feat: motor stacking, auto-exclude, refined stitching#98
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FIrgolitsch wants to merge 3 commits intomainfrom
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feat: motor stacking, auto-exclude, refined stitching#98FIrgolitsch wants to merge 3 commits intomainfrom
FIrgolitsch wants to merge 3 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
New library modules: - linumpy/stitching/motor.py — motor-only stacking - linumpy/stitching/stacking.py — stacking improvements (confidence gating, z-consistency, drift limits) New scripts: - linum_stack_motor_only.py, linum_stack_slices_motor.py - linum_stitch_motor_only.py, linum_stitch_3d_refined.py - linum_auto_exclude_slices.py Updated scripts: - linum_stack_slices_3d.py, linum_stack_slices.py, linum_stitch_3d.py - linum_align_mosaics_3d_from_shifts.py Tests: test_stitching_motor.py, test_stitching_stacking.py
This was referenced Apr 1, 2026
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PR E — Motor Stacking & Refined Stitching
New library modules
linumpy/stitching/motor.py— Motor-only stacking implementationlinumpy/stitching/stacking.py— Enhanced stacking with confidence gating, z-consistency enforcement, drift limitsNew scripts
linum_stack_motor_only.py— Motor-only slice stackinglinum_stack_slices_motor.py— Motor-based slice stackinglinum_stitch_motor_only.py— Motor-only stitchinglinum_stitch_3d_refined.py— Refined 3D stitchinglinum_auto_exclude_slices.py— Automatic slice exclusionUpdated scripts
linum_stack_slices_3d.py,linum_stack_slices.py,linum_stitch_3d.pylinum_align_mosaics_3d_from_shifts.pyTests
test_stitching_motor.py,test_stitching_stacking.pyDependencies