throw IException(IException::Unknown, msg, _FILEINFO_);
+ // }
QMutexLocker locker(m_mutex);
m_ioHandler->write(bufferToWrite);
@@ -1184,7 +1530,7 @@ namespace Isis {
m_base = 0.0;
m_multiplier = 1.0;
- double x1, x2;
+ double x1 = 0.0, x2 = 0.0;
if (m_pixelType == UnsignedByte) {
x1 = VALID_MIN1;
x2 = VALID_MAX1;
@@ -1252,14 +1598,17 @@ namespace Isis {
delete m_label;
m_label = NULL;
}
- catch (IException &) {
+ catch (IException &e) {
delete m_label;
m_label = NULL;
- throw;
+ throw e;
}
- m_storesDnData = false;
+ setLabelsAttached(Cube::ExternalLabel);
m_dataFileName = new FileName(cubeFileWithDnData);
+ FileName realDataFile = realDataFileName();
+ delete m_dataFileName;
+ m_dataFileName = new FileName(realDataFile.expanded());
delete m_labelFile;
m_labelFile = NULL;
@@ -1288,7 +1637,7 @@ namespace Isis {
*
* @param attach If false, the labels and data will be in separate files.
*/
- void Cube::setLabelsAttached(bool attach) {
+ void Cube::setLabelsAttached(LabelAttachment attach) {
openCheck();
m_attached = attach;
}
@@ -1386,7 +1735,7 @@ namespace Isis {
}
- if (m_storesDnData) {
+ if (labelsAttached() != ExternalLabel) {
throw IException(IException::Unknown,
QString("The cube [%1] stores DN data. It cannot be relocated to [%2] - "
"this is only supported for external cube label files.")
@@ -1573,7 +1922,7 @@ namespace Isis {
_FILEINFO_);
}
- if (storesDnData()) {
+ if (labelsAttached() == ExternalLabel) {
throw IException(IException::Unknown,
"Cube::getExternalCubeFileName can only be called on an external cube label "
"file",
@@ -1581,8 +1930,7 @@ namespace Isis {
}
- PvlObject &core = m_label->findObject("IsisCube").findObject("Core");
-
+ PvlObject &core = m_label->findObject("IsisCube").findObject("Core");
return core["^DnFile"][0];
}
@@ -1929,16 +2277,6 @@ namespace Isis {
}
- /**
- * This method returns a boolean value
- *
- * @return bool
- */
- bool Cube::storesDnData() const {
- return m_storesDnData;
- }
-
-
/**
* This will add the given caching algorithm to the list of attempted caching
* algorithms. The algorithms are tried in the opposite order that they
@@ -2164,6 +2502,11 @@ namespace Isis {
delete m_dataFile;
m_dataFile = NULL;
+ if (m_geodataSet) {
+ GDALClose(m_geodataSet);
+ }
+ m_geodataSet = NULL;
+
delete m_labelFileName;
m_labelFileName = NULL;
@@ -2223,6 +2566,14 @@ namespace Isis {
}
+ GDALDataset *Cube::gdalDataset() const {
+ if (!m_geodataSet) {
+ QString msg = "No GDALDataset has been constructed";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
+ return m_geodataSet;
+ }
+
/**
* This gets the file name of the file which actually contains the DN data. With ecub's, our
* data file name could be another ecub or a detached label, so using m_dataFileName is
@@ -2234,15 +2585,15 @@ namespace Isis {
FileName result;
// Attached, stores DN data - normal cube
- if (m_attached && m_storesDnData) {
+ if (labelsAttached() == LabelAttachment::AttachedLabel) {
result = *m_labelFileName;
}
// Detached, stores DN data - standard detached cube
- else if (!m_attached && m_storesDnData) {
+ else if (labelsAttached() == LabelAttachment::DetachedLabel) {
result = *m_dataFileName;
}
// External cube - go look at our external file
- else if (!m_storesDnData) {
+ else if (labelsAttached() == LabelAttachment::ExternalLabel) {
FileName guess = *m_dataFileName;
QDir dir(guess.toString());
@@ -2255,20 +2606,26 @@ namespace Isis {
guess = dir2.absolutePath() + "/" + guess.name();
}
do {
- Pvl guessLabel(guess.expanded());
+ Cube dataCube(guess.expanded());
+ Pvl guessLabel = *(dataCube.label());
- PvlObject &core = guessLabel.findObject("IsisCube").findObject("Core");
+ if (guessLabel.hasObject("IsisCube")) {
+ PvlObject &core = guessLabel.findObject("IsisCube").findObject("Core");
- if (core.hasKeyword("^DnFile")) {
- FileName currentGuess = guess;
- guess = core["^DnFile"][0];
+ if (core.hasKeyword("^DnFile")) {
+ FileName currentGuess = guess;
+ guess = core["^DnFile"][0];
- if (!guess.path().startsWith("/")) {
- guess = currentGuess.path() + "/" + guess.original();
+ if (!guess.path().startsWith("/")) {
+ guess = currentGuess.path() + "/" + guess.original();
+ }
+ }
+ else if (core.hasKeyword("^Core")) {
+ result = core["^Core"][0];
+ }
+ else {
+ result = guess;
}
- }
- else if (core.hasKeyword("^Core")) {
- result = core["^Core"][0];
}
else {
result = guess;
@@ -2299,8 +2656,7 @@ namespace Isis {
m_format = Tile;
m_pixelType = Real;
- m_attached = true;
- m_storesDnData = true;
+ m_attached = LabelAttachment::AttachedLabel;
m_labelBytes = 65536;
m_samples = 0;
@@ -2318,9 +2674,11 @@ namespace Isis {
* @param label Pvl label to initialize from
*/
void Cube::initCoreFromLabel(const Pvl &label) {
+ initialize();
+ initLabelState(label);
const PvlObject &core = label.findObject("IsisCube").findObject("Core");
- if (!core.hasKeyword("^DnFile")) {
+ if (labelsAttached() != ExternalLabel) {
// Dimensions
const PvlGroup &dims = core.findGroup("Dimensions");
m_samples = dims["Samples"];
@@ -2336,10 +2694,17 @@ namespace Isis {
// Now examine the format to see which type of handler to create
if ((QString) core["Format"] == "BandSequential") {
- m_format = Bsq;
+ m_format = Format::Bsq;
+ }
+ else if ((QString) core["Format"] == "Tile") {
+ m_format = Format::Tile;
+ }
+ else if ((QString) core["Format"] == "GTiff") {
+ m_format = Format::GTiff;
}
else {
- m_format = Tile;
+ QString msg = "Unknown format [" + (QString)core["Format"] + "]";
+ throw IException(IException::Io, msg, _FILEINFO_);
}
}
else {
@@ -2347,12 +2712,34 @@ namespace Isis {
if (!temp.expanded().startsWith("/")) {
temp = FileName(m_labelFileName->path() + "/" + temp.original());
}
-
- initCoreFromLabel(Pvl(temp.toString()));
+ try {
+ initCoreFromLabel(Pvl(temp.toString()));
+ }
+ catch (IException &e) {
+ initCoreFromGdal(temp.toString());
+ }
+ // Reset the label state as we recurse back out from initCoreFromLabel calls
+ initLabelState(label);
}
}
+ void Cube::initCoreFromGdal(const QString &labelFile) {
+ GDALDataset *geodataSet = GDALDataset::FromHandle(GDALOpen(labelFile.toStdString().c_str(), GA_ReadOnly));
+ if (!geodataSet) {
+ QString msg = "Gdal failed to open [" + labelFile + "]";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
+
+ setFormat(GTiff);
+ setDimensions(geodataSet->GetRasterXSize(), geodataSet->GetRasterYSize(), geodataSet->GetRasterCount());
+
+ GDALRasterBand *band = geodataSet->GetRasterBand(1);
+ setPixelType(GdalPixelToIsis(band->GetRasterDataType()));
+ setBaseMultiplier(band->GetOffset(), band->GetScale());
+ GDALClose(geodataSet);
+ }
+
/**
* This function initializes the Cube label from a file passed as a parameter
*
@@ -2632,19 +3019,35 @@ namespace Isis {
string msg = "Cube must be opened first before writing labels";
throw IException(IException::Programmer, msg, _FILEINFO_);
}
+
+ if (m_format == Format::GTiff && labelsAttached() == LabelAttachment::AttachedLabel) {
+ // update metadata
+ nlohmann::ordered_json jsonblob = this->label()->toJson()["Root"];
+ nlohmann::ordered_json jsonOut;
+ // std::cout << jsonblob << std::endl;
+ for (auto& [key, val] : jsonblob.items()) {
+ if (!val.contains("Bytes") || key == "Label") {
+ jsonOut[key] = val;
+ }
+ }
+ std::string jsonblobstr = jsonOut.dump();
+ std::string name = "CubeLabel";
+ gdalDataset()->SetMetadataItem(name.c_str(), jsonblobstr.c_str(), "USGS");
+ return;
+ }
// Set the pvl's format template
m_label->setFormatTemplate(m_formatTemplateFile->original());
// Write them with attached data
- if (m_attached) {
+ if (labelsAttached() != LabelAttachment::DetachedLabel) {
QMutexLocker locker(m_mutex);
QMutexLocker locker2(m_ioHandler->dataFileMutex());
ostringstream temp;
temp << *m_label << endl;
string tempstr = temp.str();
- if ((int) tempstr.length() < m_labelBytes) {
+ if ((int) tempstr.length() <= m_labelBytes) {
QByteArray labelArea(m_labelBytes, '\0');
QByteArray labelUnpaddedContents(tempstr.c_str(), tempstr.length());
labelArea.replace(0, labelUnpaddedContents.size(), labelUnpaddedContents);
@@ -2667,4 +3070,17 @@ namespace Isis {
m_label->write(m_labelFileName->expanded());
}
}
+
+ void Cube::initLabelState(const Pvl &label) {
+ const PvlObject &core = label.findObject("IsisCube").findObject("Core");
+ LabelAttachment attachmentStyle = AttachedLabel;
+ if (core.hasKeyword("^DnFile")) {
+ attachmentStyle = ExternalLabel;
+ }
+ else if (core.hasKeyword("^Core")) {
+ attachmentStyle = DetachedLabel;
+ }
+
+ setLabelsAttached(attachmentStyle);
+ }
}
diff --git a/isis/src/base/objs/Cube/Cube.h b/isis/src/base/objs/Cube/Cube.h
index 32d234367c1ceb7dac2c7909d11a4ed8eb0b33dd..6e28110aa48c659a3d81c6393ade6a323959473b 100644
--- a/isis/src/base/objs/Cube/Cube.h
+++ b/isis/src/base/objs/Cube/Cube.h
@@ -30,9 +30,9 @@ namespace Isis {
class Camera;
class CubeAttributeOutput;
class CubeCachingAlgorithm;
- class CubeIoHandler;
class CubeStretch;
class FileName;
+ class ImageIoHandler;
class Projection;
class Pvl;
class PvlGroup;
@@ -230,7 +230,29 @@ namespace Isis {
* The symbol '*' denotes tile boundaries.
* The symbols '-' and '|' denote cube boundaries.
*/
- Tile
+ Tile,
+ GTiff
+ };
+
+ /**
+ * @brief Input cube label type tracker
+ *
+ * This enumeration and its functions are for the label
+ * type of an input cube. The enum defines the type of labels (i.e.,
+ * Both the label and cube are in the same file and the label is in a
+ * separate file from the cube.
+ */
+ enum LabelAttachment {
+ AttachedLabel, //!< The input label is embedded in the image file
+ DetachedLabel, //!< The input label is in a separate data file from the image
+ /**
+ * The label is pointing to an external DN file - the label is also external to the data.
+ *
+ * This format implies that the output is a cube that contains everything except DN data
+ * (more similar to attached than detached).
+ */
+ ExternalLabel,
+ GdalLabel
};
void fromIsd(const FileName &fileName, Pvl &label, nlohmann::json &isd, QString access);
@@ -242,7 +264,7 @@ namespace Isis {
bool isProjected() const;
bool isReadOnly() const;
bool isReadWrite() const;
- bool labelsAttached() const;
+ LabelAttachment labelsAttached() const;
void attachSpiceFromIsd(nlohmann::json Isd);
void attachLineScanTableFromIsd(nlohmann::json isd);
@@ -251,7 +273,11 @@ namespace Isis {
Cube *copy(FileName newFile, const CubeAttributeOutput &newFileAttributes);
void create(const QString &cfile);
void create(const QString &cfile, const CubeAttributeOutput &att);
+ void createGdal(QString &dataFileName, QString &, char **papszOptions);
+ void checkAccess(QString access);
void open(const QString &cfile, QString access = "r");
+ void openCube(const QString &cubeFileName, QString access);
+ void openGdal(const QString &cubeFileName, QString access);
void reopen(QString access = "r");
void read(Blob &blob,
@@ -279,7 +305,8 @@ namespace Isis {
void setDimensions(int ns, int nl, int nb);
void setExternalDnData(FileName cubeFileWithDnData);
void setFormat(Format format);
- void setLabelsAttached(bool attached);
+ void setLabelsAttached(LabelAttachment attached);
+ // void setLabelsExternal(bool external);
void setLabelSize(int labelBytes);
void setPixelType(PixelType pixelType);
void setVirtualBands(const QList<QString> &vbands);
@@ -313,7 +340,6 @@ namespace Isis {
Statistics *statistics(const int &band, const double &validMin,
const double &validMax,
QString msg = "Gathering statistics");
- bool storesDnData() const;
void addCachingAlgorithm(CubeCachingAlgorithm *);
void clearIoCache();
@@ -334,9 +360,12 @@ namespace Isis {
void construct();
QFile *dataFile() const;
+ GDALDataset *gdalDataset() const;
void initialize();
void initCoreFromLabel(const Pvl &label);
+ void initCoreFromGdal(const QString &labelFile);
+ void initLabelState(const Pvl &label);
void initLabelFromFile(FileName labelFileName, bool readWrite);
void openCheck();
Pvl realDataFileLabel() const;
@@ -353,6 +382,7 @@ namespace Isis {
* If isOpen() is true, then this is allocated.
*/
QFile *m_labelFile;
+
/**
* This is only sometimes allocated. This is used for when IsOpen is true
* and labels are detached so the QFile for the labels does not give
@@ -360,11 +390,16 @@ namespace Isis {
*/
QFile *m_dataFile;
+ /**
+ * TODO: Write description
+ */
+ GDALDataset *m_geodataSet = nullptr;
+
/**
* This does the heavy lifting for cube DN IO and is always allocated
* when isOpen() is true.
*/
- CubeIoHandler *m_ioHandler;
+ ImageIoHandler *m_ioHandler;
/**
* The byte order of the opened cube; if there is no open cube then
@@ -413,14 +448,7 @@ namespace Isis {
FileName *m_formatTemplateFile;
//! True if labels are attached
- bool m_attached;
-
- /**
- * True (most common case) when the cube DN data is inside the file we're writing to. False
- * means we're referencing another cube's internal DN data for reading, and writing buffers
- * is disallowed.
- */
- bool m_storesDnData;
+ LabelAttachment m_attached;
//! The label if IsOpen(), otherwise NULL
Pvl *m_label;
diff --git a/isis/src/base/objs/Cube/CubeIoHandler.cpp b/isis/src/base/objs/Cube/CubeIoHandler.cpp
index f94d0755539e25fa853bb45a619ed11fd8e903b1..de8c20c97c1441233b48a8a5a4361c7d3a5e365d 100644
--- a/isis/src/base/objs/Cube/CubeIoHandler.cpp
+++ b/isis/src/base/objs/Cube/CubeIoHandler.cpp
@@ -59,17 +59,16 @@ namespace Isis {
* initialized into the file before this object is destructed.
*/
CubeIoHandler::CubeIoHandler(QFile * dataFile,
- const QList<int> *virtualBandList, const Pvl &label, bool alreadyOnDisk) {
+ const QList<int> *virtualBandList, const Pvl &label, bool alreadyOnDisk) :
+ ImageIoHandler(virtualBandList) {
m_byteSwapper = NULL;
m_cachingAlgorithms = NULL;
m_dataIsOnDiskMap = NULL;
m_rawData = NULL;
- m_virtualBands = NULL;
m_nullChunkData = NULL;
m_lastProcessByLineChunks = NULL;
m_writeCache = NULL;
m_ioThreadPool = NULL;
- m_writeThreadMutex = NULL;
try {
if (!dataFile) {
@@ -134,8 +133,6 @@ namespace Isis {
if(!alreadyOnDisk) {
m_dataIsOnDiskMap = new QMap<int, bool>;
}
-
- setVirtualBands(virtualBandList);
}
catch(IException &e) {
IString msg = "Constructing CubeIoHandler failed";
@@ -201,17 +198,11 @@ namespace Isis {
delete m_byteSwapper;
m_byteSwapper = NULL;
- delete m_virtualBands;
- m_virtualBands = NULL;
-
delete m_nullChunkData;
m_nullChunkData = NULL;
delete m_lastProcessByLineChunks;
m_lastProcessByLineChunks = NULL;
-
- delete m_writeThreadMutex;
- m_writeThreadMutex = NULL;
}
@@ -425,37 +416,6 @@ namespace Isis {
(BigInt)getBytesPerChunk();
}
-
- /**
- * This changes the virtual band list.
- *
- * @param virtualBandList A list where the indices are the vbands and the
- * values are the physical bands. The values are 1-based. This can
- * be specified as NULL, in which case the vbands are the physical
- * bands. The virtual band list is copied
- * (the pointer provided isn't remembered).
- */
- void CubeIoHandler::setVirtualBands(const QList<int> *virtualBandList) {
- if(m_virtualBands) {
- delete m_virtualBands;
- m_virtualBands = NULL;
- }
-
- if(virtualBandList && !virtualBandList->empty())
- m_virtualBands = new QList<int>(*virtualBandList);
- }
-
- /**
- * Get the mutex that this IO handler is using around I/Os on the given
- * data file. A lock should be acquired before doing any reads/writes on
- * the data file externally.
- *
- * @return A mutex that can guarantee exclusive access to the data file
- */
- QMutex *CubeIoHandler::dataFileMutex() {
- return m_writeThreadMutex;
- }
-
/**
* @return the number of physical bands in the cube.
*/
@@ -920,10 +880,10 @@ namespace Isis {
startX = max(cube1.getStartSample(), cube2.Sample());
startY = max(cube1.getStartLine(), cube2.Line());
startZ = max(cube1.getStartBand(), startPhysicalBand);
- endX = min(cube1.getStartSample() + cube1.sampleCount() - 1,
- cube2.Sample() + cube2.SampleDimension() - 1);
- endY = min(cube1.getStartLine() + cube1.lineCount() - 1,
- cube2.Line() + cube2.LineDimension() - 1);
+ endX = min(cube1.getStartSample() + cube1.sampleCount(),
+ cube2.Sample() + cube2.SampleDimension());
+ endY = min(cube1.getStartLine() + cube1.lineCount(),
+ cube2.Line() + cube2.LineDimension());
endZ = min(cube1.getStartBand() + cube1.bandCount() - 1,
endPhysicalBand);
}
@@ -1379,6 +1339,11 @@ namespace Isis {
const char *chunkBuf = chunk.getRawData().data();
char *buffersRawBuf = (char *)output.RawBuffer();
+
+ // Scale the sampleand line increment, only necessary in read for Q apps
+ int lineIncrement = (double)output.LineDimension() / (double)output.LineDimensionScaled();
+ int sampleIncrement = (double)output.SampleDimension() / (double)output.SampleDimensionScaled();
+
for(int z = startZ; z <= endZ; z++) {
const int &bandIntoChunk = z - chunkStartBand;
int virtualBand = z;
@@ -1388,12 +1353,16 @@ namespace Isis {
if(virtualBand != 0 && virtualBand >= bufferBand &&
virtualBand <= bufferBand + bufferBands - 1) {
- for(int y = startY; y <= endY; y++) {
+ for(int y = startY; y < endY; y = y + lineIncrement) {
const int &lineIntoChunk = y - chunkStartLine;
- int bufferIndex = output.Index(startX, y, virtualBand);
- for(int x = startX; x <= endX; x++) {
+ for(int x = startX; x < endX; x = x + sampleIncrement) {
const int &sampleIntoChunk = x - chunkStartSample;
+ int bufferIndex = output.Index(x, y, virtualBand);
+ // Avoid rolling back onto your buffer
+ if (bufferIndex >= output.size()) {
+ bufferIndex = output.size() - 1;
+ }
const int &chunkIndex = sampleIntoChunk +
(chunkLineSize * lineIntoChunk) +
@@ -1534,7 +1503,7 @@ namespace Isis {
((unsigned char *)buffersRawBuf)[bufferIndex] = raw;
}
- bufferIndex ++;
+ bufferIndex++;
}
}
}
@@ -1590,11 +1559,11 @@ namespace Isis {
if(virtualBand != 0 && virtualBand >= bufferBand &&
virtualBand <= bufferBand + bufferBands - 1) {
- for(int y = startY; y <= endY; y++) {
+ for(int y = startY; y < endY; y++) {
const int &lineIntoChunk = y - outputStartLine;
int bufferIndex = buffer.Index(startX, y, virtualBand);
- for(int x = startX; x <= endX; x++) {
+ for(int x = startX; x < endX; x++) {
const int &sampleIntoChunk = x - outputStartSample;
const int &chunkIndex = sampleIntoChunk +
diff --git a/isis/src/base/objs/Cube/CubeIoHandler.h b/isis/src/base/objs/Cube/CubeIoHandler.h
index a5114ec4fea3cd065c1734be1ae24480bf2944ae..69ce20435e3c04fc9e8a3363379517e56d26c0ac 100644
--- a/isis/src/base/objs/Cube/CubeIoHandler.h
+++ b/isis/src/base/objs/Cube/CubeIoHandler.h
@@ -13,6 +13,7 @@ find files of those names at the top level of this repository. **/
#include "Constants.h"
#include "Endian.h"
+#include "ImageIoHandler.h"
#include "PixelType.h"
class QFile;
@@ -106,19 +107,18 @@ namespace Isis {
* @history 2018-08-13 Summer Stapleton - Fixed incoming buffer comparison values for
* unsigned int type in writeIntoRaw(...).
*/
- class CubeIoHandler {
+ class CubeIoHandler : public ImageIoHandler {
public:
CubeIoHandler(QFile * dataFile, const QList<int> *virtualBandList,
const Pvl &label, bool alreadyOnDisk);
virtual ~CubeIoHandler();
- void read(Buffer &bufferToFill) const;
- void write(const Buffer &bufferToWrite);
+ virtual void read(Buffer &bufferToFill) const;
+ virtual void write(const Buffer &bufferToWrite);
- void addCachingAlgorithm(CubeCachingAlgorithm *algorithm);
- void clearCache(bool blockForWriteCache = true) const;
- BigInt getDataSize() const;
- void setVirtualBands(const QList<int> *virtualBandList);
+ virtual void addCachingAlgorithm(CubeCachingAlgorithm *algorithm);
+ virtual void clearCache(bool blockForWriteCache = true) const;
+ virtual BigInt getDataSize() const;
/**
* Function to update the labels with a Pvl object
*
@@ -126,7 +126,6 @@ namespace Isis {
*/
virtual void updateLabels(Pvl &labels) = 0;
- QMutex *dataFileMutex();
int bandCount() const;
int getBandCountInChunk() const;
BigInt getBytesPerChunk() const;
@@ -310,8 +309,6 @@ namespace Isis {
//! The map from chunk index to on-disk status, all true if not allocated.
mutable QMap<int, bool> * m_dataIsOnDiskMap;
- //! Converts from virtual band to physical band.
