🐛 Fix Broken Margin Behaviour

[measty]

Fixes a bug in MultiTaskSegmentor’s WSI probability-map vertical merging when spilling intermediate probability rows to Zarr. Previously, once a head spilled to Zarr, subsequent chunks for that same head could continue accumulating in memory instead of being appended to the Zarr. At finalization, the code preferred the Zarr array and discarded the in-memory chunks, producing truncated probability maps for only the heads that spilled resulting in the shape mismatch that was being seen by me and Jiaqi.

The fix keeps hold of the opened Zarr group after the first spill and routes later chunks for that head into the same Zarr dataset. This preserves the full merged probability-map height across all heads.

[codecov]

Codecov Report

❌ Patch coverage is 77.96610% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 99.77%. Comparing base (0202a7d) to head (e22ca77).

Files with missing lines	Patch %	Lines
tiatoolbox/models/engine/semantic_segmentor.py	76.36%	6 Missing and 7 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1067      +/-   ##
===========================================
- Coverage    99.88%   99.77%   -0.12%     
===========================================
  Files           85       85              
  Lines        11625    11658      +33     
  Branches      1524     1530       +6     
===========================================
+ Hits         11612    11632      +20     
- Misses           7       13       +6     
- Partials         6       13       +7     

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[Jiaqi-Lv]

Is this related to my issue with SemanticSegmentor? #1071 ?

[measty]

Is this related to my issue with SemanticSegmentor? #1071 ?

It fixed a similar-looking issue I was having when changing the margin (not the stride as in your case). What I was getting was basically the same error you saw:

curr_chunk[-overlap:] += next_chunk[:overlap]
ValueError: operands could not be broadcast together

On some values, but when varying margin not stride. I was hoping it might fix your issue too, but tried it on the same slide as in your issue and it does not. So, similar symptoms but not the same cause.

[measty]

This PR now fixes #1071 too

[Copilot]

Pull request overview

This PR fixes vertical probability-map merging behavior, especially when intermediate probability rows spill to Zarr during WSI segmentation, so later chunks continue appending instead of being dropped.

Changes:

• Adds generalized vertical chunk aggregation for semantic segmentation with multi-row overlap handling.
• Keeps and returns the opened Zarr group during multitask vertical probability spilling.
• Adds regression tests for multi-row overlap and continuing appends after Zarr spill.

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
tiatoolbox/models/engine/semantic_segmentor.py	Refactors vertical merging to aggregate active overlapping chunks and store finalized segments incrementally.
tiatoolbox/models/engine/multi_task_segmentor.py	Updates multitask probability spilling to retain the Zarr group for later appends.
tests/engines/test_semantic_segmentor.py	Adds coverage for a row overlapping multiple following rows.
tests/engines/test_multi_task_segmentor.py	Updates cache helper test and adds a regression test for post-spill appending.

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[Jiaqi-Lv]

Looks good.