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Support optional raw_sum, raw_sum_sq, raw_count kwargs for tracking per-label intensity statistics. Derived mean_intensity and std_intensity are computed from accumulators. Updated __add__ to merge and __eq__ to compare raw intensity fields.
…rmation New function computes per-label sum, sum of squares, and count using fastremap and bincount. get_object_information now accepts an optional raw_data kwarg and passes intensity accumulators to ObjectInformation.
Measure now accepts optional raw_path kwarg to compute per-label mean and std intensity from a raw zarr dataset. Resolution differences are handled via ImageDataInterface output_voxel_size. CSV output includes Mean Intensity and Std Intensity columns when raw_path is provided.
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #54 +/- ##
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+ Coverage 81.89% 81.92% +0.02%
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Files 24 24
Lines 3016 3076 +60
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+ Hits 2470 2520 +50
- Misses 546 556 +10 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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This pull request introduces support for measuring raw intensity statistics for segmented objects, including their mean and standard deviation, and integrates these statistics throughout the measurement pipeline. The changes add new functionality for handling raw intensity data, updating object information, and outputting these statistics, as well as comprehensive tests to ensure correctness.
Raw intensity support and integration:
raw_pathin theMeasureclass, loading raw intensity data and propagating it through blockwise measurement processing (src/cellmap_analyze/analyze/measure.py). [1] [2]src/cellmap_analyze/analyze/measure.py). [1] [2]Object information enhancements:
raw_sum,raw_sum_sq,raw_count,mean_intensity,std_intensity,has_raw_intensity) inObjectInformation, including validation and aggregation in addition and equality operations (src/cellmap_analyze/util/information_holders.py). [1] [2] [3]Measurement utilities:
get_raw_intensity_statsto efficiently compute per-label raw intensity statistics, and integrated it intoget_object_informationfor both whole and blockwise measurements (src/cellmap_analyze/util/measure_util.py). [1] [2] [3] [4]Testing improvements:
tests/conftest.py,tests/operations/test_measure.py). [1] [2] [3] [4]Expanded test coverage:
ObjectInformationobjects with raw intensity, and end-to-end measurement with raw intensity input (tests/operations/test_measure.py).