- QList<int> * m_virtualBands;
//! The number of samples in a cube chunk.
int m_samplesInChunk;
@@ -352,9 +349,6 @@ namespace Isis {
*/
bool m_useOptimizedCubeWrite;
- //! This enables us to block while the write thread is working
- QMutex *m_writeThreadMutex;
-
//! Ideal write cache flush size
mutable volatile int m_idealFlushSize;
diff --git a/isis/src/base/objs/CubeAttribute/CubeAttribute.cpp b/isis/src/base/objs/CubeAttribute/CubeAttribute.cpp
index 1402990f611d940a2a8ed8e5c236fd8c11e26757..f1d8b400db4e19449cf625e61db25850263265b2 100644
--- a/isis/src/base/objs/CubeAttribute/CubeAttribute.cpp
+++ b/isis/src/base/objs/CubeAttribute/CubeAttribute.cpp
@@ -274,6 +274,9 @@ namespace Isis {
if (formatString == "BSQ" || formatString == "BANDSEQUENTIAL")
result = Cube::Bsq;
+ else if(formatString == "GTIFF") {
+ result = Cube::GTiff;
+ }
}
return result;
@@ -286,8 +289,19 @@ namespace Isis {
void CubeAttributeOutput::setFileFormat(Cube::Format fmt) {
- setAttribute((fmt == Cube::Tile)? "Tile" : "BandSequential",
- &CubeAttributeOutput::isFileFormat);
+ if (fmt == Cube::Tile) {
+ setAttribute("Tile", &CubeAttributeOutput::isFileFormat);
+ }
+ else if (fmt == Cube::Bsq) {
+ setAttribute("BandSequential", &CubeAttributeOutput::isFileFormat);
+ }
+ else if (fmt == Cube::GTiff) {
+ setAttribute("GTiff", &CubeAttributeOutput::isFileFormat);
+ }
+ else {
+ QString msg = "Unsupported format [" + toString(fmt) + "]";
+ IException(IException::Programmer, msg, _FILEINFO_);
+ }
}
@@ -392,22 +406,22 @@ namespace Isis {
}
- void CubeAttributeOutput::setLabelAttachment(LabelAttachment attachment) {
+ void CubeAttributeOutput::setLabelAttachment(Cube::LabelAttachment attachment) {
setAttribute(LabelAttachmentName(attachment), &CubeAttributeOutput::isLabelAttachment);
}
- LabelAttachment CubeAttributeOutput::labelAttachment() const {
- LabelAttachment result = AttachedLabel;
+ Cube::LabelAttachment CubeAttributeOutput::labelAttachment() const {
+ Cube::LabelAttachment result = Cube::AttachedLabel;
QStringList labelAttachmentAtts = attributeList(&CubeAttributeOutput::isLabelAttachment);
if (!labelAttachmentAtts.isEmpty()) {
QString labelAttachmentAtt = labelAttachmentAtts.last();
if (labelAttachmentAtt == "DETACHED")
- result = DetachedLabel;
+ result = Cube::DetachedLabel;
else if (labelAttachmentAtt == "EXTERNAL")
- result = ExternalLabel;
+ result = Cube::ExternalLabel;
}
return result;
@@ -420,7 +434,7 @@ namespace Isis {
bool CubeAttributeOutput::isFileFormat(QString attribute) const {
- return QRegExp("(BANDSEQUENTIAL|BSQ|TILE)").exactMatch(attribute);
+ return QRegExp("(BANDSEQUENTIAL|BSQ|TILE|GTIFF)").exactMatch(attribute);
}
@@ -443,10 +457,21 @@ namespace Isis {
QString CubeAttributeOutput::toString(Cube::Format format) {
- QString result = "Tile";
+ QString result;
- if (format == Cube::Bsq)
+ if (format == Cube::Tile) {
+ result = "Tile";
+ }
+ else if (format == Cube::Bsq) {
result = "BandSequential";
+ }
+ else if (format == Cube::GTiff) {
+ result = "GTiff";
+ }
+ else {
+ QString msg = "Format [" + QString::number(format) + "] cannot be translated to string";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
return result;
}
diff --git a/isis/src/base/objs/CubeAttribute/CubeAttribute.h b/isis/src/base/objs/CubeAttribute/CubeAttribute.h
index 28684c4a5a7729ef21908d8bf2104e179b5b5c60..5736d1ac21651cbc31400bde5382303e40410412 100644
--- a/isis/src/base/objs/CubeAttribute/CubeAttribute.h
+++ b/isis/src/base/objs/CubeAttribute/CubeAttribute.h
@@ -20,27 +20,6 @@ find files of those names at the top level of this repository. **/
namespace Isis {
- /**
- * @brief Input cube label type tracker
- *
- * This enumeration and its functions are for the label
- * type of an input cube. The enum defines the type of labels (i.e.,
- * Both the label and cube are in the same file and the label is in a
- * separate file from the cube.
- */
- enum LabelAttachment {
- AttachedLabel, //!< The input label is embedded in the image file
- DetachedLabel, //!< The input label is in a separate data file from the image
- /**
- * The label is pointing to an external DN file - the label is also external to the data.
- *
- * This format implies that the output is a cube that contains everything except DN data
- * (more similar to attached than detached).
- */
- ExternalLabel
- };
-
-
/**
* Return the string representation of the contents of a
* variable of type LabelAttachment
@@ -49,10 +28,11 @@ namespace Isis {
*
* @return A string representation of the parameter
*/
- inline QString LabelAttachmentName(LabelAttachment labelType) {
- if(labelType == AttachedLabel) return "Attached";
- if(labelType == DetachedLabel) return "Detached";
- if(labelType == ExternalLabel) return "External";
+ inline QString LabelAttachmentName(Cube::LabelAttachment labelType) {
+ if(labelType == Cube::AttachedLabel) return "Attached";
+ if(labelType == Cube::DetachedLabel) return "Detached";
+ if(labelType == Cube::ExternalLabel) return "External";
+ if(labelType == Cube::GdalLabel) return "Gdal";
QString msg = "Invalid label attachment type [" + QString::number(labelType) + "]";
throw IException(IException::Programmer, msg, _FILEINFO_);
@@ -67,18 +47,17 @@ namespace Isis {
*
* @return The RangeType enum corresponding to the string parameter
*/
- inline LabelAttachment LabelAttachmentEnumeration(const QString &labelType) {
+ inline Cube::LabelAttachment LabelAttachmentEnumeration(const QString &labelType) {
QString temp = labelType.toUpper();
- if(temp == "ATTACHED") return AttachedLabel;
- if(temp == "DETACHED") return DetachedLabel;
- if(temp == "External") return ExternalLabel;
+ if(temp == "ATTACHED") return Cube::AttachedLabel;
+ if(temp == "DETACHED") return Cube::DetachedLabel;
+ if(temp == "EXTERNAL") return Cube::ExternalLabel;
+ if(temp == "GDAL") return Cube::GdalLabel;
QString msg = "Invalid label attachment type string [" + labelType + "]";
throw IException(IException::Unknown, msg, _FILEINFO_);
}
-
-
/**
* @brief Parent class for CubeAttributeInput and CubeAttributeOutput.
*
@@ -539,9 +518,9 @@ namespace Isis {
void setPixelType(PixelType type);
//! Set the label attachment type to the parameter value
- void setLabelAttachment(LabelAttachment attachment);
+ void setLabelAttachment(Cube::LabelAttachment attachment);
- LabelAttachment labelAttachment() const;
+ Cube::LabelAttachment labelAttachment() const;
using CubeAttribute<CubeAttributeOutput>::toString;
diff --git a/isis/src/base/objs/CubeAttribute/unitTest.cpp b/isis/src/base/objs/CubeAttribute/unitTest.cpp
index 1892e65209b2e7cdf2585023dae63b4a9c9ac6dc..d4832be86986dea6cee638843ceb7680f848899f 100644
--- a/isis/src/base/objs/CubeAttribute/unitTest.cpp
+++ b/isis/src/base/objs/CubeAttribute/unitTest.cpp
@@ -205,10 +205,10 @@ int main(int argc, char *argv[]) {
att.setPixelType(Real);
cout << att.toString() << endl;
- att.setLabelAttachment(DetachedLabel);
+ att.setLabelAttachment(Cube::DetachedLabel);
cout << att.toString() << endl;
- att.setLabelAttachment(ExternalLabel);
+ att.setLabelAttachment(Cube::ExternalLabel);
cout << att.toString() << endl;
}
catch (IException &e) {
@@ -300,8 +300,8 @@ void reportOutput(const CubeAttributeOutput &att, QString orderHint) {
}
cout << "Label attachment = ";
- if(att.labelAttachment() == AttachedLabel) cout << LabelAttachmentName(AttachedLabel) << endl;
- if(att.labelAttachment() == DetachedLabel) cout << LabelAttachmentName(DetachedLabel) << endl;
+ if(att.labelAttachment() == Cube::AttachedLabel) cout << LabelAttachmentName(Cube::AttachedLabel) << endl;
+ if(att.labelAttachment() == Cube::DetachedLabel) cout << LabelAttachmentName(Cube::DetachedLabel) << endl;
#if 0
fstream stream("CubeAttribute.truth", ios::in | ios::out);
diff --git a/isis/src/base/objs/CubeDataThread/CubeDataThread.cpp b/isis/src/base/objs/CubeDataThread/CubeDataThread.cpp
index d566ea8a4a1c839901c0d0d8fe5421d4b8d1d786..ed835e4283cb65ed2f975092a86d2ae50c8a09c2 100644
--- a/isis/src/base/objs/CubeDataThread/CubeDataThread.cpp
+++ b/isis/src/base/objs/CubeDataThread/CubeDataThread.cpp
@@ -255,13 +255,13 @@ namespace Isis {
* @param sharedLock True if read-only, false if read-write
*/
void CubeDataThread::GetCubeData(int cubeId, int ss, int sl, int es, int el,
- int band, void *caller, bool sharedLock) {
+ int band, void *caller, bool sharedLock, double scale) {
Brick *requestedBrick = NULL;
p_threadSafeMutex->lock();
requestedBrick = new Brick(*p_managedCubes->value(cubeId).second, es
- - ss + 1, el - sl + 1, 1);
+ - ss + 1, (el - sl + 1) / scale, 1, false, scale);
requestedBrick->SetBasePosition(ss, sl, band);
p_threadSafeMutex->unlock();
@@ -425,7 +425,7 @@ namespace Isis {
*/
void CubeDataThread::ReadCube(int cubeId, int startSample, int startLine,
int endSample, int endLine, int band,
- void *caller) {
+ void *caller, double scale) {
if(!p_managedCubes->contains(cubeId)) {
IString msg = "cube ID [";
@@ -434,8 +434,12 @@ namespace Isis {
throw IException(IException::Programmer, msg, _FILEINFO_);
}
+ if (scale > 1) {
+ scale = 1.0;
+ }
+
GetCubeData(cubeId, startSample, startLine, endSample, endLine, band,
- caller, true);
+ caller, true, scale);
}
/**
@@ -469,7 +473,7 @@ namespace Isis {
}
GetCubeData(cubeId, startSample, startLine, endSample, endLine, band,
- caller, false);
+ caller, false, 1);
}
/**
diff --git a/isis/src/base/objs/CubeDataThread/CubeDataThread.h b/isis/src/base/objs/CubeDataThread/CubeDataThread.h
index 4c3af01b7145364089a69016593eb760c17bbb19..94f2a1530e30a053c321d23c2abd0bf958d459f3 100644
--- a/isis/src/base/objs/CubeDataThread/CubeDataThread.h
+++ b/isis/src/base/objs/CubeDataThread/CubeDataThread.h
@@ -81,7 +81,7 @@ namespace Isis {
public slots:
void ReadCube(int cubeId, int startSample, int startLine,
- int endSample, int endLine, int band, void *caller);
+ int endSample, int endLine, int band, void *caller, double scale);
void ReadWriteCube(int cubeId, int startSample, int startLine,
int endSample, int endLine, int band, void *caller);
@@ -155,7 +155,7 @@ namespace Isis {
int instanceNum, bool &exact);
void GetCubeData(int cubeId, int ss, int sl, int es, int el, int band,
- void *caller, bool sharedLock);
+ void *caller, bool sharedLock, double scale=1);
void AcquireLock(QReadWriteLock *lockObject, bool readLock);
diff --git a/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.cpp b/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.cpp
index 8399b3bcef12decb1f7040af7ebf2bcb427776f8..50276bf5239e906bfd218dd0d7454dcd6a09b841 100644
--- a/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.cpp
+++ b/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.cpp
@@ -51,9 +51,9 @@ namespace Isis {
*/
void CubeDataThreadTester::Connect() {
connect(this,
- SIGNAL(RequestReadCube(int, int, int, int, int, int, void *)),
+ SIGNAL(RequestReadCube(int, int, int, int, int, int, void *, double)),
p_cubeDataThread,
- SLOT(ReadCube(int, int, int, int, int, int, void *)));
+ SLOT(ReadCube(int, int, int, int, int, int, void *, double)));
connect(this,
SIGNAL(RequestReadWriteCube(int, int, int, int, int, int, void *)),
@@ -98,7 +98,7 @@ namespace Isis {
*/
void CubeDataThreadTester::ReadCubeTest(int cubeId) {
cout << "=============== Testing Basic Read ===============" << endl;
- emit RequestReadCube(cubeId, 1, 1, 2, 2, 1, this);
+ emit RequestReadCube(cubeId, 1, 1, 2, 2, 1, this, 1.0);
}
@@ -113,8 +113,8 @@ namespace Isis {
"===============" << endl;
p_notifyDone = false;
- emit RequestReadCube(cubeId1, 1, 1, 3, 2, 1, this);
- emit RequestReadCube(cubeId2, 1, 2, 3, 2, 1, this);
+ emit RequestReadCube(cubeId1, 1, 1, 3, 2, 1, this, 1.0);
+ emit RequestReadCube(cubeId2, 1, 2, 3, 2, 1, this, 1.0);
}
@@ -128,8 +128,8 @@ namespace Isis {
<< endl << endl;
p_notifyDone = false;
- emit RequestReadCube(cubeId, 1, 2, 2, 2, 1, this);
- emit RequestReadCube(cubeId, 1, 2, 2, 2, 1, this);
+ emit RequestReadCube(cubeId, 1, 2, 2, 2, 1, this, 1.0);
+ emit RequestReadCube(cubeId, 1, 2, 2, 2, 1, this, 1.0);
}
@@ -141,7 +141,7 @@ namespace Isis {
void CubeDataThreadTester::WriteCubeTest(int cubeId) {
cout << "=============== Testing Basic R/W ===============" << endl << endl;
emit RequestReadWriteCube(cubeId, 1, 1, 2, 2, 1, this);
- emit RequestReadCube(cubeId, 1, 1, 2, 2, 1, this);
+ emit RequestReadCube(cubeId, 1, 1, 2, 2, 1, this, 1.0);
}
diff --git a/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.h b/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.h
index 8134df48d7919991bb52be105279ce6a4e93f77c..04c6d85334989e12b8f06050b8ed7d1ef5478029 100644
--- a/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.h
+++ b/isis/src/base/objs/CubeDataThread/CubeDataThreadTester.h
@@ -67,7 +67,7 @@ namespace Isis {
* @param caller A this pointer
*/
void RequestReadCube(int cubeId, int startSample, int startLine,
- int endSample, int endLine, int band, void *caller);
+ int endSample, int endLine, int band, void *caller, double scale);
/**
diff --git a/isis/src/base/objs/CubeManager/CubeManager.truth b/isis/src/base/objs/CubeManager/CubeManager.truth
index 064d543ea9667cfd50b0fa59e0e228d116185e1f..0465b4a2f5f975f04ae65eee8da6f2f67273c584 100644
--- a/isis/src/base/objs/CubeManager/CubeManager.truth
+++ b/isis/src/base/objs/CubeManager/CubeManager.truth
@@ -49,4 +49,6 @@ Verify isisTruth2.cub is now managed and limit of 2 is enforced:
Setting number of open cubes > 60 percent of system open file limit
Attempting to open a file that does not exist:
- **I/O ERROR** Unable to open [dne.cub].
+ **I/O ERROR** Failed to open [dne.cub].
+**PROGRAMMER ERROR** Gdal failed to open [dne.cub].
+**I/O ERROR** Unable to open [dne.cub].
diff --git a/isis/src/base/objs/EquatorialCylindricalShape/EquatorialCylindricalShape.cpp b/isis/src/base/objs/EquatorialCylindricalShape/EquatorialCylindricalShape.cpp
index ba969599db46b231beaf5b1a58ee31cfa3c9b679..777c5ee2d9858a0ae3c3abf204ac1fdb50ffa211 100644
--- a/isis/src/base/objs/EquatorialCylindricalShape/EquatorialCylindricalShape.cpp
+++ b/isis/src/base/objs/EquatorialCylindricalShape/EquatorialCylindricalShape.cpp
@@ -32,8 +32,6 @@ find files of those names at the top level of this repository. **/
using namespace std;
-#define MAX(x,y) (((x) > (y)) ? (x) : (y))
-
namespace Isis {
/**
* Initialize the ISIS Equatorial Cylindrical shape model.
@@ -222,7 +220,7 @@ namespace Isis {
// Set dalpha to be half the grid spacing for nyquist sampling
//double dalpha = (PI/180.0)/(2.0*p_demScale);
double cmin = cos((90.0 - 1.0 / (2.0 * demScale())) * DEG2RAD);
- double dalpha = MAX(cos(g1lat * DEG2RAD), cmin) / (2.0 * demScale() * RAD2DEG);
+ double dalpha = std::max(cos(g1lat * DEG2RAD), cmin) / (2.0 * demScale() * RAD2DEG);
// Previous Sensor version used local version of this method with lat and lon doubles. Steven said
// it didn't make a significant difference in speed.
@@ -390,7 +388,7 @@ namespace Isis {
// put in a test (above) for dd being smaller than the pixel
// convergence tolerance. If so the loop exits without an
// intersection
- dalpha = MAX(cos(g2lat * DEG2RAD), cmin) / (2.0 * demScale() * RAD2DEG);
+ dalpha = std::max(cos(g2lat * DEG2RAD), cmin) / (2.0 * demScale() * RAD2DEG);
} // end while
SpiceDouble intersectionPoint[3];
diff --git a/isis/src/base/objs/FileName/FileName.cpp b/isis/src/base/objs/FileName/FileName.cpp
index 425e0801a5af08f81bd93a3e6e4e6c10e21632f4..0ef719ced72f6b2edcfa22fada8efd3bfc6ecd9e 100644
--- a/isis/src/base/objs/FileName/FileName.cpp
+++ b/isis/src/base/objs/FileName/FileName.cpp
@@ -447,6 +447,9 @@ namespace Isis {
* @return Boolean
*/
bool FileName::fileExists() const {
+ if (toString().contains((QString)"https://")) {
+ return true;
+ }
return QFileInfo(expanded()).exists();
}
diff --git a/isis/src/base/objs/Gui/GuiOutputAttribute.cpp b/isis/src/base/objs/Gui/GuiOutputAttribute.cpp
index cff2ed9119b7e9dd7b4964080ba741b614eff2cc..04579559bb8d43fac8450928b53428be9a208cd7 100644
--- a/isis/src/base/objs/Gui/GuiOutputAttribute.cpp
+++ b/isis/src/base/objs/Gui/GuiOutputAttribute.cpp
@@ -244,7 +244,7 @@ namespace Isis {
p_msb->setChecked(true);
}
- if(att.labelAttachment() == AttachedLabel) {
+ if(att.labelAttachment() == Cube::AttachedLabel) {
p_attached->setChecked(true);
}
else {
diff --git a/isis/src/base/objs/IException/IException.cpp b/isis/src/base/objs/IException/IException.cpp
index cd42a87e53b18b1ac4f9860edbad56a63c225300..aa79d36efb16766f722eebaffd7865649bc297df 100644
--- a/isis/src/base/objs/IException/IException.cpp
+++ b/isis/src/base/objs/IException/IException.cpp
@@ -639,6 +639,10 @@ namespace Isis {
return *this;
}
+ int IException::length() {
+ return m_previousExceptions->length();
+ }
+
/**
* Returns the source of the error in string format for the given ErrorType.
