feat: utility modules, preprocessing improvements, galvo correction#97
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FIrgolitsch wants to merge 2 commits intomainfrom
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feat: utility modules, preprocessing improvements, galvo correction#97FIrgolitsch wants to merge 2 commits intomainfrom
FIrgolitsch wants to merge 2 commits intomainfrom
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- Replace setup.py + requirements.txt with pyproject.toml (uv) - Add .pre-commit-config.yaml (ruff-format, ruff lint, ty advisory) - Update CI workflow to use uv + ruff + ty - Update Dockerfile for uv - Add uv.lock, linumpy/py.typed - Delete setup.py, requirements.txt, requirements-pytest.txt - Run ruff format on all Python files - Run ruff check --fix (341 auto-fixes applied)
…visualization New library modules: - linumpy/preproc/normalization.py, resampling.py - linumpy/utils/image_quality.py, orientation.py, visualization.py New scripts: - linum_fix_galvo_shift_zarr.py, linum_clean_raw_data.py - linum_compare_stitching.py, linum_extract_pyramid_levels.py - linum_normalize_z_intensity.py, linum_aip_png.py - linum_screenshot_omezarr_annotated.py, linum_generate_mosaic_aips.py Updated: preprocessing, stitching, registration, I/O, metrics modules Added tests for normalization, resampling, xyzcorr, orientation, visualization
This was referenced Apr 1, 2026
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PR C — Utility Modules, Preprocessing & General Library Improvements
New library modules
linumpy/preproc/normalization.py— Intensity normalization utilitieslinumpy/preproc/resampling.py— Resampling utilitieslinumpy/utils/image_quality.py— Image quality metricslinumpy/utils/orientation.py— Orientation utilitieslinumpy/utils/visualization.py— Visualization helpersNew scripts
linum_fix_galvo_shift_zarr.py— Galvo shift correction for OME-Zarrlinum_clean_raw_data.py— Raw data cleaninglinum_compare_stitching.py— Stitching comparison toollinum_extract_pyramid_levels.py— Pyramid level extractionlinum_normalize_z_intensity.py— Z-axis intensity normalizationlinum_aip_png.py— Average intensity projection (PNG output)linum_screenshot_omezarr_annotated.py— Annotated OME-Zarr screenshotslinum_generate_mosaic_aips.py— Batch mosaic AIP generationLibrary improvements
icorr.py,xyzcorr.pywith functional improvementsmosaic_grid.py,registration.py,topology.py,FileUtils.py,manual_registration.pyzarr.py,data_io.py,thorlabs.pymetrics.py,io.pyTests added
test_preproc_normalization.py,test_preproc_resampling.py,test_preproc_xyzcorr.pytest_utils_orientation.py,test_utils_visualization.pyDependencies
linumpy/stitching/__init__.pyimportsinterpolation,motor,stackingwhich will be added by PR Add slice interpolation for missing and degraded tissue sections #87 and PR E