8000 JP-3738: Subtract pedestal dark for MIRI MRS when constructing selfcal minimum by drlaw1558 · Pull Request #8771 · spacetelescope/jwst · GitHub
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JP-3738: Subtract pedestal dark for MIRI MRS when constructing selfcal minimum #8771

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Merged
merged 5 commits into from
Sep 11, 2024
Merged

JP-3738: Subtract pedestal dark for MIRI MRS when constructing selfcal minimum #8771

merged 5 commits into from
Sep 11, 2024

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drlaw1558
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@drlaw1558 drlaw1558 commented Sep 10, 2024 •
edited by melanieclarke
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This PR addresses JP-3738 by subtracting off the MRS median pedestal dark when performing bad pixel self calibration combine of multiple input exposures.

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?
    • add an entry to CHANGES.rst within the relevant release section (otherwise add the no-changelog-entry-needed label to this PR)
    • 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

@drlaw1558 drlaw1558 requested a review from a team as a code owner September 10, 2024 18:14
@stscijgbot-jp stscijgbot-jp mentioned this pull request Sep 10, 2024
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emolter
emolter approved these changes Sep 10, 2024
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@emolter emolter left a comment •
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Looks great, it should do what is expected. Just one style nitpick.

Regression tests need to be run too. I will start those when Jenkins is free

jwst/badpix_selfcal/badpix_selfcal_step.py Outdated
Comment on lines 108 to 113
if (input_sci.meta.instrument.detector.upper() == 'MIRIFUSHORT'):
selfcal_3d.append(selfcal_model.data - np.nanmedian(selfcal_model.data[50:1024-50, 503:516]))
elif (input_sci.meta.instrument.detector.upper() == 'MIRIFULONG'):
selfcal_3d.append(selfcal_model.data - np.nanmedian(selfcal_model.data[50:1024-50, 474:507]))
else:
selfcal_3d.append(selfcal_model.data)
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Style nit-pick incoming: Oftentimes in the pipeline when we want to hard-code numbers like this, we create an all-caps variable at the top of the file (just below imports) like this example. I think it would be good to do this with the pedestal indices, e.g. PEDESTAL_IDX_LONG=(50,974,474,507) and then call that variable where needed.

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Done!

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codecov bot commented Sep 10, 2024 •
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Codecov Report

Attention: Patch coverage is 71.42857% with 2 lines in your changes missing coverage. Please review.

Project coverage is 60.79%. Comparing base (12f5d3e) to head (2ab2da9).

Files with missing lines Patch % Lines
jwst/badpix_selfcal/badpix_selfcal_step.py 71.42% 2 Missing ⚠️
Additional details and impacted files 
@@           Coverage Diff           @@
##           master    #8771   +/-   ##
=======================================
  Coverage   60.79%   60.79%           
=======================================
  Files         373      373           
  Lines       38690    38696    +6     
=======================================
+ Hits        23523    23527    +4     
- Misses      15167    15169    +2

☔ View full report in Codecov by Sentry.
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emolter commented Sep 10, 2024

regression tests started here

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emolter commented Sep 11, 2024

Regression test failures appear to match the ones from last night's nightly run, except that the two badpix_selfcal tests are now showing 1% different pixels. If those differences look ok to you @drlaw1558 then this should be good to go, and we will ok-ify those tests once this is merged.

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emolter commented Sep 11, 2024

One more thing, and sorry, I probably should have been less trigger-happy with the "approve" button. It would probably be good to add a bullet point to the Description section of the badpix selfcal docs saying that the pedestal average is subtracted from each frame for MIRI data.

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One more thing, and sorry, I probably should have been less trigger-happy with the "approve" button. It would probably be good to add a bullet point to the Description section of the badpix selfcal docs saying that the pedestal average is subtracted from each frame for MIRI data.

Good call, added.

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Regression test failures appear to match the ones from last night's nightly run, except that the two badpix_selfcal tests are now showing 1% different pixels. If those differences look ok to you @drlaw1558 then this should be good to go, and we will ok-ify those tests once this is merged.

Some small difference in the flagged pixels sounds reasonable and should be ok.

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emolter commented Sep 11, 2024

everything looks good to me now

@melanieclarke melanieclarke added this to the Build 11.1 milestone Sep 11, 2024
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LGTM! Thanks for reviewing, Ned, and for the fix, David!

@melanieclarke melanieclarke merged commit bd7d269 into spacetelescope:master Sep 11, 2024
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