diff --git a/isis/src/base/objs/IException/IException.h b/isis/src/base/objs/IException/IException.h
index 17c0c84fac20db572b8a62ed53fec208687f104f..f78f00f4913f99ff48939e9bed57a7af17d8b5f5 100644
--- a/isis/src/base/objs/IException/IException.h
+++ b/isis/src/base/objs/IException/IException.h
@@ -197,6 +197,8 @@ namespace Isis {
void swap(IException &other);
IException &operator=(const IException &rhs);
+ int length();
+
private:
static IException createStackTrace();
static ErrorType stringToErrorType(const QString &s);
diff --git a/isis/src/base/objs/ImageIoHandler/GdalIoHandler.cpp b/isis/src/base/objs/ImageIoHandler/GdalIoHandler.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a5af442c9d6c914654d6a7408d9257e8396524d5
--- /dev/null
+++ b/isis/src/base/objs/ImageIoHandler/GdalIoHandler.cpp
@@ -0,0 +1,873 @@
+#include "GdalIoHandler.h"
+
+#include "Brick.h"
+#include "Buffer.h"
+#include "CubeCachingAlgorithm.h"
+#include "IException.h"
+#include "Pvl.h"
+#include "PvlObject.h"
+#include "SpecialPixel.h"
+
+#include <QList>
+#include <QMutex>
+#include <QString>
+
+#include <iostream>
+
+using namespace std;
+
+namespace Isis {
+ GdalIoHandler::GdalIoHandler(QString &dataFilePath, const QList<int> *virtualBandList, GDALDataType pixelType, GDALAccess eAccess) :
+ ImageIoHandler(virtualBandList) {
+ GDALAllRegister();
+ m_geodataSetPath = dataFilePath.toUtf8().constData();
+ m_geodataSet = GDALDataset::FromHandle(GDALOpen(m_geodataSetPath.c_str(), eAccess));
+ m_datasetOwner = true;
+ m_pixelType = pixelType;
+ init();
+ }
+
+ GdalIoHandler::GdalIoHandler(GDALDataset *geodataSet, const QList<int> *virtualBandList, GDALDataType pixelType) :
+ ImageIoHandler(virtualBandList) {
+ m_geodataSet = geodataSet;
+ if (!m_geodataSet) {
+ QString msg = "Constructing GdalIoHandler failed. Null geodataSet pointer passed";
+ throw IException(IException::Programmer, msg, _FILEINFO_);
+ }
+ m_datasetOwner = false;
+ m_pixelType = pixelType;
+ init();
+ }
+
+ void GdalIoHandler::init() {
+ m_samples = m_geodataSet->GetRasterXSize();
+ m_lines = m_geodataSet->GetRasterYSize();
+ m_bands = m_geodataSet->GetRasterCount();
+
+ m_driverName = std::string(m_geodataSet->GetDriverName());
+
+ // Check if we need to create the mask band
+ if ((m_geodataSet->GetAccess() == GA_Update) && (m_driverName != "ISIS3")) {
+ m_geodataSet->CreateMaskBand(8);
+ m_geodataSet->GetRasterBand(1)->GetMaskBand()->Fill(255);
+ }
+
+ GDALRasterBand *band = m_geodataSet->GetRasterBand(1);
+ m_offset = band->GetOffset();
+ m_scale = band->GetScale();
+ int *pbSuccess = new int;
+ m_gdalNoDataValue = band->GetNoDataValue(pbSuccess);
+ if (!pbSuccess) {
+ m_gdalNoDataValue = NULL8;
+ }
+ delete pbSuccess;
+ }
+
+ GdalIoHandler::~GdalIoHandler() {
+ clearCache();
+ if (m_maskBuff) {
+ delete m_maskBuff;
+ }
+ if (m_geodataSet && m_datasetOwner) {
+ m_geodataSet->Close();
+ }
+ }
+
+ void GdalIoHandler::read(Buffer &bufferToFill) const {
+ GDALRasterBand *poBand;
+
+ bufferToFill = NULL8;
+ int maxBand = bufferToFill.BandDimension() + bufferToFill.Band() - 1;
+ for (int band = bufferToFill.Band(); band <= maxBand; band++) {
+ int vband = band;
+ if (m_virtualBands)
+ vband = m_virtualBands->at(band - 1);
+
+ if (vband > m_bands) {
+ return;
+ }
+
+ poBand = m_geodataSet->GetRasterBand(vband);
+
+ // Account for 1 based line and sample reading from ISIS process classes
+ // as gdal reads 0 based lines and samples
+ int lineStart = bufferToFill.Line() - 1;
+ int sampleStart = bufferToFill.Sample() - 1;
+ int lineSize = bufferToFill.LineDimension();
+ int sampleSize = bufferToFill.SampleDimension();
+
+ // Handle reading out of bound pixels as cube IO handler would
+ bool outOfBounds = false;
+ if (lineStart < 0) {
+ lineStart = 0;
+ outOfBounds = true;
+ }
+ if (lineStart + lineSize > m_lines) {
+ lineSize = m_lines - lineStart;
+ outOfBounds = true;
+ }
+ if (sampleStart < 0) {
+ sampleStart = 0;
+ outOfBounds = true;
+ }
+ if (sampleStart + sampleSize > m_samples) {
+ sampleSize = m_samples - sampleStart;
+ outOfBounds = true;
+ }
+
+ if (sampleSize > 0 && lineSize > 0) {
+ if (outOfBounds) {
+ Brick boundedBrick(sampleSize, lineSize, bufferToFill.BandDimension(), GdalPixelToIsis(m_pixelType), false, bufferToFill.scale());
+ boundedBrick.SetBasePosition(sampleStart + 1, lineStart + 1, bufferToFill.Band());
+ int bufferSize = boundedBrick.SampleDimensionScaled() * boundedBrick.LineDimensionScaled();
+ int currentBandIdx = bufferSize * (vband - boundedBrick.Band());
+ char *buffersRawBuf = &(((char *)boundedBrick.RawBuffer())[(int)(currentBandIdx * SizeOf(boundedBrick.PixelType()))]);
+ double *buffersDoubleBuf = &(boundedBrick.DoubleBuffer()[currentBandIdx]);
+ CPLErr err = poBand->RasterIO(GF_Read, sampleStart, lineStart,
+ sampleSize, lineSize,
+ buffersRawBuf,
+ boundedBrick.SampleDimensionScaled(), boundedBrick.LineDimensionScaled(),
+ m_pixelType,
+ 0, 0);
+
+ if (err >= CE_Failure) {
+ QString msg = "Failure when trying to read image";
+ throw IException(IException::Unknown, msg, _FILEINFO_);
+ }
+
+ // Handle pixel type conversion
+ for (int bufferIdx = 0; bufferIdx < bufferSize; bufferIdx++) {
+ readPixelType(buffersDoubleBuf, buffersRawBuf, bufferIdx);
+ }
+ bufferToFill.CopyOverlapFrom(boundedBrick);
+ }
+ else {
+ int bufferSize = bufferToFill.SampleDimensionScaled() * bufferToFill.LineDimensionScaled();;
+ int currentBandIdx = bufferSize * (vband - bufferToFill.Band());
+ // silence warnings
+ char *buffersRawBuf = &(((char *)bufferToFill.RawBuffer())[(int)(currentBandIdx * SizeOf(bufferToFill.PixelType()))]);
+ double *buffersDoubleBuf = &(bufferToFill.DoubleBuffer()[currentBandIdx]);
+ CPLErr err = poBand->RasterIO(GF_Read, sampleStart, lineStart,
+ sampleSize, lineSize,
+ buffersRawBuf,
+ bufferToFill.SampleDimensionScaled(), bufferToFill.LineDimensionScaled(),
+ m_pixelType,
+ 0, 0);
+ if (err >= CE_Failure) {
+ QString msg = "Failure when trying to read image";
+ throw IException(IException::Unknown, msg, _FILEINFO_);
+ }
+
+ // Handle pixel type conversion
+ for (int bufferIdx = 0; bufferIdx < bufferSize; bufferIdx++) {
+ readPixelType(buffersDoubleBuf, buffersRawBuf, bufferIdx);
+ }
+ }
+ }
+ }
+ }
+
+ void GdalIoHandler::write(const Buffer &bufferToWrite) {
+ CPLErr gdalerr;
+ GDALRasterBand *poBand;
+
+ int maxBand = bufferToWrite.BandDimension() + bufferToWrite.Band() - 1;
+ for (int band = bufferToWrite.Band(); band <= maxBand; band++) {
+ int vband = band;
+ if(m_virtualBands)
+ vband = m_virtualBands->indexOf(band) + 1;
+
+ if (band > m_bands) {
+ return;
+ }
+
+ poBand = m_geodataSet->GetRasterBand(vband);
+
+ int lineStart = bufferToWrite.Line() - 1;
+ int sampleStart = bufferToWrite.Sample() - 1;
+ int lineSize = bufferToWrite.LineDimension();
+ int sampleSize = bufferToWrite.SampleDimension();
+
+ if (lineStart < 0) {
+ lineStart = 0;
+ }
+ if (lineStart + lineSize > m_lines) {
+ lineSize = m_lines - lineStart;
+ }
+ if (sampleStart < 0) {
+ sampleStart = 0;
+ }
+ if (sampleStart + sampleSize > m_samples) {
+ sampleSize = m_samples - sampleStart;
+ }
+
+ int bufferSize = sampleSize * lineSize;
+ int currentBandIdx = bufferSize * (vband - bufferToWrite.Band());
+ m_maskBuff = (unsigned char *) CPLMalloc(sizeof(unsigned char) * bufferSize);
+ for (int i = 0; i < bufferSize; i++) {
+ m_maskBuff[i] = 255;
+ }
+
+
+ // Handle pixel type conversion
+ char *buffersRawBuf = &(((char *)bufferToWrite.RawBuffer())[(int)(currentBandIdx * SizeOf(bufferToWrite.PixelType()))]);
+ double *buffersDoubleBuf = &(bufferToWrite.DoubleBuffer()[currentBandIdx]);
+ // std::cout << buffersDoubleBuf[0] << std::endl;
+ for (int bufferIdx = 0; bufferIdx < bufferSize; bufferIdx++) {
+ if (writePixelType(buffersDoubleBuf, buffersRawBuf, bufferIdx)) {
+ m_maskBuff[bufferIdx] = 0;
+ };
+ }
+
+ // silence warning
+ gdalerr = poBand->RasterIO(GF_Write, sampleStart, lineStart,
+ sampleSize, lineSize,
+ (void *)buffersRawBuf,
+ sampleSize, lineSize,
+ m_pixelType,
+ 0, 0);
+ if (gdalerr >= CE_Failure) {
+ QString msg = "Failure when trying to write image";
+ throw IException(IException::Unknown, msg, _FILEINFO_);
+ }
+
+ if (m_driverName != "ISIS3") {
+ poBand = m_geodataSet->GetRasterBand(band)->GetMaskBand();
+ gdalerr = poBand->RasterIO(GF_Write, sampleStart, lineStart,
+ sampleSize, lineSize,
+ m_maskBuff,
+ sampleSize, lineSize,
+ GDT_Byte,
+ 0, 0);
+ if (gdalerr >= CE_Failure) {
+ QString msg = "Failure when trying to write msk file";
+ throw IException(IException::Unknown, msg, _FILEINFO_);
+ }
+ }
+ }
+
+ delete m_maskBuff;
+ m_maskBuff = NULL;
+ }
+
+ BigInt GdalIoHandler::getDataSize() const {
+ return 0;
+ }
+ /**
+ * Function to update the labels with a Pvl object
+ *
+ * @param labels Pvl object to update with
+ */
+ void GdalIoHandler::updateLabels(Pvl &labels) {
+ PvlObject &core = labels.findObject("IsisCube").findObject("Core");
+ core.addKeyword(PvlKeyword("Format", "GTiff"), PvlContainer::Replace);
+ }
+
+ void GdalIoHandler::readPixelType(double *doubleBuff, void *rawBuff, int idx) const {
+ double &bufferVal = doubleBuff[idx];
+
+ if (m_pixelType == GDT_Float64) {
+ bufferVal = ((double *)rawBuff)[idx];
+ if (bufferVal == m_gdalNoDataValue) {
+ bufferVal = NULL8;
+ }
+ }
+
+ else if(m_pixelType == GDT_Float32) {
+ float raw = ((float *)rawBuff)[idx];
+ // if(m_byteSwapper)
+ // raw = m_byteSwapper->Float(&raw);
+ if (raw == (float) m_gdalNoDataValue) {
+ raw = NULL4;
+ }
+
+ if(raw >= VALID_MIN4) {
+ bufferVal = (double) raw;
+ }
+ else {
+ if(raw == NULL4)
+ bufferVal = NULL8;
+ else if(raw == LOW_INSTR_SAT4)
+ bufferVal = LOW_INSTR_SAT8;
+ else if(raw == LOW_REPR_SAT4)
+ bufferVal = LOW_REPR_SAT8;
+ else if(raw == HIGH_INSTR_SAT4)
+ bufferVal = HIGH_INSTR_SAT8;
+ else if(raw == HIGH_REPR_SAT4)
+ bufferVal = HIGH_REPR_SAT8;
+ else
+ bufferVal = LOW_REPR_SAT8;
+ }
+
+ ((float *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Int32) {
+ int raw = ((int *)rawBuff)[idx];
+ // if(m_byteSwapper)
+ // raw = m_byteSwapper->Uint32_t(&raw);
+ if (raw == (int) m_gdalNoDataValue) {
+ raw = NULLI4;
+ }
+
+ if(raw >= VALID_MINI4) {
+ bufferVal = (double) raw * m_scale + m_offset;
+ }
+ else {
+ if (raw == NULLI4)
+ bufferVal = NULL8;
+ else if (raw == LOW_INSTR_SATI4)
+ bufferVal = LOW_INSTR_SAT8;
+ else if (raw == LOW_REPR_SATI4)
+ bufferVal = LOW_REPR_SAT8;
+ else if (raw == HIGH_INSTR_SATI4)
+ bufferVal = HIGH_INSTR_SAT8;
+ else if (raw == HIGH_REPR_SATI4)
+ bufferVal = HIGH_REPR_SAT8;
+ else
+ bufferVal = LOW_REPR_SAT8;
+ }
+ ((int *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_UInt32) {
+ unsigned int raw = ((unsigned int *)rawBuff)[idx];
+ // if(m_byteSwapper)
+ // raw = m_byteSwapper->Uint32_t(&raw);
+ if (raw == (unsigned int) m_gdalNoDataValue) {
+ raw = NULLUI4;
+ }
+
+ if(raw >= VALID_MINUI4) {
+ bufferVal = (double) raw * m_scale + m_offset;
+ if (raw >= VALID_MAXUI4) {
+ if(raw == HIGH_INSTR_SATUI4)
+ bufferVal = HIGH_INSTR_SAT8;
+ else if(raw == HIGH_REPR_SATUI4)
+ bufferVal = HIGH_REPR_SAT8;
+ else
+ bufferVal = HIGH_REPR_SAT8;
+ }
+ }
+ else {
+ if(raw == NULLUI4)
+ bufferVal = NULL8;
+ else if(raw == LOW_INSTR_SATUI4)
+ bufferVal = LOW_INSTR_SAT8;
+ else if(raw == LOW_REPR_SATUI4)
+ bufferVal = LOW_REPR_SAT8;
+ else
+ bufferVal = LOW_REPR_SAT8;
+ }
+ ((unsigned int *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Int16) {
+ short raw = ((short *)rawBuff)[idx];
+ // if(m_byteSwapper)
+ // raw = m_byteSwapper->ShortInt(&raw);
+ if (raw == (short) m_gdalNoDataValue) {
+ raw = NULL2;
+ }
+
+ if(raw >= VALID_MIN2) {
+ bufferVal = (double) raw * m_scale + m_offset;
+ }
+ else {
+ if(raw == NULL2)
+ bufferVal = NULL8;
+ else if(raw == LOW_INSTR_SAT2)
+ bufferVal = LOW_INSTR_SAT8;
+ else if(raw == LOW_REPR_SAT2)
+ bufferVal = LOW_REPR_SAT8;
+ else if(raw == HIGH_INSTR_SAT2)
+ bufferVal = HIGH_INSTR_SAT8;
+ else if(raw == HIGH_REPR_SAT2)
+ bufferVal = HIGH_REPR_SAT8;
+ else
+ bufferVal = LOW_REPR_SAT8;
+ }
+
+ ((short *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_UInt16) {
+ unsigned short raw = ((unsigned short *)rawBuff)[idx];
+ // if(m_byteSwapper)
+ // raw = m_byteSwapper->UnsignedShortInt(&raw);
+ if (raw == (unsigned short) m_gdalNoDataValue) {
+ raw = NULLU2;
+ }
+
+ if(raw >= VALID_MINU2) {
+ bufferVal = (double) raw * m_scale + m_offset;
+ if (raw > VALID_MAXU2) {
+ if(raw == HIGH_INSTR_SATU2)
+ bufferVal = HIGH_INSTR_SAT8;
+ else if(raw == HIGH_REPR_SATU2)
+ bufferVal = HIGH_REPR_SAT8;
+ else
+ bufferVal = HIGH_REPR_SAT8;
+ }
+ }
+ else {
+ if(raw == NULLU2)
+ bufferVal = NULL8;
+ else if(raw == LOW_INSTR_SATU2)
+ bufferVal = LOW_INSTR_SAT8;
+ else if(raw == LOW_REPR_SATU2)
+ bufferVal = LOW_REPR_SAT8;
+ else
+ bufferVal = LOW_REPR_SAT8;
+ }
+ ((unsigned short *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Int8) {
+ char raw = ((char *)rawBuff)[idx];
+ if (raw == (char) m_gdalNoDataValue) {
+ raw = NULLS1;
+ }
+
+ if(raw == NULLS1) {
+ bufferVal = NULL8;
+ }
+ else if(raw == HIGH_REPR_SATS1) {
+ bufferVal = HIGH_REPR_SAT8;
+ }
+ else {
+ bufferVal = (double) raw * m_scale + m_offset;
+ }
+
+ ((char *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Byte) {
+ unsigned char raw = ((unsigned char *)rawBuff)[idx];
+ if (raw == (char) m_gdalNoDataValue) {
+ raw = NULL1;
+ }
+
+ if(raw == NULL1) {
+ bufferVal = NULL8;
+ }
+ else if(raw == HIGH_REPR_SAT1) {
+ bufferVal = HIGH_REPR_SAT8;
+ }
+ else {
+ bufferVal = (double) raw * m_scale + m_offset;
+ }
+
+ ((unsigned char *)rawBuff)[idx] = raw;
+ }
+ }
+
+ bool GdalIoHandler::writePixelType(double *doubleBuff, void *rawBuff, int idx) const {
+ double bufferVal = doubleBuff[idx];
+ bool isSpecial = false;
+ if (m_pixelType == GDT_Float64) {
+ ((double *)rawBuff)[idx] = bufferVal;
+ }
+
+ else if(m_pixelType == GDT_Float32) {
+ float raw = 0;
+
+ if(bufferVal >= VALID_MIN8) {
+ double filePixelValueDbl = (bufferVal - m_offset) /
+ m_scale;
+
+ if(filePixelValueDbl < (double) VALID_MIN4) {
+ raw = LOW_REPR_SAT4;
+ isSpecial = true;
+ }
+ else if(filePixelValueDbl > (double) VALID_MAX4) {
+ raw = HIGH_REPR_SAT4;
+ isSpecial = true;
+ }
+ else {
+ raw = (float) filePixelValueDbl;
+ }
+ }
+ else {
+ if(bufferVal == NULL8) {
+ raw = NULL4;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_INSTR_SAT8) {
+ raw = LOW_INSTR_SAT4;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_REPR_SAT8) {
+ raw = LOW_REPR_SAT4;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_INSTR_SAT8) {
+ raw = HIGH_INSTR_SAT4;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_REPR_SAT8) {
+ raw = HIGH_REPR_SAT4;
+ isSpecial = true;
+ }
+ else {
+ raw = LOW_REPR_SAT4;
+ isSpecial = true;
+ }
+ }
+ ((float *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Int32) {
+ int raw;
+
+ if(bufferVal >= VALID_MINI4) {
+ double filePixelValueDbl = (bufferVal - m_offset) /
+ m_scale;
+ if(filePixelValueDbl < VALID_MINI4 - 0.5) {
+ raw = LOW_REPR_SATI4;
+ isSpecial = true;
+ }
+ if(filePixelValueDbl > VALID_MAXI4) {
+ raw = HIGH_REPR_SATI4;
+ isSpecial = true;
+ }
+ else {
+ int filePixelValue = (int)round(filePixelValueDbl);
+
+ if(filePixelValue < VALID_MINI4) {
+ raw = LOW_REPR_SATI4;
+ isSpecial = true;
+ }
+ else if(filePixelValue > VALID_MAXI4) {
+ raw = HIGH_REPR_SATI4;
+ isSpecial = true;
+ }
+ else {
+ raw = filePixelValue;
+ }
+ }
+ }
+ else {
+ if(bufferVal == NULL8) {
+ raw = NULLI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_INSTR_SAT8) {
+ raw = LOW_INSTR_SATI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_REPR_SAT8) {
+ raw = LOW_REPR_SATI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_INSTR_SAT8) {
+ raw = HIGH_INSTR_SATI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_REPR_SAT8) {
+ raw = HIGH_REPR_SATI4;
+ isSpecial = true;
+ }
+ else {
+ raw = LOW_REPR_SATI4;
+ isSpecial = true;
+ }
+ }
+ ((int *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_UInt32) {
+ unsigned int raw;
+
+ if(bufferVal >= VALID_MINUI4) {
+ double filePixelValueDbl = (bufferVal - m_offset) /
+ m_scale;
+ if(filePixelValueDbl < VALID_MINUI4 - 0.5) {
+ raw = LOW_REPR_SATUI4;
+ isSpecial = true;
+ }
+ if(filePixelValueDbl > VALID_MAXUI4) {
+ raw = HIGH_REPR_SATUI4;
+ isSpecial = true;
+ }
+ else {
+ unsigned int filePixelValue = (unsigned int)round(filePixelValueDbl);
+
+ if(filePixelValue < VALID_MINUI4) {
+ raw = LOW_REPR_SATUI4;
+ isSpecial = true;
+ }
+ else if(filePixelValue > VALID_MAXUI4) {
+ raw = HIGH_REPR_SATUI4;
+ isSpecial = true;
+ }
+ else {
+ raw = filePixelValue;
+ }
+ }
+ }
+ else {
+ if(bufferVal == NULL8) {
+ raw = NULLUI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_INSTR_SAT8) {
+ raw = LOW_INSTR_SATUI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_REPR_SAT8) {
+ raw = LOW_REPR_SATUI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_INSTR_SAT8) {
+ raw = HIGH_INSTR_SATUI4;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_REPR_SAT8) {
+ raw = HIGH_REPR_SATUI4;
+ isSpecial = true;
+ }
+ else {
+ raw = LOW_REPR_SATUI4;
+ isSpecial = true;
+ }
+ }
+ ((unsigned int *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Int16) {
+ short raw;
+
+ if(bufferVal >= VALID_MIN8) {
+ double filePixelValueDbl = (bufferVal - m_offset) /
+ m_scale;
+ if(filePixelValueDbl < VALID_MIN2 - 0.5) {
+ raw = LOW_REPR_SAT2;
+ isSpecial = true;
+ }
+ if(filePixelValueDbl > VALID_MAX2 + 0.5) {
+ raw = HIGH_REPR_SAT2;
+ isSpecial = true;
+ }
+ else {
+ int filePixelValue = (int)round(filePixelValueDbl);
+
+ if(filePixelValue < VALID_MIN2) {
+ raw = LOW_REPR_SAT2;
+ isSpecial = true;
+ }
+ else if(filePixelValue > VALID_MAX2) {
+ raw = HIGH_REPR_SAT2;
+ isSpecial = true;
+ }
+ else {
+ raw = filePixelValue;
+ }
+ }
+ }
+ else {
+ if(bufferVal == NULL8) {
+ raw = NULL2;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_INSTR_SAT8) {
+ raw = LOW_INSTR_SAT2;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_REPR_SAT8) {
+ raw = LOW_REPR_SAT2;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_INSTR_SAT8) {
+ raw = HIGH_INSTR_SAT2;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_REPR_SAT8) {
+ raw = HIGH_REPR_SAT2;
+ isSpecial = true;
+ }
+ else {
+ raw = LOW_REPR_SAT2;
+ isSpecial = true;
+ }
+ }
+ ((short *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_UInt16) {
+ unsigned short raw;
+
+ if(bufferVal >= VALID_MIN8) {
+ double filePixelValueDbl = (bufferVal - m_offset) /
+ m_scale;
+ if(filePixelValueDbl < VALID_MINU2 - 0.5) {
+ raw = LOW_REPR_SATU2;
+ isSpecial = true;
+ }
+ if(filePixelValueDbl > VALID_MAXU2 + 0.5) {
+ raw = HIGH_REPR_SATU2;
+ isSpecial = true;
+ }
+ else {
+ int filePixelValue = (int)round(filePixelValueDbl);
+
+ if(filePixelValue < VALID_MINU2) {
+ raw = LOW_REPR_SATU2;
+ isSpecial = true;
+ }
+ else if(filePixelValue > VALID_MAXU2) {
+ raw = HIGH_REPR_SATU2;
+ isSpecial = true;
+ }
+ else {
+ raw = filePixelValue;
+ }
+ }
+ }
+ else {
+ if(bufferVal == NULL8) {
+ raw = NULLU2;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_INSTR_SAT8) {
+ raw = LOW_INSTR_SATU2;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_REPR_SAT8) {
+ raw = LOW_REPR_SATU2;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_INSTR_SAT8) {
+ raw = HIGH_INSTR_SATU2;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_REPR_SAT8) {
+ raw = HIGH_REPR_SATU2;
+ isSpecial = true;
+ }
+ else {
+ raw = LOW_REPR_SATU2;
+ isSpecial = true;
+ }
+ }
+ ((unsigned short *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Int8) {
+ char raw;
+
+ if(bufferVal >= VALID_MIN8) {
+ double filePixelValueDbl = (bufferVal - m_offset) /
+ m_scale;
+ if(filePixelValueDbl < VALID_MINS1 - 0.5) {
+ raw = LOW_REPR_SATS1;
+ isSpecial = true;
+ }
+ else if(filePixelValueDbl > VALID_MAXS1 + 0.5) {
+ raw = HIGH_REPR_SATS1;
+ isSpecial = true;
+ }
+ else {
+ int filePixelValue = (int)(filePixelValueDbl + 0.5);
+ if(filePixelValue < VALID_MINS1) {
+ raw = LOW_REPR_SATS1;
+ isSpecial = true;
+ }
+ else if(filePixelValue > VALID_MAXS1) {
+ raw = HIGH_REPR_SATS1;
+ isSpecial = true;
+ }
+ else {
+ raw = (char)(filePixelValue);
+ }
+ }
+ }
+ else {
+ if(bufferVal == NULL8) {
+ raw = NULLS1;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_INSTR_SAT8) {
+ raw = LOW_INSTR_SATS1;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_REPR_SAT8) {
+ raw = LOW_REPR_SATS1;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_INSTR_SAT8) {
+ raw = HIGH_INSTR_SATS1;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_REPR_SAT8) {
+ raw = HIGH_REPR_SATS1;
+ isSpecial = true;
+ }
+ else {
+ raw = LOW_REPR_SATS1;
+ isSpecial = true;
+ }
+ }
+ ((char *)rawBuff)[idx] = raw;
+ }
+
+ else if(m_pixelType == GDT_Byte) {
+ unsigned char raw;
+
+ if(bufferVal >= VALID_MIN8) {
+ double filePixelValueDbl = (bufferVal - m_offset) /
+ m_scale;
+ if(filePixelValueDbl < VALID_MIN1 - 0.5) {
+ raw = LOW_REPR_SAT1;
+ isSpecial = true;
+ }
+ else if(filePixelValueDbl > VALID_MAX1 + 0.5) {
+ raw = HIGH_REPR_SAT1;
+ isSpecial = true;
+ }
+ else {
+ int filePixelValue = (int)(filePixelValueDbl + 0.5);
+ if(filePixelValue < VALID_MIN1) {
+ raw = LOW_REPR_SAT1;
+ isSpecial = true;
+ }
+ else if(filePixelValue > VALID_MAX1) {
+ raw = HIGH_REPR_SAT1;
+ isSpecial = true;
+ }
+ else {
+ raw = (unsigned char)(filePixelValue);
+ }
+ }
+ }
+ else {
+ if(bufferVal == NULL8) {
+ raw = NULL1;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_INSTR_SAT8) {
+ raw = LOW_INSTR_SAT1;
+ isSpecial = true;
+ }
+ else if(bufferVal == LOW_REPR_SAT8) {
+ raw = LOW_REPR_SAT1;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_INSTR_SAT8) {
+ raw = HIGH_INSTR_SAT1;
+ isSpecial = true;
+ }
+ else if(bufferVal == HIGH_REPR_SAT8) {
+ raw = HIGH_REPR_SAT1;
+ isSpecial = true;
+ }
+ else {
+ raw = LOW_REPR_SAT1;
+ isSpecial = true;
+ }
+ }
+ ((unsigned char *)rawBuff)[idx] = raw;
+ }
+ return isSpecial;
+ }
+}
\ No newline at end of file
diff --git a/isis/src/base/objs/ImageIoHandler/GdalIoHandler.h b/isis/src/base/objs/ImageIoHandler/GdalIoHandler.h
new file mode 100644
index 0000000000000000000000000000000000000000..bdc5079d815e5b3ef296bc4b26d2526e5a6ee3a5
--- /dev/null
+++ b/isis/src/base/objs/ImageIoHandler/GdalIoHandler.h
@@ -0,0 +1,85 @@
+/** This is free and unencumbered software released into the public domain.
+The authors of ISIS do not claim copyright on the contents of this file.
+For more details about the LICENSE terms and the AUTHORS, you will
+find files of those names at the top level of this repository. **/
+
+/* SPDX-License-Identifier: CC0-1.0 */
+
+#ifndef GdalIoHandler_h
+#define GdalIoHandler_h
+
+#include "Constants.h"
+#include "ImageIoHandler.h"
+#include "SpecialPixel.h"
+
+#include "gdal_priv.h"
+
+class QFile;
+class QMutex;
+class QString;
+template <typename A> class QList;
+
+namespace Isis {
+ class Buffer;
+ class CubeCachingAlgorithm;
+ class Pvl;
+
+ /**
+ * @ingroup Low Level Image IO
+ *
+ * @brief Handles converting buffers to and from disk.
+ *
+ * This class handles converting buffers to and from disk. This class holds
+ * the cube chunks in memory and is capable of reading and writing them. It
+ * asks the caching algorithms to recommend cube chunks to not keep in
+ * memory. Children need to call setChunkSizes() in their constructor.
+ *
+ * This class handles all of the virtual band conversions. This class also
+ * guarantees that unwritten cube data ends up read and written as NULLs.
+ * The default caching algorithm is a RegionalCachingAlgorithm.
