BUG: Fix wrong Subset unit when created in 2D spectrum viewer #3201

pllim · 2024-09-24T21:49:02Z

Description

This pull request is to address wrong Subset unit when it is extracted from Subset created in Specviz2d on the 2D spectrum viewer. Glue itself does not attach unit natively to Subset, so that means Jdaviz made wrong assumptions in the extraction code. Bug ticket blamed it to the Export plugin but the actual bug has nothing to do with the Export plugin, thought the plugin did expose the bug when user extracted Subset that way but you don't need the plugin to reproduce the bug.

Change log entry

Is a change log needed? If yes, is it added to CHANGES.rst? If you want to avoid merge conflicts,
list the proposed change log here for review and add to CHANGES.rst before merge. If no, maintainer
should add a no-changelog-entry-needed label.

Checklist for package maintainer(s)

This checklist is meant to remind the package maintainer(s) who will review this pull request of some common things to look for. This list is not exhaustive.

Are two approvals required? Branch protection rule does not check for the second approval. If a second approval is not necessary, please apply the trivial label.
Do the proposed changes actually accomplish desired goals? Also manually run the affected example notebooks, if necessary.
Do the proposed changes follow the STScI Style Guides?
Are tests added/updated as required? If so, do they follow the STScI Style Guides?
Are docs added/updated as required? If so, do they follow the STScI Style Guides?
Did the CI pass? If not, are the failures related?
Is a milestone set? Set this to bugfix milestone if this is a bug fix and needs to be released ASAP; otherwise, set this to the next major release milestone. Bugfix milestone also needs an accompanying backport label.
After merge, any internal documentations need updating (e.g., JIRA, Innerspace)? 🐱

pllim · 2024-09-24T21:54:37Z

jdaviz/configs/specviz2d/tests/test_parsers.py

@@ -134,6 +137,25 @@ def test_2d_1d_parser(specviz2d_helper, mos_spectrum2d, spectrum1d):
    specviz2d_helper.load_data(spectrum_2d=mos_spectrum2d, spectrum_1d=spectrum1d)
    assert specviz2d_helper.app.data_collection.labels == ['Spectrum 2D', 'Spectrum 1D']

+    spec2d_viewer = specviz2d_helper.app.get_viewer("spectrum-2d-viewer")
+    assert spec2d_viewer.figure.axes[0].label == "x: pixels"  # -0.5, 14.5
+    spec2d_viewer.apply_roi(XRangeROI(10, 12))


Could have used the API from #3104 but since it is not merged yet, I didn't.

#3104 is now merged but the API is not yet public. Should I keep this as-is or should I use the helper.plugins['Subset Tools']._obj.import_region(...) syntax here?

pllim · 2024-09-24T21:56:07Z

jdaviz/configs/specviz2d/tests/test_parsers.py

+    assert len(subsets) == 2
+    s1 = subsets["Subset 1"]
+    s2 = subsets["Subset 2"]
+    assert s1.lower.unit == s1.upper.unit == u.pix


I confirmed that this line throws exception on main without this patch, but passes with this patch. Exception on main:

> assert s1.lower.unit == s1.upper.unit == u.pix E assert Unit("Angstrom") == Unit("pix") E + where Unit("Angstrom") = <Quantity 12. Angstrom>.unit E + where <Quantity 12. Angstrom> = Spectral Region, 1 sub-regions:\n (10.0 Angstrom, 12.0 Angstrom) .upper E + and Unit("pix") = u.pix

and fixed an ambiguous specviz2d test, maybe

jdaviz/app.py

jdaviz/tests/test_subsets.py

codecov · 2024-09-24T23:14:09Z

Codecov Report

Attention: Patch coverage is 66.66667% with 5 lines in your changes missing coverage. Please review.

Project coverage is 88.44%. Comparing base (f880d55) to head (eafb391).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
jdaviz/app.py	66.66%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3201      +/-   ##
==========================================
- Coverage   88.46%   88.44%   -0.02%     
==========================================
  Files         125      125              
  Lines       18668    18676       +8     
==========================================
+ Hits        16514    16518       +4     
- Misses       2154     2158       +4

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

rosteen

Seems like it's giving the expected results in my testing, other configs appear to still work. LGTM, thanks.

pllim · 2024-09-30T17:29:48Z

@kecnry , I think I addressed your comment.

kecnry · 2024-09-30T18:48:18Z

jdaviz/app.py

+            viewer = self.get_viewer(self._jdaviz_helper._default_spectrum_viewer_reference_name)
+            data = viewer.data()
+            if data and len(data) > 0 and isinstance(data[0], Spectrum1D):
+                units = data[0].spectral_axis.unit


what does data[0] assume? That that is the full cube extracted spectrum? If that is the assumption, maybe we need to be more explicit and request it by label instead? What if that has been unloaded from the viewer?

