JP-3796: Scale barshadow correction to long slits #9085
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Running initial regression tests here: Results show differences only for NIRSpec MOS data.
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Codecov ReportAll modified and coverable lines are covered by tests ✅
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## main #9085 +/- ##
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+ Coverage 78.15% 78.16% +0.01%
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Lines 46244 46212 -32
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+ Misses 10103 10091 -12
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Resolves JP-3796
Partially resolves JP-1341
There are two approximations being made in the barshadow correction that are not scaling well to the very long "slitlet" in MOS data taken in longslit mode.
The first is related to JP-1341: there are two different definitions of slit height. The barshadow correction needs the full bar-to-bar height, but the slit coordinates in the WCS use the open area height. The barshadow code currently hard-codes the ratio between the full and open heights as 1.15, but the value actually varies a bit by quadrant. I'm proposing that we use the equation in JP-1341 to calculate and store the scale factors in the slit datamodel and use the slit.slit_yscale attribute in the barshadow correction in place of the hard-coded value. This requires an stdatamodels PR: spacetelescope/stdatamodels#379. With this change, the bars are much closer to where they need to be for long slit data.
The second approximation is that the barshadow code shifts the slit y-coordinates by the mean value for the bounding box in order to put the center of the constructed shadow at the center of the slit. This is correct if the center of the bounding box is also the center of the middle shutter, but may be a little offset if not. For the long slit test case, it introduced a shift of ~1 pixel. Changing the code to shift the constructed shadow to the fiducial shutter instead of the center of the bounding box fixes this offset as well.
This PR also includes some maintenance and minor refactoring for the barshadow step, to clean up documentation and add unit tests. I also replaced a local implementation of a bilinear interpolation algorithm with scipy.ndimage.map_coordinates: this was a simple, drop-in replacement that performs identically except that map_coordinates preserves NaNs at the edges of the arrays where there are no valid coordinates. The old interpolator extended the barshadow correction all the way to the edge of the data array in the dispersion direction.
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Build 11.3(use the latest build if not sure)no-changelog-entry-needed)changes/:echo "changed something" > changes/<PR#>.<changetype>.rst(see below for change types)docs/pageokify_regteststo update the truth filesnews fragment change types...
changes/<PR#>.general.rst: infrastructure or miscellaneous changechanges/<PR#>.docs.rstchanges/<PR#>.stpipe.rstchanges/<PR#>.datamodels.rstchanges/<PR#>.scripts.rstchanges/<PR#>.fits_generator.rstchanges/<PR#>.set_telescope_pointing.rstchanges/<PR#>.pipeline.rststage 1
changes/<PR#>.group_scale.rstchanges/<PR#>.dq_init.rstchanges/<PR#>.emicorr.rstchanges/<PR#>.saturation.rstchanges/<PR#>.ipc.rstchanges/<PR#>.firstframe.rstchanges/<PR#>.lastframe.rstchanges/<PR#>.reset.rstchanges/<PR#>.superbias.rstchanges/<PR#>.refpix.rstchanges/<PR#>.linearity.rstchanges/<PR#>.rscd.rstchanges/<PR#>.persistence.rstchanges/<PR#>.dark_current.rstchanges/<PR#>.charge_migration.rstchanges/<PR#>.jump.rstchanges/<PR#>.clean_flicker_noise.rstchanges/<PR#>.ramp_fitting.rstchanges/<PR#>.gain_scale.rststage 2
changes/<PR#>.assign_wcs.rstchanges/<PR#>.badpix_selfcal.rstchanges/<PR#>.msaflagopen.rstchanges/<PR#>.nsclean.rstchanges/<PR#>.imprint.rstchanges/<PR#>.background.rstchanges/<PR#>.extract_2d.rstchanges/<PR#>.master_background.rstchanges/<PR#>.wavecorr.rstchanges/<PR#>.srctype.rstchanges/<PR#>.straylight.rstchanges/<PR#>.wfss_contam.rstchanges/<PR#>.flatfield.rstchanges/<PR#>.fringe.rstchanges/<PR#>.pathloss.rstchanges/<PR#>.barshadow.rstchanges/<PR#>.photom.rstchanges/<PR#>.pixel_replace.rstchanges/<PR#>.resample_spec.rstchanges/<PR#>.residual_fringe.rstchanges/<PR#>.cube_build.rstchanges/<PR#>.extract_1d.rstchanges/<PR#>.resample.rststage 3
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changes/<PR#>.wfs_combine.rstchanges/<PR#>.white_light.rstchanges/<PR#>.cube_skymatch.rstchanges/<PR#>.engdb_tools.rstchanges/<PR#>.guider_cds.rst