def test_augment_artifact_polarization_from_blueprint():
test_blueprint = ObsBlueprint(polarization_axis=1)
test_blueprint.set('Chunk.polarizationAxis', '1')
test_blueprint.set('Chunk.polarization.axis.axis.ctype', 'STOKES')
test_blueprint.set('Chunk.polarization.axis.function.refCoord.pix', '1.0')
test_blueprint.set('Chunk.polarization.axis.function.refCoord.val', '1.0')
test_blueprint.set('Chunk.polarization.axis.function.delta', '1.0')
test_blueprint.set('Chunk.polarization.axis.function.naxis', '1')
test_fitsparser = FitsParser(sample_file_4axes,
test_blueprint,
uri='test_parser')
test_chunk = Chunk()
test_fitsparser._try_polarization_with_blueprint(test_chunk, 0)
ex = _get_from_str_xml(EXPECTED_POLARIZATION_XML,
ObservationReader()._get_polarization_wcs,
'polarization')
result = get_differences(ex, test_chunk.polarization)
assert result is None
def test_load_from_file_configure():
ob = ObsBlueprint()
assert not ob._pos_axes_configed, \
'Failure to initialize configure_position_axes'
assert not ob._energy_axis_configed, \
'Failure to initialize configure_energy_axis'
ob.add_fits_attribute('Chunk.position.axis.axis1.ctype', 'CTYPE1')
ob.add_fits_attribute('Chunk.position.axis.axis2.ctype', 'CTYPE2')
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._pos_axes_configed, 'Failure to call configure_position_axes'
assert ob._energy_axis_configed, 'Failure to call configure_energy_axis'
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE3', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
ob = ObsBlueprint()
ob.add_fits_attribute('Chunk.position.axis.axis1.ctype', 'CTYPE3')
ob.add_fits_attribute('Chunk.position.axis.axis2.ctype', 'CTYPE4')
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._pos_axes_configed, 'Failure to call configure_position_axes'
assert ob._energy_axis_configed, 'Failure to call configure_energy_axis'
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE1', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
ob = ObsBlueprint()
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE3', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
def test_load_from_file_configure():
ob = ObsBlueprint()
assert not ob._pos_axes_configed, \
'Failure to initialize configure_position_axes'
assert not ob._energy_axis_configed, \
'Failure to initialize configure_energy_axis'
ob.add_fits_attribute('Chunk.position.axis.axis1.ctype', 'CTYPE1')
ob.add_fits_attribute('Chunk.position.axis.axis2.ctype', 'CTYPE2')
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._pos_axes_configed, 'Failure to call configure_position_axes'
assert ob._energy_axis_configed, 'Failure to call configure_energy_axis'
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE3', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
ob = ObsBlueprint()
ob.add_fits_attribute('Chunk.position.axis.axis1.ctype', 'CTYPE3')
ob.add_fits_attribute('Chunk.position.axis.axis2.ctype', 'CTYPE4')
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._pos_axes_configed, 'Failure to call configure_position_axes'
assert ob._energy_axis_configed, 'Failure to call configure_energy_axis'
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE1', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
ob = ObsBlueprint()
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE3', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
def test_has_chunk():
# the CFHT case
ob = ObsBlueprint()
ob.configure_position_axes((1, 2))
ob.set('Chunk', '{ignore}')
ob.set('Chunk.position.axis.axis1.ctype', 'RA---SIN', 1)
assert not ob.has_chunk(0)
assert ob.has_chunk(1)
# the OMM case
ob = ObsBlueprint()
ob.configure_position_axes((1, 2))
ob.set('Chunk', '{ignore}', 1)
assert ob.has_chunk(0)
assert not ob.has_chunk(1)
def test_has_chunk():
# the CFHT case
ob = ObsBlueprint()
ob.configure_position_axes((1, 2))
ob.set('Chunk', '{ignore}')
ob.set('Chunk.position.axis.axis1.ctype', 'RA---SIN', 1)
assert not ob.has_chunk(0)
assert ob.has_chunk(1)
# the OMM case
ob = ObsBlueprint()
ob.configure_position_axes((1, 2))
ob.set('Chunk', '{ignore}', 1)
assert ob.has_chunk(0)
assert not ob.has_chunk(1)
def test_augment_observation():
test_obs_blueprint = ObsBlueprint(position_axes=(1, 2))
test_obs_blueprint.set('Observation.target.name', 'CGPS Mosaic MA1')
test_obs_blueprint.set('Observation.target.standard', False)
test_obs_blueprint.set('Observation.telescope.name', 'DRAO-ST')
test_obs_blueprint.set('Observation.instrument.name', 'DRAO-ST')
