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

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

  - numpy 

  - pyproj 

  - h5py 

  - pvl 

  - pvl >= 1.0 

  - scipy 

  - protobuf 

  - affine 

            #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)

                    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():

    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)

            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):

                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)

    - python

    - setuptools

    - numpy

    - pvl

    - pvl >= 1.0

    - protobuf

    - gdal

    - icu