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Add transform widget #88

Merged
merged 10 commits into from
Jul 31, 2024
Merged

Add transform widget #88

merged 10 commits into from
Jul 31, 2024

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adamltyson
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@adamltyson adamltyson commented Jul 15, 2024

Closes #26. I decided to "brand" this widget as brainmapper as it essentially adds the missing functionality of brainmapper to napari.

This also effectively reverses #84, as we now need napari.

I'm struggling to get the tests cache to work, so they're taking much longer than they should.

Docs and a tutorial need to be added, but I'm holding off doing this until this PR is merged, as the docs will depend on the final UI. Basic instructions are:

  • Open napari
  • Register data with brainreg
  • Detect (with any method) points in the raw data that was registered
  • Open plugin
  • Set "points layer" to be the detected points
  • Load the raw data originally registered, and set as "Raw data layer"
  • Click "transform points" and select the brainreg output directory when prompted
  • The summary results will be displayed in a table, and the transformed cells added as layers. More detailed info can be exported using the new buttons that will appear under the table.

Once this is merged we should:

  • Update the docs
  • Release a new version of brainglobe-utils
  • Update the brainglobe-utils version in the metapackage
  • Release the new version of the metapackage

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codecov bot commented Jul 15, 2024

Codecov Report

Attention: Patch coverage is 99.18367% with 2 lines in your changes missing coverage. Please review.

Project coverage is 92.68%. Comparing base (78533f8) to head (52aab75).

Files Patch % Lines
brainglobe_utils/brainmapper/transform_widget.py 99.01% 2 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #88      +/-   ##
==========================================
+ Coverage   91.59%   92.68%   +1.08%     
==========================================
  Files          35       37       +2     
  Lines        1607     1845     +238     
==========================================
+ Hits         1472     1710     +238     
  Misses        135      135              
Flag Coverage Δ
numba 92.62% <99.18%> (+1.09%) ⬆️

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@alessandrofelder alessandrofelder marked this pull request as ready for review July 29, 2024 13:49
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@alessandrofelder alessandrofelder left a comment

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Thanks @adamltyson - looking good.

I made a few nitpicky comments that I think would help with legibility.

I opened an issue to address the cache issues separately #92

brainglobe_utils/brainmapper/transform_widget.py Outdated Show resolved Hide resolved
brainglobe_utils/qtpy/table.py Show resolved Hide resolved
brainglobe_utils/brainmapper/transform_widget.py Outdated Show resolved Hide resolved
@adamltyson adamltyson merged commit 7098eb8 into main Jul 31, 2024
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@adamltyson adamltyson deleted the transform branch July 31, 2024 11:33
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[Feature] Create cells transform widget
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