test_obs_blueprint.set('Observation.telescope.geoLocationX',
'-2100330.87517')
test_obs_blueprint.set('Observation.telescope.geoLocationY',
'-3694247.82445')
test_obs_blueprint.set('Observation.telescope.geoLocationZ',
'4741018.33097')
test_obs_blueprint.set('Plane.dataProductType', 'cube')
test_obs_blueprint.set('Artifact.productType', 'info')
test_obs_blueprint.set('Artifact.releaseType', 'data')
test_obs_blueprint.set('Plane.calibrationLevel', '2')
test_fitsparser = FitsParser(sample_file_4axes_obs, test_obs_blueprint)
test_fitsparser.blueprint = test_obs_blueprint
test_obs = SimpleObservation('collection', 'MA1_DRAO-ST',
Algorithm('exposure'))
test_fitsparser.augment_observation(test_obs,
sample_file_4axes_uri,
product_id='HI-line')
assert test_obs is not None
assert test_obs.planes is not None
assert len(test_obs.planes) == 1
test_plane = test_obs.planes['HI-line']
assert test_plane.artifacts is not None
assert len(test_plane.artifacts) == 1
test_artifact = test_plane.artifacts[sample_file_4axes_uri]
assert test_artifact is not None
test_part = test_artifact.parts['0']
# remove the chunk bit, as it's part of other tests -
# results in <caom2:chunks/> xml output
test_part.chunks.pop()
output = BytesIO()
ow = ObservationWriter(False, False, "caom2",
obs_reader_writer.CAOM20_NAMESPACE)
ow.write(test_obs, output)
result = output.getvalue().decode('UTF-8')
output.close()
expected = _get_obs(EXPECTED_OBS_XML)
actual = _get_obs(result)
diff_result = get_differences(expected, actual, 'Observation')
assert diff_result is None
def test_augment_artifact_time_from_blueprint():
test_blueprint = ObsBlueprint(time_axis=1)
test_blueprint.set('Chunk.timeAxis', '1')
test_blueprint.set('Chunk.time.exposure', '0.02')
test_blueprint.set('Chunk.time.resolution', '0.02')
test_blueprint.set('Chunk.time.timesys', 'UTC')
test_blueprint.set('Chunk.time.axis.axis.ctype', 'TIME')
test_blueprint.set('Chunk.time.axis.axis.cunit', 'd')
test_blueprint.set('Chunk.time.axis.error.syser', '1e-07')
test_blueprint.set('Chunk.time.axis.error.rnder', '1e-07')
test_blueprint.set('Chunk.time.axis.function.refCoord.pix', '0.5')
test_blueprint.set('Chunk.time.axis.function.refCoord.val',
'56789.4298069')
test_blueprint.set('Chunk.time.axis.function.delta', '2.31481e-07')
test_blueprint.set('Chunk.time.axis.function.naxis', '1')
test_fitsparser = FitsParser(sample_file_4axes,
test_blueprint,
uri='ad:TEST/test_blueprint')
test_chunk = Chunk()
test_fitsparser._try_time_with_blueprint(test_chunk, 0)
ex = _get_from_str_xml(EXPECTED_CFHT_WIRCAM_RAW_GUIDE_CUBE_TIME,
ObservationReader()._get_temporal_wcs, 'time')
result = get_differences(ex, test_chunk.time)
assert result is None
def test_augment_artifact_position_from_blueprint():
test_blueprint = ObsBlueprint(position_axes=(1, 2))
test_blueprint.set('Chunk.positionAxis1', '1')
test_blueprint.set('Chunk.positionAxis2', '2')
test_blueprint.set('Chunk.position.axis.axis1.ctype', 'GLON-CAR')
test_blueprint.set('Chunk.position.axis.axis1.cunit', 'deg')
test_blueprint.set('Chunk.position.axis.axis2.ctype', 'GLAT-CAR')
test_blueprint.set('Chunk.position.axis.axis2.cunit', 'deg')
test_blueprint.set('Chunk.position.axis.function.cd11', '-0.004999999')
test_blueprint.set('Chunk.position.axis.function.cd12', '0.0')
test_blueprint.set('Chunk.position.axis.function.cd21', '0.0')
test_blueprint.set('Chunk.position.axis.function.cd22', '0.004999999')
test_blueprint.set('Chunk.position.axis.function.dimension.naxis1', '1')
test_blueprint.set('Chunk.position.axis.function.dimension.naxis2', '1')
test_blueprint.set('Chunk.position.axis.range.start.coord1.pix', '513.0')
test_blueprint.set('Chunk.position.axis.range.start.coord1.val',
'128.7499990027')
test_blueprint.set('Chunk.position.axis.range.start.coord2.pix', '513.0')
test_blueprint.set('Chunk.position.axis.range.start.coord2.val',
'-0.9999999922536')
test_fitsparser = FitsParser(sample_file_4axes,
test_blueprint,
uri='test_parser')
test_chunk = Chunk()
test_fitsparser._try_position_with_blueprint(test_chunk, 0)
ex = _get_from_str_xml(EXPECTED_POSITION_XML,
ObservationReader()._get_spatial_wcs, 'position')
result = get_differences(ex, test_chunk.position)
assert result is None
def test_augment_artifact_energy_from_blueprint():
test_blueprint = ObsBlueprint(energy_axis=1)
test_blueprint.set('Chunk.energyAxis', 1)
test_blueprint.set('Chunk.energy.specsys', 'LSRK')