+ *
+ * @author 2024-04-30 Adam Paquette
+ *
+ */
+ class GdalIoHandler : public ImageIoHandler {
+ public:
+ GdalIoHandler(QString &dataFilePath, const QList<int> *virtualBandList, GDALDataType pixelType = GDT_Float64, GDALAccess eAccess=GA_ReadOnly);
+ GdalIoHandler(GDALDataset *geodataSet, const QList<int> *virtualBandList, GDALDataType pixelType = GDT_Float64);
+ void init();
+ virtual ~GdalIoHandler();
+
+ virtual void read(Buffer &bufferToFill) const;
+ virtual void write(const Buffer &bufferToWrite);
+
+ virtual BigInt getDataSize() const;
+ /**
+ * Function to update the labels with a Pvl object
+ *
+ * @param labels Pvl object to update with
+ */
+ virtual void updateLabels(Pvl &labels);
+
+ virtual void clearCache(bool blockForWriteCache=false) {
+ m_geodataSet->FlushCache(blockForWriteCache);
+ }
+
+ private:
+ void readPixelType(double *doubleBuff, void *rawBuff, int idx) const;
+ bool writePixelType(double *doubleBuff, void *rawBuff, int idx) const;
+
+ GDALDataset *m_geodataSet = nullptr;
+ std::string m_geodataSetPath = "";
+ GDALDataType m_pixelType;
+ int m_lines;
+ int m_samples;
+ int m_bands;
+ double m_offset;
+ double m_scale;
+ unsigned char *m_maskBuff = nullptr;
+ bool m_datasetOwner = false;
+ double m_gdalNoDataValue = NULL8;
+ std::string m_driverName;
+ };
+}
+
+#endif
diff --git a/isis/src/base/objs/ImageIoHandler/ImageIoHandler.cpp b/isis/src/base/objs/ImageIoHandler/ImageIoHandler.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..7965c69e2b82b76acd0a4a43d401870cc27c98fc
--- /dev/null
+++ b/isis/src/base/objs/ImageIoHandler/ImageIoHandler.cpp
@@ -0,0 +1,61 @@
+#include "ImageIoHandler.h"
+
+#include "Buffer.h"
+#include "CubeCachingAlgorithm.h"
+
+#include <QList>
+#include <QMutex>
+
+using namespace std;
+
+namespace Isis {
+ ImageIoHandler::ImageIoHandler(const QList<int> *virtualBandList) {
+ m_writeThreadMutex = NULL;
+ m_writeThreadMutex = new QMutex;
+ m_virtualBands = NULL;
+
+ setVirtualBands(virtualBandList);
+ }
+
+ ImageIoHandler::~ImageIoHandler() {
+ delete m_virtualBands;
+ m_virtualBands = NULL;
+
+ delete m_writeThreadMutex;
+ m_writeThreadMutex = NULL;
+ }
+
+ void ImageIoHandler::addCachingAlgorithm(CubeCachingAlgorithm *algorithm) {}
+
+ void ImageIoHandler::clearCache(bool blockForWriteCache) const {}
+
+ /**
+ * This changes the virtual band list.
+ *
+ * @param virtualBandList A list where the indices are the vbands and the
+ * values are the physical bands. The values are 1-based. This can
+ * be specified as NULL, in which case the vbands are the physical
+ * bands. The virtual band list is copied
+ * (the pointer provided isn't remembered).
+ */
+ void ImageIoHandler::setVirtualBands(const QList<int> *virtualBandList) {
+ if(m_virtualBands) {
+ delete m_virtualBands;
+ m_virtualBands = NULL;
+ }
+
+ if(virtualBandList && !virtualBandList->empty())
+ m_virtualBands = new QList<int>(*virtualBandList);
+ }
+
+ /**
+ * Get the mutex that this IO handler is using around I/Os on the given
+ * data file. A lock should be acquired before doing any reads/writes on
+ * the data file externally.
+ *
+ * @return A mutex that can guarantee exclusive access to the data file
+ */
+ QMutex *ImageIoHandler::dataFileMutex() {
+ return m_writeThreadMutex;
+ }
+}
\ No newline at end of file
diff --git a/isis/src/base/objs/ImageIoHandler/ImageIoHandler.h b/isis/src/base/objs/ImageIoHandler/ImageIoHandler.h
new file mode 100644
index 0000000000000000000000000000000000000000..baab584cd7a709116151238a7a0a94a946dc1a2d
--- /dev/null
+++ b/isis/src/base/objs/ImageIoHandler/ImageIoHandler.h
@@ -0,0 +1,128 @@
+/** This is free and unencumbered software released into the public domain.
+The authors of ISIS do not claim copyright on the contents of this file.
+For more details about the LICENSE terms and the AUTHORS, you will
+find files of those names at the top level of this repository. **/
+
+/* SPDX-License-Identifier: CC0-1.0 */
+
+#ifndef ImageIoHandler_h
+#define ImageIoHandler_h
+
+#include "Constants.h"
+
+class QFile;
+class QMutex;
+template <typename A> class QList;
+
+namespace Isis {
+ class Buffer;
+ class CubeCachingAlgorithm;
+ class Pvl;
+
+ /**
+ * @ingroup Low Level Image IO
+ *
+ * @brief Handles converting buffers to and from disk.
+ *
+ * This class handles converting buffers to and from disk. This class holds
+ * the cube chunks in memory and is capable of reading and writing them. It
+ * asks the caching algorithms to recommend cube chunks to not keep in
+ * memory. Children need to call setChunkSizes() in their constructor.
+ *
+ * This class handles all of the virtual band conversions. This class also
+ * guarantees that unwritten cube data ends up read and written as NULLs.
+ * The default caching algorithm is a RegionalCachingAlgorithm.
+ *
+ * @author 2011-??-?? Jai Rideout and Steven Lambright
+ *
+ * @internal
+ * @history 2011-06-27 Steven Lambright - Added addCachingAlgorithm()
+ * @history 2011-07-18 Jai Rideout and Steven Lambright - Added
+ * unimplemented copy constructor and assignment
+ * operator.
+ * @history 2011-07-18 Jai Rideout and Steven Lambright - getDataFile() is
+ * no longer const, along with readRaw() and
+ * writeRaw().
+ * @history 2011-11-23 Jai Rideout - Added fix to findCubeChunks() and
+ * findIntersection() so that requested areas that
+ * are outside of the virtual bands of the cube will
+ * no longer fail, but instead will fill the buffer
+ * with nulls.
+ * @history 2012-02-17 Steven Lambright - The read() method is now const -
+ * the caching should be transparent to the API. It
+ * is still important to note that you cannot call
+ * read() and write() simultaneously - Cube is
+ * guaranteeing this. Backgrounded writes are now
+ * implemented and fully supported. Timing tests
+ * show results like this:
+ * Before:
+ * User: 358.71 Kernel: 38.29 Total Elapsed: 6:49.83
+ * After:
+ * User: 380.01 Kernel: 44.97 Total Elapsed: 6:19.96
+ * User- user-space CPU time consumed.
+ * Kernel- kernel-space CPU time consumed.
+ * The CPU consumption and kernel time consumption
+ * goes up, but the overall run time is lower. This
+ * makes the option perfectly viable for typical
+ * multi-core desktop solutions. Turning off the
+ * cube write optimization results in equivalent run
+ * times as before implementation. These time tests
+ * were run before the adaptive cache flush size was
+ * added, which improved performance further.
+ * References #727.
+ * @history 2012-06-06 Jeff Anderson - The read() method was modified to
+ * improve the speed for small buffer sizes as seen
+ * in ProcessByBoxcar and ProcessRubbersheet. The
+ * internal cache was always checked to be minimized
+ * which is slow for every read. Now the cache is
+ * only mimimized if it changed in size.
+ * Reference #894.
+ * @history 2014-04-07 Kimberly Oyama and Stuart Sides - Modified the findCubeChunks,
+ * writeIntoDouble, and writeIntoRaw methods to handle
+ * repeating virtual bands. Fixes #1927.
+ * @history 2014-09-30 Ian Humphrey - Modified read method to correctly access virtual bands
+ * when cube dimensions and buffer shape are same size. Fixes #1689.
+ * @history 2015-01-30 Ian Humphrey - Modified destructor to free m_writThreadMutex to
+ * prevent memory leaks upon destruction. Fixes #2082.
+ * @history 2016-04-21 Makayla Shepherd - Added UnsignedWord pixel type handling.
+ * @history 2016-06-21 Kris Becker - Properly forward declare QPair as struct not class
+ * @history 2016-08-28 Kelvin Rodriguez - updateLabels now a pure virtual, it had no
+ * implementation causing warnings in clang. Part of OS X 10.11 porting.
+ * QPair forward declaration now properly claims it as a struct.
+ * @history 2017-09-22 Cole Neubauer - Fixed documentation. References #4807
+ * @history 2018-07-20 Tyler Wilson - Added support for unsigned integer special pixel values.
+ * in functions writeIntoRaw(...) and writeIntoDouble(...)
+ * References #971.
+ * @history 2018-08-13 Summer Stapleton - Fixed incoming buffer comparison values for
+ * unsigned int type in writeIntoRaw(...).
+ */
+ class ImageIoHandler {
+ public:
+ ImageIoHandler(const QList<int> *virtualBandList);
+ virtual ~ImageIoHandler();
+
+ virtual void read(Buffer &bufferToFill) const = 0;
+ virtual void write(const Buffer &bufferToWrite) = 0;
+
+ virtual void addCachingAlgorithm(CubeCachingAlgorithm *algorithm);
+ virtual void clearCache(bool blockForWriteCache = true) const;
+ virtual BigInt getDataSize() const = 0;
+ void setVirtualBands(const QList<int> *virtualBandList);
+ /**
+ * Function to update the labels with a Pvl object
+ *
+ * @param labels Pvl object to update with
+ */
+ virtual void updateLabels(Pvl &labels) = 0;
+ QMutex *dataFileMutex();
+
+ protected:
+ //! This enables us to block while the write thread is working
+ QMutex *m_writeThreadMutex;
+
+ //! Converts from virtual band to physical band.
+ QList<int> *m_virtualBands;
+ };
+}
+
+#endif
diff --git a/isis/src/base/objs/PixelType/PixelType.h b/isis/src/base/objs/PixelType/PixelType.h
index c9f5868fe88850d988a55c5620f2e63068f938a1..8f2de66d2c8bd13f680c40f9657aeb9af6c38d58 100644
--- a/isis/src/base/objs/PixelType/PixelType.h
+++ b/isis/src/base/objs/PixelType/PixelType.h
@@ -8,6 +8,8 @@ find files of those names at the top level of this repository. **/
/* SPDX-License-Identifier: CC0-1.0 */
#include <QString>
+#include "gdal_priv.h"
+
namespace Isis {
/**
* @brief Enumerations for Isis Pixel Types
@@ -98,6 +100,31 @@ namespace Isis {
if(temp == "DOUBLE") return Isis::Double;
return Isis::None;
}
+
+ inline Isis::PixelType GdalPixelToIsis(GDALDataType type) {
+ if (type == GDT_Byte) return Isis::UnsignedByte;
+ if (type == GDT_Int8) return Isis::SignedByte;
+ if (type == GDT_UInt16) return Isis::UnsignedWord;
+ if (type == GDT_Int16) return Isis::SignedWord;
+ if (type == GDT_UInt32) return Isis::UnsignedInteger;
+ if (type == GDT_Int32) return Isis::SignedInteger;
+ if (type == GDT_Float32) return Isis::Real;
+ if (type == GDT_Float64) return Isis::Double;
+ return Isis::None;
+ }
+
+ inline GDALDataType IsisPixelToGdal(Isis::PixelType type) {
+ if(type == Isis::None) return GDT_Unknown;
+ if(type == Isis::UnsignedByte) return GDT_Byte;
+ if(type == Isis::SignedByte) return GDT_Int8;
+ if(type == Isis::UnsignedWord) return GDT_UInt16;
+ if(type == Isis::SignedWord) return GDT_Int16;
+ if(type == Isis::UnsignedInteger) return GDT_UInt32;
+ if(type == Isis::SignedInteger) return GDT_Int32;
+ if(type == Isis::Real) return GDT_Float32;
+ if(type == Isis::Double) return GDT_Float64;
+ return GDT_Unknown;
+ }
}
#endif
diff --git a/isis/src/base/objs/Process/Process.cpp b/isis/src/base/objs/Process/Process.cpp
index b0046635298415d142b27003c9bc5b5efb39d4f7..0d00aafe736d37bde495f171957f3388fbc14f63 100644
--- a/isis/src/base/objs/Process/Process.cpp
+++ b/isis/src/base/objs/Process/Process.cpp
@@ -330,7 +330,7 @@ Isis::Cube *Process::SetOutputCubeStretch(const QString ¶meter, const int ns
cube->setDimensions(ns, nl, nb);
cube->setByteOrder(att.byteOrder());
cube->setFormat(att.fileFormat());
- cube->setLabelsAttached(att.labelAttachment() == AttachedLabel);
+ cube->setLabelsAttached(att.labelAttachment());
if(att.propagatePixelType()) {
if(InputCubes.size() > 0) {
cube->setPixelType(InputCubes[0]->pixelType());
diff --git a/isis/src/base/objs/ProcessMapMosaic/ProcessMapMosaic.cpp b/isis/src/base/objs/ProcessMapMosaic/ProcessMapMosaic.cpp
index 90368f87ce5b1d126f56a45bcc0f133d01ad74a0..48d9292d49efead3769693bcb3f113b412380e75 100644
--- a/isis/src/base/objs/ProcessMapMosaic/ProcessMapMosaic.cpp
+++ b/isis/src/base/objs/ProcessMapMosaic/ProcessMapMosaic.cpp
@@ -508,7 +508,8 @@ namespace Isis {
double xmin, double xmax, double ymin, double ymax,
double slat, double elat, double slon, double elon, int nbands,
CubeAttributeOutput &oAtt, const QString &mosaicFile, bool latlonflag) {
- Pvl fileLab(inputFile);
+ Cube cube(inputFile);
+ Pvl fileLab = *cube.label();
PvlGroup &mapping = fileLab.findGroup("Mapping", Pvl::Traverse);
// All mosaicking programs use only the upper left x and y to determine where to
diff --git a/isis/src/base/objs/Pvl/Pvl.cpp b/isis/src/base/objs/Pvl/Pvl.cpp
index 1c6240509303098d37e4bb79bcd0c0c3050731fe..318913bca1b12a016ce52572d71c5782542d5c0b 100644
--- a/isis/src/base/objs/Pvl/Pvl.cpp
+++ b/isis/src/base/objs/Pvl/Pvl.cpp
@@ -11,6 +11,11 @@ find files of those names at the top level of this repository. **/
#include <locale>
#include <fstream>
#include <sstream>
+#include <cctype>
+
+#include <filesystem>
+#include <random>
+#include <nlohmann/json.hpp>
#include "FileName.h"
#include "IException.h"
@@ -18,6 +23,10 @@ find files of those names at the top level of this repository. **/
#include "PvlTokenizer.h"
#include "PvlFormat.h"
+namespace fs = std::filesystem;
+using json = nlohmann::json;
+using ordered_json = nlohmann::ordered_json;
+
using namespace std;
namespace Isis {
//! Constructs an empty Pvl object.
@@ -36,7 +45,6 @@ namespace Isis {
read(file);
}
-
//! Copy constructor
Pvl::Pvl(const Pvl &other) : PvlObject::PvlObject(other) {
m_internalTemplate = false;
@@ -51,6 +59,109 @@ namespace Isis {
m_internalTemplate = false;
}
+ // This function specifically reads from GDAL-style JSON metadata.
+ Isis::PvlObject &Pvl::readObject(Isis::PvlObject &pvlobj, nlohmann::ordered_json jdata) {
+ for(auto &[key, value] : jdata.items()) {
+ string name = key;
+ if(value.contains("_type")) {
+ string type = value.at("_type");
+ value.erase("_type");
+ if (value.contains("_container_name")) {
+ name = value["_container_name"];
+ value.erase("_container_name");
+ }
+
+ if(type == "object") {
+ PvlObject nestedObj(QString::fromStdString(name));
+ pvlobj.addObject(readObject(nestedObj, value));
+ }
+ if(type == "group") {
+ // parse keys
+ PvlGroup group(QString::fromStdString(name));
+ for(auto &[pvlkeyword, pvlvalue] : value.items()) {
+ PvlKeyword keyword;
+ keyword.setName(QString::fromStdString(pvlkeyword));
+ if (pvlvalue.is_array())
+ keyword.addJsonArrayValue(pvlvalue);
+ else
+ keyword.setJsonValue(pvlvalue);
+ group.addKeyword(keyword);
+ }
+ pvlobj.addGroup(group);
+ } // end of group
+ } // end of _type search
+
+ // not a group or object, must be a keyword
+ else if (key != "_type" && key != "_filename" && key != "Data") {
+ PvlKeyword keyword;
+ keyword.setName(QString::fromStdString(key));
+ if (value.is_array())
+ keyword.setJsonArrayValue(value);
+ else
+ keyword.setJsonValue(value);
+
+ pvlobj.addKeyword(keyword);
+ }
+ }
+ return pvlobj;
+ }
+
+
+ ordered_json Pvl::toJson() {
+ // needs to be a function because recursion
+ function<ordered_json(PvlObject&)> pvlobject_to_json = [&](PvlObject &pvlobj) -> ordered_json {
+ ordered_json jsonobj;
+ string okey = (pvlobj.name()).toStdString();
+ if (pvlobj.hasKeyword("Name")) {
+ okey = (pvlobj.name()+"_"+(QString)pvlobj.findKeyword("Name")).toStdString();
+ }
+ jsonobj[okey] = {};
+ if (pvlobj.hasKeyword("Name")) {
+ jsonobj[okey]["_container_name"] = pvlobj.name().toStdString();
+ }
+
+ if (okey != "Root") {
+ jsonobj[okey]["_type"] = "object";
+ }
+
+ for (int i=0; i < pvlobj.objects(); i++) {
+ jsonobj[okey].merge_patch(pvlobject_to_json(pvlobj.object(i)));
+ }
+
+ for (int i=0; i<pvlobj.groups(); i++) {
+ PvlGroup g = pvlobj.group(i);
+ string gkey = (g.name()).toStdString();
+ if (g.hasKeyword("Name")) {
+ gkey = (g.name()+"_"+(QString)g.findKeyword("Name")).toStdString();
+ }
+ jsonobj[okey][gkey] = {};
+ if (g.hasKeyword("Name")) {
+ jsonobj[okey][gkey]["_container_name"] = g.name().toStdString();
+ }
+ jsonobj[okey][gkey]["_type"] = "group";
+
+ // go through keywords
+ for(int j =0; j<g.keywords();j++) {
+ PvlKeyword k=g[j];
+ jsonobj[okey][gkey][k.name().toStdString()] = k.toJson();
+ }
+ }
+
+ // get left over keywords
+ for(int i =0; i<pvlobj.keywords();i++) {
+ PvlKeyword k=pvlobj[i];
+ jsonobj[okey][k.name().toStdString()] = k.toJson();
+ }
+ return jsonobj;
+ };
+
+ if (this->name() == "Root" && this->objects() == 1) {
+ return pvlobject_to_json(this->object(0));
+ }
+ else {
+ return pvlobject_to_json(*this);
+ }
+ }
/**
* Load PVL information from a string
diff --git a/isis/src/base/objs/Pvl/Pvl.h b/isis/src/base/objs/Pvl/Pvl.h
index d634ac5a6dcd5b6e37a424372133585303804e37..df89e8db6ca3f757fccfdf0b439ec12686f0e3b4 100644
--- a/isis/src/base/objs/Pvl/Pvl.h
+++ b/isis/src/base/objs/Pvl/Pvl.h
@@ -8,8 +8,11 @@ find files of those names at the top level of this repository. **/
/* SPDX-License-Identifier: CC0-1.0 */
#include <fstream>
+
#include "PvlObject.h"
+#include <gdal_priv.h>
+
namespace Isis {
/**
* @brief Container for cube-like labels
@@ -126,12 +129,15 @@ namespace Isis {
friend std::ostream &operator<<(std::ostream &os, Isis::Pvl &pvl);
void fromString(const std::string &str);
+ static Isis::PvlObject &readObject(Isis::PvlObject &pvlobj, nlohmann::ordered_json jdata);
+ nlohmann::ordered_json toJson();
+
~Pvl() {
if(m_internalTemplate) delete m_formatTemplate;
};
void read(const QString &file);
-
+
void write(const QString &file);
void append(const QString &file);
diff --git a/isis/src/base/objs/PvlKeyword/PvlKeyword.cpp b/isis/src/base/objs/PvlKeyword/PvlKeyword.cpp
index 0fa0aca35bf96376bd7c480f309f65c98a2f72f3..4fa5c779d20fcda30bde1c4c197d0fb533aa6ba2 100644
--- a/isis/src/base/objs/PvlKeyword/PvlKeyword.cpp
+++ b/isis/src/base/objs/PvlKeyword/PvlKeyword.cpp
@@ -19,6 +19,7 @@ find files of those names at the top level of this repository. **/
using namespace std;
using json = nlohmann::json;
+
namespace Isis {
//! Constructs a blank PvlKeyword object.
PvlKeyword::PvlKeyword() {
@@ -172,10 +173,9 @@ namespace Isis {
*
* @see addJsonValue()
*/
- void PvlKeyword::setJsonValue(json jsonobj, QString unit)
- {
+ void PvlKeyword::setJsonValue(json jsonobj) {
clear();
- addJsonValue(jsonobj, unit);
+ addJsonValue(jsonobj);
}
/**
@@ -301,31 +301,108 @@ namespace Isis {
*
* @throws Isis::iException::Unknown - jsonobj cannot be an array of values
*/
- void PvlKeyword::addJsonValue(json jsonobj, QString unit) {
+ void PvlKeyword::addJsonValue(json jsonobj) {
QString value;
- if (jsonobj.is_array()) {
+ QString unit = "";
+ json jvalue = jsonobj;
+ if (jsonobj.contains("unit")) {
+ unit = QString::fromStdString(jsonobj["unit"].get<string>());
+ jvalue = jsonobj["value"];
+ }
+
+ if (jvalue.is_array()) {
QString msg = "Unable to convert " + name() + " with nested json array value into PvlKeyword";
throw IException(IException::Unknown, msg, _FILEINFO_);
}
- else if (jsonobj.is_number())
- {
- value = QString::number(jsonobj.get<double>(), 'g', 16);
+ else if (jvalue.is_number()) {
+ value = QString::number(jvalue.get<double>(), 'g', 16);
}
- else if (jsonobj.is_boolean())
- {
- value = QString(jsonobj.get<bool>() ? "true" : "false");
+ else if (jvalue.is_boolean()) {
+ value = QString(jvalue.get<bool>() ? "true" : "false");
}
- else if (jsonobj.is_null())
- {
+ else if (jvalue.is_null()) {
value = QString("Null");
}
- else
- {
- value = QString::fromStdString(jsonobj);
+ else {
+ value = QString::fromStdString(jvalue);
}
addValue(value, unit);
}
+ /**
+ * Adds multiple items from a json array.
+ *
+ * If no current value exists, this method sets the given json value.
+ * Otherwise, it retains any current values and adds the json value
+ * given to the array of values for this PvlKeyword object using addValue.
+ * Defaults to unit = "" (empty QString).
+ *
+ * @param jsonobj New jsonobj to be parsed and assigned.
+ * @param unit Units of measurement corresponding to the value.
+ *
+ * @see setJsonValue()
+ * @see addValue()
+ *
+ * @throws Isis::iException::Unknown - jsonobj must be a json array
+ */
+ void PvlKeyword::addJsonArrayValue(json jsonobj) {
+ if(!jsonobj.is_array()) {
+ QString msg = "Unable to convert to a json array:\n" + QString::fromStdString(jsonobj.dump());
+ throw IException(IException::Unknown, msg, _FILEINFO_);
+ }
+
+ for(auto ar = jsonobj.begin(); ar!=jsonobj.end(); ar++) {
+ try {
+ addJsonValue(*ar);
+ }
+ catch (IException &e) {
+ QString msg = "While attempting to parse " + name() + " the following occured";
+ throw IException(e, IException::Unknown, msg, _FILEINFO_);
+ }
+ }
+ }
+
+
+ json PvlKeyword::toJson() {
+ if(size() == 1) {
+ if(unit() == "") {
+ return this->operator[](0).toStdString();
+ } else {
+ return {{"unit", unit().toStdString()}, {"value", this->operator[](0).toStdString()}};
+ }
+ } else {
+ // it's an array
+ json jsonarr = json::array();
+ for(int i = 0; i < size(); i++) {
+ jsonarr += this->operator[](i).toStdString();
+ }
+ return jsonarr;
+ }
+ }
+
+
+ /**
+ * sets multiple items from a json array.
+ *
+ * If no current value exists, this method sets the given json value.
+ * Otherwise, it retains any current values and adds the json value
+ * given to the array of values for this PvlKeyword object using addValue.
+ * Defaults to unit = "" (empty QString).
+ *
+ * @param jsonobj New jsonobj to be parsed and assigned.
+ * @param unit Units of measurement corresponding to the value.
+ *
+ * @see setJsonValue()
+ * @see addValue()
+ *
+ * @throws Isis::iException::Unknown - jsonobj must be a json array
+ */
+ void PvlKeyword::setJsonArrayValue(json jsonobj) {
+ clear();
+ addJsonArrayValue(jsonobj);
+ }
+
+
/**
* Adds a value.
