def compare(cls, reference_file, test_file, atol=None, rtol=None):
import astropy
from astropy.io.fits.diff import FITSDiff
from astropy.utils.introspection import minversion
if minversion(astropy, '2.0'):
diff = FITSDiff(reference_file, test_file, rtol=rtol)
else:
diff = FITSDiff(reference_file, test_file, tolerance=rtol)
return diff.identical, diff.report()
def test_partially_identical_files3(self):
"""
Test files that have some identical HDUs but a different extension
name.
"""
phdu = PrimaryHDU()
ehdu = ImageHDU(name='FOO')
hdula = HDUList([phdu, ehdu])
ehdu = BinTableHDU(name='BAR')
ehdu.header['EXTVER'] = 2
ehdu.header['EXTLEVEL'] = 3
hdulb = HDUList([phdu, ehdu])
diff = FITSDiff(hdula, hdulb)
assert not diff.identical
assert diff.diff_hdus[0][0] == 1
hdu_diff = diff.diff_hdus[0][1]
assert hdu_diff.diff_extension_types == ('IMAGE', 'BINTABLE')
assert hdu_diff.diff_extnames == ('FOO', 'BAR')
assert hdu_diff.diff_extvers == (1, 2)
assert hdu_diff.diff_extlevels == (1, 3)
report = diff.report()
assert 'Extension types differ' in report
assert 'a: IMAGE\n b: BINTABLE' in report
assert 'Extension names differ' in report
assert 'a: FOO\n b: BAR' in report
assert 'Extension versions differ' in report
assert 'a: 1\n b: 2' in report
assert 'Extension levels differ' in report
assert 'a: 1\n b: 2' in report
def test_nircam_setpointing_tsimg(_jail, rtdata, fitsdiff_default_kwargs):
"""
Regression test of the set_telescope_pointing script on a level-1b
NIRCam TSO imaging file.
"""
# Get SIAF PRD database file
siaf_path = rtdata.get_data("common/prd.db")
rtdata.get_data(
"nircam/tsimg/jw00312006001_02102_00001-seg001_nrcb1_uncal.fits")
# The add_wcs function overwrites its input, so output = input
rtdata.output = rtdata.input
# Call the WCS routine, using the ENGDB_Service
try:
add_wcs(rtdata.input, siaf_path=siaf_path)
except ValueError:
pytest.skip('Engineering Database not available.')
rtdata.get_truth(
"truth/test_nircam_setpointing/jw00312006001_02102_00001-seg001_nrcb1_uncal.fits"
)
fitsdiff_default_kwargs['rtol'] = 1e-6
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_miri_setpointing(_jail, rtdata, fitsdiff_default_kwargs):
"""
Regression test of the set_telescope_pointing script on a level-1b MIRI image.
"""
# Get SIAF PRD database file
siaf_path = rtdata.get_data("common/prd.db")
# Get the input level-1b file
rtdata.get_data("miri/image/jw80600010001_02101_00001_mirimage_uncal.fits")
# The add_wcs function overwrites its input, so output = input
rtdata.output = rtdata.input
# Call the WCS routine, using the ENGDB_Service
# Note that there aren't any quaternion mnemonics in the ENGDB for the time
# range of this exposure, so we set "allow_default" to tell add_wcs to use
# default values for the pointing-related keywords. Keyword values retrieved
# from the SIAF will be good.
add_wcs(rtdata.input, allow_default=True, siaf_path=siaf_path)
# Compare the results
rtdata.get_truth(
"truth/test_miri_setpointing/jw80600010001_02101_00001_mirimage_uncal.fits"
)
fitsdiff_default_kwargs['rtol'] = 1e-6
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nirspec_ifu_mbkg_user(rtdata, fitsdiff_default_kwargs):
"""Test NIRSpec IFU data with a user-supplied background file."""
