Transform widget (2nd iteration)

[alessandrofelder]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?

What does this PR do?

• adds a widget to transform cells into atlas space
• adds a smoke test that checks that running the widgets adds an extra points layer.

References

This PR builds on top of the abandoned #117 PR and fixes brainglobe/cellfinder#316.

Differences to #117

• layer needs to be added to viewer instead of returned by magicgui
• main branch has sinced moved to using pyproject.toml so new dependencies need to be included there
• test data should be hosted on gin-gnode (instead of included with git-lfs)
• test data should be accessed with pooch
• problems with real-life data (see Widget to transform cells to an atlas space #117 (comment)) should be reproduced, fixed, and tested.
  • I could reproduce this manually by creating "untransformed" points outside the source image bounds
  • the cause of the error is that the point is not inside the deformation field tiff and therefore https://github.com/brainglobe/cellfinder/blob/main/cellfinder/analyse/analyse.py#L271 throws. We need to think about how to handle this error (and general error-handling across BrainGlobe so it feels consistent.

How has this PR been tested?

Please explain how any new code has been tested, and how you have ensured that no existing functionality has changed.

Is this a breaking change?

No, just adds an additional widget.

Does this PR require an update to the documentation?

If any features have changed, or have been added. Please explain how the documentation has been updated (and link to the associated PR). See here for details.

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[deprecated-napari-hub-preview-bot]

Preview page for your plugin is ready here:
https://preview.napari-hub.org/brainglobe/cellfinder-napari/153
Updated: 2023-04-05T14:45:29.386108

[codecov]

Codecov Report

Patch coverage: 91.52% and project coverage change: -0.27 ⚠️

Comparison is base (d66f030) 95.35% compared to head (97b9c3d) 95.09%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     brainglobe/cellfinder-napari#153      +/-   ##
==========================================
- Coverage   95.35%   95.09%   -0.27%     
==========================================
  Files          17       19       +2     
  Lines         797      856      +59     
==========================================
+ Hits          760      814      +54     
- Misses         37       42       +5     

Impacted Files	Coverage Δ
cellfinder_napari/transform.py	84.84% <84.84%> (ø)
cellfinder_napari/tests/test_transform.py	100.00% <100.00%> (ø)

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[alessandrofelder]

closing, see #117 for explanation.