I still wish this could be generalized, but I see how its difficult since data in the else is the glue component, but data in the if is a Spectrum1D (or other translated object). Although the else in the else then uses a handler to convert to a Spectrum1D anyways. 🤔

If all we need here are the units of the x-axis of the spectrum viewer... can we just access the display units? Or do we need the native units of the "reference" data?

I don't know the answers. This block is really for Cubeviz and I am trying to patch Specviz2D. Do I really have to fix Cubeviz too?

Fair, ignore my first line of questions then since those do apply to the old code. But I think if we can have a general block here that applies to cubeviz and specviz2d, that would be easier to maintain than if-statements, right? There is even a TODO comment immediately above suggesting switching to display units - so maybe we can simplify this all down to one line once @gibsongreen enables display units across all configs?

(or maybe it makes sense to get this in like this now and either roll that into @gibsongreen's WIP or as a tech-debt follow-up after that makes it in as well?)

ok, we have decided to revisit this after unit conversion is enabled across all configs and merge the logic as-is until then. 🐱

pllim · 2024-10-01T13:36:09Z

Actually I am not going to backport this because it is unlikely the backport will be clean due to unit conversion stuff.

pllim · 2024-10-01T14:18:16Z

Thanks, all!

pllim added 2 commits September 24, 2024 17:15

BUG: Fix wrong Subset unit in Specviz2d

b1a3031

Add test and change log

9dc6d6e

pllim added bug Something isn't working 💤backport-v3.10.x on-merge: backport to v3.10.x labels Sep 24, 2024

pllim added this to the 3.10.4 milestone Sep 24, 2024

github-actions bot added the specviz2d label Sep 24, 2024

pllim commented Sep 24, 2024

View reviewed changes

cubeviz is so special

fe250fa

and fixed an ambiguous specviz2d test, maybe

pllim commented Sep 24, 2024

View reviewed changes

jdaviz/app.py Outdated Show resolved Hide resolved

jdaviz/tests/test_subsets.py Outdated Show resolved Hide resolved

pllim marked this pull request as ready for review September 24, 2024 23:14

pllim requested review from rosteen, javerbukh, kecnry, bmorris3, haticekaratay, cshanahan1 and gibsongreen as code owners September 24, 2024 23:14

rosteen approved these changes Sep 25, 2024

View reviewed changes

pllim added 2 commits September 30, 2024 12:46

Address comment from kecnry

e4d6311

Merge branch 'main' into specviz2d-subset-unit

3e501c0

kecnry reviewed Sep 30, 2024

View reviewed changes

kecnry approved these changes Oct 1, 2024

View reviewed changes

pllim removed the 💤backport-v3.10.x on-merge: backport to v3.10.x label Oct 1, 2024

pllim modified the milestones: 3.10.4, 4.0 Oct 1, 2024

Move change log to match new milestone

eafb391

pllim merged commit 23fec46 into spacetelescope:main Oct 1, 2024
17 of 19 checks passed

pllim deleted the specviz2d-subset-unit branch October 1, 2024 14:18

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

BUG: Fix wrong Subset unit when created in 2D spectrum viewer #3201

BUG: Fix wrong Subset unit when created in 2D spectrum viewer #3201

pllim commented Sep 24, 2024 •

edited

Loading

pllim Sep 24, 2024

pllim Sep 30, 2024

pllim Sep 24, 2024

codecov bot commented Sep 24, 2024 •

edited

Loading

rosteen left a comment

pllim commented Sep 30, 2024

kecnry Sep 30, 2024

pllim Sep 30, 2024

kecnry Sep 30, 2024

kecnry Sep 30, 2024

kecnry Oct 1, 2024

pllim commented Oct 1, 2024

pllim commented Oct 1, 2024

BUG: Fix wrong Subset unit when created in 2D spectrum viewer #3201

BUG: Fix wrong Subset unit when created in 2D spectrum viewer #3201

Conversation

pllim commented Sep 24, 2024 • edited Loading

Description

Change log entry

Checklist for package maintainer(s)

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

codecov bot commented Sep 24, 2024 • edited Loading

Codecov Report

rosteen left a comment

Choose a reason for hiding this comment

pllim commented Sep 30, 2024

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

pllim commented Oct 1, 2024

pllim commented Oct 1, 2024

pllim commented Sep 24, 2024 •

edited

Loading

codecov bot commented Sep 24, 2024 •

edited

Loading