Use nanmedian3D for TSO data in outlier detection

[emolter]

#8782 added the nanmedian3D() convenience function to outlier detection, which calls np.nanmedian on the zeroth axis in a way that avoids allocating a float64 array that is the same size as the input data, and also suppresses "all-NaN slice encountered" warnings. This PR replaces a single instance of np.nanmedian() with nanmedian3D for TSO data when a rolling median (the default) is NOT requested.

Testing on one fake dataset, constructed by repeating the calints files from regtest/run_nircam_tsimage.py along the time axis until the input data shape was (2000, 64, 64), showed that this change makes no difference to the peak memory usage of the step. The reasons are that (1) the memory performance of np.nanmedian does not scale as poorly when the time axis gets large as when the spatial axes get large; and (2) computing the weights and their associated thresholds also scales with the input data size and turns out to use more memory than np.nanmedian.

Nevertheless, this change is probably worth implementing. It ensures the median call does not become a memory performance problem if the memory usage elsewhere in the step is ever optimized, and if nothing else it suppresses the "all-NaN" warnings.

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

[emolter]

regression tests started here

Not sure if I'm using the no-changelog-entry-needed flag properly here or not. My logic is that this change doesn't do anything that a user of the code would care about.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 61.79%. Comparing base (32f744d) to head (7c3639b).
Report is 2 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #8859   +/-   ##
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  Coverage   61.79%   61.79%           
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  Files         377      377           
  Lines       38827    38827           
=======================================
+ Hits        23992    23994    +2     
+ Misses      14835    14833    -2     

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[braingram]

LGTM.

[melanieclarke]

This looks fine to me by eye, but it looks the code is not covered by either unit test or regression test. Can we add a quick test for TSO with non-rolling median?

[melanieclarke]

LGTM, thanks for adding the test!