Add image quality, orientation, visualisation and normalisation modules#89
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FIrgolitsch wants to merge 10 commits intomainfrom
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Add image quality, orientation, visualisation and normalisation modules#89FIrgolitsch wants to merge 10 commits intomainfrom
FIrgolitsch wants to merge 10 commits intomainfrom
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New modules: utils/image_quality.py (sharpness/contrast/SNR metrics), utils/orientation.py (RAS reorientation), utils/visualization.py (pipeline quality summary plots), preproc/normalization.py (percentile/ zscore/histogram-eq), preproc/resampling.py. Enhanced preproc/xyzcorr.py with galvo confidence scoring and preproc/icorr.py with improved illumination correction. Adds linum_generate_slice_config.py and linum_create_masks.py scripts, plus unit tests for all new modules.
…tions for anatomical labeling
…move unused _auto_slice_indices function
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Closing in favour of #97 (recreated with squashed commits as part of the PR split plan refresh). |
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Summary
Adds several general-purpose library modules used by downstream pipeline steps and scripts, plus improvements to existing preprocessing code.
New Modules
linumpy/utils/image_quality.pylinumpy/utils/orientation.pyparse_orientation_code,get_reorient_transform,reorient_volumeto RAS conventionlinumpy/utils/visualization.pycreate_registration_summary_plot,create_quality_heatmap, pipeline quality summary figureslinumpy/preproc/normalization.pynormalize_volume(percentile/z-score/histogram-eq)linumpy/preproc/resampling.pyImprovements to Existing Code
linumpy/preproc/xyzcorr.py— galvo artefact detection now returns a confidence score; low-confidence detections can be skipped via a thresholdlinumpy/preproc/icorr.py— improved illumination correctionlinumpy/segmentation.py—create_maskwith normalisation optionlinumpy/utils/io.py—add_overwrite_arg, improved logging helperslinumpy/utils/mosaic_grid.py— improved grid pattern detection, auto-detection for cleaned data directory structureNew Scripts
linum_generate_slice_config.py— generates a slice config CSV (slice_id,use,galvo_confidence,notes) from mosaic directorieslinum_create_masks.py— CPU-based mask creationTests
New
linumpy/tests/__init__.pymarks the tests as a package. New tests for normalization, resampling, xyzcorr, orientation, and visualisation.Dependencies
Depends on PR #85 (thread config module).