*
diff --git a/isis/src/base/objs/PvlKeyword/PvlKeyword.h b/isis/src/base/objs/PvlKeyword/PvlKeyword.h
index ba9800c6a166f6011a2ffbf7ccfea956f64b500d..fff827b1995e5d680ef00299a5882a47cc654b28 100644
--- a/isis/src/base/objs/PvlKeyword/PvlKeyword.h
+++ b/isis/src/base/objs/PvlKeyword/PvlKeyword.h
@@ -117,7 +117,9 @@ namespace Isis {
};
void setValue(QString value, QString unit = "");
- void setJsonValue(nlohmann::json jsonobj, QString unit = "");
+ void setJsonValue(nlohmann::json jsonobj);
+ void setJsonArrayValue(nlohmann::json jsonobj);
+
void setUnits(QString units);
void setUnits(QString value, QString units);
@@ -125,7 +127,8 @@ namespace Isis {
PvlKeyword &operator=(QString value);
void addValue(QString value, QString unit = "");
- void addJsonValue(nlohmann::json jsonobj, QString unit = "");
+ void addJsonValue(nlohmann::json jsonobj);
+ void addJsonArrayValue(nlohmann::json jsonobj);
PvlKeyword &operator+=(QString value);
@@ -155,6 +158,8 @@ namespace Isis {
operator QString() const;
+ nlohmann::json toJson();
+
const QString &operator[](int index) const;
QString &operator[](int index);
QString unit(const int index = 0) const;
diff --git a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth
index 2750ff4e6556d5a9e169bf94617f5c705cd0fd00..0ea1a8227ae49ad2f78e95158f5cd25d2f6fa63a 100644
--- a/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth
+++ b/isis/src/base/objs/ShapeModelFactory/ShapeModelFactory.truth
@@ -39,6 +39,8 @@ Unit test for Isis::ShapeModel
**PROGRAMMER ERROR** Unable to create a shape model from given target and pvl.
**I/O ERROR** Invalid shape model file [NotAFile] in Kernels group.
**ERROR** The given shape model file is not a valid ISIS DEM. Unable to open as an ISIS cube.
+**I/O ERROR** Failed to open [NotAFile].
+**PROGRAMMER ERROR** Gdal failed to open [NotAFile].
**I/O ERROR** Unable to open [NotAFile].
**ERROR** The given shape model file is not a valid NAIF DSK file. Unable to construct a NAIF DSK shape model.
**USER ERROR** NAIF DSK file [NotAFile] does not exist.
diff --git a/isis/src/base/objs/SpecialPixel/SpecialPixel.h b/isis/src/base/objs/SpecialPixel/SpecialPixel.h
index 2d1c56ed98fbd77c9f8ad2ef0192efb6059f155e..277c7e877bbfeb49b92b3edd5e3757c7da35d6d1 100644
--- a/isis/src/base/objs/SpecialPixel/SpecialPixel.h
+++ b/isis/src/base/objs/SpecialPixel/SpecialPixel.h
@@ -150,10 +150,10 @@ namespace Isis {
const int IVALID_MAX4 = (*((const int *) &VALID_MAX4));
// 2-byte signed special pixel values
- const short VALID_MIN2 = ((short)(-32752));
- const short NULL2 = ((short)(-32768));
- const short LOW_REPR_SAT2 = ((short)(-32767));
- const short LOW_INSTR_SAT2 = ((short)(-32766));
+ const short VALID_MIN2 = ((short)(-32752));
+ const short NULL2 = ((short)(-32768));
+ const short LOW_REPR_SAT2 = ((short)(-32767));
+ const short LOW_INSTR_SAT2 = ((short)(-32766));
const short HIGH_INSTR_SAT2 = ((short)(-32765));
const short HIGH_REPR_SAT2 = ((short)(-32764));
const short VALID_MAX2 = ((short) 32767);
@@ -167,6 +167,15 @@ namespace Isis {
const unsigned short HIGH_REPR_SATU2 = ((unsigned short) 65535);
const unsigned short VALID_MAXU2 = ((unsigned short) 65522);
+ // 4-byte signed special pixel values
+ const int VALID_MINI4 = ((int)(-2147483632));
+ const int NULLI4 = ((int)(-2147483648));
+ const int LOW_REPR_SATI4 = ((int)(-2147483647));
+ const int LOW_INSTR_SATI4 = ((int)(-2147483646));
+ const int HIGH_INSTR_SATI4 = ((int)(-2147483645));
+ const int HIGH_REPR_SATI4 = ((int)(-2147483644));
+ const int VALID_MAXI4 = ((int) 2147483647 );
+
// 4-byte unsigned special pixel values
const unsigned int VALID_MINUI4 = ((unsigned int) 3);
const unsigned int NULLUI4 = ((unsigned int) 0);
@@ -176,8 +185,16 @@ namespace Isis {
const unsigned int HIGH_REPR_SATUI4 = ((unsigned int) 4294967295);
const unsigned int VALID_MAXUI4 = ((unsigned int) 4294967282);
+ // 1-byte signed special pixel values
+ const char VALID_MINS1 = ((char) -126);
+ const char NULLS1 = ((char) -128);
+ const char LOW_REPR_SATS1 = ((char) -128);
+ const char LOW_INSTR_SATS1 = ((char) -128);
+ const char HIGH_INSTR_SATS1 = ((char) -127);
+ const char HIGH_REPR_SATS1 = ((char) -127);
+ const char VALID_MAXS1 = ((char) 127);
- // 1-byte special pixel values
+ // 1-byte unsigned special pixel values
const unsigned char VALID_MIN1 = ((unsigned char) 1);
const unsigned char NULL1 = ((unsigned char) 0);
const unsigned char LOW_REPR_SAT1 = ((unsigned char) 0);
diff --git a/isis/src/base/objs/SpectralDefinitionFactory/SpectralDefinitionFactory.truth b/isis/src/base/objs/SpectralDefinitionFactory/SpectralDefinitionFactory.truth
index 4c5ff858d38dba84df0d9c9fe6a537cc9a9ab651..de5d45ce46ae401e349a9d100b7c1d8e2066fbfa 100644
--- a/isis/src/base/objs/SpectralDefinitionFactory/SpectralDefinitionFactory.truth
+++ b/isis/src/base/objs/SpectralDefinitionFactory/SpectralDefinitionFactory.truth
@@ -1,5 +1,9 @@
----- Testing SpectralDefinitionFactory -----
**ERROR** Unable to open input file [assets/test.csv]. Is it a valid CSV?.
**USER ERROR** Unable to open file [assets/test.csv].
+**I/O ERROR** Failed to open [assets/test.txt].
+**PROGRAMMER ERROR** Gdal failed to open [assets/test.txt].
**I/O ERROR** Unable to open [assets/test.txt].
+**I/O ERROR** Failed to open [assets/cube.cub].
+**PROGRAMMER ERROR** Gdal failed to open [assets/cube.cub].
**I/O ERROR** Unable to open [assets/cube.cub].
diff --git a/isis/src/base/objs/Spice/Spice.cpp b/isis/src/base/objs/Spice/Spice.cpp
index 1e357c77d7d6d802379863617e36665c856cea2b..b940718b806c01a9e717e6628f95bd7ae8207137 100644
--- a/isis/src/base/objs/Spice/Spice.cpp
+++ b/isis/src/base/objs/Spice/Spice.cpp
@@ -68,9 +68,37 @@ namespace Isis {
}
else {
PvlGroup kernels = lab.findGroup("Kernels", Pvl::Traverse);
- bool hasTables = (kernels["TargetPosition"][0] == "Table");
+
// BONUS TODO: update to pull out separate init methods
- init(lab, !hasTables);
+ // try using ALE
+ bool hasTables = (kernels["TargetPosition"][0] == "Table");
+ m_usingNaif = !lab.hasObject("NaifKeywords") || !hasTables;
+ m_usingAle = false;
+
+ if (m_usingNaif) {
+ try {
+ std::ostringstream kernel_pvl;
+ kernel_pvl << kernels;
+
+ json props;
+ if (kernels["InstrumentPointing"][0].toUpper() == "NADIR") {
+ props["nadir"] = true;
+ }
+
+ props["kernels"] = kernel_pvl.str();
+
+ json isd = ale::load(lab.fileName().toStdString(), props.dump(), "ale", false, false, true);
+ m_usingAle = true;
+
+ isdInit(lab, isd);
+ }
+ catch(...) {
+ init(cube, lab, !hasTables);
+ }
+ }
+ else {
+ init(cube, lab, !hasTables);
+ }
}
}
@@ -82,7 +110,209 @@ namespace Isis {
* @param isd ALE Json ISD
*/
Spice::Spice(Pvl &lab, json isd) {
- init(lab, true, isd);
+ // Set the expected member states for other parts of the Spice
+ // class
+ m_usingNaif = true;
+ m_usingAle = true;
+
+ isdInit(lab, isd);
+ }
+
+ void Spice::isdInit(Pvl &lab, json isd) {
+ NaifStatus::CheckErrors();
+ // Initialize members
+ defaultInit();
+
+ m_spkCode = new SpiceInt;
+ m_ckCode = new SpiceInt;
+ m_ikCode = new SpiceInt;
+ m_sclkCode = new SpiceInt;
+ m_spkBodyCode = new SpiceInt;
+ m_bodyFrameCode = new SpiceInt;
+
+ m_naifKeywords = new PvlObject("NaifKeywords");
+
+ // Get the kernel group and load main kernels
+ PvlGroup kernels = lab.findGroup("Kernels", Pvl::Traverse);
+
+ // Get the time padding first
+ if (kernels.hasKeyword("StartPadding")) {
+ *m_startTimePadding = toDouble(kernels["StartPadding"][0]);
+ }
+ else {
+ *m_startTimePadding = 0.0;
+ }
+
+ if (kernels.hasKeyword("EndPadding")) {
+ *m_endTimePadding = toDouble(kernels["EndPadding"][0]);
+ }
+ else {
+ *m_endTimePadding = 0.0;
+ }
+
+ try {
+ json aleNaifKeywords = isd["naif_keywords"];
+ m_naifKeywords = new PvlObject("NaifKeywords", aleNaifKeywords);
+
+ // Still need to load clock kernels for now
+ load(kernels["LeapSecond"], true);
+ if ( kernels.hasKeyword("SpacecraftClock")) {
+ load(kernels["SpacecraftClock"], true);
+ }
+ }
+ catch(IException &e) {
+ QString msg = "Failed to read naif_keywords from ISD";
+ throw IException(e, IException::Programmer, msg, _FILEINFO_);
+ }
+
+ // Moved the construction of the Target after the NAIF kenels have been loaded or the
+ // NAIF keywords have been pulled from the cube labels, so we can find target body codes
+ // that are defined in kernels and not just body codes build into spicelib
+ // TODO: Move this below the else once the rings code below has been refactored
+ m_target = new Target(this, lab);
+
+ // This should not be here. Consider having spiceinit add the necessary rings kernels to the
+ // Extra parameter if the user has set the shape model to RingPlane.
+ // If Target is Saturn and ShapeModel is RingPlane, load the extra rings pck file
+ // which changes the prime meridian values to report longitudes with respect to
+ // the ascending node of the ringplane.
+ if (m_target->name().toUpper() == "SATURN" && m_target->shape()->name().toUpper() == "PLANE") {
+ PvlKeyword ringPck = PvlKeyword("RingPCK","$cassini/kernels/pck/saturnRings_v001.tpc");
+ load(ringPck, true);
+ }
+
+ // Get NAIF ik, spk, sclk, and ck codes
+ //
+ // Use ikcode to get parameters from instrument kernel such as focal
+ // length, distortions, focal plane maps, etc
+ //
+ // Use spkcode to get spacecraft position from spk file
+ //
+ // Use sclkcode to transform times from et to tics
+ //
+ // Use ckcode to transform between frames
+ //
+ // Use bodycode to obtain radii and attitude (pole position/omega0)
+ //
+ // Use spkbodycode to read body position from spk
+
+ QString trykey = "NaifIkCode";
+ if (kernels.hasKeyword("NaifFrameCode")) trykey = "NaifFrameCode";
+ *m_ikCode = toInt(kernels[trykey][0]);
+
+ *m_spkCode = *m_ikCode / 1000;
+ *m_sclkCode = *m_spkCode;
+ *m_ckCode = *m_ikCode;
+
+ if (!m_target->isSky()) {
+ // Get target body code and radii and store them in the Naif group
+ // DAC modified to look for and store body code so that the radii keyword name
+ // will be able to be constructed even for new bodies not in the standard PCK yet.
+ QString radiiKey = "BODY" + Isis::toString(m_target->naifBodyCode()) + "_RADII";
+ QVariant result = m_target->naifBodyCode();
+ storeValue("BODY_CODE", 0, SpiceIntType, result);
+ std::vector<Distance> radii(3,Distance());
+ radii[0] = Distance(getDouble(radiiKey, 0), Distance::Kilometers);
+ radii[1] = Distance(getDouble(radiiKey, 1), Distance::Kilometers);
+ radii[2] = Distance(getDouble(radiiKey, 2), Distance::Kilometers);
+ // m_target doesn't have the getDouble method so Spice gets the radii for it
+ m_target->setRadii(radii);
+ }
+
+ *m_spkBodyCode = m_target->naifBodyCode();
+
+ // Override them if they exist in the labels
+ if (kernels.hasKeyword("NaifSpkCode")) {
+ *m_spkCode = (int) kernels["NaifSpkCode"];
+ }
+
+ if (kernels.hasKeyword("NaifCkCode")) {
+ *m_ckCode = (int) kernels["NaifCkCode"];
+ }
+
+ if (kernels.hasKeyword("NaifSclkCode")) {
+ *m_sclkCode = (int) kernels["NaifSclkCode"];
+ }
+
+ if (!m_target->isSky()) {
+ if (kernels.hasKeyword("NaifSpkBodyCode")) {
+ *m_spkBodyCode = (int) kernels["NaifSpkBodyCode"];
+ }
+ }
+
+ if (m_target->isSky()) {
+ // Create the identity rotation for sky targets
+ // Everything in bodyfixed will really be J2000
+ m_bodyRotation = new SpiceRotation(1);
+ }
+ else {
+ SpiceInt frameCode;
+ try {
+ frameCode = getInteger("BODY_FRAME_CODE", 0);
+ }
+ catch(IException &e) {
+ QString msg = "Unable to read BODY_FRAME_CODE from naifkeywords group";
+ throw IException(IException::Io, msg, _FILEINFO_);
+ }
+
+ m_bodyRotation = new SpiceRotation(frameCode);
+ *m_bodyFrameCode = frameCode;
+ }
+
+ m_instrumentRotation = new SpiceRotation(*m_ckCode);
+
+ // Set up for observer/target and light time correction to between s/c
+ // and target body.
+ LightTimeCorrectionState ltState(*m_ikCode, this);
+ ltState.checkSpkKernelsForAberrationCorrection();
+
+ vector<Distance> radius = m_target->radii();
+ Distance targetRadius((radius[0] + radius[2])/2.0);
+ m_instrumentPosition = new SpacecraftPosition(*m_spkCode, *m_spkBodyCode,
+ ltState, targetRadius);
+
+ m_sunPosition = new SpicePosition(10, m_target->naifBodyCode());
+
+
+ // Check to see if we have nadir pointing that needs to be computed &
+ // See if we have table blobs to load
+ m_sunPosition->LoadCache(isd["sun_position"]);
+ if (m_sunPosition->cacheSize() > 3) {
+ m_sunPosition->Memcache2HermiteCache(0.01);
+ }
+ m_bodyRotation->LoadCache(isd["body_rotation"]);
+ m_bodyRotation->MinimizeCache(SpiceRotation::DownsizeStatus::Yes);
+ if (m_bodyRotation->cacheSize() > 5) {
+ m_bodyRotation->LoadTimeCache();
+ }
+ solarLongitude();
+
+ // We can't assume InstrumentPointing & InstrumentPosition exist, old
+ // files may be around with the old keywords, SpacecraftPointing &
+ // SpacecraftPosition. The old keywords were in existance before the
+ // Table option, so we don't need to check for Table under the old
+ // keywords.
+ if (kernels["InstrumentPointing"].size() == 0) {
+ throw IException(IException::Unknown,
+ "No camera pointing available",
+ _FILEINFO_);
+ }
+
+ m_instrumentRotation->LoadCache(isd["instrument_pointing"]);
+ m_instrumentRotation->MinimizeCache(SpiceRotation::DownsizeStatus::Yes);
+ if (m_instrumentRotation->cacheSize() > 5) {
+ m_instrumentRotation->LoadTimeCache();
+ }
+
+
+ if (kernels["InstrumentPosition"].size() == 0) {
+ throw IException(IException::Unknown,
+ "No instrument position available",
+ _FILEINFO_);
+ }
+
+ m_instrumentPosition->LoadCache(isd["instrument_position"]);
+ NaifStatus::CheckErrors();
}
@@ -151,7 +381,7 @@ namespace Isis {
* @internal
* @history 2011-02-08 Jeannie Walldren - Initialize pointers to null.
*/
- void Spice::init(Pvl &lab, bool noTables, json isd) {
+ void Spice::init(Cube &cube, Pvl &lab, bool noTables) {
NaifStatus::CheckErrors();
// Initialize members
defaultInit();
@@ -184,73 +414,40 @@ namespace Isis {
*m_endTimePadding = 0.0;
}
- // We should remove this completely in the near future
- m_usingNaif = !lab.hasObject("NaifKeywords") || noTables;
- m_usingAle = false;
-
-
// Modified to load planetary ephemeris SPKs before s/c SPKs since some
// missions (e.g., MESSENGER) may augment the s/c SPK with new planet
// ephemerides. (2008-02-27 (KJB))
if (m_usingNaif) {
- try {
- if (isd == NULL) {
- // try using ALE
- std::ostringstream kernel_pvl;
- kernel_pvl << kernels;
-
- json props;
- if (kernels["InstrumentPointing"][0].toUpper() == "NADIR") {
- props["nadir"] = true;
- }
-
- props["kernels"] = kernel_pvl.str();
-
- isd = ale::load(lab.fileName().toStdString(), props.dump(), "ale", false, false, true);
- }
-
- json aleNaifKeywords = isd["naif_keywords"];
- m_naifKeywords = new PvlObject("NaifKeywords", aleNaifKeywords);
-
- // Still need to load clock kernels for now
- load(kernels["LeapSecond"], noTables);
- if ( kernels.hasKeyword("SpacecraftClock")) {
- load(kernels["SpacecraftClock"], noTables);
- }
- m_usingAle = true;
+ // Backup to standard ISIS implementation
+ if (noTables) {
+ load(kernels["TargetPosition"], noTables);
+ load(kernels["InstrumentPosition"], noTables);
+ load(kernels["InstrumentPointing"], noTables);
}
- catch(...) {
- // Backup to standard ISIS implementation
- if (noTables) {
- load(kernels["TargetPosition"], noTables);
- load(kernels["InstrumentPosition"], noTables);
- load(kernels["InstrumentPointing"], noTables);
- }
- if (kernels.hasKeyword("Frame")) {
- load(kernels["Frame"], noTables);
- }
+ if (kernels.hasKeyword("Frame")) {
+ load(kernels["Frame"], noTables);
+ }
- load(kernels["TargetAttitudeShape"], noTables);
- if (kernels.hasKeyword("Instrument")) {
- load(kernels["Instrument"], noTables);
- }
- // Always load after instrument
- if (kernels.hasKeyword("InstrumentAddendum")) {
- load(kernels["InstrumentAddendum"], noTables);
- }
+ load(kernels["TargetAttitudeShape"], noTables);
+ if (kernels.hasKeyword("Instrument")) {
+ load(kernels["Instrument"], noTables);
+ }
+ // Always load after instrument
+ if (kernels.hasKeyword("InstrumentAddendum")) {
+ load(kernels["InstrumentAddendum"], noTables);
+ }
- // Still need to load clock kernels for now
- load(kernels["LeapSecond"], noTables);
- if ( kernels.hasKeyword("SpacecraftClock")) {
- load(kernels["SpacecraftClock"], noTables);
- }
+ // Still need to load clock kernels for now
+ load(kernels["LeapSecond"], noTables);
+ if ( kernels.hasKeyword("SpacecraftClock")) {
+ load(kernels["SpacecraftClock"], noTables);
+ }
- // Modified to load extra kernels last to allow overriding default values
- // (2010-04-07) (DAC)
- if (kernels.hasKeyword("Extra")) {
- load(kernels["Extra"], noTables);
- }
+ // Modified to load extra kernels last to allow overriding default values
+ // (2010-04-07) (DAC)
+ if (kernels.hasKeyword("Extra")) {
+ load(kernels["Extra"], noTables);
}
// Moved the construction of the Target after the NAIF kenels have been loaded or the
@@ -347,7 +544,7 @@ namespace Isis {
else {
// JAA - Modified to store and look for the frame body code in the cube labels
SpiceInt frameCode;
- if (((m_usingNaif) || (!m_naifKeywords->hasKeyword("BODY_FRAME_CODE"))) && !isUsingAle()) {
+ if ((m_usingNaif) || (!m_naifKeywords->hasKeyword("BODY_FRAME_CODE"))) {
char frameName[32];
SpiceBoolean found;
cidfrm_c(*m_spkBodyCode, sizeof(frameName), &frameCode, frameName, &found);
@@ -396,23 +593,11 @@ namespace Isis {
// Check to see if we have nadir pointing that needs to be computed &
// See if we have table blobs to load
- if (m_usingAle) {
- m_sunPosition->LoadCache(isd["sun_position"]);
- if (m_sunPosition->cacheSize() > 3) {
- m_sunPosition->Memcache2HermiteCache(0.01);
- }
- m_bodyRotation->LoadCache(isd["body_rotation"]);
- m_bodyRotation->MinimizeCache(SpiceRotation::DownsizeStatus::Yes);
- if (m_bodyRotation->cacheSize() > 5) {
- m_bodyRotation->LoadTimeCache();
- }
- solarLongitude();
- }
- else if (kernels["TargetPosition"][0].toUpper() == "TABLE") {
- Table t("SunPosition", lab.fileName(), lab);
+ if (kernels["TargetPosition"][0].toUpper() == "TABLE") {
+ Table t = cube.readTable("SunPosition");
m_sunPosition->LoadCache(t);
- Table t2("BodyRotation", lab.fileName(), lab);
+ Table t2 = cube.readTable("BodyRotation");
m_bodyRotation->LoadCache(t2);
if (t2.Label().hasKeyword("SolarLongitude")) {
*m_solarLongitude = Longitude(t2.Label()["SolarLongitude"],
@@ -437,7 +622,7 @@ namespace Isis {
// 2009-03-18 Tracie Sucharski - Removed test for old keywords, any files
// with the old keywords should be re-run through spiceinit.
