✨ Add dict_to_store_semantic_segmentor

[shaneahmed]

• Add a function to convert the output of TIAToolbox segmentation engine to AnnotationStore.

[shaneahmed]

@adamshephard @measty @mbasheer04 I have created this PR separately so we can work towards different scenarios particularly where the annotations have holes.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.69%. Comparing base (3eea490) to head (9ba6908).
⚠️ Report is 15 commits behind head on develop.

Additional details and impacted files

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##           develop     #926   +/-   ##
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  Coverage    99.69%   99.69%           
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  Files           71       71           
  Lines         8874     8921   +47     
  Branches      1159     1168    +9     
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+ Hits          8847     8894   +47     
  Misses          23       23           
  Partials         4        4           

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[adamshephard]

This still doesn't handle the holes issue. In the last test I have added, you can see that the inner contour/hole is treated the same as the outer contour, resulting in a store of length 2 (i.e. inner and outer). When these contours are drawn, any holes present will be filled in as a result by the hole contour.

[Copilot]

Pull Request Overview

This PR adds a new helper function, dict_to_store_semantic_segmentor, to convert the TIAToolbox SemanticSegmentor engine output into an AnnotationStore while introducing process_contours to handle segmentation contours. The changes include new functions in tiatoolbox/utils/misc.py and several tests to verify behavior for various segmentation outputs and contour‐hole scenarios.

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.

File	Description
tiatoolbox/utils/misc.py	Added process_contours and dict_to_store_semantic_segmentor functions.
tests/test_utils.py	Added multiple tests to verify different segmentation, holes, and save_path scenarios.