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Suppress warnings about NaNs in input data from TweakRegStep #8308

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merged 5 commits into from
Feb 28, 2024
Merged

Suppress warnings about NaNs in input data from TweakRegStep #8308

merged 5 commits into from
Feb 28, 2024

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jdavies-st
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@jdavies-st jdavies-st commented Feb 26, 2024 •
edited by hbushouse
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Currently TweakRegStep logs lots of warnings like the following:

2024-02-26 14:09:45,740 - stpipe.tweakreg - WARNING - /Users/jdavies/miniconda3/envs/jwst-dev/lib/python3.11/site-packages/photutils/background/background_2d.py:273: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically masked.
2024-02-26 14:09:45,740 - stpipe.tweakreg - WARNING -   warnings.warn('Input data contains invalid values (NaNs or '
2024-02-26 14:09:45,740 - stpipe.tweakreg - WARNING - 
2024-02-26 14:09:46,597 - stpipe.tweakreg - INFO - Detected 106 sources in jw01345002001_14201_00002_nrcalong_cal.fits.
2024-02-26 14:09:46,608 - stpipe.tweakreg - WARNING - /Users/jdavies/miniconda3/envs/jwst-dev/lib/python3.11/site-packages/photutils/background/background_2d.py:273: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically masked.
2024-02-26 14:09:46,608 - stpipe.tweakreg - WARNING -   warnings.warn('Input data contains invalid values (NaNs or '
2024-02-26 14:09:46,608 - stpipe.tweakreg - WARNING - 
2024-02-26 14:09:47,422 - stpipe.tweakreg - INFO - Detected 115 sources in jw01345002001_14201_00003_nrcalong_cal.fits.
2024-02-26 14:09:47,433 - stpipe.tweakreg - WARNING - /Users/jdavies/miniconda3/envs/jwst-dev/lib/python3.11/site-packages/photutils/background/background_2d.py:273: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically masked.
2024-02-26 14:09:47,433 - stpipe.tweakreg - WARNING -   warnings.warn('Input data contains invalid values (NaNs or '
2024-02-26 14:09:47,433 - stpipe.tweakreg - WARNING - 
2024-02-26 14:09:48,253 - stpipe.tweakreg - INFO - Detected 95 sources in jw01345002001_14201_00001_nrcalong_cal.fits.
2024-02-26 14:09:48,265 - stpipe.tweakreg - WARNING - /Users/jdavies/miniconda3/envs/jwst-dev/lib/python3.11/site-packages/photutils/background/background_2d.py:273: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically masked.
2024-02-26 14:09:48,266 - stpipe.tweakreg - WARNING -   warnings.warn('Input data contains invalid values (NaNs or '
2024-02-26 14:09:48,266 - stpipe.tweakreg - WARNING - 
2024-02-26 14:09:49,092 - stpipe.tweakreg - INFO - Detected 100 sources in jw01345002001_14201_00001_nrcblong_cal.fits.
2024-02-26 14:09:49,950 - stpipe.tweakreg - WARNING - /Users/jdavies/miniconda3/envs/jwst-dev/lib/python3.11/site-packages/photutils/background/background_2d.py:273: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically masked.
2024-02-26 14:09:49,950 - stpipe.tweakreg - WARNING -   warnings.warn('Input data contains invalid values (NaNs or '
2024-02-26 14:09:49,950 - stpipe.tweakreg - WARNING - 
2024-02-26 14:09:50,762 - stpipe.tweakreg - INFO - Detected 94 sources in jw01345002001_14201_00002_nrcblong_cal.fits.
2024-02-26 14:09:50,775 - stpipe.tweakreg - WARNING - /Users/jdavies/miniconda3/envs/jwst-dev/lib/python3.11/site-packages/photutils/background/background_2d.py:273: AstropyUserWarning: Input data contains invalid values (NaNs or infs), which were automatically masked.
2024-02-26 14:09:50,775 - stpipe.tweakreg - WARNING -   warnings.warn('Input data contains invalid values (NaNs or '
2024-02-26 14:09:50,775 - stpipe.tweakreg - WARNING - 
2024-02-26 14:09:51,584 - stpipe.tweakreg - INFO - Detected 98 sources in jw01345002001_14201_00003_nrcblong_cal.fits.

