def test_fitcoord_table_and_gwcs_match(ad, change_working_dir):
"""
Runs determineDistortion and checks that the model in the gWCS is the same
as the model in the FITCOORD table. The FITCOORD table is never used by
DRAGONS.
Parameters
----------
ad: pytest.fixture (AstroData)
Fixture that reads the filename and loads as an AstroData object.
change_working_dir : pytest.fixture
Fixture that changes the working directory
(see :mod:`astrodata.testing`).
"""
with change_working_dir():
logutils.config(file_name='log_match_{:s}.txt'.format(ad.data_label()))
p = GMOSLongslit([ad])
p.viewer = geminidr.dormantViewer(p, None)
p.determineDistortion(**fixed_parameters_for_determine_distortion)
distortion_determined_ad = p.writeOutputs().pop()
model = distortion_determined_ad[0].wcs.get_transform(
"pixels", "distortion_corrected")
fitcoord = distortion_determined_ad[0].FITCOORD
fitcoord_model = am.table_to_model(fitcoord[0])
fitcoord_inv = am.table_to_model(fitcoord[1])
np.testing.assert_allclose(model[1].parameters, fitcoord_model.parameters)
np.testing.assert_allclose(model.inverse[1].parameters,
fitcoord_inv.parameters)
def test_regression_for_determine_distortion_using_wcs(ad, change_working_dir,
ref_ad_factory):
"""
Runs the `determineDistortion` primitive on a preprocessed data and compare
its model with the one in the reference file. The distortion model needs to
be reconstructed because different coefficients might return same results.
Parameters
----------
ad : pytest.fixture (AstroData)
Fixture that reads the filename and loads as an AstroData object.
change_working_dir : pytest.fixture
Fixture that changes the working directory
(see :mod:`astrodata.testing`).
reference_ad : pytest.fixture
Fixture that contains a function used to load the reference AstroData
object (see :mod:`recipe_system.testing`).
"""
with change_working_dir():
logutils.config(
file_name='log_fitcoord_{:s}.txt'.format(ad.data_label()))
p = GMOSLongslit([ad])
p.viewer = geminidr.dormantViewer(p, None)
p.determineDistortion(**fixed_parameters_for_determine_distortion)
distortion_determined_ad = p.writeOutputs().pop()
ref_ad = ref_ad_factory(distortion_determined_ad.filename)
model = distortion_determined_ad[0].wcs.get_transform(
"pixels", "distortion_corrected")[1]
ref_model = ref_ad[0].wcs.get_transform("pixels",
"distortion_corrected")[1]
X, Y = np.mgrid[:ad[0].shape[0], :ad[0].shape[1]]
np.testing.assert_allclose(model(X, Y), ref_model(X, Y), atol=1)
def test_regression_for_determine_distortion_using_models_coefficients(
ad, change_working_dir, ref_ad_factory, request):
"""
Runs the `determineDistortion` primitive on a preprocessed data and compare
its model with the one in the reference file.
Parameters
----------
ad : pytest.fixture (AstroData)
Fixture that reads the filename and loads as an AstroData object.
change_working_dir : pytest.fixture
Fixture that changes the working directory
(see :mod:`astrodata.testing`).
reference_ad : pytest.fixture
Fixture that contains a function used to load the reference AstroData
object (see :mod:`recipe_system.testing`).
request : pytest.fixture
PyTest built-in containing command line options.
"""
with change_working_dir():
logutils.config(file_name='log_model_{:s}.txt'.format(ad.data_label()))
p = GMOSLongslit([ad])
p.viewer = geminidr.dormantViewer(p, None)
p.determineDistortion(**fixed_parameters_for_determine_distortion)
distortion_determined_ad = p.writeOutputs().pop()
ref_ad = ref_ad_factory(distortion_determined_ad.filename)
assert_have_same_distortion(distortion_determined_ad, ref_ad, atol=1)
if request.config.getoption("--do-plots"):
do_plots(distortion_determined_ad, ref_ad)
def process_arc(filename, suffix="distortionDetermined"):
"""
Helper recipe to reduce the arc file.
Returns
-------
AstroData
Processed arc.
"""
from astrodata.testing import download_from_archive
from geminidr.gmos.primitives_gmos_longslit import GMOSLongslit
processed_filename, ext = os.path.splitext(filename)
processed_filename += "_{:s}{:s}".format(suffix, ext)
if os.path.exists(processed_filename):
ad = astrodata.open(processed_filename)
else:
if os.path.exists(filename):
ad = astrodata.open(filename)
else:
ad = astrodata.open(
download_from_archive(filename,
path='',
env_var='DRAGONS_TEST'))
p = GMOSLongslit([ad])
p.prepare()
p.addDQ(static_bpm=None)
p.addVAR(read_noise=True)
p.overscanCorrect()
# p.biasCorrect()
p.ADUToElectrons()
p.addVAR(poisson_noise=True)
p.mosaicDetectors()
p.makeIRAFCompatible()
p.determineWavelengthSolution()
p.determineDistortion()
ad = p.streams['main'][0]
ad.write(overwrite=True)
return ad
def test_distortion_correction_is_applied_the_same_way(config):
"""
Applies the same distortion correction model to both output and reference
arcs and compares the results.
