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JP-3858-superbias #9232

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penaguerrero
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Resolves partially JP-3858

Closes #

This PR addresses style changes to superbias in the jwst repo.

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#>.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

@penaguerrero penaguerrero requested review from a team as code owners February 27, 2025 20:25
kmacdonald-stsci
kmacdonald-stsci approved these changes Feb 27, 2025
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jwst/superbias/bias_sub.py
The DQ flags in the bias reference image are propagated into the science
data pixeldq array. The error array is unchanged.
data pixel dq array. The error array is unchanged.
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I recommend capitalizing "DQ" here, since it's now changed to an acronym, instead of a variable name.

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codecov bot commented Feb 27, 2025

Codecov Report

Attention: Patch coverage is 75.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 73.65%. Comparing base (2eae615) to head (33bd228).
Report is 4 commits behind head on main.

Files with missing lines Patch % Lines
jwst/superbias/superbias_step.py 62.50% 3 Missing ⚠️
Additional details and impacted files 
@@           Coverage Diff           @@
##             main    #9232   +/-   ##
=======================================
  Coverage   73.65%   73.65%           
=======================================
  Files         368      368           
  Lines       36374    36374           
=======================================
  Hits        26792    26792           
  Misses       9582     9582

☔ View full report in Codecov by Sentry.
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emolter
emolter reviewed Feb 27, 2025
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Thanks for doing this Maria! I left a few comments

jwst/superbias/bias_sub.py

bias_model: super-bias model object
bias data
input_model : data model object
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Here and elsewhere, it might be good to be more specific about which types of JWSTDataModels are acceptable, and use specific class names (i.e., what would come out of type(input_model))

I assume the bias model needs to be specifically a SuperBiasModel, for example.

jwst/superbias/bias_sub.py
Comment on lines +45 to +47
Subtract a superbias image from a science data set.

Subtract the superbias from each group of each integration in the science data.
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These lines seem redundant with one another

jwst/superbias/superbias_step.py
Comment on lines +11 to +13
Perform super-bias subtraction.

Subtract super-bias reference data from the input science data model.
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Same here, seems redundant

jwst/superbias/superbias_step.py

Parameters
----------
step_input : data model object
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does this have to be a datamodel? I think it could also be a string pointing to a filename containing a datamodel

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@kmacdonald-stsci kmacdonald-stsci kmacdonald-stsci approved these changes

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@penaguerrero @emolter @kmacdonald-stsci