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Fix compatibility with recent JWST pipeline and stdatamodels versions #69

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Merged
jruffio merged 2 commits into from
Aug 7, 2026
Merged

Fix compatibility with recent JWST pipeline and stdatamodels versions #69

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a658ad7
Fix compatibility with recent JWST pipeline and stdatamodels versions…
mperrin Aug 6, 2026
66e5f46
use standard gWCS function call API for better compatibility
mperrin Aug 7, 2026
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4 changes: 2 additions & 2 deletions breads/instruments/jwstnirspec_cal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def _init_wcs(self, filename):
from gwcs import wcstools

hdulist = pyfits.open(filename)
calfile = jwst.datamodels.open(hdulist) # save time opening by passing the already opened file
calfile = datamodels.open(filename)
photom_dataset = DataSet(calfile)

# Compute 2D wavelength and pixel area arrays for the whole image
Expand Down Expand Up @@ -135,7 +135,7 @@ def _init_wcs(self, filename):
y = y.reshape(y.shape[0], 1) * np.ones((1, xmax - xmin))

# Transform all those pixels to RA, Dec, wavelength
skycoords, speccoord = wcses[i](x, y, with_units=True)
skycoords, speccoord = wcses[i].pixel_to_world(x, y)

ra_array[ymin:ymax, xmin:xmax] = skycoords.ra
dec_array[ymin:ymax, xmin:xmax] = skycoords.dec
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5 changes: 4 additions & 1 deletion breads/jwst_tools/reduction_utils.py
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Expand Up @@ -244,6 +244,9 @@ def run_stage2(rate_files, output_dir, skip_cubes=True, overwrite=False, TA=Fals

pathloss_skip = TA # For target acq images, skip the pathloss step, otherwise don't skip it.

from packaging.version import Version
clean_flicker_step = 'clean_flicker_noise' if Version(jwst.__version__) > Version("1.20") else 'nsclean'

step_parameters = {
# spec2.assign_wcs.skip = False
# spec2.bkg_subtract.skip = False
Expand All @@ -253,7 +256,7 @@ def run_stage2(rate_files, output_dir, skip_cubes=True, overwrite=False, TA=Fals
# spec2.flat_field.skip = False
# spec2.pathloss.skip = False
'pathloss':{'skip':pathloss_skip},
'nsclean':{'skip':nsclean_skip},
clean_flicker_step: {'skip': nsclean_skip},
# spec2.photom.skip = False
'cube_build': {'skip': skip_cubes}, # We do not want or need interpolated cubes
'extract_1d': {'skip': True},
Expand Down
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