"""
# Process the output file ---
basename, ext = os.path.splitext(config.filename)
basename, _ = basename.split("_")[0], basename.split("_")[1:]
arc_basename = "{:s}_{:s}{:s}".format(basename, "distortionDetermined",
ext)
arc_name = os.path.join(config.output_dir, arc_basename)
if not os.path.exists(arc_name):
pytest.skip("Arc file not found: {}".format(arc_name))
ad_out = config.ad
p = GMOSLongslit([])
ad_out = p.distortionCorrect(adinputs=[ad_out], arc=arc_name)[0]
filename = ad_out.filename
ad_out = p.determineDistortion(adinputs=[ad_out])[0]
for ext in ad_out:
assert "distortion_corrected" in ext.wcs.available_frames
ad_out.write(filename=filename, overwrite=True)
# assert False
# # Reads the reference file ---
# reference = os.path.join(config.ref_dir, ad_out.filename)
#
# if not os.path.exists(reference):
# pytest.fail('Reference file not found: {}'.format(reference))
#
# ad_ref = astrodata.open(reference)
os.rename(filename, os.path.join(config.output_dir, filename))
def create_inputs_recipe():
"""
Creates input data for tests using pre-processed standard star and its
calibration files.
The raw files will be downloaded and saved inside the path stored in the
`$DRAGONS_TEST/raw_inputs` directory. Processed files will be stored inside
a new folder called "dragons_test_inputs". The sub-directory structure
should reflect the one returned by the `path_to_inputs` fixture.
"""
import os
from astrodata.testing import download_from_archive
from recipe_system.reduction.coreReduce import Reduce
from gempy.utils import logutils
from astrodata.testing import get_associated_calibrations
associated_calibrations = {
"S20190808S0048.fits": 'S20190808S0167.fits',
"S20190808S0049.fits": 'S20190808S0168.fits',
"S20190808S0053.fits": 'S20190808S0169.fits',
"N20180106S0025.fits": 'N20180115S0264.fits',
"N20180106S0026.fits": 'N20180115S0264.fits',
"N20180106S0028.fits": 'N20180115S0264.fits',
"N20180106S0029.fits": 'N20180115S0264.fits',
}
root_path = os.path.join("./dragons_test_inputs/")
module_path = "geminidr/gmos/spect/{}".format(__file__.split('.')[0])
path = os.path.join(root_path, module_path)
os.makedirs(path, exist_ok=True)
os.chdir(path)
os.makedirs("./inputs", exist_ok=True)
print('Current working directory:\n {:s}'.format(os.getcwd()))
for fname, arc_fname in associated_calibrations.items():
sci_path = download_from_archive(fname)
arc_path = download_from_archive(arc_fname)
sci_ad = astrodata.open(sci_path)
data_label = sci_ad.data_label()
print('Reducing ARC for {:s}'.format(data_label))
logutils.config(file_name='log_arc_{}.txt'.format(data_label))
if os.path.exists(
arc_fname.replace('.fits', '_distortionDetermined.fits')):
arc = astrodata.open(
arc_fname.replace('.fits', '_distortionDetermined.fits'))
else:
p = GMOSLongslit([astrodata.open(arc_path)])
p.prepare()
p.addDQ(static_bpm=None)
p.addVAR(read_noise=True)
p.overscanCorrect()
p.ADUToElectrons()
p.addVAR(poisson_noise=True)
p.mosaicDetectors()
p.makeIRAFCompatible()
p.determineWavelengthSolution()
p.determineDistortion()
arc = p.writeOutputs().pop()
print('Reducing pre-processed data:')
logutils.config(file_name='log_{}.txt'.format(data_label))
p = GMOSLongslit([sci_ad])
p.prepare()
p.addDQ(static_bpm=None)
p.addVAR(read_noise=True)
p.overscanCorrect()
p.ADUToElectrons()
p.addVAR(poisson_noise=True)
p.mosaicDetectors()
p.distortionCorrect(arc=arc)
p.findSourceApertures(max_apertures=1)
p.skyCorrectFromSlit()
os.chdir("inputs/")
_ = p.writeOutputs().pop()
os.chdir("../")