JP-3739: Update NRM geometry, affine distortion use

[rcooper295]

Resolves JP-3739

This PR addresses JP-3739, which includes updates associated with the mask geometry. The NRM reference file is being updated to be distorted by the affine transform parameters derived during commissioning, and the datamodel definitions have also been updated to allow the AMI3 code to read the mask hole centers and other pupil geometry from the reference file datamodel, rather than it being hardcoded in mask_definitions.py. The new mask_definition_ami.NRM_definition largely keeps the same structure as mask_definitions.NRM_mask_definitions but is simplified because there is only one NRM on JWST. A special input argument for affine2d, 'commissioning' is the new default and uses the commissioning affine parameters for the analytical form of the mask (rather than distortion-free or rotation-only).

(to be merged after #8846

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/.general.rst``: infrastructure or miscellaneous change - ``changes/.docs.rst`` - ``changes/.stpipe.rst`` - ``changes/.datamodels.rst`` - ``changes/.scripts.rst`` - ``changes/.fits_generator.rst`` - ``changes/.set_telescope_pointing.rst`` - ``changes/.pipeline.rst`` ## stage 1 - ``changes/.group_scale.rst`` - ``changes/.dq_init.rst`` - ``changes/.emicorr.rst`` - ``changes/.saturation.rst`` - ``changes/.ipc.rst`` - ``changes/.firstframe.rst`` - ``changes/.lastframe.rst`` - ``changes/.reset.rst`` - ``changes/.superbias.rst`` - ``changes/.refpix.rst`` - ``changes/.linearity.rst`` - ``changes/.rscd.rst`` - ``changes/.persistence.rst`` - ``changes/.dark_current.rst`` - ``changes/.charge_migration.rst`` - ``changes/.jump.rst`` - ``changes/.clean_flicker_noise.rst`` - ``changes/.ramp_fitting.rst`` - ``changes/.gain_scale.rst`` ## stage 2 - ``changes/.assign_wcs.rst`` - ``changes/.badpix_selfcal.rst`` - ``changes/.msaflagopen.rst`` - ``changes/.nsclean.rst`` - ``changes/.imprint.rst`` - ``changes/.background.rst`` - ``changes/.extract_2d.rst`` - ``changes/.master_background.rst`` - ``changes/.wavecorr.rst`` - ``changes/.srctype.rst`` - ``changes/.straylight.rst`` - ``changes/.wfss_contam.rst`` - ``changes/.flatfield.rst`` - ``changes/.fringe.rst`` - ``changes/.pathloss.rst`` - ``changes/.barshadow.rst`` - ``changes/.photom.rst`` - ``changes/.pixel_replace.rst`` - ``changes/.resample_spec.rst`` - ``changes/.residual_fringe.rst`` - ``changes/.cube_build.rst`` - ``changes/.extract_1d.rst`` - ``changes/.resample.rst`` ## stage 3 - ``changes/.assign_mtwcs.rst`` - ``changes/.mrs_imatch.rst`` - ``changes/.tweakreg.rst`` - ``changes/.skymatch.rst`` - ``changes/.exp_to_source.rst`` - ``changes/.outlier_detection.rst`` - ``changes/.tso_photometry.rst`` - ``changes/.stack_refs.rst`` - ``changes/.align_refs.rst`` - ``changes/.klip.rst`` - ``changes/.spectral_leak.rst`` - ``changes/.source_catalog.rst`` - ``changes/.combine_1d.rst`` - ``changes/.ami.rst`` ## other - ``changes/.wfs_combine.rst`` - ``changes/.white_light.rst`` - ``changes/.cube_skymatch.rst`` - ``changes/.engdb_tools.rst`` - ``changes/.guider_cds.rst``

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 24.56140% with 172 lines in your changes missing coverage. Please review.

Project coverage is 62.52%. Comparing base (5a2d0cd) to head (8f38d3f). Report is 19 commits behind head on main.

Files with missing lines	Patch %	Lines
jwst/ami/oifits.py	7.54%	98 Missing :warning:
jwst/ami/ami_analyze_step.py	28.20%	28 Missing :warning:
jwst/ami/leastsqnrm.py	9.52%	19 Missing :warning:
jwst/ami/mask_definition_ami.py	63.15%	14 Missing :warning:
jwst/ami/lg_model.py	28.57%	5 Missing :warning:
jwst/ami/ami_analyze.py	62.50%	3 Missing :warning:
jwst/ami/instrument_data.py	66.66%	2 Missing :warning:
jwst/ami/find_affine2d_parameters.py	0.00%	1 Missing :warning:
jwst/ami/mask_definitions.py	0.00%	1 Missing :warning:
jwst/ami/nrm_core.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #8974 +/- ## ========================================== - Coverage 64.52% 62.52% -2.01% ========================================== Files 375 376 +1 Lines 38739 38921 +182 ========================================== - Hits 24997 24335 -662 - Misses 13742 14586 +844 ```

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