Add a new button to import an existing layers from other plugins

[adamltyson]

Description

There's now a good number of segmentation plugins in napari. Following a conversation with @SaraMederos, it seems like a good idea to be able to "import" these results into brainreg-segment so that they can be analysed in the context of the atlas.
What is this PR

• Bug fix
• Addition of a new feature
• Other

What does this PR do?

• Adds a Add region from selected layer to the region segmentation panel that will add the selected layer (e.g. from a segmentation plugin) to the list of layers to be analysed.

• Adds a Add track from selected layer to the track segmentation panel that will add the selected layer (e.g. from another plugin) to the list of layers to be analysed.

References

Closes #73

How has this PR been tested?

No automated tests yet, as all the tests are broken in some way.

Is this a breaking change?

No

Does this PR require an update to the documentation?

Yes, it will, not added yet though.

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

[adamltyson]

Converted to draft as I'd like to get some feedback on the tool from a user POV, and also add similar functionality for tracks.

[adamltyson]

Also need to add tests

[deprecated-napari-hub-preview-bot]

Preview page for your plugin is ready here:
https://preview.napari-hub.org/brainglobe/brainreg-segment/74
Updated: 2023-04-25T10:48:19.241060

[codecov]

Codecov Report

Patch coverage: 78.12% and project coverage change: +0.61 🎉

Comparison is base (d0bfd87) 59.86% compared to head (ed2d4c0) 60.48%.

❗ Current head ed2d4c0 differs from pull request most recent head 5a09d31. Consider uploading reports for the commit 5a09d31 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #74      +/-   ##
==========================================
+ Coverage   59.86%   60.48%   +0.61%     
==========================================
  Files          20       20              
  Lines         887      916      +29     
==========================================
+ Hits          531      554      +23     
- Misses        356      362       +6     

Impacted Files	Coverage Δ
brainreg_segment/layout/utils.py	37.50% <50.00%> (+4.16%)	⬆️
brainreg_segment/segmentation_panels/tracks.py	83.83% <75.00%> (-1.39%)	⬇️
brainreg_segment/segmentation_panels/regions.py	76.92% <78.57%> (-0.86%)	⬇️
brainreg_segment/regions/layers.py	100.00% <100.00%> (ø)
brainreg_segment/tracks/layers.py	100.00% <100.00%> (ø)

... and 5 files with indirect coverage changes

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[adamltyson]

Moved the test changes from this branch into #77

[dstansby]

Three major comments:

• See inline comments, I think worth checking the layer type and erroring when adding the existing layers in the functions that do the adding.
• I can't get any of the info boxes to pop up, even when trying to add a layer that is the wrong type. Not sure what the best way to debug this is though...
• This could really do with some user facing docs, but I guess we don't have anywhere to put them right now? Perhaps a simple markdown file with a short "how to import existing layers" section could be started, and then when a proper doc structure is added to the repo it can be migrated there.

[adamltyson]

Thanks @dstansby I've addressed these issues. I'll document this feature in the new docs site before the new version is released. @SaraMederos is also kindly developing a tutorial from the researchers point of view.

[dstansby]

I haven't checked this works as intended, but I have smoke checked it and the info boxes seem to be working now 👍