def test_range1d_to_interval(self):
# happy path
wcs = CustomTestUtil.good_wcs()
start = RefCoord(float(0.9), float(1.1))
end = RefCoord(float(10.9), float(11.1))
range_1d = CoordRange1D(start, end)
actual_interval = wcs_util.CustomAxisUtil.range1d_to_interval(
wcs, range_1d)
expected_interval = Interval(1.1, 11.1)
self.assertEqual(expected_interval.lower, actual_interval.lower)
self.assertEqual(expected_interval.upper, actual_interval.upper)
self.assertEqual(None, actual_interval.samples)
# function_1d.delta == 0.0 && function_1d.naxis > 1
start = RefCoord(float(0.9), float(1.1))
end = RefCoord(float(10.9), float(1.1))
range_1d = CoordRange1D(start, end)
with pytest.raises(ValueError) as ex:
wcs_util.CustomAxisUtil.range1d_to_interval(wcs, range_1d)
assert ('Invalid CoordRange1D:' in str(ex.value))
def test_val2pix(self):
# happy path
wcs = CustomTestUtil.good_wcs()
naxis = int(100)
delta = -0.01
ref_coord = RefCoord(0.0, 0.0)
func = CoordFunction1D(naxis, delta, ref_coord)
val = 0.1
pix = wcs_util.CustomAxisUtil.val2pix(wcs, func, val)
expected_pix = -10.0
self.assertEqual(pix, expected_pix)
def _update_ngvs_time(chunk, provenance, obs_id):
logging.debug(f'Begin _update_ngvs_time for {obs_id}')
if (chunk is not None and provenance is not None and
len(provenance.inputs) > 0):
# bounds = ctor
config = mc.Config()
config.get_executors()
subject = mc.define_subject(config)
client = CAOM2RepoClient(
subject, config.logging_level, 'ivo://cadc.nrc.ca/ams')
metrics = mc.Metrics(config)
bounds = CoordBounds1D()
min_date = 0
max_date = sys.float_info.max
exposure = 0
for entry in provenance.inputs:
ip_obs_id, ip_product_id = mc.CaomName.decompose_provenance_input(
entry.uri)
logging.info(f'Retrieving provenance metadata for {ip_obs_id}.')
ip_obs = mc.repo_get(client, 'CFHT', ip_obs_id, metrics)
if ip_obs is not None:
ip_plane = ip_obs.planes.get(ip_product_id)
if (ip_plane is not None and ip_plane.time is not None and
ip_plane.time.bounds is not None):
bounds.samples.append(CoordRange1D(
RefCoord(pix=0.5, val=ip_plane.time.bounds.lower),
RefCoord(pix=1.5, val=ip_plane.time.bounds.upper)))
min_date = min(ip_plane.time.bounds.lower, min_date)
max_date = max(ip_plane.time.bounds.upper, max_date)
exposure += ip_plane.time.exposure
axis = Axis(ctype='TIME', cunit='d')
time_axis = CoordAxis1D(axis=axis,
error=None,
range=None,
bounds=bounds,
function=None)
temporal_wcs = TemporalWCS(axis=time_axis, timesys=None, trefpos=None,
mjdref=None, exposure=mc.to_float(exposure),
resolution=None)
chunk.time = temporal_wcs
logging.debug(f'End _update_ngvs_time.')
def test_function1d_to_interval_happy_path(self):
# happy path
wcs = CustomTestUtil.good_wcs()
naxis = int(100)
delta = -0.2
ref_coord = RefCoord(0.0, 0.0)
function_1d = CoordFunction1D(naxis, delta, ref_coord)
actual_interval = wcs_util.CustomAxisUtil.function1d_to_interval(
wcs, function_1d)
expected_interval = Interval(-502.5, -2.5)
self.assertEqual(expected_interval.lower, actual_interval.lower)
self.assertEqual(expected_interval.upper, actual_interval.upper)
self.assertEqual(None, actual_interval.samples)
# function_1d.delta == 0.0 && function_1d.naxis > 1
naxis = int(100)
delta = 0.0
ref_coord = RefCoord(0.0, 0.0)
function_1d = CoordFunction1D(naxis, delta, ref_coord)
with pytest.raises(ValueError) as ex:
wcs_util.CustomAxisUtil.function1d_to_interval(wcs, function_1d)
assert ('Invalid CoordFunction1D:' in str(ex.value))
def get_test_function_with_function(ctype, unit, px, sx, nx, ds):
error = None
range = None
bounds = None
naxis = int(1)
delta = float(2.5)
ref_coord = wcs.RefCoord(float(1.0), float(2.0))
function = CoordFunction1D(naxis, delta, ref_coord)
axis_1d = CoordAxis1D(wcs.Axis(ctype, unit), error, range, bounds,
function)
ref_coord = RefCoord(px, sx)
axis_1d.function = CoordFunction1D(nx, ds, ref_coord)
custom_wcs = chunk.CustomWCS(axis_1d)
return custom_wcs
def _update_time(self, chunk, obs_id):
"""Create TemporalWCS information using FITS header information.
