def test_verify_image2(run_image2, rtdata_module, fitsdiff_default_kwargs,
suffix):
"""Test results of the detector1 and image2 processing"""
rtdata = rtdata_module
rtdata.input = replace_suffix(ROOT, 'uncal') + '.fits'
output = replace_suffix(ROOT, suffix) + '.fits'
rtdata.output = output
rtdata.get_truth('truth/test_nirspec_verify/' + output)
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def run_spec3(jail, run_spec2):
"""Run the Spec3Pipeline on the results from the Spec2Pipeline run"""
rtdata = run_spec2
# Create the level 3 `spec3` association from the output product
# name of `run_spec2`
product = run_spec2.asn['products'][0]['name']
input_name = replace_suffix(product, 'cal') + '.fits'
asn = asn_from_list([input_name], product_name=product)
_, serialized = asn.dump()
asn_name = product + '_spec3_asn.json'
with open(asn_name, 'w') as asn_fh:
asn_fh.write(serialized)
# Set the input in the RegtestData instance to avoid download.
rtdata.input = asn_name
step_params = {
'step': 'calwebb_spec3.cfg',
'args': [
'--steps.master_background.save_results=true',
'--steps.mrs_imatch.save_results=true',
'--steps.outlier_detection.save_results=true',
'--steps.resample_spec.save_results=true',
'--steps.cube_build.save_results=true',
'--steps.extract_1d.save_results=true',
'--steps.combine_1d.save_results=true',
]
}
rtdata = rt.run_step_from_dict(rtdata, **step_params)
return rtdata
def run_image2(run_detector1, rtdata_module):
"""Run NRS_VERIFY through image2"""
rtdata = rtdata_module
# Get some predefined references due to insufficient coverage
# from CRDS.
refs = [
'jwst_nirspec_fpa_0005.asdf', 'jwst_nirspec_flat_0061.fits',
'jwst_nirspec_area_0001.fits'
]
for ref in refs:
rtdata.get_data('nirspec/imaging/' + ref)
rtdata.input = replace_suffix(ROOT, 'rate') + '.fits'
args = [
'jwst.pipeline.Image2Pipeline',
rtdata.input,
'--steps.assign_wcs.save_results=true',
'--steps.assign_wcs.override_fpa=jwst_nirspec_fpa_0005.asdf',
'--steps.flat_field.save_results=true',
'--steps.flat_field.override_flat=jwst_nirspec_flat_0061.fits',
'--steps.flat_field.override_sflat=N/A',
'--steps.flat_field.override_fflat=N/A',
'--steps.flat_field.override_dflat=N/A',
'--steps.photom.save_results=true',
'--steps.photom.override_area=jwst_nirspec_area_0001.fits',
]
Step.from_cmdline(args)
def test_suffix_replacement(suffix,
enable_logging,
base='file',
new='junk',
sep='_'):
"""Test suffix replacement"""
full_path = base + sep + suffix
replaced = s.replace_suffix(full_path, new)
assert replaced == base + sep + new
def is_like_truth(rtdata,
fitsdiff_default_kwargs,
suffix,
truth_path='truth/fgs/test_fgs_guider'):
"""Compare step outputs with truth"""
output = replace_suffix(
os.path.splitext(os.path.basename(rtdata.input))[0], suffix) + '.fits'
rtdata.output = output
rtdata.get_truth(os.path.join(truth_path, output))
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nirspec_brightobj_spec2(run_tso_spec2_pipeline, fitsdiff_default_kwargs, suffix):
"""
Regression test of calwebb_spec2 pipeline performed on NIRSpec
fixed-slit data that uses the NRS_BRIGHTOBJ mode (S1600A1 slit).
"""
rtdata = run_tso_spec2_pipeline
output = replace_suffix(
os.path.splitext(os.path.basename(rtdata.input))[0], suffix) + '.fits'
rtdata.output = output
# Get the truth files
rtdata.get_truth(os.path.join("truth/test_nirspec_brightobj_spec2", output))
# Compare the results
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def test_nirspec_lamp_ifu_spec2(run_pipeline, fitsdiff_default_kwargs, suffix):
"""Regression test of the calwebb_spec2 pipeline on a
NIRSpec lamp exposure in IFU mode."""