which is caused by passing _cal.fits data with NaNs to photutils.background.Background2D:

https://github.com/astropy/photutils/blob/d5e8bc9afebd758087ea47874aff0a1788e22587/photutils/background/background_2d.py#L287-L289

All JWST input data for this step has NaNs, so warning about them is not informative. This PR suppresses those warnings, so we now get:

2024-02-26 14:13:18,475 - stpipe.tweakreg - INFO - Detected 106 sources in jw01345002001_14201_00002_nrcalong_cal.fits.
2024-02-26 14:13:19,287 - stpipe.tweakreg - INFO - Detected 115 sources in jw01345002001_14201_00003_nrcalong_cal.fits.
2024-02-26 14:13:20,097 - stpipe.tweakreg - INFO - Detected 95 sources in jw01345002001_14201_00001_nrcalong_cal.fits.
2024-02-26 14:13:20,903 - stpipe.tweakreg - INFO - Detected 100 sources in jw01345002001_14201_00001_nrcblong_cal.fits.
2024-02-26 14:13:22,522 - stpipe.tweakreg - INFO - Detected 94 sources in jw01345002001_14201_00002_nrcblong_cal.fits.
2024-02-26 14:13:23,345 - stpipe.tweakreg - INFO - Detected 98 sources in jw01345002001_14201_00003_nrcblong_cal.fits.

Possible upstream fix for this in astropy/photutils#1712

Checklist for maintainers

  • added entry in CHANGES.rst within the relevant release section
  • updated or added relevant tests
  • updated relevant documentation
  • added relevant milestone
  • added relevant label(s)
  • ran regression tests, post a link to the Jenkins job below.
    How to run regression tests on a PR
  • Make sure the JIRA ticket is resolved properly

@jdavies-st jdavies-st requested a review from a team as a code owner February 26, 2024 13:31
@jdavies-st jdavies-st force-pushed the tweakreg-silence-photutils-warnings branch from 46dc688 to d102466 Compare February 26, 2024 13:33
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codecov bot commented Feb 26, 2024 •
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Codecov Report

Attention: Patch coverage is 62.50000% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 75.21%. Comparing base (4cc0ac1) to head (d879a7f).
Report is 2 commits behind head on master.

❗ Current head d879a7f differs from pull request most recent head bb89734. Consider uploading reports for the commit bb89734 to get more accurate results

Files Patch % Lines
jwst/source_catalog/detection.py 62.50% 3 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master    #8308      +/-   ##
==========================================
+ Coverage   75.15%   75.21%   +0.05%     
==========================================
  Files         470      474       +4     
  Lines       38604    38812     +208     
==========================================
+ Hits        29014    29191     +177     
- Misses       9590     9621      +31
Flag Coverage Δ *Carryforward flag
nightly 77.36% <ø> (-0.03%) ⬇️ Carriedforward from 4cc0ac1

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

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larrybradley
larrybradley suggested changes Feb 26, 2024
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Thanks, @jdavies-st.

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@larrybradley PEP8 cleanup on aisle 7 is done.

@hbushouse hbushouse added this to the Build 10.2 milestone Feb 27, 2024
hbushouse
hbushouse reviewed Feb 27, 2024
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hbushouse
hbushouse reviewed Feb 27, 2024
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Regression test run started at https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1236

@jdavies-st jdavies-st force-pushed the tweakreg-silence-photutils-warnings branch from b80f5e9 to bb89734 Compare February 28, 2024 15:22
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Regression test run started at https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1236

Regression test run is clean, as expected.

@hbushouse hbushouse merged commit f5f4826 into spacetelescope:master Feb 28, 2024
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@jdavies-st jdavies-st deleted the tweakreg-silence-photutils-warnings branch February 29, 2024 09:13
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@larrybradley larrybradley larrybradley approved these changes

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