- if (kernels["InstrumentPointing"][0].toUpper() == "NADIR" && !isUsingAle()) {
+ if (kernels["InstrumentPointing"][0].toUpper() == "NADIR") {
if (m_instrumentRotation) {
delete m_instrumentRotation;
m_instrumentRotation = NULL;
@@ -445,15 +630,8 @@ namespace Isis {
m_instrumentRotation = new SpiceRotation(*m_ikCode, *m_spkBodyCode);
}
- else if (m_usingAle) {
- m_instrumentRotation->LoadCache(isd["instrument_pointing"]);
- m_instrumentRotation->MinimizeCache(SpiceRotation::DownsizeStatus::Yes);
- if (m_instrumentRotation->cacheSize() > 5) {
- m_instrumentRotation->LoadTimeCache();
- }
- }
else if (kernels["InstrumentPointing"][0].toUpper() == "TABLE") {
- Table t("InstrumentPointing", lab.fileName(), lab);
+ Table t = cube.readTable("InstrumentPointing");
m_instrumentRotation->LoadCache(t);
}
@@ -464,13 +642,11 @@ namespace Isis {
_FILEINFO_);
}
- if (m_usingAle) {
- m_instrumentPosition->LoadCache(isd["instrument_position"]);
- }
- else if (kernels["InstrumentPosition"][0].toUpper() == "TABLE") {
- Table t("InstrumentPosition", lab.fileName(), lab);
+ if (kernels["InstrumentPosition"][0].toUpper() == "TABLE") {
+ Table t = cube.readTable("InstrumentPosition");
m_instrumentPosition->LoadCache(t);
}
+
NaifStatus::CheckErrors();
}
diff --git a/isis/src/base/objs/Spice/Spice.h b/isis/src/base/objs/Spice/Spice.h
index f95b73cec2501e82686b45f143bd1e1dedf3b21d..4ffa4097cb30744970bec2f060f31cdbd62ff6f2 100644
--- a/isis/src/base/objs/Spice/Spice.h
+++ b/isis/src/base/objs/Spice/Spice.h
@@ -284,7 +284,7 @@ namespace Isis {
public:
// constructors
Spice(Cube &cube);
- Spice(Pvl &lab, nlohmann::json);
+ Spice(Pvl &lab, nlohmann::json isd);
// destructor
virtual ~Spice();
@@ -387,7 +387,8 @@ namespace Isis {
Spice(const Spice &other);
Spice &operator=(const Spice &other);
- void init(Pvl &pvl, bool noTables, nlohmann::json isd = NULL);
+ void init(Cube &cube, Pvl &pvl, bool noTables);
+ void isdInit(Pvl &pvl, nlohmann::json isd);
void csmInit(Cube &cube, Pvl label);
void defaultInit();
diff --git a/isis/src/lro/apps/lronac2isis/lronac2isis.cpp b/isis/src/lro/apps/lronac2isis/lronac2isis.cpp
index d24d3ba0a8c183bc05abf51bab63dfb6df58b5fa..addabeb0e544d9dfeff9333367d7473b7219b392 100644
--- a/isis/src/lro/apps/lronac2isis/lronac2isis.cpp
+++ b/isis/src/lro/apps/lronac2isis/lronac2isis.cpp
@@ -107,7 +107,7 @@ namespace Isis {
g_ocube->setByteOrder(outAtt.byteOrder());
g_ocube->setFormat(outAtt.fileFormat());
g_ocube->setMinMax((double) VALID_MIN2, (double) VALID_MAX2);
- g_ocube->setLabelsAttached(outAtt.labelAttachment() == AttachedLabel);
+ g_ocube->setLabelsAttached(outAtt.labelAttachment());
g_ocube->setDimensions(p.Samples(), p.Lines(), p.Bands());
g_ocube->setPixelType(Isis::Real);
g_ocube->create(ui.GetCubeName("TO"));
diff --git a/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp b/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp
index 7f0a2b9b16bb1eda4cdd97ed9055ffcf8d90dca7..24272da3562db6b66443d5afcd0d11d8a279967d 100644
--- a/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp
+++ b/isis/src/mex/apps/hrsc2isis/hrsc2isis.cpp
@@ -149,7 +149,7 @@ namespace Isis{
outCube->setByteOrder(outAtt.byteOrder());
outCube->setFormat(outAtt.fileFormat());
- outCube->setLabelsAttached(outAtt.labelAttachment() == AttachedLabel);
+ outCube->setLabelsAttached(outAtt.labelAttachment());
TableField ephTimeField("EphemerisTime", TableField::Double);
TableField expTimeField("ExposureTime", TableField::Double);
diff --git a/isis/src/mro/apps/ctxcal/ctxcal.cpp b/isis/src/mro/apps/ctxcal/ctxcal.cpp
index 6969f691cc86ce21704fc06126f8df662a91efc2..04d9289a725d3fca36a1fce0a3005a6c9fedd1d1 100644
--- a/isis/src/mro/apps/ctxcal/ctxcal.cpp
+++ b/isis/src/mro/apps/ctxcal/ctxcal.cpp
@@ -45,7 +45,7 @@ namespace Isis {
// We will be processing by line
ProcessByLine p;
- Isis::Pvl lab(icube->fileName());
+ Isis::Pvl lab = *(icube->label());
Isis::PvlGroup &inst =
lab.findGroup("Instrument", Pvl::Traverse);
diff --git a/isis/src/mro/apps/marcical/marcical.cpp b/isis/src/mro/apps/marcical/marcical.cpp
index f5592320a28851351def72b940dcbc5ca9a154d4..f2b203f262cbff89c1f9604e0a3f5588816a4146 100644
--- a/isis/src/mro/apps/marcical/marcical.cpp
+++ b/isis/src/mro/apps/marcical/marcical.cpp
@@ -297,7 +297,7 @@ namespace Isis {
ocube.setDimensions(icube.sampleCount(), icube.lineCount(), icube.bandCount());
ocube.setByteOrder(outAtt.byteOrder());
ocube.setFormat(outAtt.fileFormat());
- ocube.setLabelsAttached(outAtt.labelAttachment() == AttachedLabel);
+ ocube.setLabelsAttached(outAtt.labelAttachment());
ocube.setPixelType(outAtt.pixelType());
ocube.create(FileName(ui.GetCubeName("TO")).expanded());
diff --git a/isis/src/odyssey/apps/thmvisflat/main.cpp b/isis/src/odyssey/apps/thmvisflat/main.cpp
index 64982a03bc1bb56a82543044e7a0b5ee1be3f063..afaf6bedc84347f5ea420aa85916f88c64df6621 100644
--- a/isis/src/odyssey/apps/thmvisflat/main.cpp
+++ b/isis/src/odyssey/apps/thmvisflat/main.cpp
@@ -68,7 +68,7 @@ void IsisMain() {
ocube.setDimensions(icube.sampleCount(), icube.lineCount(), icube.bandCount());
ocube.setByteOrder(outAtt.byteOrder());
ocube.setFormat(outAtt.fileFormat());
- ocube.setLabelsAttached(outAtt.labelAttachment() == AttachedLabel);
+ ocube.setLabelsAttached(outAtt.labelAttachment());
ocube.setPixelType(outAtt.pixelType());
ocube.create(FileName(ui.GetCubeName("TO")).expanded());
diff --git a/isis/src/qisis/apps/qview/main.cpp b/isis/src/qisis/apps/qview/main.cpp
index 69f06fe013e070d47fb29fee2c50d51db97fd28f..eb8a1198e25641dbdd40771384d1c1120dceeb57 100644
--- a/isis/src/qisis/apps/qview/main.cpp
+++ b/isis/src/qisis/apps/qview/main.cpp
@@ -104,7 +104,7 @@ int main(int argc, char *argv[]) {
*/
QChar escape(27);
for (int i = 1; i < argc; i++) {
- temp += QFileInfo(FileName(argv[i]).expanded()).absoluteFilePath();
+ temp += FileName(argv[i]).expanded();
temp += QString(escape);
}
temp += "raise";
diff --git a/isis/src/qisis/objs/CubeViewport/ViewportBuffer.cpp b/isis/src/qisis/objs/CubeViewport/ViewportBuffer.cpp
index 6dbecb5d681a5a5f8efebd6458367a09e61132a8..4d2579a8dedff9225636f470c81bb7d3ca458e9b 100644
--- a/isis/src/qisis/objs/CubeViewport/ViewportBuffer.cpp
+++ b/isis/src/qisis/objs/CubeViewport/ViewportBuffer.cpp
@@ -61,8 +61,8 @@ namespace Isis {
p_requestedFillArea = 0.0;
p_bricksOrdered = true;
- connect(this, SIGNAL(ReadCube(int, int, int, int, int, int, void *)),
- p_dataThread, SLOT(ReadCube(int, int, int, int, int, int, void *)));
+ connect(this, SIGNAL(ReadCube(int, int, int, int, int, int, void *, double)),
+ p_dataThread, SLOT(ReadCube(int, int, int, int, int, int, void *, double)));
connect(p_dataThread, SIGNAL(ReadReady(void *, int, const Isis::Brick *)),
this, SLOT(DataReady(void *, int, const Isis::Brick *)));
@@ -76,8 +76,8 @@ namespace Isis {
*
*/
ViewportBuffer::~ViewportBuffer() {
- disconnect(this, SIGNAL(ReadCube(int, int, int, int, int, int, void *)),
- p_dataThread, SLOT(ReadCube(int, int, int, int, int, int, void *)));
+ disconnect(this, SIGNAL(ReadCube(int, int, int, int, int, int, void *, double)),
+ p_dataThread, SLOT(ReadCube(int, int, int, int, int, int, void *, double)));
disconnect(p_dataThread, SIGNAL(ReadReady(void *, int, const Isis::Brick *)),
this, SLOT(DataReady(void *, int, const Isis::Brick *)));
@@ -238,24 +238,22 @@ namespace Isis {
p_bricksOrdered = true;
}
- double samp;
-
// Loop through x values of rect on screen that we want to fill
+ int brickIndex = 0;
for(int x = rect->left(); x <= rect->right(); x++) {
// Index into internal buffer is minus leftmost/topmost pixel
int xIndex = x - fill->getLeftmostPixelPosition();
int yIndex = y - fill->getTopmostPixelPosition();
- samp = fill->viewportToSample(x);
-
- // Index into buffer is current sample - start sample
- // *Brick indices are in units of cube pixels, not screen pixels
- int brickIndex = (int)(samp + 0.5) - brick->Sample();
+ int scaledBufferIndex = brickIndex;
+ if (fill->scale() > 1.0) {
+ scaledBufferIndex /= fill->scale();
+ }
- if(brickIndex < 0) {
+ if(scaledBufferIndex < 0) {
p_buffer.at(yIndex).at(xIndex) = brick->at(0);
}
- else if(brickIndex >= brick->size()) {
+ else if(scaledBufferIndex >= brick->size()) {
p_buffer.at(yIndex).at(xIndex) = brick->at(brick->size() - 1);
}
else {
@@ -277,7 +275,8 @@ namespace Isis {
throw IException(IException::Programmer, msg, _FILEINFO_);
}
else {
- p_buffer.at(yIndex).at(xIndex) = brick->at(brickIndex);
+ p_buffer.at(yIndex).at(xIndex) = brick->at(scaledBufferIndex);
+ brickIndex++;
}
}
}
@@ -547,17 +546,18 @@ namespace Isis {
double esamp = fill->viewportToSample(rect.right());
- int brickWidth = (int)(ceil(esamp) - floor(ssamp)) + 1;
+ int brickWidth = (int)(ceil(esamp) - floor(ssamp));
if(brickWidth <= 0)
return;
double line = fill->viewportToLine(fill->getRequestPosition());
+ line -= (1 / fill->scale()) / 2.0;
int roundedSamp = (int)(ssamp + 0.5);
int roundedLine = (int)(line + 0.5);
- emit ReadCube(p_cubeId, roundedSamp, roundedLine, roundedSamp + brickWidth,
- roundedLine, p_band, this);
+ emit ReadCube(p_cubeId, roundedSamp, roundedLine, roundedSamp + brickWidth - 1,
+ roundedLine, p_band, this, fill->scale());
fill->incRequestPosition();
}
diff --git a/isis/src/qisis/objs/CubeViewport/ViewportBuffer.h b/isis/src/qisis/objs/CubeViewport/ViewportBuffer.h
index 747dbbe15b1b1d5f72b7d069fccf56ce5764a1c6..bf9b0b00c1490d8a3d8721c966e3fa7cf64176c1 100644
--- a/isis/src/qisis/objs/CubeViewport/ViewportBuffer.h
+++ b/isis/src/qisis/objs/CubeViewport/ViewportBuffer.h
@@ -125,7 +125,7 @@ namespace Isis {
* @param caller
*/
void ReadCube(int cubeId, int startSample, int startLine,
- int endSample, int endLine, int band, void *caller);
+ int endSample, int endLine, int band, void *caller, double scale);
//! Tell cube data thread we're done with a brick
void DoneWithData(int, const Isis::Brick *);
diff --git a/isis/src/qisis/objs/CubeViewport/ViewportBufferFill.h b/isis/src/qisis/objs/CubeViewport/ViewportBufferFill.h
index 55428fc197120c6b634c7f1f25341b3683db8620..71224c09e1f2ad344d708e36787a6d215d0635fc 100644
--- a/isis/src/qisis/objs/CubeViewport/ViewportBufferFill.h
+++ b/isis/src/qisis/objs/CubeViewport/ViewportBufferFill.h
@@ -111,6 +111,9 @@ namespace Isis {
void stop();
+ double scale() {
+ return p_xScale;
+ }
private:
//! Position of the cube reads
diff --git a/isis/src/qisis/objs/FileDialog/FileDialog.cpp b/isis/src/qisis/objs/FileDialog/FileDialog.cpp
index 0f4b95ff595c708f45f22c149f08b16839d684cb..30446bfaf3474ba1332e213050f76c6297ac1ef4 100644
--- a/isis/src/qisis/objs/FileDialog/FileDialog.cpp
+++ b/isis/src/qisis/objs/FileDialog/FileDialog.cpp
@@ -20,7 +20,7 @@ namespace Isis {
this->setOptions(QFileDialog::DontUseNativeDialog);
this->setWindowTitle(title);
- this->setFileMode(QFileDialog::ExistingFiles);
+ this->setFileMode(QFileDialog::AnyFile);
if(parent != 0) {
parent->installEventFilter(this);
p_appName = parent->windowTitle();
diff --git a/isis/src/qisis/objs/FileTool/FileTool.cpp b/isis/src/qisis/objs/FileTool/FileTool.cpp
index 214013ed26ba716c5c2251696b3a2bd24c66342b..d56fb76284c727c2b837339fea25c0094b414ae7 100644
--- a/isis/src/qisis/objs/FileTool/FileTool.cpp
+++ b/isis/src/qisis/objs/FileTool/FileTool.cpp
@@ -559,7 +559,7 @@ namespace Isis {
ocube->setDimensions(piNumSamples, piNumLines, piNumBands);
ocube->setByteOrder(outAtt.byteOrder());
ocube->setFormat(outAtt.fileFormat());
- ocube->setLabelsAttached(outAtt.labelAttachment() == AttachedLabel);
+ ocube->setLabelsAttached(outAtt.labelAttachment());
if (outAtt.propagatePixelType()) {
ocube->setPixelType(icube->pixelType());
diff --git a/isis/src/qisis/objs/Image/Image.cpp b/isis/src/qisis/objs/Image/Image.cpp
index 576f8fc9a72381f3e0932c58abd7a1382238dc1f..9a19d368ac54e97c9325c23cbf4b63f68bc37a52 100644
--- a/isis/src/qisis/objs/Image/Image.cpp
+++ b/isis/src/qisis/objs/Image/Image.cpp
@@ -525,7 +525,7 @@ namespace Isis {
// If this is an ecub (it should be) and is pointing to a relative file name,
// then we want to copy the DN cube also.
- if (!origImage.storesDnData() ) {
+ if ( origImage.labelsAttached() == Cube::ExternalLabel) {
if (origImage.externalCubeFileName().path() == ".") {
Cube dnFile(
FileName(m_fileName).path() + "/" + origImage.externalCubeFileName().name());
diff --git a/isis/src/qisis/objs/Shape/Shape.cpp b/isis/src/qisis/objs/Shape/Shape.cpp
index 0061a412fe7d98340683fd2a65a57825260b2645..405fabdb8f0b25b97251a49bd842eb9688818d56 100644
--- a/isis/src/qisis/objs/Shape/Shape.cpp
+++ b/isis/src/qisis/objs/Shape/Shape.cpp
@@ -548,7 +548,7 @@ namespace Isis {
// If this is an ecub (it should be) and is pointing to a relative file name,
// then we want to copy the DN cube also.
- if (!origShape.storesDnData()) {
+ if ( origShape.labelsAttached() == Cube::ExternalLabel ) {
if (origShape.externalCubeFileName().path() == ".") {
Cube dnFile(
FileName(m_fileName).path() + "/" + origShape.externalCubeFileName().name());
diff --git a/isis/src/system/apps/blobdump/main.cpp b/isis/src/system/apps/blobdump/main.cpp
index 22c57e817ccfc3b31d5df9483190666b14ed6750..55c1d5056a3c78fac3883ed67886925a5bfc780d 100644
--- a/isis/src/system/apps/blobdump/main.cpp
+++ b/isis/src/system/apps/blobdump/main.cpp
@@ -37,7 +37,14 @@ void IsisMain() {
FileName file = ui.GetCubeName("FROM");
QString blobname = ui.GetString("NAME");
QString blobtype = ui.GetString("TYPE");
- Blob blob(blobname, blobtype, file.expanded());
+ Blob blob(blobname, blobtype);
+ try {
+ blob.Read(file.expanded());
+ }
+ catch (...) {
+ Cube cube(file);
+ cube.read(blob);
+ }
FileName outfname = ui.GetFileName("TO");
blob.Write(outfname.expanded());
}
@@ -49,7 +56,14 @@ void helperButtonGetBlobList() {
UserInterface &ui = Application::GetUserInterface();
QString currentFile = ui.GetCubeName("FROM");
- const Pvl label(FileName(currentFile).expanded());
+ Pvl label;
+ try {
+ label = Pvl(FileName(currentFile).expanded());
+ }
+ catch (...) {
+ Cube cube(FileName(currentFile).expanded());
+ label = *cube.label();
+ }
// Check to see if the "FILE" parameter has changed since last press
if(currentFile != previousFile) {
diff --git a/isis/tests/BlobTests.cpp b/isis/tests/BlobTests.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..9f9afeb88ad5c3cdfd0225679b0e1c28e3ae6ede
--- /dev/null
+++ b/isis/tests/BlobTests.cpp
@@ -0,0 +1,125 @@
+#include <QTemporaryFile>
+#include <QString>
+#include <iostream>
+
+#include "Blob.h"
+
+#include "TempFixtures.h"
+#include "TiffFixtures.h"
+#include "TestUtilities.h"
+
+#include "gmock/gmock.h"
+
+using namespace Isis;
+
+class DefaultBlob : public TempTestingFiles {
+
+ protected:
+ Blob *testBlob;
+ QString testBlobPath = tempDir.path() + "/junk_blob.pvl";
+
+ void SetUp() override {
+ TempTestingFiles::SetUp();
+
+ testBlob = new Blob("UnitTest", "Blob");
+ char buf[] = {"ABCD"};
+ testBlob->setData(buf, 4);
+ testBlob->Write(testBlobPath);
+ }
+
+ void TearDown() override {
+ delete testBlob;
+ }
+
+};
+
+TEST_F(TempTestingFiles, TestBlobDefault) {
+ Blob b("UnitTest", "Blob");
+ char buf[] = {"ABCD"};
+ b.setData(buf, 4);
+ b.Write("junk");
+
+ EXPECT_EQ("UnitTest", b.Name());
+ EXPECT_EQ(4, b.Size());
+ EXPECT_EQ("Blob", b.Type());
+}
+
+TEST_F(DefaultBlob, TestBlobRead) {
+ Blob b("UnitTest", "Blob", testBlobPath);
+
+ EXPECT_EQ("UnitTest", b.Name());
+ EXPECT_EQ(4, b.Size());
+ EXPECT_EQ("Blob", b.Type());
+
+ std::string buffStr(b.getBuffer());
+ EXPECT_EQ("ABCD", buffStr);
+}
+
+TEST_F(DefaultBlob, TestBlobWriteExisting) {
+ Isis::Pvl pvl(testBlobPath);
+ std::fstream strm;
+ strm.open(testBlobPath.toStdString(), std::ios::binary | std::ios::out);
+ char buf[] = {"ABCD"};
+ testBlob->setData(buf, 3);
+ testBlob->Write(pvl, strm);
+ strm.seekp(0, std::ios::beg);
+ strm << pvl;
+ EXPECT_EQ("UnitTest", testBlob->Name());
+ EXPECT_EQ(3, testBlob->Size());
+ EXPECT_EQ("Blob", testBlob->Type());
+ strm.close();
+
+ Blob b("UnitTest", "Blob", testBlobPath);
+
+ EXPECT_EQ("UnitTest", b.Name());
+ EXPECT_EQ(3, b.Size());
+ EXPECT_EQ("Blob", b.Type());
+}
+
+TEST_F(DefaultBlob, TestBlobWriteExistingEOF) {
+ Isis::Pvl pvl("junk");
+ std::fstream strm;
+ strm.open(testBlobPath.toStdString(), std::ios::binary | std::ios::out);
+ char buf[] = {"ABCD"};
+ testBlob->setData(buf, 4);
+ testBlob->Write(pvl, strm);
+ strm.seekp(0, std::ios::beg);
+ strm << pvl;
+ EXPECT_EQ("UnitTest", testBlob->Name());
+ EXPECT_EQ(4, testBlob->Size());
+ EXPECT_EQ("Blob", testBlob->Type());
+ strm.close();
+
+ Blob b("UnitTest", "Blob", testBlobPath);
+
+ EXPECT_EQ("UnitTest", b.Name());
+ EXPECT_EQ(4, b.Size());
+ EXPECT_EQ("Blob", b.Type());
+}
+
+TEST_F(ReadWriteTiff, TestBlobWriteReadGdal) {
+ createTiff(UnsignedByte, false);
+ GDALDataset *dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_Update));
+
+ Blob writeBlob("UnitTest", "Blob");
+ char buf[] = {"ABCD"};
+ writeBlob.setData(buf, 4);
+ writeBlob.WriteGdal(dataset);
+
+ GDALClose(dataset);
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_Update));
+
+ Blob readBlob("UnitTest", "Blob");
+ readBlob.ReadGdal(dataset);
+
+ EXPECT_EQ(writeBlob.Name(), readBlob.Name());
+ EXPECT_EQ(writeBlob.Size(), readBlob.Size());
+ EXPECT_EQ(writeBlob.Type(), readBlob.Type());
+
+ std::string writeBuff(writeBlob.getBuffer());
+ std::string readBuff(readBlob.getBuffer());
+
+ EXPECT_EQ(writeBuff, readBuff);
+
+ GDALClose(dataset);
+}
\ No newline at end of file
diff --git a/isis/tests/BufferTests.cpp b/isis/tests/BufferTests.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..49126fc251d4021f53a03830bb33d19a89906873
--- /dev/null
+++ b/isis/tests/BufferTests.cpp
@@ -0,0 +1,157 @@
+#include <QTemporaryFile>
+#include <QString>
+#include <iostream>
+
+#include "Buffer.h"
+
+#include "TempFixtures.h"
+#include "TestUtilities.h"
+
+#include "gmock/gmock.h"
+
+using namespace Isis;
+
+TEST(BufferTest, TestBufferDefault) {
+ Buffer b(4, 3, 2, Isis::SignedInteger);
+
+ for(int i = 0; i < b.size(); i++) {
+ b[i] = i;
+ }
+
+ EXPECT_EQ(b.SampleDimension(), 4);
+ EXPECT_EQ(b.LineDimension(), 3);
+ EXPECT_EQ(b.BandDimension(), 2);
+ EXPECT_EQ(b.size(), 24);
+
+ EXPECT_EQ(b.Sample(), 0);
+ EXPECT_EQ(b.Line(), 0);
+ EXPECT_EQ(b.Band(), 0);
+
+ int samp, line, band;
+ b.Position(0, samp, line, band);
+ EXPECT_EQ(samp, 0);
+ EXPECT_EQ(line, 0);
+ EXPECT_EQ(band, 0);
+
+ EXPECT_EQ(b.Index(samp, line, band), 0);
+
+ EXPECT_EQ(b.at(0), 0);
+ EXPECT_EQ(b.at(10), 10);
+ EXPECT_EQ(b.at(23), 23);
+ EXPECT_EQ(b[0], 0);
+ EXPECT_EQ(b[10], 10);
+ EXPECT_EQ(b[23], 23);
+
+ // b.SetBasePosition(3, 2, 1);
+ // EXPECT_EQ(b.Sample(), 3);
+ // EXPECT_EQ(b.Line(), 2);
+ // EXPECT_EQ(b.Band(), 1);
+
+ // b.Position(0, samp, line, band);
+ // EXPECT_EQ(samp, 3);
+ // EXPECT_EQ(line, 2);
+ // EXPECT_EQ(band, 1);
+
+ // EXPECT_EQ(b.Index(samp, line, band), 0);
+
+ // EXPECT_EQ(b.Sample(16), 3);
+ // EXPECT_EQ(b.Line(16), 3);
+ // EXPECT_EQ(b.Band(16), 2);
+
+ // b.Position(16, samp, line, band);
+ // EXPECT_EQ(samp, 3);
+ // EXPECT_EQ(line, 3);
+ // EXPECT_EQ(band, 2);
+
+ // EXPECT_EQ(b.Index(samp, line, band), 16);
+}
+
+TEST(BufferTest, TestBufferCopy) {
+ Buffer b(4, 3, 2, Isis::SignedInteger);
+
+ for(int i = 0; i < b.size(); i++) {
+ b[i] = i;
+ }
+
+ Buffer a = b;
+
+ EXPECT_TRUE(a.DoubleBuffer() != b.DoubleBuffer());
+
+ EXPECT_EQ(a.SampleDimension(), 4);
+ EXPECT_EQ(a.LineDimension(), 3);
+ EXPECT_EQ(a.BandDimension(), 2);
+ EXPECT_EQ(a.size(), 24);
+
+ EXPECT_EQ(a[0], 0);
+ EXPECT_EQ(a[23], 23);
+
+ EXPECT_EQ(Isis::PixelTypeName(a.PixelType()), "SignedInteger");
+}
+
+TEST(BufferTest, TestBufferDefaultConstructor) {
+ Buffer nullbuf;
+ EXPECT_EQ(nullbuf.size(), 0);
+}
+
+TEST(BufferTest, TestBufferAssignment) {
+ Buffer b(2, 2, 2, Isis::Double);
+ b = 999.0;
+
+ EXPECT_EQ(b.size(), 8);
+ EXPECT_EQ(b[0], 999.0);
+ EXPECT_EQ(b[2], 999.0);
+ EXPECT_EQ(b[b.size()-1], 999.0);
+}
+
+TEST(BufferTest, TestBufferOutOfBound) {