test_blueprint.set('Chunk.energy.axis.axis.ctype', 'VRAD')
test_blueprint.set('Chunk.energy.axis.axis.cunit', 'm / s')
test_blueprint.set('Chunk.energy.axis.function.refCoord.pix', '145.0')
test_blueprint.set('Chunk.energy.axis.function.refCoord.val', '-60000.0')
test_blueprint.set('Chunk.energy.axis.function.delta', '-824.46002')
test_blueprint.set('Chunk.energy.axis.function.naxis', '1')
test_fitsparser = FitsParser(sample_file_4axes,
test_blueprint,
uri='ad:TEST/test_blueprint')
test_chunk = Chunk()
test_fitsparser._try_energy_with_blueprint(test_chunk, 0)
ex = _get_from_str_xml(EXPECTED_ENERGY_XML,
ObservationReader()._get_spectral_wcs, 'energy')
result = get_differences(ex, test_chunk.energy)
assert result is None
def test_augment_artifact_bounds_range_from_blueprint():
test_blueprint = ObsBlueprint(energy_axis=1,
time_axis=2,
polarization_axis=3,
position_axes=(4, 5))
test_blueprint.set('Chunk.energy.axis.range.start.pix', '145.0')
test_blueprint.set('Chunk.energy.axis.range.start.val', '-60000.0')
test_blueprint.set('Chunk.energy.axis.range.end.pix', '-824.46002')
test_blueprint.set('Chunk.energy.axis.range.end.val', '1')
test_blueprint.set('Chunk.time.axis.range.start.pix', '145.0')
test_blueprint.set('Chunk.time.axis.range.start.val', '-60000.0')
test_blueprint.set('Chunk.time.axis.range.end.pix', '-824.46002')
test_blueprint.set('Chunk.time.axis.range.end.val', '1')
test_blueprint.set('Chunk.polarization.axis.range.start.pix', '145.0')
test_blueprint.set('Chunk.polarization.axis.range.start.val', '-60000.0')
test_blueprint.set('Chunk.polarization.axis.range.end.pix', '-824.46002')
test_blueprint.set('Chunk.polarization.axis.range.end.val', '1')
test_blueprint.set('Chunk.position.axis.range.start.coord1.pix', '145.0')
test_blueprint.set('Chunk.position.axis.range.start.coord1.val',
'-60000.0')
test_blueprint.set('Chunk.position.axis.range.end.coord1.pix',
'-824.46002')
test_blueprint.set('Chunk.position.axis.range.end.coord1.val', '1')
test_blueprint.set('Chunk.position.axis.range.start.coord2.pix', '145.0')
test_blueprint.set('Chunk.position.axis.range.start.coord2.val',
'-60000.0')
test_blueprint.set('Chunk.position.axis.range.end.coord2.pix',
'-824.46002')
test_blueprint.set('Chunk.position.axis.range.end.coord2.val', '1')
test_fitsparser = FitsParser(sample_file_4axes,
test_blueprint,
uri='ad:TEST/test_blueprint')
test_chunk = Chunk()
test_chunk.energy = SpectralWCS(CoordAxis1D(Axis('WAVE', 'm')), 'TOPOCENT')
test_chunk.time = TemporalWCS(CoordAxis1D(Axis('TIME', 'd')))
test_chunk.polarization = PolarizationWCS(CoordAxis1D(Axis('STOKES')))
test_chunk.position = SpatialWCS(
CoordAxis2D(Axis('RA', 'deg'), Axis('DEC', 'deg')))
test_fitsparser._try_range_with_blueprint(test_chunk, 0)
assert test_chunk.energy.axis.range is not None, \
'chunk.energy.axis.range should be declared'
assert test_chunk.time.axis.range is not None, \
'chunk.time.axis.range should be declared'
assert test_chunk.polarization.axis.range is not None, \
'chunk.polarization.axis.range should be declared'
assert test_chunk.position.axis.range is not None, \
'chunk.position.axis.range should be declared'
ex = _get_from_str_xml(EXPECTED_ENERGY_RANGE_BOUNDS_XML,
ObservationReader()._get_spectral_wcs, 'energy')
assert ex is not None, \
'energy string from expected output should be declared'
result = get_differences(ex, test_chunk.energy)
assert result is None
ex = _get_from_str_xml(EXPECTED_TIME_RANGE_BOUNDS_XML,
ObservationReader()._get_temporal_wcs, 'time')
assert ex is not None, \
'time string from expected output should be declared'
result = get_differences(ex, test_chunk.time)
assert result is None
ex = _get_from_str_xml(EXPECTED_POL_RANGE_BOUNDS_XML,
ObservationReader()._get_polarization_wcs,
'polarization')
assert ex is not None, \
'polarization string from expected output should be declared'
result = get_differences(ex, test_chunk.polarization)
assert result is None
ex = _get_from_str_xml(EXPECTED_POS_RANGE_BOUNDS_XML,
ObservationReader()._get_spatial_wcs, 'position')
assert ex is not None, \
'position string from expected output should be declared'
result = get_differences(ex, test_chunk.position)
assert result is None
def test_obs_blueprint():
# test the CAOM2_ELEMENTS property
assert ObsBlueprint.CAOM2_ELEMENTS == ObsBlueprint._CAOM2_ELEMENTS
# updating the CAOM2_ELEMENTS property should not update the original
elems = ObsBlueprint.CAOM2_ELEMENTS
elems = elems[2:]
