🐛 Fix padded contours for Visualization

[shaneahmed]

• This commit fixes visualization of contour overlays with padded values.
• padded values were introduced to make the contours rectangular in an effort to make np arrays compatible with zarr v3

fixed

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.88%. Comparing base (1c94d65) to head (1299f47).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1095   +/-   ##
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  Coverage    99.88%   99.88%           
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  Files           86       86           
  Lines        11661    11675   +14     
  Branches      1531     1533    +2     
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+ Hits         11648    11662   +14     
  Misses           7        7           
  Partials         6        6           

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[Copilot]

Pull request overview

Fixes visualization of instance contour overlays when contours have been padded (to support rectangular arrays for Zarr v3 compatibility), by stripping the padding before drawing contours.

Changes:

• Add a utility (remove_padded_values_in_contours) to remove padding rows from contour arrays.
• Invoke the new utility in overlay_prediction_contours so padded contours render correctly.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
tiatoolbox/utils/visualization.py	Applies padded-contour cleanup before calling cv2.drawContours so overlays render correctly.
tiatoolbox/utils/misc.py	Introduces helper to remove padded rows from contour arrays saved in rectangular form for Zarr v3.

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[Jiaqi-Lv]

Yes the fix works, I've tested on my side.