# Get user-supplied background
user_background = "prism_bkg_x1d.fits"
rtdata.get_data(f"nirspec/ifu/{user_background}")
# Get input data
rtdata.get_data("nirspec/ifu/prism_sci_bkg_cal.fits")
collect_pipeline_cfgs("config")
args = [
"config/master_background.cfg", rtdata.input, "--user_background",
user_background
]
Step.from_cmdline(args)
output = "prism_sci_bkg_master_background.fits"
rtdata.output = output
# Get the truth file
rtdata.get_truth(f"truth/test_nirspec_ifu_mbkg_user/{output}")
# Compare the results
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_miri_lrs_slitless_tso3(
run_spec3_pipeline,
generate_tso3_asn,
rtdata_module,
fitsdiff_default_kwargs,
step_suffix,
filename_extension,
is_product,
diff_astropy_tables,
):
"""Compare the output of a MIRI LRS slitless calwebb_tso3 step."""
rtdata = rtdata_module
_, asn_id = generate_tso3_asn
if is_product:
output_filename = f"{PRODUCT_NAME}_{step_suffix}.{filename_extension}"
else:
output_filename = f"{DATASET_ID}_{asn_id}_{step_suffix}.{filename_extension}"
rtdata.output = output_filename
rtdata.get_truth(f"truth/test_miri_lrs_slitless_tso3/{output_filename}")
if filename_extension == "fits":
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
else:
diff = diff_astropy_tables(rtdata.output, rtdata.truth)
assert len(diff) == 0, "\n".join(diff)
def test_level_1(out_dir):
l0 = test_data.products.L0_LightCurve_fits
l1 = Level1(out_dir / 'LB', out_dir)
res = sorted(l1.process_fits_files(files=l0))
assert len(res) == 2
# test for https://github.com/i4Ds/STIXCore/issues/180
# TODO remove when solved
lc1 = Product(res[0])
lc2 = Product(res[1])
t = np.hstack((np.array(lc1.data['time']), (np.array(lc2.data['time']))))
td = np.hstack(
(np.array(lc1.data['timedel']), (np.array(lc2.data['timedel']))))
range(len(lc1.data['time']) - 3, len(lc1.data['time']) + 3)
assert np.all((t[1:] - t[0:-1]) == td[0:-1])
# end test for https://github.com/i4Ds/STIXCore/issues/180
for fits in res:
diff = FITSDiff(
test_data.products.DIR / fits.name,
fits,
ignore_keywords=['CHECKSUM', 'DATASUM', 'DATE', 'VERS_SW'])
if not diff.identical:
print(diff.report())
assert diff.identical
def fits_osiris_allclose(a, b):
"""Assert that two OSIRIS fits files are close."""
a = fits.open(a)
b = fits.open(b)
try:
del a[0].header['COMMENT']
del b[0].header['COMMENT']
report = StringIO()
diff = FITSDiff(a,
b,
ignore_keywords=["COMMENT"],
ignore_comments=["SIMPLE"],
ignore_fields=[],
ignore_blanks=True,
ignore_blank_cards=True,
tolerance=1e-5)
diff.report(fileobj=report)
assert diff.identical, report.getvalue()
finally:
a.close()
b.close()
def test_image3_closedfile(run_image3_closedfile, rtdata, fitsdiff_default_kwargs):
"""Ensure production of Image3Pipeline output with data having closed file issues"""
rtdata.output = 'jw00617-o082_t001_nircam_clear-f090w-sub320_i2d.fits'
rtdata.get_truth('truth/test_nircam_image/jw00617-o082_t001_nircam_clear-f090w-sub320_i2d.fits')
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def fitsdiff(input1,
input2,
comment_excl_list='',
value_excl_list='',
field_excl_list='',
maxdiff=10,
delta=0.0,
neglect_blanks=True,
output=None):
if isinstance(comment_excl_list, string_types):
comment_excl_list = list_parse(comment_excl_list)
if isinstance(value_excl_list, string_types):
value_excl_list = list_parse(value_excl_list)
if isinstance(field_excl_list, string_types):
field_excl_list = list_parse(field_excl_list)
diff = FITSDiff(input1,
input2,
ignore_keywords=value_excl_list,
ignore_comments=comment_excl_list,
ignore_fields=field_excl_list,
numdiffs=maxdiff,
tolerance=delta,
ignore_blanks=neglect_blanks)
if output is None:
output = sys.stdout
diff.report(output)
return diff.identical
def test_miri_lrs_extract1d_from_cal(run_pipeline, rtdata_module, fitsdiff_default_kwargs):
rtdata = rtdata_module
rtdata.input = "jw00623032001_03102_00001_mirimage_cal.fits"
Extract1dStep.call(rtdata.input, save_results=True)
output = "jw00623032001_03102_00001_mirimage_extract1dstep.fits"
rtdata.output = output
rtdata.get_truth(f"truth/test_miri_lrs_slit_spec2/{output}")
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_miri_image3_i2d(run_image3, rtdata_module, fitsdiff_default_kwargs):
rtdata = rtdata_module
rtdata.input = "det_dithered_5stars_image3_asn.json"
rtdata.output = "det_dithered_5stars_f770w_i2d.fits"
rtdata.get_truth("truth/test_miri_image_stages/det_dithered_5stars_f770w_i2d.fits")
fitsdiff_default_kwargs["rtol"] = 1e-4
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_miri_image2(run_pipeline, fitsdiff_default_kwargs, output):
"""Regression test of calwebb_image2 pipeline performed on MIRI data."""