+ Buffer b(4, 3, 2, Isis::SignedInteger);
+ for(int i = 0; i < b.size(); i++) {
+ b[i] = i;
+ }
+
+ try {
+ b.at(-1);
+ }
+ catch(Isis::IException &e) {
+ EXPECT_TRUE(e.toString().toLatin1().contains("Array subscript [-1] is out of array bounds"))
+ << e.toString().toStdString();
+ }
+
+ try {
+ b.at(24);
+ }
+ catch(Isis::IException &e) {
+ EXPECT_TRUE(e.toString().toLatin1().contains("Array subscript [24] is out of array bounds"))
+ << e.toString().toStdString();
+ }
+}
+
+TEST(BufferTest, TestBufferScale) {
+ Buffer b(4, 3, 2, Isis::SignedInteger, 0.5);
+
+ EXPECT_EQ(b.SampleDimension(), 4);
+ EXPECT_EQ(b.LineDimension(), 3);
+ EXPECT_EQ(b.BandDimension(), 2);
+
+ EXPECT_EQ(b.SampleDimensionScaled(), 2);
+ EXPECT_EQ(b.LineDimensionScaled(), 1);
+
+ EXPECT_EQ(b.size(), 4);
+
+ for(int i = 0; i < b.size(); i++) {
+ b[i] = i;
+ }
+
+ Buffer d(4, 3, 2, Isis::SignedInteger, 1);
+ d.CopyOverlapFrom(b);
+ std::vector<int> truthBuffer = {0, 0, 1, 1,
+ 0, 0, 1, 1,
+ 0, 0, 1, 1,
+ // Second band
+ 2, 2, 3, 3,
+ 2, 2, 3, 3,
+ 2, 2, 3, 3};
+ for (int i = 0; i < truthBuffer.size(); i++) {
+ EXPECT_EQ(truthBuffer[i], d[i]);
+ }
+}
\ No newline at end of file
diff --git a/isis/tests/CubeTests.cpp b/isis/tests/CubeTests.cpp
index 81261407067a1f1bd632a83dfc45472bd0ba6eba..538fcae47b6e733e6422520bb1c341b73cf73f43 100644
--- a/isis/tests/CubeTests.cpp
+++ b/isis/tests/CubeTests.cpp
@@ -30,7 +30,7 @@ void check_cube(Cube &cube,
double base,
double multiplier,
int pixelType,
- bool attached,
+ int attachType,
int format,
int isOpen,
int isReadOnly,
@@ -43,7 +43,7 @@ void check_cube(Cube &cube,
EXPECT_EQ(cube.base(), base);
EXPECT_EQ(cube.multiplier(), multiplier);
EXPECT_EQ(cube.pixelType(), pixelType);
- EXPECT_EQ(cube.labelsAttached(), attached);
+ EXPECT_EQ(cube.labelsAttached(), attachType);
EXPECT_EQ(cube.format(), format);
EXPECT_EQ(cube.isOpen(), isOpen);
if (cube.isOpen()) {
@@ -270,7 +270,7 @@ TEST(CubeTest, TestCubeAttachSpiceFromIsd) {
EXPECT_PRED_FORMAT2(AssertQStringsEqual, cam->instrumentNameLong(), "Visual Imaging Subsystem Camera B");
}
-TEST(CubeTest, TestCubeAttachLineScanTableFromIsd) {
+TEST_F(TempTestingFiles, TestCubeAttachLineScanTableFromIsd) {
std::istringstream labelStrm(R"(
Object = IsisCube
Object = Core
@@ -786,9 +786,8 @@ TEST(CubeTest, TestCubeAttachLineScanTableFromIsd) {
Pvl label;
labelStrm >> label;
- QTemporaryFile tempFile;
Cube testCube;
- testCube.fromIsd(tempFile.fileName() + ".cub", label, isd, "rw");
+ testCube.fromIsd(tempDir.path() + "/test.cub", label, isd, "rw");
PvlGroup kernels = testCube.group("Kernels");
@@ -820,11 +819,11 @@ TEST_F(SmallCube, TestCubeHasBlob) {
TEST_F(TempTestingFiles, TestCubeCreateWriteCopy) {
Cube out;
QString file = "";
- check_cube(out, file, 0, 0, 0, 0, 1, 7, 1, 1, 0, 0, 0, 65536);
+ check_cube(out, file, 0, 0, 0, 0, 1, 7, 0, 1, 0, 0, 0, 65536);
out.setDimensions(150, 200, 2);
file = QString(tempDir.path() + "/IsisCube_00.cub");
out.create(file);
- check_cube(out, file, 150, 200, 2, 0, 1, 7, 1, 1, 1, 0, 1, 65536);
+ check_cube(out, file, 150, 200, 2, 0, 1, 7, 0, 1, 1, 0, 1, 65536);
LineManager line(out);
long j = 0;
@@ -844,7 +843,7 @@ TEST_F(TempTestingFiles, TestCubeCreateWriteCopy) {
// Test the open and read methods
Cube in(file2);
- check_cube(in, file2, 150, 200, 2, 0, 1, 7, 1, 1, 1, 1, 0, 6563);
+ check_cube(in, file2, 150, 200, 2, 0, 1, 7, 0, 1, 1, 1, 0, 6563);
LineManager inLine(in);
j = 0;
@@ -862,15 +861,15 @@ TEST_F(TempTestingFiles, TestCubeCreateWriteCopy) {
TEST_F(TempTestingFiles, TestCubeCreateWrite8bit) {
Cube out;
QString file = "";
- check_cube(out, file, 0, 0, 0, 0, 1, 7, 1, 1, 0, 0, 0, 65536);
+ check_cube(out, file, 0, 0, 0, 0, 1, 7, 0, 1, 0, 0, 0, 65536);
out.setDimensions(150, 200, 1);
- out.setLabelsAttached(0);
+ out.setLabelsAttached(Cube::DetachedLabel);
out.setBaseMultiplier(200.0, -1.0);
out.setByteOrder(ISIS_LITTLE_ENDIAN ? Msb : Lsb);
out.setFormat(Cube::Bsq);
out.setLabelSize(1000);
out.setPixelType(UnsignedByte);
- check_cube(out, file, 150, 200, 1, 200, -1, 1, 0, 0, 0, 0, 0, 1000);
+ check_cube(out, file, 150, 200, 1, 200, -1, 1, 1, 0, 0, 0, 0, 1000);
file = QString(tempDir.path() + "/IsisCube_00.cub");
out.create(file);
@@ -894,7 +893,7 @@ TEST_F(TempTestingFiles, TestCubeCreateWrite8bit) {
catch (IException &e) {
e.print();
}
- check_cube(in, file, 150, 200, 1, 200, -1, 1, 0, 0, 1, 1, 0, 419);
+ check_cube(in, file, 150, 200, 1, 200, -1, 1, 1, 0, 1, 1, 0, 419);
j = 0;
LineManager inLine(in);
for(inLine.begin(); !inLine.end(); inLine++) {
@@ -911,12 +910,12 @@ TEST_F(TempTestingFiles, TestCubeCreateWrite8bit) {
TEST_F(TempTestingFiles, TestCubeCreateWrite16bit) {
Cube out;
QString file = "";
- check_cube(out, file, 0, 0, 0, 0, 1, 7, 1, 1, 0, 0, 0, 65536);
+ check_cube(out, file, 0, 0, 0, 0, 1, 7, 0, 1, 0, 0, 0, 65536);
out.setDimensions(150, 200, 2);
out.setBaseMultiplier(30000.0, -1.0);
out.setByteOrder(ISIS_LITTLE_ENDIAN ? Msb : Lsb);
out.setPixelType(SignedWord);
- check_cube(out, file, 150, 200, 2, 30000, -1, 4, 1, 1, 0, 0, 0, 65536);
+ check_cube(out, file, 150, 200, 2, 30000, -1, 4, 0, 1, 0, 0, 0, 65536);
file = QString(tempDir.path() + "/IsisCube.cub");
out.create(file);
@@ -939,7 +938,7 @@ TEST_F(TempTestingFiles, TestCubeCreateWrite16bit) {
catch (IException &e) {
e.print();
}
- check_cube(in, file, 150, 200, 2, 30000, -1, 4, 1, 1, 1, 1, 0, 65536);
+ check_cube(in, file, 150, 200, 2, 30000, -1, 4, 0, 1, 1, 1, 0, 65536);
j = 0;
LineManager inLine(in);
for(inLine.begin(); !inLine.end(); inLine++) {
@@ -1053,16 +1052,16 @@ TEST_F(SmallCube, TestCubeVirutalBands) {
TEST_F(SmallCube, TestCubeReopenRW) {
QString path = testCube->fileName();
- check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 1, 1, 1, 0, 1, 65536);
+ check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 0, 1, 1, 0, 1, 65536);
testCube->reopen("rw");
- check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 1, 1, 1, 0, 1, 65536);
+ check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 0, 1, 1, 0, 1, 65536);
}
TEST_F(SmallCube, TestCubeReopenR) {
QString path = testCube->fileName();
- check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 1, 1, 1, 0, 1, 65536);
+ check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 0, 1, 1, 0, 1, 65536);
testCube->reopen("r");
- check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 1, 1, 1, 1, 0, 65536);
+ check_cube(*testCube, path, 10, 10, 10, 0, 1, 7, 0, 1, 1, 1, 0, 65536);
}
TEST_F(SmallCube, TestCubeAlreadyOpenOpen) {
@@ -1374,14 +1373,15 @@ TEST_F(ECube, TestCubeECubeWrite) {
for (int index = 0; index < writeBrick.size(); index++) {
writeBrick[index] = 1.0;
}
- try {
- testECube->write(writeBrick);
- FAIL();
- }
- catch(IException &e) {
- EXPECT_TRUE(e.toString().toLatin1().contains("The cube [external.ecub] does not support storing DN data because it is using an external file for DNs."))
- << e.toString().toStdString();
+ testECube->write(writeBrick);
+
+ Brick readBrick(3, 3, 2, testECube->pixelType());
+ readBrick.SetBasePosition(1, 1, 1);
+ testECube->read(readBrick);
+ for (int index = 0; index < readBrick.size(); index++) {
+ EXPECT_EQ(readBrick[index], 1);
}
+
}
TEST_F(ECube, TestCubeECubeFromECubeRead) {
diff --git a/isis/tests/FunctionalTestsCubeatt.cpp b/isis/tests/FunctionalTestsCubeatt.cpp
index 174474920cb636b19d31672c64dd14ccd8640bd9..673161d5291fc18533d178eea8cffdf21806d357 100644
--- a/isis/tests/FunctionalTestsCubeatt.cpp
+++ b/isis/tests/FunctionalTestsCubeatt.cpp
@@ -46,7 +46,7 @@ TEST_F(SmallCube, FunctionalTestCubeattNoChange) {
// Check attributes: pixel type, storage format, label format, storage order, pixel range, bands
EXPECT_EQ(outputCube.pixelType(), PixelType::Real);
EXPECT_EQ(outputCube.format(), Cube::Format::Tile);
- EXPECT_TRUE(outputCube.labelsAttached());
+ EXPECT_EQ(outputCube.labelsAttached(), Cube::AttachedLabel);
EXPECT_EQ(outputCube.byteOrder(), ByteOrder::Lsb);
// Setting the pixel range modifies the base/multiplier, so check those.
EXPECT_EQ(outputCube.base(), 0);
diff --git a/isis/tests/FunctionalTestsShadow.cpp b/isis/tests/FunctionalTestsShadow.cpp
index 3efb78c57966e4d2510c58aaf98ace185842751d..c1c9acfa6e014bd52843c1d792d2c1cf20381e0f 100644
--- a/isis/tests/FunctionalTestsShadow.cpp
+++ b/isis/tests/FunctionalTestsShadow.cpp
@@ -37,10 +37,10 @@ TEST_F(DemCube, FunctionalTestShadowMatch) {
EXPECT_DOUBLE_EQ(double(shadowStats["MinimumElevation"]), 90.0);
EXPECT_DOUBLE_EQ(double(shadowStats["MaximumElevation"]), 90.0);
- EXPECT_EQ(int(shadowStats["NumRays"]), 5551);
- EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 5551);
+ EXPECT_EQ(int(shadowStats["NumRays"]), 5550);
+ EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 5550);
EXPECT_DOUBLE_EQ(double(shadowStats["AverageRayDemIntersectionsPerRay"]), 1.0);
- EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5551);
+ EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5550);
EXPECT_EQ(int(shadowStats["NumShadowedPixels"]), 0);
EXPECT_EQ(int(shadowStats["NumSpecialPixels"]), 2800);
EXPECT_EQ(int(shadowStats["NumPixelsShadowedByRays"]), 0);
@@ -49,10 +49,10 @@ TEST_F(DemCube, FunctionalTestShadowMatch) {
std::unique_ptr<Histogram> hist (shadowCube.histogram());
- EXPECT_NEAR(hist->Average(), 0.00084506527240706553, 1e-11);
- EXPECT_NEAR(hist->Sum(), 4.6909573271316205, 1e-11);
- ASSERT_EQ(hist->ValidPixels(), 5551);
- EXPECT_NEAR(hist->StandardDeviation(), 0.0010084740620921499, 1e-11);
+ EXPECT_NEAR(hist->Average(), 0.00084519596669997796, 1e-11);
+ EXPECT_NEAR(hist->Sum(), 4.6908376151848774, 1e-11);
+ EXPECT_EQ(hist->ValidPixels(), 5550);
+ EXPECT_NEAR(hist->StandardDeviation(), 0.0010084895548001136, 1e-11);
}
TEST_F(DemCube, FunctionalTestShadowTime) {
@@ -77,8 +77,8 @@ TEST_F(DemCube, FunctionalTestShadowTime) {
EXPECT_DOUBLE_EQ(double(shadowStats["MaximumElevation"]), 55.260883777776002);
EXPECT_EQ(int(shadowStats["NumRays"]), 9604);
- EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 10177);
- EXPECT_DOUBLE_EQ(double(shadowStats["AverageRayDemIntersectionsPerRay"]), 1.0596626405664);
+ EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 10159);
+ EXPECT_DOUBLE_EQ(double(shadowStats["AverageRayDemIntersectionsPerRay"]), 1.0577884214910001);
EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 9500);
EXPECT_EQ(int(shadowStats["NumShadowedPixels"]), 104);
EXPECT_EQ(int(shadowStats["NumSpecialPixels"]), 2800);
@@ -88,10 +88,10 @@ TEST_F(DemCube, FunctionalTestShadowTime) {
std::unique_ptr<Histogram> hist (shadowCube.histogram());
- EXPECT_NEAR(hist->Average(), 0.57755590112585775, 1e-11);
- EXPECT_NEAR(hist->Sum(), 5486.7810606956482, 1e-11);
- ASSERT_EQ(hist->ValidPixels(), 9500);
- EXPECT_NEAR(hist->StandardDeviation(), 0.0027122379225963896, 1e-11);
+ EXPECT_NEAR(hist->Average(), 0.5775715160056164, 1e-11);
+ EXPECT_NEAR(hist->Sum(), 5486.9294020533562, 1e-11);
+ EXPECT_EQ(hist->ValidPixels(), 9500);
+ EXPECT_NEAR(hist->StandardDeviation(), 0.0027113945565730518, 1e-11);
}
TEST_F(DemCube, FunctionalTestShadowNoShadow) {
@@ -116,7 +116,7 @@ TEST_F(DemCube, FunctionalTestShadowNoShadow) {
EXPECT_EQ(int(shadowStats["NumRays"]), 0);
EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 0);
- EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5551);
+ EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5550);
EXPECT_EQ(int(shadowStats["NumShadowedPixels"]), 0);
EXPECT_EQ(int(shadowStats["NumSpecialPixels"]), 2800);
EXPECT_EQ(int(shadowStats["NumPixelsShadowedByRays"]), 0);
@@ -125,10 +125,10 @@ TEST_F(DemCube, FunctionalTestShadowNoShadow) {
std::unique_ptr<Histogram> hist (shadowCube.histogram());
- EXPECT_NEAR(hist->Average(), 0.00084506527240706553, 1e-11);
- EXPECT_NEAR(hist->Sum(), 4.6909573271316205, 1e-11);
- EXPECT_EQ(hist->ValidPixels(), 5551);
- EXPECT_NEAR(hist->StandardDeviation(), 0.0010084740620921499, 1e-11);
+ EXPECT_NEAR(hist->Average(), 0.00084519596669997796, 1e-11);
+ EXPECT_NEAR(hist->Sum(), 4.6908376151848774, 1e-11);
+ EXPECT_EQ(hist->ValidPixels(), 5550);
+ EXPECT_NEAR(hist->StandardDeviation(), 0.0010084895548001136, 1e-11);
}
TEST_F(DemCube, FunctionalTestShadowAccurate) {
@@ -149,10 +149,10 @@ TEST_F(DemCube, FunctionalTestShadowAccurate) {
EXPECT_DOUBLE_EQ(double(shadowStats["MinimumElevation"]), 90.0);
EXPECT_DOUBLE_EQ(double(shadowStats["MaximumElevation"]), 90.0);
- EXPECT_EQ(int(shadowStats["NumRays"]), 5551);
- EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 5551);
+ EXPECT_EQ(int(shadowStats["NumRays"]), 5550);
+ EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 5550);
EXPECT_DOUBLE_EQ(double(shadowStats["AverageRayDemIntersectionsPerRay"]), 1.0);
- EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5551);
+ EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5550);
EXPECT_EQ(int(shadowStats["NumShadowedPixels"]), 0);
EXPECT_EQ(int(shadowStats["NumSpecialPixels"]), 2800);
EXPECT_EQ(int(shadowStats["NumPixelsShadowedByRays"]), 0);
@@ -161,10 +161,10 @@ TEST_F(DemCube, FunctionalTestShadowAccurate) {
std::unique_ptr<Histogram> hist (shadowCube.histogram());
- EXPECT_NEAR(hist->Average(), 0.00084506527240706553, 1e-11);
- EXPECT_NEAR(hist->Sum(), 4.6909573271316205, 1e-11);
- ASSERT_EQ(hist->ValidPixels(), 5551);
- EXPECT_NEAR(hist->StandardDeviation(), 0.0010084740620921499, 1e-11);
+ EXPECT_NEAR(hist->Average(), 0.00084519596669997796, 1e-11);
+ EXPECT_NEAR(hist->Sum(), 4.6908376151848774, 1e-11);
+ EXPECT_EQ(hist->ValidPixels(), 5550);
+ EXPECT_NEAR(hist->StandardDeviation(), 0.0010084895548001136, 1e-11);
}
TEST_F(DemCube, FunctionalTestShadowCustom) {
@@ -185,10 +185,10 @@ TEST_F(DemCube, FunctionalTestShadowCustom) {
EXPECT_DOUBLE_EQ(double(shadowStats["MinimumElevation"]), 90.0);
EXPECT_DOUBLE_EQ(double(shadowStats["MaximumElevation"]), 90.0);
- EXPECT_EQ(int(shadowStats["NumRays"]), 5551);
- EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 5551);
+ EXPECT_EQ(int(shadowStats["NumRays"]), 5550);
+ EXPECT_EQ(int(shadowStats["NumRayDemIntersections"]), 5550);
EXPECT_DOUBLE_EQ(double(shadowStats["AverageRayDemIntersectionsPerRay"]), 1.0);
- EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5551);
+ EXPECT_EQ(int(shadowStats["NumLightedPixels"]), 5550);
EXPECT_EQ(int(shadowStats["NumShadowedPixels"]), 0);
EXPECT_EQ(int(shadowStats["NumSpecialPixels"]), 2800);
EXPECT_EQ(int(shadowStats["NumPixelsShadowedByRays"]), 0);
@@ -197,10 +197,10 @@ TEST_F(DemCube, FunctionalTestShadowCustom) {
std::unique_ptr<Histogram> hist (shadowCube.histogram());
- EXPECT_NEAR(hist->Average(), 0.00084506527240706553, 1e-11);
- EXPECT_NEAR(hist->Sum(), 4.6909573271316205, 1e-11);
- ASSERT_EQ(hist->ValidPixels(), 5551);
- EXPECT_NEAR(hist->StandardDeviation(), 0.0010084740620921499, 1e-11);
+ EXPECT_NEAR(hist->Average(), 0.00084519596669997796, 1e-11);
+ EXPECT_NEAR(hist->Sum(), 4.6908376151848774, 1e-11);
+ EXPECT_EQ(hist->ValidPixels(), 5550);
+ EXPECT_NEAR(hist->StandardDeviation(), 0.0010084895548001136, 1e-11);
}
TEST_F(DemCube, FunctionalTestShadowErrors) {
diff --git a/isis/tests/GTiffTests.cpp b/isis/tests/GTiffTests.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..704c8c0679af265a0f3cfde78f228eaa26056225
--- /dev/null
+++ b/isis/tests/GTiffTests.cpp
@@ -0,0 +1,225 @@
+#include <QTemporaryFile>
+#include <QString>
+#include <iostream>
+
+#include <nlohmann/json.hpp>
+using json = nlohmann::json;
+
+#include "Blob.h"
+#include "Brick.h"
+#include "Camera.h"
+#include "Cube.h"
+#include "CubeAttribute.h"
+#include "Histogram.h"
+#include "LineManager.h"
+#include "Statistics.h"
+#include "Table.h"
+#include "TableField.h"
+#include "TableRecord.h"
+
+#include "CubeFixtures.h"
+#include "TestUtilities.h"
+
+#include "gmock/gmock.h"
+
+using namespace Isis;
+
+void check_tiff(Cube &cube,
+ QString &file,
+ int sampleCount,
+ int lineCount,
+ int bandCount,
+ double base,
+ double multiplier,
+ int pixelType,
+ int attachType,
+ int format,
+ int isOpen,
+ int isReadOnly,
+ int isReadWrite,
+ int labelSize) {
+ EXPECT_EQ(cube.fileName().toStdString(), file.toStdString());
+ EXPECT_EQ(cube.sampleCount(), sampleCount);
+ EXPECT_EQ(cube.lineCount(), lineCount);
+ EXPECT_EQ(cube.bandCount(), bandCount);
+ EXPECT_EQ(cube.base(), base);
+ EXPECT_EQ(cube.multiplier(), multiplier);
+ EXPECT_EQ(cube.pixelType(), pixelType);
+ EXPECT_EQ(cube.labelsAttached(), attachType);
+ EXPECT_EQ(cube.format(), format);
+ EXPECT_EQ(cube.isOpen(), isOpen);
+ if (cube.isOpen()) {
+ EXPECT_EQ(cube.isReadOnly(), isReadOnly);
+ EXPECT_EQ(cube.isReadWrite(), isReadWrite);
+ }
+ EXPECT_EQ(cube.labelSize(), labelSize);
+}
+
+
+TEST_F(TempTestingFiles, TestGTiffCreateWriteCopy) {
+ Cube out;
+ QString file = "";
+ check_tiff(out, file, 0, 0, 0, 0, 1, 7, 0, 1, 0, 0, 0, 65536);
+ out.setDimensions(150, 200, 2);
+ out.setFormat(Isis::Cube::GTiff);
+ file = QString(tempDir.path() + "/IsisCube_00.tiff");
+ out.create(file);
+ check_tiff(out, file, 150, 200, 2, 0, 1, 7, 0, 2, 1, 0, 1, 65536);
+
+ LineManager line(out);
+ long j = 0;
+ for(line.begin(); !line.end(); line++) {
+ for(int i = 0; i < line.size(); i++) {
+ line[i] = (double) j;
+ j++;
+ }
+ j--;
+ out.write(line);
+ }
+
+ // Copy returns the resulting Cube, we don't care about it (but we need it to flush) so delete
+ QString file2 = tempDir.path() + "/IsisCube_01.tiff";
+ CubeAttributeOutput outAtt;
+ outAtt.setFileFormat(Isis::Cube::GTiff);
+ delete out.copy(file2, outAtt);
+ out.close();
+
+ // Test the open and read methods
+ Cube in(file2);
+ check_tiff(in, file2, 150, 200, 2, 0, 1, 7, 0, 2, 1, 1, 0, 65536);
+
+ LineManager inLine(in);
+ j = 0;
+ for(inLine.begin(); !inLine.end(); inLine++) {
+ in.read(inLine);
+ for(int i = 0; i < inLine.size(); i++) {
+ EXPECT_NEAR(inLine[i], (double) j, 1e-15);
+ j++;
+ }
+ j--;
+ }
+ in.close();
+}
+
+class GdalDnTypeGenerator: public TempTestingFiles, public ::testing::WithParamInterface<Isis::PixelType> {
+ // Intentionally left empty
+ void SetUp() {
+ TempTestingFiles::SetUp();
+ }
+};
+
+INSTANTIATE_TEST_SUITE_P (GdalDnPixelTypes,
+ GdalDnTypeGenerator,
+ ::testing::Values(Isis::UnsignedByte,
+ Isis::SignedByte,
+ Isis::UnsignedWord,
+ Isis::SignedWord,
+ Isis::UnsignedInteger,
+ Isis::SignedInteger,
+ Isis::Real,
+ Isis::Double));
+
+TEST_P(GdalDnTypeGenerator, TestGTiffCreateWrite) {
+ Cube out;
+ QString file = "";
+ check_tiff(out, file, 0, 0, 0, 0, 1, 7, 0, 1, 0, 0, 0, 65536);
+ int lines = 200;
+ int samples = 150;
+ int bands = 4;
+ out.setDimensions(samples, lines, bands);
+ out.setBaseMultiplier(0.0, 1.0);
+ out.setFormat(Cube::GTiff);
+ out.setPixelType(GetParam());
+ check_tiff(out, file, samples, lines, bands, 0, 1, GetParam(), 0, 2, 0, 0, 0, 65536);
+ file = QString(tempDir.path() + "/IsisCube_00.tiff");
+ out.create(file);
+
+ // Only write DNs between 3 and 127 as those are valid
+ // DN values for all pixel types
+ // All special pixel input and output tests are handled in the
+ // GdalIoHandler tests
+ int min = 3;
+ int max = 127;
+
+ long j = min;
+ LineManager oline(out);
+ for(oline.begin(); !oline.end(); oline++) {
+ for(int i = 0; i < oline.size(); i++) {
+ oline[i] = (double) j;
+ }
+ out.clearIoCache();
+ out.write(oline);
+ j++;
+ if (j > max) {
+ j = min;
+ }
+ }
+ out.close();
+
+ Cube in;
+ try {
+ in.open(file);
+ }
+ catch (IException &e) {
+ e.print();
+ }
+ check_tiff(in, file, samples, lines, bands, 0, 1, GetParam(), 0, 2, 1, 1, 0, 65536);
+
+ Statistics *cubeStats = in.statistics(0);
+ EXPECT_DOUBLE_EQ(cubeStats->Average(), 62.65625);
+ EXPECT_DOUBLE_EQ(cubeStats->StandardDeviation(), 36.277390383170371);
+ EXPECT_DOUBLE_EQ(cubeStats->TotalPixels(), 120000);
+ EXPECT_DOUBLE_EQ(cubeStats->NullPixels(), 0);
+ delete cubeStats;
+ in.close();
+}
+
+// Add Test for GTiff with no ISIS metadata
+
+TEST_F(TempTestingFiles, TableTestsWriteReadGdal) {
+ TableField f1("Column1", TableField::Integer);
+ TableField f2("Column2", TableField::Double);
