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Refactor cubeviz parser and plugins for specutils 2.0 compatibility #2762

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Refactor cubeviz parser and plugins for specutils 2.0 compatibility #2762

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@rosteen rosteen commented Mar 19, 2024 •
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Tests are expected to fail on this, since it requires specutils v2.0-dev and the glue-astronomy compatibility PR to work. But I'd like to get this in front of other people for testing sooner rather than later.

Current known to-do items, I will add to these as new issues they are discovered and update when fixed:

  • Deprecate _parse_jwst_s3d now that specutils and glue-astronomy handle GWCS.
  • Test JWST ESA 3d file to see if _parse_esa_s3d can be offloaded to Spectrum1D.read like _parse_jwst_s3d was.
  • Fix slice plugin getting values from wrong axis.
  • Fix coords info showing 0 or NaN for the value on hover.
  • Verify that coords_info is giving flux for correct pixel.
  • Spectral extraction is failing with an error in the glue-astronomy NDData translator.
  • Aperture photometry fails due to attempting to operate on the wrong axis.

@rosteen rosteen added this to the 3.10 milestone Mar 19, 2024
@github-actions github-actions bot added imviz plugin Label for plugins common to multiple configurations labels Mar 19, 2024
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rosteen commented Mar 19, 2024 •
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I confirmed offline that the ESA parser can be removed, it was specifically to support commissioning.

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rosteen commented Mar 25, 2024

It looks like the pixel coords_info is returning a value for is off by one in the y-direction, not immediately obvious to me why (I don't think GWCS is 1-indexed...).

@rosteen
Remove jwst s3d parser now that it can be handled by Spectrum1D
ae654e2
@rosteen
Starting to debug slice
ed4a3a4
@rosteen
Fix coords mouseover when SkyCoord is before SpectralCoord
c5266d1
@rosteen
More debugging
ee0cb79
@rosteen
Fix slice with different spectral_axis_index, add specutils_format kw…
1586e8d 
…arg to cubeviz parser
@rosteen
Remove unused import
fe37147
@rosteen
Remove ESA parser from commissioning [skip ci]
4506524
@rosteen
Generalizing coords_info to handle spectral axis first or last [ci skip]
0eb9cb6
@rosteen
Working on debugging aperture photometry
6565e9d
@rosteen
Need to pull meta from data not comp
1304cca
@rosteen
Fix aperture photometry and wrong coord order in coords_info
b7c27d6
@rosteen
Fix codestyle, delete defunct case in parser
379f98c
@rosteen
Change Spectrum1D to Spectrum
007ae6e
@rosteen
Debugging
eb35397
@rosteen
Change class name in recent code additions
a70e082
@rosteen
Get spectral extraction working again for cylinder case
85c86df
@rosteen
Debugging wavelength dependent case
217a5bd
@rosteen
Make sure spectral extraction result is linked when added to data col…
d832c5c 
…lection
@rosteen
Moved fix to correct place
49e94b3
@rosteen
Fix indents
c65f091
@rosteen
Revert this change from rebase to match main
06819df
@bmorris3 bmorris3 modified the milestones: 3.10, 3.11 May 3, 2024
pllim
pllim reviewed May 14, 2024
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pyproject.toml
@@ -23,7 +23,7 @@ dependencies = [
"ipywidgets>=8.0.6",
"voila>=0.4,<0.5",
"pyyaml>=5.4.1",
"specutils>=1.9",
"specutils>=2.0",
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Same as glue-viz/glue-astronomy#100 (review)

Suggested change
"specutils>=2.0",
"specutils>=2.0.dev",

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But then we'll see all the test failures that I haven't updated to fix 😭 😆

@rosteen rosteen mentioned this pull request Jun 20, 2024
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@rosteen rosteen modified the milestones: 3.11, 4.1 Oct 17, 2024
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