assert elems != ObsBlueprint.CAOM2_ELEMENTS
# default config (one entry per row...)
assert str(ObsBlueprint()).count('\n') == 24
print(ObsBlueprint())
# default config with WCS info
assert str(
ObsBlueprint(position_axes=(1, 2),
energy_axis=3,
polarization_axis=4,
time_axis=5,
obs_axis=6,
custom_axis=7)).count('\n') == 90
ob = ObsBlueprint()
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
ob.configure_observable_axis(axis=6)
ob.configure_custom_axis(axis=7)
# test that configuring something that's already configured doesn't break
# anything
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
ob.configure_observable_axis(axis=6)
ob.configure_custom_axis(axis=7)
# set attribute
ob.set('Observation.instrument.name', 'NIRI')
assert ob._plan['Observation.instrument.name'] == 'NIRI'
assert 'Observation.instrument.name = NIRI' in str(ob)
# set default
ob.clear('Observation.instrument.keywords')
ob.add_fits_attribute('Observation.instrument.keywords', 'INSTMODE')
assert "Observation.instrument.keywords = ['INSTMODE'], default = None" \
in str(ob)
ob.set_default('Observation.instrument.keywords', 'TEST')
assert ob._plan['Observation.instrument.keywords'][1] == 'TEST'
assert ob._plan['Observation.instrument.keywords'][0] == ['INSTMODE']
assert "Observation.instrument.keywords = ['INSTMODE'], default = TEST" \
in str(ob)
# set fits attribute
ob.add_fits_attribute('Observation.proposal.id', 'PROP')
ob.add_fits_attribute('Observation.proposal.id', 'PROP2')
ob.set_default('Observation.proposal.id', 'NOPROP')
assert ob._plan['Observation.proposal.id'][0] == ['PROP2', 'PROP', 'RUNID']
assert ob._plan['Observation.proposal.id'][1] == 'NOPROP'
if sys.version.startswith('2.7.'):
assert ("Observation.proposal.id = ['PROP2', 'PROP', u'RUNID'], "
"default = NOPROP") in str(ob)
else:
assert ("Observation.proposal.id = ['PROP2', 'PROP', 'RUNID'], "
"default = NOPROP") in str(ob)
# set in extension
ob.set('Chunk.energy.velang', 33, extension=1)
extension1_str = str(ob)[str(ob).index('extension 1'):]
assert 'Chunk.energy.velang = 33' in extension1_str
# set fits attribute in extension
ob.add_fits_attribute('Chunk.energy.axis.axis.ctype',
'MYCTYPE',
extension=1)
ob.add_fits_attribute('Chunk.energy.axis.axis.ctype',
'MYCTYPE2',
extension=1)
ob.set_default('Chunk.energy.axis.axis.ctype', 'NOCTYPE', extension=1)
extension1_str = str(ob)[str(ob).index('extension 1'):]
assert ("Chunk.energy.axis.axis.ctype = ['MYCTYPE2', 'MYCTYPE'], "
"default = NOCTYPE") in extension1_str
# set in a different extension
ob.set('Chunk.energy.velang', 44, extension=2)
extension2_str = str(ob)[str(ob).index('extension 2'):]
assert 'Chunk.energy.velang = 44' in extension2_str
# test get
assert ob._get('Observation.instrument.name') == 'NIRI'
assert ob._get('Observation.instrument.keywords')[0] == ['INSTMODE']
assert ob._get('Observation.instrument.keywords')[1] == 'TEST'
assert ob._get('Chunk.energy.velang', extension=2) == 44
assert ob._get('Chunk.energy.velang', extension=1) == 33
assert ob._get('Chunk.energy.axis.axis.ctype', extension=1)[0] ==\
['MYCTYPE2', 'MYCTYPE']
assert ob._get('Chunk.energy.axis.axis.ctype', extension=1)[1] == 'NOCTYPE'
# test get when keyword not present in extension and the default is used
assert ob._get('Chunk.energy.specsys', extension=33)[0] == ['SPECSYS']
assert ob._get('Chunk.energy.specsys', extension=44)[1] is None
# get element not set
assert 'Observation.target.redshift' not in ob._plan
assert ob._get('Observation.target.redshift') is None
# bintable :)
ob.add_table_attribute('CompositeObservation.members', 'FICS', extension=0)
result = ob._get('CompositeObservation.members', extension=0)
assert result is not None
assert len(result) == 3, len(result)
# delete attributes
assert len(ob._plan) != 0
assert len(ob._extensions) != 0
for i in ObsBlueprint.CAOM2_ELEMENTS:
ob.delete(i)
assert len(ob._plan) == 0
# clear
ob.clear('Chunk.energy.axis.axis.ctype', extension=1)
# delete attributes from extensions
ob.delete('Chunk.energy.velang', extension=1)
ob.delete('Chunk.energy.axis.axis.ctype', extension=1)
ob.delete('CompositeObservation.members', extension=0)
ob.delete('Chunk.energy.velang', extension=2)
assert len(ob._extensions) == 0
# set defaults in extension
ob.set_default('Chunk.energy.axis.axis.ctype', 'NOCTYPE', extension=3)
extension3_str = str(ob)[str(ob).index('extension 3'):]
assert "Chunk.energy.axis.axis.ctype = NOCTYPE" in extension3_str
assert len(ob._extensions) == 1
# testing error cases
ob = ObsBlueprint()
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
# non CAOM2 element name
with pytest.raises(KeyError):
ob.set('Nonexistent', 33)
with pytest.raises(KeyError):
ob.add_fits_attribute('Nonexistent', 33)
with pytest.raises(KeyError):
ob.set_default('Nonexistent', 33)
with pytest.raises(KeyError):
ob._get('Nonexistent')
with pytest.raises(KeyError):
ob.delete('Nonexistent')
with pytest.raises(KeyError):
ob.clear('Nonexistent')
# repeat with extension specified
with pytest.raises(KeyError):
ob.set('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob.add_fits_attribute('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob.set_default('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob._get('Nonexistent', extension=33)
with pytest.raises(KeyError):
ob.delete('Chunk.Nonexistent', extension=1)
with pytest.raises(KeyError):
ob.clear('Chunk.Nonexistent', extension=1)
# CAOM2 element not Chunk with extension specified
with pytest.raises(ValueError):
ob.set('Observation.observationID', 33, extension=1)
with pytest.raises(ValueError):
ob.set_default('Observation.observationID', 33, extension=1)
with pytest.raises(ValueError):
ob.add_fits_attribute('Observation.observationID', 'AA', extension=1)
with pytest.raises(ValueError):
ob.delete('Observation.observationID', extension=1)
with pytest.raises(ValueError):
ob.clear('Observation.observationID', extension=1)
# CAOM2 element Chunk with extension
with pytest.raises(ValueError):
