docs: update documentation and add RECONST_2_5D_WORKFLOW#105
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FIrgolitsch wants to merge 529 commits intopr-a-build-toolingfrom
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docs: update documentation and add RECONST_2_5D_WORKFLOW#105FIrgolitsch wants to merge 529 commits intopr-a-build-toolingfrom
FIrgolitsch wants to merge 529 commits intopr-a-build-toolingfrom
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Copilot recommendation Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Charles Poirier <41654474+CHrlS98@users.noreply.github.com>
Co-authored-by: Charles Poirier <41654474+CHrlS98@users.noreply.github.com>
…ss slices in parallel
…saic_parallel # Conflicts: # linumpy/reconstruction.py
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
…act step handling, adding unreliable transition refinement via image registration, and improving inter-slice shift estimation from tile stage positions.
Improve pairwise registration: multi-scale ITK, shift filtering, motor-position mode
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Relocates thread-pool configuration into a dedicated config sub-package.
- Remove dead modules data_io.py and npz.py (unused). - Move Allen brain atlas helpers from io/allen.py into a new linumpy.reference sub-package. - Drop star imports from io/__init__.py. - Modernize remaining io/ modules (Path, type hints, docstrings).
- Move utils/io.py argparse helpers to a new linumpy.cli.args module. - Move utils/metrics.py into a top-level linumpy.metrics package. - Remove now-empty linumpy.utils package.
…in.py Promotes the single-file linumpy.segmentation module into a package with a dedicated brain.py module for clarity and future extension.
- imaging/transform.py: image transformation helpers. - imaging/overlay.py: overlay/composite helpers.
…osaic.quick_stitch - mosaic/discovery.py: tile-discovery helpers. - mosaic/quick_stitch.py: quick low-resolution stitching helpers.
- mosaic/grid.py: grid construction (from stitching/mosaic_grid.py).
- mosaic/overlap.py: tile overlap helpers (extracted from stitching).
- registration/manual.py: interactive registration GUI
(from stitching/manual_registration.py).
- registration/sitk.py: SimpleITK-based registration
(from stitching/registration.py).
- registration/phase_correlation.py: phase-correlation registration.
- registration/refinement.py: multi-stage refinement helpers.
- registration/transforms.py: affine/rigid transform utilities.
- Drop dead modules stitching/FileUtils.py, stitching/topology.py,
stitching/stitch_utils.py.
…ckage Splits the 1786-line linumpy/preproc/icorr.py module into focused modules: - intensity/normalize.py: intensity normalization helpers. - intensity/attenuation.py: attenuation correction. - intensity/psf_model.py: PSF-model-based illumination correction. - intensity/vignette.py: vignetting correction. - intensity/artifact.py: artifact removal helpers. - intensity/convert.py: intensity conversion helpers.
…ckage Splits xyzcorr.py into focused modules: - geometry/crop.py: volume cropping helpers. - geometry/resample.py: resampling utilities. - geometry/interface.py: tissue-interface detection and fitting. - geometry/galvo.py: galvo / scanner geometry helpers. Repoints linumpy.microscope.oct to use the new geometry.galvo module.
…it utils.py - stack_alignment/io.py: I/O helpers (CSV/JSON read/write). - stack_alignment/units.py: unit conversion helpers. - stack_alignment/filter.py: outlier filtering helpers. Renames the corresponding test module from test_utils_shifts.py to test_stack_alignment.py.
- psf/synthetic.py: synthesize_3d_psf helper (renamed from get_3d_psf for clarity). - psf/extract.py: extract experimental PSFs from data.
Updates all 43 linum_*.py scripts plus 2 script tests to use the
new sub-packages introduced in this refactor:
linumpy.preproc.icorr -> linumpy.intensity.{normalize,attenuation,
psf_model,vignette,
artifact,convert}
linumpy.preproc.xyzcorr -> linumpy.geometry.{crop,resample,
interface,galvo}
linumpy.shifts.utils -> linumpy.stack_alignment.{io,units,filter}
linumpy.psf.psf_estimator -> linumpy.psf.{synthetic,extract}
linumpy.stitching -> linumpy.mosaic.{grid,overlap,discovery,
quick_stitch} and
linumpy.registration.{manual,sitk,
phase_correlation,
refinement,transforms}
linumpy.utils_images -> linumpy.imaging.{transform,overlay}
linumpy.utils.io -> linumpy.cli.args
linumpy.utils.metrics -> linumpy.metrics
linumpy.io.allen -> linumpy.reference.allen
linumpy.segmentation -> linumpy.segmentation.brain
linumpy.reconstruction -> linumpy.mosaic.{discovery,quick_stitch}
linumpy._thread_config -> linumpy.config.threads
- Update setuptools `packages.find` and ruff `per-file-ignores` to reflect the renamed/split modules (intensity/, geometry/, mosaic/, registration/, stack_alignment/, etc.). - Update isort `thread-config` section to reference linumpy.config.threads. - Refresh uv.lock to pick up incidental dependency updates. - Pre-existing tooling tweaks (expanded ruff rule set, ty config, GPU dependency cleanup) carried in the working tree.
Refreshes all transitive package versions to current resolutions (idna, magicgui, ome-zarr, pre-commit, pydantic, pytest, ruff, ty, typer, virtualenv, etc.).
Removed pins on numpy, scipy, hyperactive, pynrrd, and numcodecs. basicpy 2.0.0 (latest available) transitively pins scipy<1.13, which forces numpy<2; override that ceiling via [tool.uv].override-dependencies so we resolve modern numpy 2.x and scipy 1.17 across the stack.
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Docs update: refresh existing docs and add RECONST_2_5D_WORKFLOW.md.
Stacks on top of #95 (pr-a-build-tooling).