This information should always be available from the file."""
self._logger.debug('Begin _update_time.')
mc.check_param(chunk, Chunk)
mjd_start = self._headers[0].get('MJD_STAR')
mjd_end = self._headers[0].get('MJD_END')
if mjd_start is None or mjd_end is None:
mjd_start, mjd_end = ac.find_time_bounds(self._headers)
if mjd_start is None or mjd_end is None:
chunk.time = None
self._logger.debug(
f'Cannot calculate MJD_STAR {mjd_start} or ' f'MDJ_END'
f' {mjd_end}'
)
elif mjd_start == 'NaN' or mjd_end == 'NaN':
raise mc.CadcException(
f'Invalid time values MJD_STAR {mjd_start} or MJD_END '
f'{mjd_end} for {obs_id}, stopping ingestion.'
)
else:
self._logger.debug(
f'Calculating range with start {mjd_start} and end {mjd_end}.'
)
start = RefCoord(0.5, mjd_start)
end = RefCoord(1.5, mjd_end)
time_cf = CoordFunction1D(1, self._headers[0].get('TEFF'), start)
time_axis = CoordAxis1D(Axis('TIME', 'd'), function=time_cf)
time_axis.range = CoordRange1D(start, end)
chunk.time = TemporalWCS(time_axis)
chunk.time.exposure = self._headers[0].get('TEFF')
chunk.time.resolution = 0.1
chunk.time.timesys = 'UTC'
chunk.time.trefpos = 'TOPOCENTER'
chunk.time_axis = None
self._logger.debug('Done _update_time.')
def _update_time(part, chunk, header, obs_id):
logging.debug(f'Begin _update_time for {obs_id} part {part.name}.')
# DB 02-07-20
# time metadata comes from MJD_OBS and EXPTIME, it's not
# an axis requiring cutout support
exp_time = header.get('EXPTIME')
mjd_obs = header.get('MJD_OBS')
if exp_time is None or mjd_obs is None:
chunk.time = None
else:
if chunk.time is None:
coord_error = CoordError(syser=1e-07, rnder=1e-07)
time_axis = CoordAxis1D(axis=Axis('TIME', 'd'), error=coord_error)
chunk.time = TemporalWCS(axis=time_axis, timesys='UTC')
ref_coord = RefCoord(pix=0.5, val=mjd_obs)
chunk.time.axis.function = CoordFunction1D(
naxis=1, delta=mc.convert_to_days(exp_time), ref_coord=ref_coord)
chunk.time.exposure = float(exp_time)
chunk.time.resolution = mc.convert_to_days(exp_time)
logging.debug(f'End _update_time.')
def get_test_function_with_bounds_3_samples(ctype, unit, px, sx, nx, ds):
error = None
range = None
start = RefCoord(float(0.8), float(1.1))
end = RefCoord(float(10.8), float(11.1))
b_range_1 = CoordRange1D(start, end)
start = RefCoord(float(0.9), float(1.2))
end = RefCoord(float(10.9), float(11.2))
b_range_2 = CoordRange1D(start, end)
start = RefCoord(float(-0.9), float(-1.2))
end = RefCoord(float(0.6), float(0.2))
b_range_3 = CoordRange1D(start, end)
samples = caom_util.TypedList(CoordRange1D, b_range_1, b_range_2,
b_range_3)
bounds = CoordBounds1D(samples)
axis_1d = wcs.CoordAxis1D(wcs.Axis(ctype, unit), error, range, bounds)
ref_coord = wcs.RefCoord(px, sx)
axis_1d.function = wcs.CoordFunction1D(nx, ds, ref_coord)
custom_wcs = chunk.CustomWCS(axis_1d)
return custom_wcs
def test_bounds(self):
# Polarization bounds is None, should not produce an error
axis = Axis("STOKES", "cunit")
axis_1d = CoordAxis1D(axis)
polarization = PolarizationWCS(axis_1d)
wcsvalidator._validate_polarization_wcs(polarization)
# Polarization axis bounds contains one valid range
start = RefCoord(float(0.9), float(1.1))
end = RefCoord(float(9.9), float(10.1))
p_range = CoordRange1D(start, end)
samples = caom_util.TypedList(CoordRange1D, p_range)
axis_1d.bounds = CoordBounds1D(samples)
polarization = PolarizationWCS(axis_1d)
wcsvalidator._validate_polarization_wcs(polarization)
# Polarization axis bounds contains more than one valid range
start = RefCoord(float(0.9), float(1.1))
end = RefCoord(float(9.9), float(10.1))
p_range = CoordRange1D(start, end)
start = RefCoord(float(-8.1), float(-7.9))
end = RefCoord(float(-1.1), float(-0.9))
n_range = CoordRange1D(start, end)
samples = caom_util.TypedList(CoordRange1D, p_range, n_range)
axis_1d.bounds = CoordBounds1D(samples)
polarization = PolarizationWCS(axis_1d)
wcsvalidator._validate_polarization_wcs(polarization)
# Polarization axis bounds contains one invalid range
start = RefCoord(float(0.9), float(1.1))
end = RefCoord(float(10.9), float(11.1))
p_range = CoordRange1D(start, end)
samples = caom_util.TypedList(CoordRange1D, p_range)