ob.clear('Chunk.energy.axis.axis.cunit', extension=33)
# add FITS attribute to element that does not exist
assert 'Chunk.energy.transition' not in ob._plan
ob.set('Chunk.energy.transition', 'Name')
with pytest.raises(AttributeError):
ob.add_fits_attribute('Chunk.energy.transition', 'BP')
# call set_fits_attribute with argument other than list
with pytest.raises(AttributeError):
ob.add_fits_attribute('Chunk.energy.transition', 33)
# delete element from a non-existent extension
with pytest.raises(ValueError):
ob.delete('Chunk.energy.transition', extension=66)
# adding the same thing twice does nothing - the test values are defaults
result = ob._get('Observation.metaRelease')
initial_result_length = (len(result[0]))
ob.add_fits_attribute('Observation.metaRelease', 'DATE-OBS')
result = ob._get('Observation.metaRelease')
add_result_length = (len(result[0]))
assert initial_result_length == add_result_length
# in an extension
result = ob._get('Chunk.energy.specsys', extension=1)
initial_result_length = (len(result[0]))
ob.add_fits_attribute('Chunk.energy.specsys', 'SPECSYS')
result = ob._get('Chunk.energy.specsys', extension=1)
add_result_length = (len(result[0]))
assert initial_result_length == add_result_length, result
def test_load_from_file_configure():
ob = ObsBlueprint()
assert not ob._pos_axes_configed, \
'Failure to initialize configure_position_axes'
assert not ob._energy_axis_configed, \
'Failure to initialize configure_energy_axis'
assert not ob._custom_axis_configed, 'custom config'
assert not ob._obs_axis_configed, 'obs config'
assert not ob._polarization_axis_configed, 'pol config'
assert not ob._time_axis_configed, 'time config'
ob.add_fits_attribute('Chunk.position.axis.axis1.ctype', 'CTYPE1')
ob.add_fits_attribute('Chunk.position.axis.axis2.ctype', 'CTYPE2')
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._pos_axes_configed, 'Failure to call configure_position_axes'
assert ob._energy_axis_configed, 'Failure to call configure_energy_axis'
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE3', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
ob = ObsBlueprint()
ob.add_fits_attribute('Chunk.position.axis.axis1.ctype', 'CTYPE3')
ob.add_fits_attribute('Chunk.position.axis.axis2.ctype', 'CTYPE4')
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._pos_axes_configed, 'Failure to call configure_position_axes'
assert ob._energy_axis_configed, 'Failure to call configure_energy_axis'
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE1', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
ob = ObsBlueprint()
ob.set('Chunk.energy.axis.axis.ctype', 'WAVE')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE3', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
ob = ObsBlueprint()
ob.set('Chunk.polarization.axis.axis.ctype', 'STOKES')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.polarization.axis.axis.ctype'] == 'CTYPE5', \
ob._wcs_std['Chunk.polarization.axis.axis.ctype']
assert ob._polarization_axis_configed, 'pol config'
ob = ObsBlueprint()
ob.set('Chunk.observable.axis.axis.ctype', 'COUNT')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.observable.axis.axis.ctype'] == 'CTYPE6', \
ob._wcs_std['Chunk.observable.axis.axis.ctype']
assert ob._obs_axis_configed, 'obs config'
ob = ObsBlueprint()
ob.set('Chunk.custom.axis.axis.ctype', 'FARDEP')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.custom.axis.axis.ctype'] == 'CTYPE7', \
ob._wcs_std['Chunk.custom.axis.axis.ctype']
assert ob._custom_axis_configed, 'custom config'
ob = ObsBlueprint()
ob.set('Chunk.time.axis.axis.ctype', 'TIME')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.time.axis.axis.ctype'] == 'CTYPE4', \
ob._wcs_std['Chunk.time.axis.axis.ctype']
assert ob._time_axis_configed, 'time config'
# should get the position axes by default
ob = ObsBlueprint()
ob._guess_axis_info_from_plan()
assert ob._pos_axes_configed, 'pos config'
assert not ob._energy_axis_configed, 'energy config'
assert not ob._custom_axis_configed, 'custom config'
assert not ob._obs_axis_configed, 'obs config'
assert not ob._polarization_axis_configed, 'pol config'
assert not ob._time_axis_configed, 'time config'
# for the truly creative instrument scientist
ob = ObsBlueprint()
ob.add_fits_attribute('Chunk.polarization.axis.axis.ctype', 'CTYPE1')
ob.add_fits_attribute('Chunk.custom.axis.axis.ctype', 'CTYPE2')
ob.add_fits_attribute('Chunk.position.axis.axis1.ctype', 'CTYPE3')
ob.add_fits_attribute('Chunk.position.axis.axis2.ctype', 'CTYPE4')
ob.add_fits_attribute('Chunk.time.axis.axis.ctype', 'CTYPE5')
ob.add_fits_attribute('Chunk.energy.axis.axis.ctype', 'CTYPE6')
ob.add_fits_attribute('Chunk.observable.axis.axis.ctype', 'CTYPE7')
ob._guess_axis_info_from_plan()
assert ob._wcs_std['Chunk.polarization.axis.axis.ctype'] == 'CTYPE1', \
ob._wcs_std['Chunk.polarization.axis.axis.ctype']
assert ob._wcs_std['Chunk.custom.axis.axis.ctype'] == 'CTYPE2', \
ob._wcs_std['Chunk.custom.axis.axis.ctype']
assert ob._wcs_std['Chunk.position.axis.axis1.ctype'] == 'CTYPE3', \
ob._wcs_std['Chunk.position.axis.axis1.ctype']
assert ob._wcs_std['Chunk.position.axis.axis2.ctype'] == 'CTYPE4', \
ob._wcs_std['Chunk.position.axis.axis2.ctype']
assert ob._wcs_std['Chunk.time.axis.axis.ctype'] == 'CTYPE5', \
ob._wcs_std['Chunk.time.axis.axis.ctype']
assert ob._wcs_std['Chunk.energy.axis.axis.ctype'] == 'CTYPE6', \
ob._wcs_std['Chunk.energy.axis.axis.ctype']
assert ob._wcs_std['Chunk.observable.axis.axis.ctype'] == 'CTYPE7', \
ob._wcs_std['Chunk.observable.axis.axis.ctype']
with pytest.raises(ValueError):
ob = ObsBlueprint()
ob.add_fits_attribute('Chunk.polarization.axis.axis.ctype', 'CTYPE1')
ob._guess_axis_info_from_plan()
def test_obs_blueprint():
# test the CAOM2_ELEMENTS property
assert ObsBlueprint.CAOM2_ELEMENTS == ObsBlueprint._CAOM2_ELEMENTS
# updating the CAOM2_ELEMENTS property should not update the original
elems = ObsBlueprint.CAOM2_ELEMENTS
elems = elems[2:]
