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Move common resample code to stcal #8986

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@mcara mcara commented Nov 27, 2024

Closes #8695

This PR add the common resample code used by both JWST and Roman pipelines to stcal. For now only imaging mode was switched to the new code. This PR supersedes #8695

This work is related to https://jira.stsci.edu/browse/AL-835

The code in this PR requires the code from spacetelescope/stcal#320

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

@mcara mcara added the resample label Nov 27, 2024
@mcara mcara self-assigned this Nov 27, 2024
@mcara mcara requested a review from a team as a code owner November 27, 2024 17:00
@mcara mcara force-pushed the new-resample-cls2 branch from adc3ca4 to c7286ee Compare November 27, 2024 17:21
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codecov bot commented Nov 27, 2024

Codecov Report

Attention: Patch coverage is 91.94444% with 29 lines in your changes missing coverage. Please review.

Project coverage is 76.64%. Comparing base (e3d263f) to head (a4301e9).
Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
jwst/resample/resample_spec_step.py 62.50% 9 Missing ⚠️
jwst/resample/resample_spec.py 91.39% 8 Missing ⚠️
jwst/resample/resample.py 96.36% 6 Missing ⚠️
jwst/resample/resample_utils.py 89.74% 4 Missing ⚠️
jwst/resample/resample_step.py 75.00% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #8986      +/-   ##
==========================================
- Coverage   76.81%   76.64%   -0.18%     
==========================================
  Files         496      496              
  Lines       45610    45421     -189     
==========================================
- Hits        35034    34811     -223     
- Misses      10576    10610      +34     
Flag Coverage Δ *Carryforward flag
nightly 77.33% <ø> (-0.10%) ⬇️ Carriedforward from aff1ded

*This pull request uses carry forward flags. Click here to find out more.

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@braingram braingram left a comment

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Thanks for putting this together.

I'd like to see the CI run and regression tests for this PR. I added one comment about psutil which should fix one of the issues preventing the CI from running.

Would you update the pyproject.toml to point to the source branch of spacetelescope/stcal#320? That should (hopefully) allow the CI to run so we can see the coverage and test results with this PR.

Also would you queue up a regtest run?

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mcara commented Nov 28, 2024

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Same question here: weren't a lot of the functions in here moved to stcal, so shouldn't they be removed from here?

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mcara commented Dec 4, 2024

Initial regression tests that were using the new code only for imaging are: https://github.com/spacetelescope/RegressionTests/actions/runs/12146883313

After switching spectral code to use the new class, here are the results of regression tests: https://github.com/spacetelescope/RegressionTests/actions/runs/12155412170

I most failures that I see are unrelated to my code, I think (such as test_miri_image_detector1[ramp], test_miri_image_detector1[rate], ...). The spectral test failures have new header cards and these could be OKified. Spectral tests are easily identifiable by Extra keyword 'NDRIZ' - these are spectral tests with extra meta info (related to resample). Imaging tests should be OK.

@mcara mcara marked this pull request as ready for review December 4, 2024 14:42
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This is looking great Mihai! Thanks for all the hard work. Most of these comments are minor.

It still feels a bit sad to have to convert the datamodels into dictionaries to pass into stcal, but I can't really think of a better way to do it while maintaining the observatory-agnostic nature of stcal. So I guess I'm happy with it. Maybe it's a bit easier on the romancal side when working with asdf files as compared with fits?

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Comment on lines +252 to +258
# delete these to reduce the number of failures in the regression tests
# TODO: this is helpful info that should be stored in products.
# del model.meta.resample.pixel_scale_ratio
# del model.meta.resample.pixfrac
# del model.meta.resample.weight_type
# del model.meta.resample.pointings
# del model.meta.cal_step.resample
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Can you elaborate on why these cause failures? should these be reinstated before merge?

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It seems like currently for spectral data none of the above fields related to resample info are being set. So, if I turn this ON right now, you will see multiple failures in the regression tests. I think these should be turned on before merging, if @melanieclarke is not against storing this info for spectral data.

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I am all for storing this info for spectral data! I thought these were added, though, in the ResampleSpecStep? There may be some weirdness around what happens with MultiSlitModels.

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@melanieclarke melanieclarke added this to the Build 11.3 milestone Dec 12, 2024
@mcara mcara force-pushed the new-resample-cls2 branch from bb0839e to aff1ded Compare December 15, 2024 11:24
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LGTM

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