+ TableField f3("Column3", TableField::Text, 10);
+ TableField f4("Column4", TableField::Double);
+ TableRecord rec;
+ rec += f1;
+ rec += f2;
+ rec += f3;
+ rec += f4;
+ Table t("UNITTEST", rec);
+
+ t.SetAssociation(Table::Lines);
+
+ rec[0] = 5;
+ rec[1] = 3.14;
+ rec[2] = "PI";
+ rec[3] = 3.14159;
+ t += rec;
+
+ rec[0] = -1;
+ rec[1] = 0.5;
+ rec[2] = "HI";
+ rec[3] = -0.55;
+ t += rec;
+
+ QString cubeFile = tempDir.path() + "/testTable.tiff";
+ Cube cube;
+ cube.setDimensions(10, 10, 1);
+ cube.setFormat(Isis::Cube::GTiff);
+ cube.create(cubeFile);
+ cube.write(t);
+ Blob tableBlob("UNITTEST", "Table");
+ cube.read(tableBlob);
+ Table t2(tableBlob);
+
+ EXPECT_EQ(t.RecordFields(), t2.RecordFields());
+ EXPECT_EQ(t.RecordSize(), t2.RecordSize());
+ EXPECT_EQ(t.IsSampleAssociated(), t2.IsSampleAssociated());
+ EXPECT_EQ(t.IsLineAssociated(), t2.IsLineAssociated());
+ EXPECT_EQ(t.IsBandAssociated(), t2.IsBandAssociated());
+
+ ASSERT_EQ(t.Records(), t2.Records());
+ for (int i = 0; i < t.Records(); i++) {
+ EXPECT_EQ(TableRecord::toString(t[i]).toStdString(), TableRecord::toString(t2[i]).toStdString());
+ }
+}
\ No newline at end of file
diff --git a/isis/tests/GdalIoHandlerTests.cpp b/isis/tests/GdalIoHandlerTests.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..166bbf84ec0beebd28ac43be3983109ab4bb22a6
--- /dev/null
+++ b/isis/tests/GdalIoHandlerTests.cpp
@@ -0,0 +1,672 @@
+#include <QTemporaryFile>
+#include <QString>
+#include <iostream>
+#include <iomanip>
+
+#include <nlohmann/json.hpp>
+using json = nlohmann::json;
+
+#include "Brick.h"
+#include "PixelType.h"
+#include "GdalIoHandler.h"
+#include "SpecialPixel.h"
+#include "TiffFixtures.h"
+
+#include "TestUtilities.h"
+
+#include "gmock/gmock.h"
+
+using namespace Isis;
+
+TEST_F(ReadWriteTiff, GdalIoTestsDefaulWrite) {
+ PixelType isisPixelType = Double;
+ createTiff(isisPixelType, false);
+
+ {
+ const QList<int> *bandList = new QList<int>;
+
+ GdalIoHandler handler(path, bandList, GDT_Float64, GA_Update);
+ Brick localBrick(6, 1, 1, isisPixelType);
+
+ localBrick.SetBasePosition(1, 1, 1);
+ // init everything to 100
+ for (int i = 0; i < localBrick.size(); i++) {
+ localBrick[i] = 100;
+ }
+
+ handler.write(localBrick);
+ } // file is closed
+
+ // read it back
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (double *) CPLMalloc(sizeof(double)*6*1);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ for (int i = 0; i<6*1; i++) {
+ ASSERT_EQ(((double *) dbuf)[i], 100);
+ }
+
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadFloat64) {
+ PixelType isisPixelType = Double;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], LOW_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[3], LOW_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 1000.0);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadFloat32) {
+ PixelType isisPixelType = Real;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], LOW_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[3], LOW_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 1000.0);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadInt32) {
+ PixelType isisPixelType = SignedInteger;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], LOW_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[3], LOW_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 1000.0);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadUInt32) {
+ PixelType isisPixelType = UnsignedInteger;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], LOW_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[3], LOW_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 1000.0);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadInt16) {
+ PixelType isisPixelType = SignedWord;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], LOW_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[3], LOW_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 1000.0);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadUInt16) {
+ PixelType isisPixelType = UnsignedWord;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], LOW_INSTR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[3], LOW_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 1000.0);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadInt8) {
+ PixelType isisPixelType = SignedByte;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], NULL8);
+ EXPECT_EQ(brickDoubleBuff[3], NULL8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 50);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadUInt8) {
+ PixelType isisPixelType = UnsignedByte;
+ createTiff(isisPixelType);
+
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType));
+ handler.read(*localBrick);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ EXPECT_EQ(brickDoubleBuff[0], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(brickDoubleBuff[2], NULL8);
+ EXPECT_EQ(brickDoubleBuff[3], NULL8);
+ EXPECT_EQ(brickDoubleBuff[4], NULL8);
+ EXPECT_EQ(brickDoubleBuff[5], 50);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteFloat64) {
+ PixelType isisPixelType = Double;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 1000;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (double *)CPLMalloc(sizeof(double) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((double *)dbuf)[0], HIGH_INSTR_SAT8);
+ EXPECT_EQ(((double *)dbuf)[1], HIGH_REPR_SAT8);
+ EXPECT_EQ(((double *)dbuf)[2], LOW_INSTR_SAT8);
+ EXPECT_EQ(((double *)dbuf)[3], LOW_REPR_SAT8);
+ EXPECT_EQ(((double *)dbuf)[4], NULL8);
+ EXPECT_EQ(((double *)dbuf)[5], 1000);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteFloat32) {
+ PixelType isisPixelType = Real;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 1000;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (float *)CPLMalloc(sizeof(float) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((float *)dbuf)[0], HIGH_INSTR_SAT4);
+ EXPECT_EQ(((float *)dbuf)[1], HIGH_REPR_SAT4);
+ EXPECT_EQ(((float *)dbuf)[2], LOW_INSTR_SAT4);
+ EXPECT_EQ(((float *)dbuf)[3], LOW_REPR_SAT4);
+ EXPECT_EQ(((float *)dbuf)[4], NULL4);
+ EXPECT_EQ(((float *)dbuf)[5], 1000);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteInt32) {
+ PixelType isisPixelType = SignedInteger;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 1000;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (unsigned int *)CPLMalloc(sizeof(unsigned int) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((unsigned int *)dbuf)[0], HIGH_INSTR_SATI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[1], HIGH_REPR_SATI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[2], LOW_INSTR_SATI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[3], LOW_REPR_SATI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[4], NULLI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[5], 1000);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteUInt32) {
+ PixelType isisPixelType = UnsignedInteger;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 1000;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (unsigned int *)CPLMalloc(sizeof(unsigned int) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((unsigned int *)dbuf)[0], HIGH_INSTR_SATUI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[1], HIGH_REPR_SATUI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[2], LOW_INSTR_SATUI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[3], LOW_REPR_SATUI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[4], NULLUI4);
+ EXPECT_EQ(((unsigned int *)dbuf)[5], 1000);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteInt16) {
+ PixelType isisPixelType = SignedWord;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 1000;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (short *)CPLMalloc(sizeof(short) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((short *)dbuf)[0], HIGH_INSTR_SAT2);
+ EXPECT_EQ(((short *)dbuf)[1], HIGH_REPR_SAT2);
+ EXPECT_EQ(((short *)dbuf)[2], LOW_INSTR_SAT2);
+ EXPECT_EQ(((short *)dbuf)[3], LOW_REPR_SAT2);
+ EXPECT_EQ(((short *)dbuf)[4], NULL2);
+ EXPECT_EQ(((short *)dbuf)[5], 1000);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteUInt16) {
+ PixelType isisPixelType = UnsignedWord;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 1000;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (unsigned short *)CPLMalloc(sizeof(unsigned short) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((unsigned short *)dbuf)[0], HIGH_INSTR_SATU2);
+ EXPECT_EQ(((unsigned short *)dbuf)[1], HIGH_REPR_SATU2);
+ EXPECT_EQ(((unsigned short *)dbuf)[2], LOW_INSTR_SATU2);
+ EXPECT_EQ(((unsigned short *)dbuf)[3], LOW_REPR_SATU2);
+ EXPECT_EQ(((unsigned short *)dbuf)[4], NULLU2);
+ EXPECT_EQ(((unsigned short *)dbuf)[5], 1000);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteInt8) {
+ PixelType isisPixelType = SignedByte;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 50;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (char *)CPLMalloc(sizeof(char) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((char *)dbuf)[0], HIGH_INSTR_SATS1);
+ EXPECT_EQ(((char *)dbuf)[1], HIGH_REPR_SATS1);
+ EXPECT_EQ(((char *)dbuf)[2], LOW_INSTR_SATS1);
+ EXPECT_EQ(((char *)dbuf)[3], LOW_REPR_SATS1);
+ EXPECT_EQ(((char *)dbuf)[4], NULLS1);
+ EXPECT_EQ(((char *)dbuf)[5], 50);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsWriteUInt8) {
+ PixelType isisPixelType = UnsignedByte;
+ createTiff(isisPixelType, false);
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ const QList<int> *bandList = new QList<int>;
+ GdalIoHandler handler(path, bandList, IsisPixelToGdal(isisPixelType), GA_Update);
+
+ localBrick = new Brick(6, 1, 1, isisPixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+
+ brickDoubleBuff[0] = HIGH_INSTR_SAT8;
+ brickDoubleBuff[1] = HIGH_REPR_SAT8;
+ brickDoubleBuff[2] = LOW_INSTR_SAT8;
+ brickDoubleBuff[3] = LOW_REPR_SAT8;
+ brickDoubleBuff[4] = NULL8;
+ brickDoubleBuff[5] = 50;
+
+ handler.write(*localBrick);
+ }
+
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_ReadOnly));
+ dbuf = (unsigned char *)CPLMalloc(sizeof(unsigned char) * 6);
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Read, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to read tiff";
+ }
+
+ EXPECT_EQ(((unsigned char *)dbuf)[0], HIGH_INSTR_SAT1);
+ EXPECT_EQ(((unsigned char *)dbuf)[1], HIGH_REPR_SAT1);
+ EXPECT_EQ(((unsigned char *)dbuf)[2], LOW_INSTR_SAT1);
+ EXPECT_EQ(((unsigned char *)dbuf)[3], LOW_REPR_SAT1);
+ EXPECT_EQ(((unsigned char *)dbuf)[4], NULL1);
+ EXPECT_EQ(((unsigned char *)dbuf)[5], 50);
+}
+
+TEST_F(ReadWriteTiff, GdalIoTestsReadOutside) {
+ PixelType isisPixelType = SignedWord;
+ const QList<int> *bandList = new QList<int>;
+
+ // Create a context so the handler goes out of scope and closes the file
+ {
+ int samples = 5;
+ int lines = 5;
+ createSizedTiff(samples, lines, 1, isisPixelType);
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_Update));
+ dbuf = (void *)CPLMalloc(sizeof(short) * samples * lines);
+
+ for (short i = 0; i < samples * lines; i++) {
+ ((short *)dbuf)[i] = i;
+ }
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Write, 0, 0,
+ samples, lines,
+ dbuf,
+ samples, lines,
+ IsisPixelToGdal(isisPixelType),
+ 0, 0);
+
+ if (err > CE_Failure) {
+ FAIL() << "Failed to write tiff";
+ }
+
+ dataset->Close();
+ }
+
+ GdalIoHandler gdalHandler(path, bandList, IsisPixelToGdal(isisPixelType));
+
+ delete localBrick;
+ localBrick = NULL;
+ localBrick = new Brick(4, 4, 1, isisPixelType);
+
+ // Test out of bounds read at the topleft
+ localBrick->SetBasePosition(-1, -1, 1);
+ gdalHandler.read(*localBrick);
+ double *brickDoubleBuff = localBrick->DoubleBuffer();
+ std::vector<double> resultVec = {NULL8, NULL8, NULL8, NULL8,
+ NULL8, NULL8, NULL8, NULL8,
+ NULL8, NULL8, 0, 1,
+ NULL8, NULL8, 5, 6};
+ for (short i = 0; i < 4 * 4; i++) {
+ EXPECT_EQ(brickDoubleBuff[i], resultVec[i]);
+ }
+
+ // Test out of bounds read at the bottom right
+ localBrick->SetBasePosition(4, 4, 1);
+ gdalHandler.read(*localBrick);
+ brickDoubleBuff = localBrick->DoubleBuffer();
+ resultVec = { 18, 19, NULL8, NULL8,
+ 23, 24, NULL8, NULL8,
+ NULL8, NULL8, NULL8, NULL8,
+ NULL8, NULL8, NULL8, NULL8};
+ for (short i = 0; i < 4 * 4; i++) {
+ EXPECT_EQ(brickDoubleBuff[i], resultVec[i]);
+ }
+
+ delete localBrick;
+ localBrick = NULL;
+ localBrick = new Brick(7, 7, 1, isisPixelType);
+ localBrick->SetBasePosition(0, 0, 1);
+
+ // Test filling a larger buffer than is in the image
+ gdalHandler.read(*localBrick);
+ brickDoubleBuff = localBrick->DoubleBuffer();
+ resultVec = {NULL8, NULL8, NULL8, NULL8, NULL8, NULL8, NULL8,
+ NULL8, 0, 1, 2, 3, 4, NULL8,
+ NULL8, 5, 6, 7, 8, 9, NULL8,
+ NULL8, 10, 11, 12, 13, 14, NULL8,
+ NULL8, 15, 16, 17, 18, 19, NULL8,
+ NULL8, 20, 21, 22, 23, 24, NULL8,
+ NULL8, NULL8, NULL8, NULL8, NULL8, NULL8, NULL8};
+ for (short i = 0; i < 7 * 7; i++) {
+ EXPECT_EQ(brickDoubleBuff[i], resultVec[i]);
+ }
+
+ // Test reading completely outside of an image
+ delete localBrick;
+ localBrick = NULL;
+ localBrick = new Brick(2, 2, 1, isisPixelType);
+
+ // Read non-NULL8 data
+ localBrick->SetBasePosition(2, 2, 1);
+ gdalHandler.read(*localBrick);
+
+ // Read over to ensure brick is updated back to NULL8s
+ localBrick->SetBasePosition(8, 8, 1);
+ gdalHandler.read(*localBrick);
+ brickDoubleBuff = localBrick->DoubleBuffer();
+ resultVec = {NULL8, NULL8,
+ NULL8, NULL8};
+ for (short i = 0; i < 2 * 2; i++) {
+ EXPECT_EQ(brickDoubleBuff[i], resultVec[i]);
+ }
+
+ delete localBrick;
+ localBrick = NULL;
+ localBrick = new Brick(2, 2, 1, isisPixelType);
+
+ // Read non-NULL8 data
+ localBrick->SetBasePosition(2, 2, 1);
+ gdalHandler.read(*localBrick);
+
+ // Read over to ensure brick is updated back to NULL8s
+ localBrick->SetBasePosition(-4, -4, 1);
+ gdalHandler.read(*localBrick);
+ brickDoubleBuff = localBrick->DoubleBuffer();
+ resultVec = {NULL8, NULL8,
+ NULL8, NULL8};
+ for (short i = 0; i < 2 * 2; i++) {
+ EXPECT_EQ(brickDoubleBuff[i], resultVec[i]);
+ }
+}
diff --git a/isis/tests/TiffFixtures.cpp b/isis/tests/TiffFixtures.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..c7af4a096a334c5bfebd945e8c0e81b30ad6e483
--- /dev/null
+++ b/isis/tests/TiffFixtures.cpp
@@ -0,0 +1,177 @@
+#include "TiffFixtures.h"
+
+#include "Brick.h"
+#include "PixelType.h"
+#include "SpecialPixel.h"
+
+namespace Isis {
+
+ void ReadWriteTiff::SetUp() {
+ TempTestingFiles::SetUp();
+
+ path = tempDir.path() + "/tiny.tiff";
+ }
+
+ void ReadWriteTiff::TearDown() {
+ if (dataset) {
+ delete dataset;
+ }
+ if (localBrick) {
+ delete localBrick;
+ }
+ if (dbuf) {
+ CPLFree(dbuf);
+ }
+ }
+
+ void ReadWriteTiff::createSizedTiff(int samples, int lines, int bands, PixelType pixelType) {
+ GDALAllRegister();
+ GDALDriver* driver = GetGDALDriverManager()->GetDriverByName("GTiff");
+ if (driver) {
+ char **papszOptions = NULL;
+ dataset = driver->Create(path.toStdString().c_str(), samples, lines, bands, IsisPixelToGdal(pixelType), papszOptions);
+ if (dataset) {
+ double noDataValue;
+ switch (pixelType) {
+ case UnsignedByte:
+ noDataValue = (double) NULL1;
+ break;
+ case SignedByte:
+ noDataValue = (double) NULLS1;
+ break;
+ case UnsignedWord:
+ noDataValue = (double) NULLU2;
+ break;
+ case SignedWord:
+ noDataValue = (double) NULL2;
+ break;
+ case UnsignedInteger:
+ noDataValue = (double) NULLUI4;
+ break;
+ case SignedInteger:
+ noDataValue = (double) NULLI4;
+ break;
+ case Real:
+ noDataValue = (double) NULL4;
+ break;
+
+ default:
+ noDataValue = NULL8;
+ break;
+ }
+ for (int i = 1; i <= bands; i++) {
+ GDALRasterBand *band = dataset->GetRasterBand(i);
+ band->SetScale(1);
+ band->SetOffset(0);
+ band->SetNoDataValue(noDataValue);
+ }
+ dataset->CreateMaskBand(GMF_ALPHA);
+ dataset->GetRasterBand(1)->GetMaskBand()->Fill(255);
+ dataset->Close();
+ }
+ }
+ }
+
+ void ReadWriteTiff::createTiff(PixelType pixelType, bool write) {
+ createSizedTiff(6, 1, 1, pixelType);
+ if (write) {
+ dataset = GDALDataset::FromHandle(GDALOpen(path.toStdString().c_str(), GA_Update));
+ if (pixelType == Double) {
+ dbuf = (void *)CPLMalloc(sizeof(double) * 6);
+
+ ((double *)dbuf)[0] = HIGH_INSTR_SAT8;
+ ((double *)dbuf)[1] = HIGH_REPR_SAT8;
+ ((double *)dbuf)[2] = LOW_INSTR_SAT8;
+ ((double *)dbuf)[3] = LOW_REPR_SAT8;
+ ((double *)dbuf)[4] = NULL8;
+ ((double *)dbuf)[5] = 1000;
+ }
+ else if (pixelType == Real) {
+ dbuf = (void *)CPLMalloc(sizeof(float) * 6);
+
+ ((float *)dbuf)[0] = HIGH_INSTR_SAT4;
+ ((float *)dbuf)[1] = HIGH_REPR_SAT4;
+ ((float *)dbuf)[2] = LOW_INSTR_SAT4;
+ ((float *)dbuf)[3] = LOW_REPR_SAT4;
+ ((float *)dbuf)[4] = NULL4;
+ ((float *)dbuf)[5] = 1000;
+ }
+ else if (pixelType == SignedInteger) {
+ dbuf = (void *)CPLMalloc(sizeof(int) * 6);
+
+ ((int *)dbuf)[0] = HIGH_INSTR_SATI4;
+ ((int *)dbuf)[1] = HIGH_REPR_SATI4;
+ ((int *)dbuf)[2] = LOW_INSTR_SATI4;
+ ((int *)dbuf)[3] = LOW_REPR_SATI4;
+ ((int *)dbuf)[4] = NULLI4;
+ ((int *)dbuf)[5] = 1000;
+ }
+ else if (pixelType == UnsignedInteger) {
+ dbuf = (void *)CPLMalloc(sizeof(unsigned int) * 6);
+
+ ((unsigned int *)dbuf)[0] = HIGH_INSTR_SATUI4;
+ ((unsigned int *)dbuf)[1] = HIGH_REPR_SATUI4;
+ ((unsigned int *)dbuf)[2] = LOW_INSTR_SATUI4;
+ ((unsigned int *)dbuf)[3] = LOW_REPR_SATUI4;
+ ((unsigned int *)dbuf)[4] = NULLUI4;
+ ((unsigned int *)dbuf)[5] = 1000;
+ }
+ else if (pixelType == SignedWord) {
+ dbuf = (void *)CPLMalloc(sizeof(short) * 6);
+
+ ((short *)dbuf)[0] = HIGH_INSTR_SAT2;
+ ((short *)dbuf)[1] = HIGH_REPR_SAT2;
+ ((short *)dbuf)[2] = LOW_INSTR_SAT2;
+ ((short *)dbuf)[3] = LOW_REPR_SAT2;
+ ((short *)dbuf)[4] = NULL2;
+ ((short *)dbuf)[5] = 1000;
+ }
+ else if (pixelType == UnsignedWord) {
+ dbuf = (void *)CPLMalloc(sizeof(unsigned short) * 6);
+
+ ((unsigned short *)dbuf)[0] = HIGH_INSTR_SATU2;
+ ((unsigned short *)dbuf)[1] = HIGH_REPR_SATU2;
+ ((unsigned short *)dbuf)[2] = LOW_INSTR_SATU2;
+ ((unsigned short *)dbuf)[3] = LOW_REPR_SATU2;
+ ((unsigned short *)dbuf)[4] = NULLU2;
+ ((unsigned short *)dbuf)[5] = 1000;
+ }
+ else if (pixelType == SignedByte) {
+ dbuf = (void *)CPLMalloc(sizeof(char) * 6);
+
+ ((char *)dbuf)[0] = HIGH_INSTR_SATS1;
+ ((char *)dbuf)[1] = HIGH_REPR_SATS1;
+ ((char *)dbuf)[2] = LOW_INSTR_SATS1;
+ ((char *)dbuf)[3] = LOW_REPR_SATS1;
+ ((char *)dbuf)[4] = NULLS1;
+ ((char *)dbuf)[5] = 50;
+ }
+ else if (pixelType == UnsignedByte) {
+ dbuf = (void *)CPLMalloc(sizeof(unsigned char) * 6);
+
+ ((unsigned char *)dbuf)[0] = HIGH_INSTR_SAT1;
+ ((unsigned char *)dbuf)[1] = HIGH_REPR_SAT1;
+ ((unsigned char *)dbuf)[2] = LOW_INSTR_SAT1;
+ ((unsigned char *)dbuf)[3] = LOW_REPR_SAT1;
+ ((unsigned char *)dbuf)[4] = NULL1;
+ ((unsigned char *)dbuf)[5] = 50;
+ }
+
+ localBrick = new Brick(6, 1, 1, pixelType);
+ localBrick->SetBasePosition(1, 1, 1);
+
+ GDALRasterBand *poBand = dataset->GetRasterBand(1);
+ CPLErr err = poBand->RasterIO(GF_Write, 0, 0,
+ 6, 1,
+ dbuf,
+ 6, 1,
+ IsisPixelToGdal(pixelType),
+ 0, 0);
+ if (err > CE_Failure) {
+ FAIL() << "Failed to write tiff";
+ }
+
+ dataset->Close();
+ }
+ }
+}
\ No newline at end of file
diff --git a/isis/tests/TiffFixtures.h b/isis/tests/TiffFixtures.h
new file mode 100644
index 0000000000000000000000000000000000000000..9a9819ce4baa710cf823d49de4bb8c04f5065fae
--- /dev/null
+++ b/isis/tests/TiffFixtures.h
@@ -0,0 +1,28 @@
+#ifndef TiffFixtures_h
+#define TiffFixtures_h
+
+#include "gtest/gtest.h"
+
+#include "Brick.h"
+#include "PixelType.h"
+#include "TempFixtures.h"
+
+#include "gdal_priv.h"
+
+namespace Isis {
+
+ class ReadWriteTiff : public TempTestingFiles {
+ protected:
+ void *dbuf = NULL;
+ GDALDataset *dataset = NULL;
+ Brick *localBrick = NULL;
+ QString path;
+
+ void SetUp() override;
+ void TearDown() override;
+ void createSizedTiff(int samples, int lines, int bands, PixelType pixelType);
+ void createTiff(PixelType pixelType, bool write=true);
+ };
+}
+
+#endif
\ No newline at end of file