assert elems != ObsBlueprint.CAOM2_ELEMENTS
# default config (one entry per row...)
assert str(ObsBlueprint()).count('\n') == 20
print(ObsBlueprint())
# default config with WCS info
assert str(
ObsBlueprint(position_axis=(1, 2),
energy_axis=3,
polarization_axis=4,
time_axis=5)).count('\n') == 77
ob = ObsBlueprint()
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
# set attribute
ob.set('Observation.instrument.name', 'NIRI')
assert ob._plan['Observation.instrument.name'] == 'NIRI'
assert 'Observation.instrument.name = NIRI' in str(ob)
# set default
ob.set_fits_attribute('Observation.instrument.keywords', [str('INSTMODE')])
assert "Observation.instrument.keywords = ['INSTMODE'], default = None" \
in str(ob)
ob.set_default('Observation.instrument.keywords', 'TEST')
assert ob._plan['Observation.instrument.keywords'][1] == 'TEST'
assert ob._plan['Observation.instrument.keywords'][0] == ['INSTMODE']
assert "Observation.instrument.keywords = ['INSTMODE'], default = TEST" \
in str(ob)
# set fits attribute
ob.set_fits_attribute('Observation.proposal.id', [str('PROP')])
ob.add_fits_attribute('Observation.proposal.id', str('PROP2'))
ob.set_default('Observation.proposal.id', 'NOPROP')
assert ob._plan['Observation.proposal.id'][0] == ['PROP2', 'PROP']
assert ob._plan['Observation.proposal.id'][1] == 'NOPROP'
assert ("Observation.proposal.id = ['PROP2', 'PROP'], "
"default = NOPROP") in str(ob)
# set in extension
ob.set('Chunk.energy.velang', 33, extension=1)
extension1_str = str(ob)[str(ob).index('extension 1'):]
assert 'Chunk.energy.velang = 33' in extension1_str
# set fits attribute in extension
ob.set_fits_attribute('Chunk.energy.axis.axis.ctype', [str('MYCTYPE')],
extension=1)
ob.add_fits_attribute('Chunk.energy.axis.axis.ctype',
str('MYCTYPE2'),
extension=1)
ob.set_default('Chunk.energy.axis.axis.ctype', 'NOCTYPE', extension=1)
extension1_str = str(ob)[str(ob).index('extension 1'):]
assert ("Chunk.energy.axis.axis.ctype = ['MYCTYPE2', 'MYCTYPE'], "
"default = NOCTYPE") in extension1_str
# set in a different extension
ob.set('Chunk.energy.velang', 44, extension=2)
extension2_str = str(ob)[str(ob).index('extension 2'):]
assert 'Chunk.energy.velang = 44' in extension2_str
# test get
assert ob._get('Observation.instrument.name') == 'NIRI'
assert ob._get('Observation.instrument.keywords')[0] == ['INSTMODE']
assert ob._get('Observation.instrument.keywords')[1] == 'TEST'
assert ob._get('Chunk.energy.velang', extension=2) == 44
assert ob._get('Chunk.energy.velang', extension=1) == 33
assert ob._get('Chunk.energy.axis.axis.ctype', extension=1)[0] ==\
['MYCTYPE2', 'MYCTYPE']
assert ob._get('Chunk.energy.axis.axis.ctype', extension=1)[1] == 'NOCTYPE'
# test get when keyword not present in extension and the default is used
assert ob._get('Chunk.energy.specsys', extension=33)[0] == ['SPECSYS']
assert ob._get('Chunk.energy.specsys', extension=44)[1] is None
# get element not set
assert 'Observation.target.redshift' not in ob._plan
assert ob._get('Observation.target.redshift') is None
# delete attributes
assert len(ob._plan) != 0
assert len(ob._extensions) != 0
for i in ObsBlueprint.CAOM2_ELEMENTS:
ob.delete(i)
assert len(ob._plan) == 0
# delete attributes from extensions
ob.delete('Chunk.energy.velang', extension=1)
ob.delete('Chunk.energy.axis.axis.ctype', extension=1)
ob.delete('Chunk.energy.velang', extension=2)
assert len(ob._extensions) == 0
# testing error cases
ob = ObsBlueprint()
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
# non CAOM2 element name
with pytest.raises(KeyError):
ob.set('Nonexistent', 33)
with pytest.raises(KeyError):
ob.set_fits_attribute('Nonexistent', 33)
with pytest.raises(KeyError):
ob.add_fits_attribute('Nonexistent', 33)
with pytest.raises(KeyError):
ob.set_default('Nonexistent', 33)
with pytest.raises(KeyError):
ob._get('Nonexistent')
with pytest.raises(KeyError):
ob.delete('Nonexistent')
# repeat with extension specified
with pytest.raises(KeyError):
ob.set('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob.set_fits_attribute('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob.add_fits_attribute('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob.set_default('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob._get('Nonexistent', extension=33)
with pytest.raises(KeyError):
ob.delete('Chunk.Nonexistent', extension=1)
# CAOM2 element not Chunk with extension specified
with pytest.raises(ValueError):
ob.set('Observation.observationID', 33, extension=1)
with pytest.raises(ValueError):
ob.set_fits_attribute('Observation.observationID', ['AA'], extension=1)
with pytest.raises(ValueError):
ob.set_default('Observation.observationID', 33, extension=1)
with pytest.raises(ValueError):
ob.add_fits_attribute('Observation.observationID', 'AA', extension=1)
with pytest.raises(ValueError):