axis_1d.bounds = CoordBounds1D(samples)
polarization = PolarizationWCS(axis_1d)
with pytest.raises(InvalidWCSError) as ex:
wcsvalidator._validate_polarization_wcs(polarization)
assert ('Invalid Polarization WCS' in str(ex.value))
assert ('11' in str(ex.value))
# Polarization axis bounds contains more than one invalid range
start = RefCoord(float(0.9), float(1.1))
end = RefCoord(float(9.9), float(10.1))
p_range = CoordRange1D(start, end)
start = RefCoord(float(-9.1), float(-8.9))
end = RefCoord(float(-1.1), float(-0.9))
n_range = CoordRange1D(start, end)
samples = caom_util.TypedList(CoordRange1D, p_range, n_range)
axis_1d.bounds = CoordBounds1D(samples)
polarization = PolarizationWCS(axis_1d)
with pytest.raises(InvalidWCSError) as ex:
wcsvalidator._validate_polarization_wcs(polarization)
assert ('Invalid Polarization WCS' in str(ex.value))
assert ('-9' in str(ex.value))
def _update_from_comment(observation, phangs_name, headers):
# From ER: 04-03-21
# COMMENT Produced with PHANGS-ALMA pipeline version 4.0 Build 935
# - Provenance.version
# COMMENT Galaxy properties from PHANGS sample table version 1.6
# COMMENT Calibration Level 4 (ANALYSIS_PRODUCT)
# - Calibration level (either 3 or 4)
# COMMENT PHANGS-ALMA Public Release 1
# - Provenance.project = PHANGS-ALMA
# COMMENT Generated by the Physics at High Angular resolution
# COMMENT in nearby GalaxieS (PHANGS) collaboration
# - Provenance.organization = PHANGS
# COMMENT Canonical Reference: Leroy et al. (2021), ApJ, Submitted
# - Update to reference when accepted
# COMMENT Release generated at 2021-03-04T07:28:10.245340
# - Provenance.lastExecuted
# COMMENT Data from ALMA Proposal ID: 2017.1.00886.L
# - Proposal.proposalID
# COMMENT ALMA Proposal PI: Schinnerer, Eva
# - Proposal.pi_name
# COMMENT Observed in MJD interval [58077.386275,58081.464121]
# COMMENT Observed in MJD interval [58290.770032,58365.629222]
# COMMENT Observed in MJD interval [58037.515807,58047.541173]
# COMMENT Observed in MJD interval [58353.589805,58381.654757]
# COMMENT Observed in MJD interval [58064.3677,58072.458597]
# COMMENT Observed in MJD interval [58114.347649,58139.301879]
chunk = None
for plane in observation.planes.values():
if plane.product_id != phangs_name.product_id:
continue
if plane.provenance is None:
plane.provenance = Provenance(name='PHANGS-ALMA pipeline')
for artifact in plane.artifacts.values():
if artifact.uri != phangs_name.file_uri:
continue
for part in artifact.parts.values():
chunk = part.chunks[0]
break
for entry in headers[0].get('COMMENT'):
if 'pipeline version ' in entry:
plane.provenance.version = entry.split(' version ')[1]
elif 'Calibration Level' in entry:
level = entry.split()[2]
if level == '4':
plane.calibration_level = CalibrationLevel.ANALYSIS_PRODUCT
elif 'PHANGS-ALMA Public Release' in entry:
plane.provenance.project = 'PHANGS-ALMA'
elif 'in nearby GalaxieS (PHANGS) collaboration' in entry:
plane.provenance.organization = 'PHANGS'
elif 'Release generated at ' in entry:
plane.provenance.last_executed = mc.make_time_tz(
entry.split(' at ')[1])
elif 'Data from ALMA Proposal ID:' in entry:
observation.proposal = Proposal(entry.split(':')[1].strip())
elif 'Canonical Reference: ' in entry:
plane.provenance.producer = entry.split(': ')[1]
elif 'ALMA Proposal PI:' in entry:
observation.proposal.pi_name = entry.split(': ')[1]
elif 'Observed in MJD interval ' in entry:
if chunk is not None:
bits = entry.split()[4].split(',')
start_ref_coord = RefCoord(
0.5, mc.to_float(bits[0].replace('[', '')))
end_ref_coord = RefCoord(
1.5, mc.to_float(bits[1].replace(']', '')))
sample = CoordRange1D(start_ref_coord, end_ref_coord)
if chunk.time is None:
coord_bounds = CoordBounds1D()
axis = CoordAxis1D(axis=Axis('TIME', 'd'))
chunk.time = TemporalWCS(axis, timesys='UTC')
chunk.time.axis.bounds = coord_bounds
chunk.time.axis.bounds.samples.append(sample)
def get_test_function(ctype, unit, px, sx, nx, ds):
axis_1d = CoordAxis1D(wcs.Axis(ctype, unit))
ref_coord = RefCoord(px, sx)
axis_1d.function = CoordFunction1D(nx, ds, ref_coord)
custom_wcs = chunk.CustomWCS(axis_1d)
return custom_wcs
