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Jan 26, 2026
sophiamaedler
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- fixes pandas 3.0.0 breaks tests #354
…ea-specific normalization
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Pull request overview
This PR fixes issues in the featurization pipeline related to mask-based intensity calculations. The changes address a bug where summed intensities were not properly handling NaN values from masked regions and were incorrectly normalizing by the last mask's area instead of each mask's own area.
Changes:
- Fixed summed intensity calculation to use
nansuminstead ofsumto properly handle masked (NaN) values - Fixed area normalization to use each mask's corresponding area instead of always using the last mask's area
- Added comprehensive test coverage to verify correct intensity calculations and area normalization
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Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.
| File | Description |
|---|---|
| src/scportrait/pipeline/featurization.py | Fixed bug in intensity sum calculation and area normalization by using nansum and pairing masks with their corresponding areas |
| tests/unit_tests/pipeline/test_featurization.py | Added test assertions to verify NaN handling and correct values for summed intensities with proper area normalization |
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…ion and project pipelines to fix Fixes #354
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Pull request overview
Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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