ob.delete('Observation.observationID', extension=1)
# add FITS attribute to element that does not exist
assert 'Chunk.energy.transition' not in ob._plan
with pytest.raises(KeyError):
ob.add_fits_attribute('Chunk.energy.transition', 'BP')
ob.set('Chunk.energy.transition', 'Name')
with pytest.raises(AttributeError):
ob.add_fits_attribute('Chunk.energy.transition', 'BP')
# call set_fits_attribute with argument other than list
with pytest.raises(AssertionError):
ob.set_fits_attribute('Chunk.energy.transition', 33)
# delete element from a non-existent extension
with pytest.raises(ValueError):
ob.delete('Chunk.energy.transition', extension=66)
def test_augment_observation(test_file, test_file_uri):
# logging.basicConfig(level=logging.DEBUG, stream=sys.stdout)
test_obs_blueprint = ObsBlueprint(position_axis=(1, 2))
test_obs_blueprint.set('Observation.target.name', 'CGPS Mosaic MA1')
test_obs_blueprint.set('Observation.telescope.name', 'DRAO-ST')
test_obs_blueprint.set('Observation.instrument.name', 'DRAO-ST')
test_obs_blueprint.set('Observation.telescope.geoLocationX',
'-2100330.87517')
test_obs_blueprint.set('Observation.telescope.geoLocationY',
'-3694247.82445')
test_obs_blueprint.set('Observation.telescope.geoLocationZ',
'4741018.33097')
test_obs_blueprint.set('Plane.dataProductType', 'cube')
test_obs_blueprint.set('Plane.calibrationLevel', '2')
test_fitsparser = FitsParser(test_file, test_obs_blueprint)
test_fitsparser.blueprint = test_obs_blueprint
test_obs = Observation('collection', 'MA1_DRAO-ST', Algorithm('exposure'))
test_fitsparser.augment_observation(test_obs,
test_file_uri,
product_id='HI-line')
assert test_obs is not None
assert test_obs.planes is not None
assert len(test_obs.planes) == 1
test_plane = test_obs.planes['HI-line']
assert test_plane.artifacts is not None
assert len(test_plane.artifacts) == 1
test_artifact = test_plane.artifacts[test_file_uri]
assert test_artifact is not None
test_part = test_artifact.parts['0']
# remove the chunk bit, as it's part of other tests -
# results in <caom2:chunks/> xml output
test_part.chunks.pop()
output = BytesIO()
ow = ObservationWriter(False, False, "caom2",
obs_reader_writer.CAOM20_NAMESPACE)
ow.write(test_obs, output)
result = output.getvalue().decode('UTF-8')
output.close()
compare = re.sub(r'caom2:id=".*"', 'caom2:id=""', result)
assert compare == EXPECTED_OBS_XML # , result
def test_obs_blueprint():
# test the CAOM2_ELEMENTS property
assert ObsBlueprint.CAOM2_ELEMENTS == ObsBlueprint._CAOM2_ELEMENTS
# updating the CAOM2_ELEMENTS property should not update the original
elems = ObsBlueprint.CAOM2_ELEMENTS
elems = elems[2:]
assert elems != ObsBlueprint.CAOM2_ELEMENTS
# default config (one entry per row...)
assert str(ObsBlueprint()).count('\n') == 21
print(ObsBlueprint())
# default config with WCS info
assert str(ObsBlueprint(position_axes=(1, 2), energy_axis=3,
polarization_axis=4, time_axis=5,
obs_axis=6)).count('\n') == 81
ob = ObsBlueprint()
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
ob.configure_observable_axis(axis=6)
# test that configuring something that's already configured doesn't break
# anything
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
ob.configure_observable_axis(axis=6)
# set attribute
ob.set('Observation.instrument.name', 'NIRI')
assert ob._plan['Observation.instrument.name'] == 'NIRI'
assert 'Observation.instrument.name = NIRI' in str(ob)
# set default
ob.clear('Observation.instrument.keywords')
ob.add_fits_attribute('Observation.instrument.keywords', str('INSTMODE'))
assert "Observation.instrument.keywords = ['INSTMODE'], default = None" \
in str(ob)
ob.set_default('Observation.instrument.keywords', 'TEST')
assert ob._plan['Observation.instrument.keywords'][1] == 'TEST'
assert ob._plan['Observation.instrument.keywords'][0] == ['INSTMODE']
assert "Observation.instrument.keywords = ['INSTMODE'], default = TEST" \
in str(ob)
# set fits attribute
ob.add_fits_attribute('Observation.proposal.id', str('PROP'))
ob.add_fits_attribute('Observation.proposal.id', str('PROP2'))
ob.set_default('Observation.proposal.id', 'NOPROP')
assert ob._plan['Observation.proposal.id'][0] == ['PROP2', 'PROP', 'RUNID']
assert ob._plan['Observation.proposal.id'][1] == 'NOPROP'
if sys.version.startswith('2.7.'):
assert ("Observation.proposal.id = ['PROP2', 'PROP', u'RUNID'], "
"default = NOPROP") in str(ob)
else:
assert ("Observation.proposal.id = ['PROP2', 'PROP', 'RUNID'], "
"default = NOPROP") in str(ob)
# set in extension
ob.set('Chunk.energy.velang', 33, extension=1)
extension1_str = str(ob)[str(ob).index('extension 1'):]
assert 'Chunk.energy.velang = 33' in extension1_str
# set fits attribute in extension
ob.add_fits_attribute('Chunk.energy.axis.axis.ctype', str('MYCTYPE'),
extension=1)
ob.add_fits_attribute('Chunk.energy.axis.axis.ctype', str('MYCTYPE2'),