# Run the pipeline and retrieve outputs
rtdata = run_pipeline
output = replace_suffix(
os.path.splitext(os.path.basename(rtdata.input))[0], suffix) + '.fits'
rtdata.output = output
# Get the truth files
rtdata.get_truth(os.path.join("truth/test_nirspec_lamp_spec2", output))
# Compare the results
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def is_like_truth(rtdata,
fitsdiff_default_kwargs,
output,
truth_path,
is_suffix=True):
"""Compare step outputs with truth
Parameters
----------
rtdata: RegtestData
The artifactory object from the step run.
fitsdiff_default_kwargs: dict
The `fitsdiff` keyword arguments
output: str
The suffix or full file name to check on.
truth_path: str
Location of the truth files.
is_suffix: bool
Interpret `output` as just a suffix on the expected output root.
Otherwise, assume it is a full file name
"""
# If given only a suffix, get the root to change the suffix of.
# If the input was an association, the output should be the name of the product
# Otherwise, output is based on input.
if is_suffix:
suffix = output
if rtdata.asn:
output = rtdata.asn['products'][0]['name']
else:
output = os.path.splitext(os.path.basename(rtdata.input))[0]
output = replace_suffix(output, suffix) + '.fits'
rtdata.output = output
rtdata.get_truth(os.path.join(truth_path, output))
diff = FITSDiff(rtdata.output, rtdata.truth, **fitsdiff_default_kwargs)
assert diff.identical, diff.report()
def run_spec2(jail, rtdata_module):
"""Run the Spec2Pipeline on a single exposure"""
rtdata = rtdata_module
# Setup the inputs
asn_name = 'ifushort_ch12_rate_asn3.json'
rtdata.get_data(INPUT_PATH + '/' + asn_name)
asn_path = rtdata.input
with open(asn_path, 'r') as asn_fh:
asn = load_asn(asn_fh)
member_path = Path(asn['products'][0]['members'][0]['expname'])
rate_path = member_path.stem
rate_path = replace_suffix(rate_path, 'rate')
rate_path = INPUT_PATH + '/' + rate_path + member_path.suffix
# Run the pipeline
step_params = {
'input_path':
rate_path,
'step':
'calwebb_spec2.cfg',
'args': [
'--steps.bkg_subtract.save_results=true',
'--steps.assign_wcs.save_results=true',
'--steps.imprint_subtract.save_results=true',
'--steps.msa_flagging.save_results=true',
'--steps.extract_2d.save_results=true',
'--steps.flat_field.save_results=true',
'--steps.srctype.save_results=true',
'--steps.straylight.save_results=true',
'--steps.fringe.save_results=true',
'--steps.pathloss.save_results=true',
'--steps.barshadow.save_results=true',
'--steps.photom.save_results=true',
'--steps.resample_spec.save_results=true',
'--steps.cube_build.save_results=true',
'--steps.extract_1d.save_results=true',
]
}
rtdata = rt.run_step_from_dict(rtdata, **step_params)
return rtdata, asn_path
def run_detector1(rtdata_module):
"""Run NRS_VERIFY through detector1"""
rtdata = rtdata_module
rtdata.get_data('nirspec/imaging/' + replace_suffix(ROOT, 'uncal') +
'.fits')
collect_pipeline_cfgs('config')
args = [
'config/calwebb_detector1.cfg',
rtdata.input,
'--steps.dq_init.save_results=True',
'--steps.saturation.save_results=True',
'--steps.superbias.save_results=True',
'--steps.refpix.save_results=True',
'--steps.linearity.save_results=True',
'--steps.dark_current.save_results=True',
'--steps.jump.save_results=True',
]
Step.from_cmdline(args)
