JP-251: Optimal extraction support for MIRI LRS

[melanieclarke]

Resolves JP-251

Work in progress: first version with PSF profile support, for testing. Since the PSF model is not in CRDS yet, the only existing example is hard-coded: the MIRI_LRS_SLIT_EPSF_20240602_WAVE_1D.fits file must exist in the current working directory to reduce MIRI LRS fixed slit data with extraction_type = 'optimal'.

This PR builds on changes in #8961; that PR should be merged first.

This PR also requires datamodels changes in spacetelescope/stdatamodels#336, which are still to-be-finalized.

Tasks

• request a review from someone specific, to avoid making the maintainers review every PR
• add a build milestone, i.e. Build 11.3 (use the latest build if not sure)
• Does this PR change user-facing code / API? (if not, label with no-changelog-entry-needed)
  • write news fragment(s) in changes/: echo "changed something" > changes/<PR#>.<changetype>.rst (see below for change types)
  • update or add relevant tests
  • update relevant docstrings and / or docs/ page
  • start a regression test and include a link to the running job (click here for instructions)
    • Do truth files need to be updated ("okified")?
      • after the reviewer has approved these changes, run okify_regtests to update the truth files
• if a JIRA ticket exists, make sure it is resolved properly

news fragment change types...

• changes/<PR#>.general.rst: infrastructure or miscellaneous change
• changes/<PR#>.docs.rst
• changes/<PR#>.stpipe.rst
• changes/<PR#>.datamodels.rst
• changes/<PR#>.scripts.rst
• changes/<PR#>.fits_generator.rst
• changes/<PR#>.set_telescope_pointing.rst
• changes/<PR#>.pipeline.rst

stage 1

• changes/<PR#>.group_scale.rst
• changes/<PR#>.dq_init.rst
• changes/<PR#>.emicorr.rst
• changes/<PR#>.saturation.rst
• changes/<PR#>.ipc.rst
• changes/<PR#>.firstframe.rst
• changes/<PR#>.lastframe.rst
• changes/<PR#>.reset.rst
• changes/<PR#>.superbias.rst
• changes/<PR#>.refpix.rst
• changes/<PR#>.linearity.rst
• changes/<PR#>.rscd.rst
• changes/<PR#>.persistence.rst
• changes/<PR#>.dark_current.rst
• changes/<PR#>.charge_migration.rst
• changes/<PR#>.jump.rst
• changes/<PR#>.clean_flicker_noise.rst
• changes/<PR#>.ramp_fitting.rst
• changes/<PR#>.gain_scale.rst

stage 2

• changes/<PR#>.assign_wcs.rst
• changes/<PR#>.badpix_selfcal.rst
• changes/<PR#>.msaflagopen.rst
• changes/<PR#>.nsclean.rst
• changes/<PR#>.imprint.rst
• changes/<PR#>.background.rst
• changes/<PR#>.extract_2d.rst
• changes/<PR#>.master_background.rst
• changes/<PR#>.wavecorr.rst
• changes/<PR#>.srctype.rst
• changes/<PR#>.straylight.rst
• changes/<PR#>.wfss_contam.rst
• changes/<PR#>.flatfield.rst
• changes/<PR#>.fringe.rst
• changes/<PR#>.pathloss.rst
• changes/<PR#>.barshadow.rst
• changes/<PR#>.photom.rst
• changes/<PR#>.pixel_replace.rst
• changes/<PR#>.resample_spec.rst
• changes/<PR#>.residual_fringe.rst
• changes/<PR#>.cube_build.rst
• changes/<PR#>.extract_1d.rst
• changes/<PR#>.resample.rst

stage 3

• changes/<PR#>.assign_mtwcs.rst
• changes/<PR#>.mrs_imatch.rst
• changes/<PR#>.tweakreg.rst
• changes/<PR#>.skymatch.rst
• changes/<PR#>.exp_to_source.rst
• changes/<PR#>.outlier_detection.rst
• changes/<PR#>.tso_photometry.rst
• changes/<PR#>.stack_refs.rst
• changes/<PR#>.align_refs.rst
• changes/<PR#>.klip.rst
• changes/<PR#>.spectral_leak.rst
• changes/<PR#>.source_catalog.rst
• changes/<PR#>.combine_1d.rst
• changes/<PR#>.ami.rst

other

• changes/<PR#>.wfs_combine.rst
• changes/<PR#>.white_light.rst
• changes/<PR#>.cube_skymatch.rst
• changes/<PR#>.engdb_tools.rst
• changes/<PR#>.guider_cds.rst

[codecov]

Codecov Report

Attention: Patch coverage is 5.32151% with 427 lines in your changes missing coverage. Please review.

Project coverage is 59.59%. Comparing base (a9ab10a) to head (cb7df62).
Report is 7 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/extract_1d/psf_profile.py	4.00%	144 Missing ⚠️
jwst/extract_1d/extract1d.py	4.28%	134 Missing ⚠️
jwst/extract_1d/extract_1d_step.py	0.00%	121 Missing ⚠️
jwst/extract_1d/ifu.py	17.64%	28 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #8967      +/-   ##
==========================================
- Coverage   64.54%   59.59%   -4.95%     
==========================================
  Files         375      376       +1     
  Lines       38737    37966     -771     
==========================================
- Hits        25002    22626    -2376     
- Misses      13735    15340    +1605     

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