extension=1)
ob.set_default('Chunk.energy.axis.axis.ctype', 'NOCTYPE', extension=1)
extension1_str = str(ob)[str(ob).index('extension 1'):]
assert ("Chunk.energy.axis.axis.ctype = ['MYCTYPE2', 'MYCTYPE'], "
"default = NOCTYPE") in extension1_str
# set in a different extension
ob.set('Chunk.energy.velang', 44, extension=2)
extension2_str = str(ob)[str(ob).index('extension 2'):]
assert 'Chunk.energy.velang = 44' in extension2_str
# test get
assert ob._get('Observation.instrument.name') == 'NIRI'
assert ob._get('Observation.instrument.keywords')[0] == ['INSTMODE']
assert ob._get('Observation.instrument.keywords')[1] == 'TEST'
assert ob._get('Chunk.energy.velang', extension=2) == 44
assert ob._get('Chunk.energy.velang', extension=1) == 33
assert ob._get('Chunk.energy.axis.axis.ctype', extension=1)[0] ==\
['MYCTYPE2', 'MYCTYPE']
assert ob._get('Chunk.energy.axis.axis.ctype', extension=1)[1] == 'NOCTYPE'
# test get when keyword not present in extension and the default is used
assert ob._get('Chunk.energy.specsys', extension=33)[0] == ['SPECSYS']
assert ob._get('Chunk.energy.specsys', extension=44)[1] is None
# get element not set
assert 'Observation.target.redshift' not in ob._plan
assert ob._get('Observation.target.redshift') is None
# bintable :)
ob.add_table_attribute('CompositeObservation.members', 'FICS', extension=0)
result = ob._get('CompositeObservation.members', extension=0)
assert result is not None
assert len(result) == 3, len(result)
# delete attributes
assert len(ob._plan) != 0
assert len(ob._extensions) != 0
for i in ObsBlueprint.CAOM2_ELEMENTS:
ob.delete(i)
assert len(ob._plan) == 0
# clear
ob.clear('Chunk.energy.axis.axis.ctype', extension=1)
# delete attributes from extensions
ob.delete('Chunk.energy.velang', extension=1)
ob.delete('Chunk.energy.axis.axis.ctype', extension=1)
ob.delete('CompositeObservation.members', extension=0)
ob.delete('Chunk.energy.velang', extension=2)
assert len(ob._extensions) == 0
# testing error cases
ob = ObsBlueprint()
ob.configure_position_axes(axes=(1, 2))
ob.configure_energy_axis(axis=3)
ob.configure_polarization_axis(axis=4)
ob.configure_time_axis(axis=5)
# non CAOM2 element name
with pytest.raises(KeyError):
ob.set('Nonexistent', 33)
with pytest.raises(KeyError):
ob.add_fits_attribute('Nonexistent', 33)
with pytest.raises(KeyError):
ob.set_default('Nonexistent', 33)
with pytest.raises(KeyError):
ob._get('Nonexistent')
with pytest.raises(KeyError):
ob.delete('Nonexistent')
with pytest.raises(KeyError):
ob.clear('Nonexistent')
# repeat with extension specified
with pytest.raises(KeyError):
ob.set('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob.add_fits_attribute('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob.set_default('Chunk.Nonexistent', 33, extension=1)
with pytest.raises(KeyError):
ob._get('Nonexistent', extension=33)
with pytest.raises(KeyError):
ob.delete('Chunk.Nonexistent', extension=1)
with pytest.raises(KeyError):
ob.clear('Chunk.Nonexistent', extension=1)
# CAOM2 element not Chunk with extension specified
with pytest.raises(ValueError):
ob.set('Observation.observationID', 33, extension=1)
with pytest.raises(ValueError):
ob.set_default('Observation.observationID', 33, extension=1)
with pytest.raises(ValueError):
ob.add_fits_attribute('Observation.observationID', 'AA', extension=1)
with pytest.raises(ValueError):
ob.delete('Observation.observationID', extension=1)
with pytest.raises(ValueError):
ob.clear('Observation.observationID', extension=1)
# CAOM2 element Chunk with extension
with pytest.raises(ValueError):
ob.clear('Chunk.energy.axis.axis.cunit', extension=33)
# add FITS attribute to element that does not exist
assert 'Chunk.energy.transition' not in ob._plan
ob.set('Chunk.energy.transition', 'Name')
with pytest.raises(AttributeError):
ob.add_fits_attribute('Chunk.energy.transition', 'BP')
# call set_fits_attribute with argument other than list
with pytest.raises(AttributeError):
ob.add_fits_attribute('Chunk.energy.transition', 33)
# delete element from a non-existent extension
with pytest.raises(ValueError):
ob.delete('Chunk.energy.transition', extension=66)
# adding the same thing twice does nothing - the test values are defaults
result = ob._get('Observation.metaRelease')
initial_result_length = (len(result[0]))
ob.add_fits_attribute('Observation.metaRelease', 'DATE-OBS')
result = ob._get('Observation.metaRelease')
add_result_length = (len(result[0]))
assert initial_result_length == add_result_length
# in an extension
result = ob._get('Chunk.energy.specsys', extension=1)
initial_result_length = (len(result[0]))
ob.add_fits_attribute('Chunk.energy.specsys', 'SPECSYS')
result = ob._get('Chunk.energy.specsys', extension=1)
add_result_length = (len(result[0]))
assert initial_result_length == add_result_length, result