rtdata = run_pipeline
rtdata.output = output
rtdata.get_truth(os.path.join("truth/test_miri_image2_cal", output))
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def _test_write_string_bytes_io(self, fileobj):
"""
Implemented for both test_write_stringio and test_write_bytesio.
"""
with fits.open(self.data('test0.fits')) as hdul:
hdul.writeto(fileobj)
hdul2 = fits.HDUList.fromstring(fileobj.getvalue())
assert FITSDiff(hdul, hdul2).identical
def test_nircam_image_stages12(run_pipelines, fitsdiff_default_kwargs, suffix):
"""Regression test of detector1 and image2 pipelines performed on NIRCam data."""
rtdata = run_pipelines
rtdata.input = "jw42424001001_01101_00001_nrca5_uncal.fits"
output = "jw42424001001_01101_00001_nrca5_" + suffix + ".fits"
rtdata.output = output
rtdata.get_truth("truth/test_nircam_image_stages/" + output)
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_spec3(run_spec3, fitsdiff_default_kwargs, output):
"""Regression test matching output files"""
rtdata = run_spec3
rtdata.output = output
rtdata.get_truth(os.path.join(TRUTH_PATH, rtdata.output))
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_niriss_soss_stage3_x1dints(run_pipelines, fitsdiff_default_kwargs):
rtdata = run_pipelines
rtdata.input = "jw00625-o023_20191210t204036_tso3_001_asn.json"
rtdata.output = "jw00625-o023_t001_niriss_clear-gr700xd-substrip256_x1dints.fits"
rtdata.get_truth(
"truth/test_niriss_soss_stages/jw00625-o023_t001_niriss_clear-gr700xd-substrip256_x1dints.fits"
)
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nirspec_detector1(run_pipeline, fitsdiff_default_kwargs, output):
"""
Regression test of calwebb_detector1 pipeline performed on NIRSpec data.
"""
rtdata = run_pipeline
rtdata.output = output
rtdata.get_truth(os.path.join("truth/test_nirspec_subarray", output))
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_spec2(rtdata_module, run_spec2, fitsdiff_default_kwargs, suffix):
"""Test ensuring the calwebb_tso-spec2 is operating appropriately for MIRI MRS TSO data"""
rtdata = rtdata_module
output = f"jw80600018001_02101_00003_mirifushort_{suffix}.fits"
rtdata.output = output
rtdata.get_truth(f"{TRUTH_PATH}/{output}")
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_fits_file_bytes_object(self):
"""
Testing when fits file is passed as bytes.
