JP-3470: Add ifu covariance scaling to extract1d

[drlaw1558]

Resolves JP-3470 by allowing for a parameter to be passed into extract1d accounting for IFU cube covariance.

Closes #8083

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

[codecov]

Codecov Report

Attention: Patch coverage is 13.33333% with 13 lines in your changes missing coverage. Please review.

Project coverage is 57.98%. Comparing base (781e0e0) to head (85eefe9).
Report is 294 commits behind head on master.

Files	Patch %	Lines
jwst/extract_1d/ifu.py	13.33%	13 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #8457      +/-   ##
==========================================
+ Coverage   57.93%   57.98%   +0.05%     
==========================================
  Files         387      387              
  Lines       38839    38826      -13     
==========================================
+ Hits        22502    22514      +12     
+ Misses      16337    16312      -25     

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[jemorrison]

Looks like a straight forward addition.

[hbushouse]

Looks good. Just one comment on the updated documentation.

[hbushouse]

regtest run started at https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1424

[hbushouse]

CI tests are failing with:

self = <LogRecord: stpipe, 20, /home/runner/work/jwst/jwst/jwst/extract_1d/ifu.py, 248, "Applying ERR covariance prefactor of %g">

    def getMessage(self):
        """
        Return the message for this LogRecord.
    
        Return the message for this LogRecord after merging any user-supplied
        arguments with the message.
        """
        msg = str(self.msg)
        if self.args:
>           msg = msg % self.args
E           TypeError: must be real number, not NoneType

[drlaw1558]

CI tests are failing with:

self = <LogRecord: stpipe, 20, /home/runner/work/jwst/jwst/jwst/extract_1d/ifu.py, 248, "Applying ERR covariance prefactor of %g">

    def getMessage(self):
        """
        Return the message for this LogRecord.
    
        Return the message for this LogRecord after merging any user-supplied
        arguments with the message.
        """
        msg = str(self.msg)
        if self.args:
>           msg = msg % self.args
E           TypeError: must be real number, not NoneType

Hm, I thought the default argument of 1.0 in the function call would be enough to deal with this, but I guess not. Added a check for value defined prior to doing anything with it.

[nden]

I'd like to check the issue with the parameter default value not being picked up before we merge this, to verify it's not a larger issue.

[hbushouse]

Started another regtest run at https://plwishmaster.stsci.edu:8081/job/RT/job/JWST-Developers-Pull-Requests/1454

And the CI tests seem to suddenly be working OK. Not sure why ...

[hbushouse]

Latest regtest run is clean. Only failures are unrelated (ref file updates).

So this is ready to merge as soon as @nden is OK with the earlier issue with function arguments.

[nden]

I tracked the problem with the arguments to a test
jwst/extract_1d/tests/test_ifu_image_ref.py: test_ifu_3d
which calls extract.do_extract_1d directly without passing a value for the parameter and so it uses the default in the do_extract1d function which is None.

So passing of parameters works as expected but if extract.do_extract_1d is to be called on its own I suggest we set a default value in the signature as well. Also remove the condition here.

[hbushouse]

Alternatively, instead of removing the condition here, it could be modified to only trigger when ifu_covar_scale is not equal to 1.0. That way you avoid having the unnecessary message about it being applied when it really isn't having any effect on the data.

[drlaw1558]

I've changed that None default to 1.0, and changed the conditional to trigger when the value is not 1.0

[hbushouse]

Final updates look good to me. Merging.