feat(io): native OME-TIFF/OME-Zarr metadata parsing and axis-aware volumetric reads - #397
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feat(io): native OME-TIFF/OME-Zarr metadata parsing and axis-aware volumetric reads#397darkclad wants to merge 3 commits into
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July 30, 2026 12:35
…of the IO series) Foundation branch for the main-io-reorg-* stack. Bundles oracle-vetting promotions for the moments/GLCM/GLRLM/GLSZM/GLDM/morphology/caliper feature families, a release-please manifest fix, and the CLAUDE.md workflow guide -- none of which are IO/OME work. Kept separate from the 4 IO PRs; should be reviewed/merged via its own track. Absorbed commits (oldest to newest): 73f6ca8 fix(moments): correct Hu invariant h5/h6 formulas (9x bracket, stray +eta03) a500bd9 ci(release-please): use manifest config so 0.x breaking = minor, and pin 0.12.0 79d0974 fix(3d): compute 3ROBUST_MEAN (was hardcoded 0) + vet 18 3D first-order features 60a1ebb fix(glcm): normalize HOM2/ENTROPY by sum_p (2D+3D) + fully oracle-vet GLCM d44dde7 test(glrlm): vet 12 2D gray-level-run joint-emphasis features vs IBSI cb07b9d test(glrlm): vet 14 3D _AVE features vs PyRadiomics -> glrlm 100% 285bc39 docs(vetting): record the config scope of the glrlm promotions 7db4532 test(glszm): vet 6 2D gray-level-zone joint-emphasis features vs IBSI -> glszm 100% c4bb8b1 docs(vetting): record the config scope of the glszm promotions d213b50 test(gldm): vet 14 2D grey-level-dependence features vs IBSI -> gldm 100% 0780912 docs(vetting): record the config scope of the gldm promotions (7 are mode-invariant) 0af100b fix(3d-shape): correct mislabeled axis lengths + vet 7 morphology features bc3e92a fix(caliper): correct Martin/Nassenstein diameters + vet 12 features vs imea 059998c test(morphology): vet Feret diameters vs imea + promote 6 features 701201b test(morphology): vet min-enclosing-circle diameter vs imea/cv2 965ab47 test(morphology): vet 8 EXTREMA coords vs matlab regionprops 992d5e6 test(morphology): promote FRACT_DIM_BOXCOUNT/PERIMETER (fraclac oracle) a9ddc15 test(morphology): vet FRACT_DIM (fraclac) + CIRCULARITY/ROUNDNESS (analytic) 3377183 fix(caliper): float-precision hull rotation + address PR PolusAI#381 review cc5b4de docs(caliper): correct inaccurate/stale comments (no code change) b924f8e docs(vetting): retract unproven 3D NGLDM "ibsi" promotions; document MIRP disagreement e301fe6 docs: add CLAUDE.md codebase and workflow guide a548b57 docs(CLAUDE): add git workflow and tests/vetting conformance rules 466c038 docs(CLAUDE): address PR PolusAI#388 review - C++20; agentic git workflow 4235e0c docs(CLAUDE): address PR PolusAI#388 review - generalize paths, drop z5py pin, add no-local-paths rule
…lumetric reads Step 1 of the IO project: lays the groundwork for native 5D (X,Y,Z,C,T) OME input. Adds the OmeAxes descriptor and OME metadata parsers with unified format detection, axis-aware tile loading (channel/timeframe), native OME-TIFF and OME-Zarr reads honoring the file's own DimensionOrder, ImageLoader::load_volume to assemble a whole X*Y*Z volume for the volumetric pipeline, and wires all 3D volumetric consumers onto it. A NIfTI load_volume equivalence guard protects the existing consumer path through the rewrite. Absorbed commits (oldest to newest): c916752 feat(io): OmeAxes descriptor, OME metadata parsers, unified format detection 364e802 feat(io): axis-aware loadTileFromFile (channel/timeframe) + 5D OME-Zarr addressability tests 33686dd feat(io): OME-Zarr native axis-order read via OmeAxes + rank/order/negative tests a0d88be feat(io): OME-TIFF native read, full DimensionOrder permutations, adversarial hardening eba3d4a feat(io): ImageLoader::load_volume - assemble whole X*Y*Z volume for the volumetric pipeline 958e1e1 test(io): NIfTI load_volume equivalence guard for the volumetric consumer rewrite 3e613cf feat(io): wire all 3D volumetric consumers onto load_volume + end-to-end consumer tests
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Part 1 of 4 of the native 5D (X,Y,Z,C,T) OME-TIFF/OME-Zarr IO series. Stacked on
main-io-reorg-vetting— please review/merge that one first; this PR's base will be retargeted tomainonce it lands.Lays the groundwork for native OME input:
OmeAxesdescriptor + OME metadata parsers, with unified format detectionDimensionOrderImageLoader::load_volumeto assemble a whole X*Y*Z volume for the volumetric pipelineload_volumeload_volumeequivalence regression guard, protecting the existing consumer path through the rewriteStandalone build/test verified green (C++ gtest +
pytest tests/python/).