"""
with fits.open(self.data('tdim.fits').encode()) as hdulist:
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
with fits.open(self.data('tdim.fits')) as hdulist2:
assert FITSDiff(hdulist2, hdulist).identical is True
def test_nircam_tsgrism_stage3_x1dints(run_pipelines, fitsdiff_default_kwargs):
rtdata = run_pipelines
rtdata.input = "jw00721-o012_20191119t043909_tso3_001_asn.json"
rtdata.output = "jw00721-o012_t004_nircam_f444w-grismr-subgrism256_x1dints.fits"
rtdata.get_truth(
"truth/test_nircam_tsgrism_stages/jw00721-o012_t004_nircam_f444w-grismr-subgrism256_x1dints.fits"
)
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nircam_image_stage3_segm(run_image3pipeline, rtdata_module, fitsdiff_default_kwargs):
"""Test that segmentation map looks good for NIRCam imaging"""
rtdata = rtdata_module
rtdata.input = "jw42424-o002_20191220t214154_image3_001_asn.json"
output = "jw42424-o002_t001_nircam_clear-f444w_segm.fits"
rtdata.output = output
rtdata.get_truth(f"truth/test_nircam_image_stages/{output}")
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nircam_coron3_product(run_pipeline, suffix, fitsdiff_default_kwargs):
"""Check final products of calwebb_coron3"""
rtdata = run_pipeline
output = "jw99999-a3001_t1_nircam_f140m-maskbar_" + suffix + ".fits"
rtdata.output = output
rtdata.get_truth("truth/test_nircam_coron3/" + output)
fitsdiff_default_kwargs['atol'] = 1e-5
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_miri_lrs_slitless_spec2(run_spec2_pipeline, rtdata_module,
fitsdiff_default_kwargs, step_suffix):
"""Compare the output of a MIRI LRS slitless calwebb_tso-spec2 step."""
rtdata = rtdata_module
output_filename = f"{DATASET_ID}_{step_suffix}.fits"
rtdata.output = output_filename
rtdata.get_truth(f"truth/test_miri_lrs_slitless_spec2/{output_filename}")
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nircam_tsimg_stage2(run_pipelines, fitsdiff_default_kwargs, suffix):
"""Regression test of tso-image2 pipeline performed on NIRCam TSIMG data."""
rtdata = run_pipelines
rtdata.input = "jw00312006001_02102_00001-seg001_nrcb1_rateints.fits"
output = "jw00312006001_02102_00001-seg001_nrcb1_" + suffix + ".fits"
rtdata.output = output
rtdata.get_truth("truth/test_nircam_tsimg_stage23/" + output)
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_miri_lrs_slitless_tso3_x1dints(run_tso3_pipeline, rtdata_module,
fitsdiff_default_kwargs):
"""Compare the output of a MIRI LRS slitless calwebb_tso3 pipeline."""
rtdata = rtdata_module
output_filename = f"{PRODUCT_NAME}_x1dints.fits"
rtdata.output = output_filename
rtdata.get_truth(f"truth/test_miri_lrs_slitless_tso3/{output_filename}")
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_fits_file_path_object(self):
"""
Testing when fits file is passed as pathlib.Path object #4412.
"""
fpath = pathlib.Path(self.data('tdim.fits'))
with fits.open(fpath) as hdulist:
assert hdulist[0].filebytes() == 2880
assert hdulist[1].filebytes() == 5760
with fits.open(self.data('tdim.fits')) as hdulist2:
assert FITSDiff(hdulist2, hdulist).identical is True
def test_niriss_soss_stage2(run_pipelines, fitsdiff_default_kwargs, suffix):
"""Regression test of tso-spec2 pipeline performed on NIRISS SOSS data."""
rtdata = run_pipelines
rtdata.input = "jw00625023001_03101_00001-seg001_nis_rateints.fits"
output = "jw00625023001_03101_00001-seg001_nis_" + suffix + ".fits"
rtdata.output = output
rtdata.get_truth("truth/test_niriss_soss_stages/" + output)
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_miri_image_stage3_i2d(run_pipelines, fitsdiff_default_kwargs):
rtdata = run_pipelines
rtdata.input = "det_dithered_5stars_image3_asn.json"
rtdata.output = "det_dithered_5stars_f770w_i2d.fits"
rtdata.get_truth(
"truth/test_miri_image_stages/det_dithered_5stars_f770w_i2d.fits")
fitsdiff_default_kwargs['ignore_fields'] = ['date', 'filename']
fitsdiff_default_kwargs['ignore_keywords'] += ['naxis1', 'tform*']
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nircam_coron3_exp(run_pipeline, suffix, exposure, fitsdiff_default_kwargs):
"""Check intermediate results of calwebb_coron3"""
rtdata = run_pipeline
output = "jw9999947001_02102_" + exposure + "_nrcb3_a3001_" + suffix + ".fits"
rtdata.output = output
rtdata.get_truth("truth/test_nircam_coron3/" + output)
fitsdiff_default_kwargs["atol"] = 1e-5
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
