Adds dynamic reference indices to ISIS network writes (#157)

* Adds dynamic reference indices to ISIS network writes

* Updates for comments

* Stub failing test

* Adds tests for referenceIndex in cnets

* Updates tests to check for warnings

* Removes travis

.travis.yml

-language: generic
-sudo: false
-
-branches:
-  only:
-    - master
-
-os:
-  - linux
-  - osx
-
-env:
-  - PYTHON_VERSION=3.6 HAS_GDAL=true
-  - PYTHON_VERSION=3.6 HAS_GDAL=false
-  - PYTHON_VERSION=3.7 HAS_GDAL=true
-  - PYTHON_VERSION=3.7 HAS_GDAL=false
-  - PYTHON_VERSION=3.8 HAS_GDAL=true
-  - PYTHON_VERSION=3.8 HAS_GDAL=false
-before_install:
-  # We do this conditionally because it saves us some downloading if the
-  # version is the same.
-  - if [ "$TRAVIS_OS_NAME" == "linux" ]; then
-      wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-    else
-      curl -o miniconda.sh  https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh;
-    fi
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  # Useful for debugging any issues with conda
-  - conda info -a
-  # Create the env
-  - conda create -q -n test python=$PYTHON_VERSION
-  - source activate test
-  # https://github.com/travis-ci/travis-ci/issues/8982
-  - python -c "import fcntl; fcntl.fcntl(1, fcntl.F_SETFL, 0)"
-
-install:
-  - conda config --add channels usgs-astrogeology
-  - conda config --add channels conda-forge
-  - if $HAS_GDAL; then
-      conda env update -n test -f environment.yml;
-    else
-      conda env update -n test -f environment_noGDAL.yml;
-    fi
-
-script:
-  - pytest --cov=plio
-
-after_success:
-  - coveralls
-  # Need to do the build in the root
-  - source deactivate
-  - conda install -q conda-build anaconda-client
-  - conda config --set anaconda_upload no
-  - travis_wait conda build recipe -q
-  - travis_wait builddir=(`conda build recipe --output`)
-  - |
-    if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then
-      anaconda -t="$CONDA_UPLOAD_TOKEN" upload -l dev --force $builddir;
-    fi
-
-  # Docs to gh-pages
-  - source activate test  # Reactivate the env to have all deps installed.
-  - pip install travis-sphinx
-  - travis-sphinx build --source=docs --nowarn # The sphinx build script
-  - travis-sphinx deploy
-
-notifications:
-  webhooks:
-    on_success: always
-    on_failure: always
-    on_start: never
-  email:
-      recipients:
-        - jlaura@usgs.gov
-      on_success: always
-      on_failure: always

environment.yml

@@ -8,7 +8,7 @@ dependencies:
   - numpy 
   - pyproj 
   - h5py 
-  - pvl 
+  - pvl >= 1.0 
   - scipy 
   - protobuf 
   - affine 

plio/io/io_controlnetwork.py

@@ -335,6 +335,11 @@ class IsisStore(object):
             #point_spec.id = _set_pid(i)
             point_spec.id = _set_pid(i)
             point_spec.type = g.iloc[0].pointType
+            try:
+                point_spec.referenceIndex = g.iloc[0].referenceIndex
+            except:
+                warnings.warn(f'Unable to identify referenceIndex for point {point_spec.id}. Defaulting to index 0.')
+                point_spec.referenceIndex = 0
             for attr, attrtype in self.point_attrs:
                 # Un-mangle common attribute names between points and measures
                 df_attr = self.point_field_map.get(attr, attr)
@@ -356,8 +361,6 @@ class IsisStore(object):
                     else:
                         setattr(point_spec, attr, attrtype(g.iloc[0][df_attr]))
 
-            # The reference index should always be the image with the lowest index
-            point_spec.referenceIndex = 0
             # A single extend call is cheaper than many add calls to pack points
             measure_iterable = []
             for node_id, m in g.iterrows():

plio/io/tests/test_io_controlnetwork.py

@@ -72,15 +72,16 @@ def cnet_dataframe(tmpdir):
     serials = {i:'APOLLO15/METRIC/{}'.format(j) for i, j in enumerate(serial_times.values())}
     columns = ['id', 'pointType', 'serialnumber', 'measureType',
                'sample', 'line', 'image_index', 'pointLog', 'measureLog',
-               'aprioriCovar']
+               'aprioriCovar', 'referenceIndex']
 
     data = []
     for i in range(npts):
         aprioriCovar = None
         if i == npts - 1:
             aprioriCovar = np.ones((2,3))
-        data.append((i, 2, serials[0], 2, 0, 0, 0, [], [], aprioriCovar))
-        data.append((i, 2, serials[1], 2, 0, 0, 1, [], [io_controlnetwork.MeasureLog(2, 0.5)],aprioriCovar))
+        reference_idx = i % 2
+        data.append((i, 2, serials[0], 2, 0, 0, 0, [], [], aprioriCovar,reference_idx))
+        data.append((i, 2, serials[1], 2, 0, 0, 1, [], [io_controlnetwork.MeasureLog(2, 0.5)],aprioriCovar, reference_idx))
 
     df = pd.DataFrame(data, columns=columns)
     
@@ -121,6 +122,9 @@ def test_create_point(cnet_dataframe, tmpdir):
             point_protocol.ParseFromString(raw_point)
             assert str(i) == point_protocol.id
             assert 2 == point_protocol.type
+
+            assert i % 2 == point_protocol.referenceIndex
+
             if i == cnet_dataframe.npts - 1:
                 assert point_protocol.aprioriCovar == [1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
             for j, m in enumerate(point_protocol.measures):
@@ -128,6 +132,21 @@ def test_create_point(cnet_dataframe, tmpdir):
                 assert 2 == m.type
                 assert len(m.log) == j  # Only the second measure has a message
 
+def test_create_point_wo_reference_index(cnet_dataframe, tmpdir):
+    # cnet_dataframe has 5 points. Set the reference on one of those to be 
+    # the second measure.
+    reference_idx = [0,0,0,0,0,0,0,0,0,0]
+    new_cnet_dataframe = cnet_dataframe.drop(columns='referenceIndex')
+    cnet_file = tmpdir.join('test_w_reference.net')
+
+    # Check that the warn is raised properly
+    with pytest.warns(UserWarning, match='Unable to identify referenceIndex (.*)'):
+        io_controlnetwork.to_isis(new_cnet_dataframe, cnet_file, mode='wb', targetname='Moon')
+        
+    # Check that nothing in == zeros out
+    test_cnet = io_controlnetwork.from_isis(cnet_file)
+    assert (test_cnet.referenceIndex == reference_idx).all()
+
 def test_create_pvl_header(cnet_dataframe, tmpdir):
     with open(tmpdir.join('test.net'), 'rb') as f:
         pvl_header = pvl.load(f)

recipe/meta.yaml

@@ -36,7 +36,7 @@ requirements:
     - python
     - setuptools
     - numpy
-    - pvl
+    - pvl >= 1.0
     - protobuf
     - gdal
     - icu

setup.py

@@ -8,8 +8,8 @@ with open('README.md', 'r') as f:
 def setup_package():
     setup(
         name = "plio",
-        version = '1.2.4',
-        author = "Jay Laura",
+        version = '1.3.0',
+        author = "USGS Astrogeology",
         author_email = "jlaura@usgs.gov",
         description = ("I/O API to support planetary data formats."),
         long_description = long_description,