fix(io): reconcile with upstream, harden calibration/build paths, and document native 3D input - #400
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fix(io): reconcile with upstream, harden calibration/build paths, and document native 3D input#400darkclad wants to merge 5 commits into
fix(io): reconcile with upstream, harden calibration/build paths, and document native 3D input#400darkclad wants to merge 5 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
…ion, and Zarr v3/tiled OME-TIFF hardening Step 2 of the IO project: builds multi-dimensional addressing and physical calibration on top of the Step 1 native-read foundation, and hardens it with the fixes and edge-case coverage that came from exercising it against real fixtures. Adds per-channel/timeframe volumetric featurization with a c_index output column, opt-in physical-voxel-spacing calibration with phys_x/y/z/unit output columns, tiled multi-plane OME-TIFF (z,c,t)->IFD support, and native OME-Zarr 0.5 (Zarr v3) reads including zstd. The remaining commits fix correctness issues this surfaced: prescan out-of-bounds reads, CSV output overwriting itself across channels/ timeframes, partial edge tiles, Zarr v3 sharding/blosc/pyramidal reads, non-canonical OME-XML TiffData plane->IFD mapping, a multi-timeframe segmented OME-TIFF crash, and an end-to-end anisotropy-rescaling check. Absorbed commits (oldest to newest): 4d2afda feat(io): per-channel/timeframe volumetric featurization + c_index output column dd01c6e feat(io): opt-in physical-voxel-spacing calibration + phys_x/y/z/unit output columns 5839643 test(io): cover resolve_slide_anisotropy and out-of-range volume reads 9a24427 fix(io): reuse a single-channel mask across all intensity channels 7a19496 fix(io): pass use_physical_spacing to initialize_environment from the 3D Python classes c06a2d7 feat(io): tiled multi-plane OME-TIFF - (z,c,t)->IFD in the tile loaders 9157d34 feat(io): read OME-Zarr 0.5 (Zarr v3), incl. zstd - via z5, no tensorstore 4df18ba fix(3d): whole-volume featurization threw "illegal call" and produced no output 2c72a85 fix(3d): prescan read out-of-bounds garbage and covered only (c0,t0) 6f3ce30 test(python): drop index/calibration columns by name in the 3D IBSI check 6267d16 fix(io): assemble volumes from the whole tile grid, and stream the prescan 4e8766a fix(io): stop CSV output from overwriting itself once per channel/timeframe 66b5d31 test(io): cover partial edge tiles in the volumetric assembly b68bbb5 test(io): verify Zarr v3 sharding (sharding_indexed codec) reads end-to-end 3831675 fix(io): honor OME-XML <TiffData> plane->IFD mapping (non-canonical layouts) fd81d63 test(io): cover Zarr v3 blosc and pyramidal (SubIFD) OME-TIFF reads 302a4b7 fix(io): clamp mask timeframe -- multi-timeframe segmented OME-TIFF crashed 374bbd5 test(io): positive + negative edge coverage across the OME read surfaces 2c916fe test(io): assert anisotropy actually rescales ROI geometry end-to-end
…feature families Step 3 of the IO project: the out-of-core streaming capability. Volumetric ROIs too large to hold in RAM are now streamed rather than rejected, across every 3D feature family -- whole-volume assembly, intensity/histogram, surface, GLCM/GLDM/NGLDM/NGTDM, GLRLM, and GLSZM/GLDZM (via streaming connected-component labeling) -- plus a fix to the 2D out-of-core intensity dispatch that predates the 3D work. Includes the negative-path test coverage that caught a degenerate-ROI bug, Zarr v3 sharding validated at multi-shard-file scale, and a chunk-depth read fix. Absorbed commits (oldest to newest): 80614c4 fix(3d): oversized whole volume fails loudly instead of emitting zeros 4222cdc fix(3d): whole-volume oversized check must use the 3D footprint estimator 6bef8bd fix(io): correct 2D out-of-core intensity features (dispatch + 3 latent bugs) 696061f feat(io): stream 3D intensity/histogram out-of-core for oversized volumetric ROIs 025a658 feat(io): stream 3D surface features out-of-core for oversized volumetric ROIs 8c848aa feat(io): stream 3D GLCM/GLDM/NGLDM/NGTDM out-of-core for oversized volumetric ROIs d003cc0 feat(io): stream 3D GLRLM out-of-core; fix latent grey-LUT gaps in GLCM/GLDM 67adfff feat(io): stream 3D GLSZM/GLDZM out-of-core via streaming connected-component labeling d469e0e test(io): add negative-path tests for the 3D out-of-core stream; fix a degenerate-ROI bug they caught a141d98 feat(io): stream oversized 3D whole-volume ROIs out-of-core 12adfe5 docs(vetting): register test_ooc_mechanics.py on the 3D features it covers 0fbe34b test(omezarr): validate Zarr v3 sharding at multi-shard-FILE scale 6da2482 fix(omezarr): read the full chunk depth instead of one Z-plane
… document native 3D input Step 4 of the IO project: closes out the branch. Reconciles with upstream after rebasing main-io onto PolusAI/nyxus main (carrying an upstream 3D surface axis-length fix into the out-of-core path it predated), then hardens calibration and read correctness -- physical-size-unit canonicalization, float-precision-free OME size parsing, a whole-volume anisotropic-resampling hang fix, a RAM-footprint-estimate underflow at n_rois==0, and a degenerate- segmented-image prescan fix. Also fixes two build issues (a missing zstd header check, a GCC-only constexpr link error), hardens a host-memory- dependent test, removes dead code and dedupes the Zarr loaders/histogram paths, drops machine-specific paths and stale planning-phase language from tests/comments, and documents native OME 3D input and physical voxel spacing in the README. Absorbed commits (oldest to newest): 43d1343 fix(io): reconcile with upstream after rebasing main-io onto PolusAI/nyxus main bcf93b1 fix(prescan): COVERED_IMAGE_INTENSITY_RANGE degenerate for any segmented image (2D+3D) 7908ffd fix(ome): canonicalize physical-size units to micrometer d626794 fix(3d): whole-volume anisotropic-resampling hang + 3 related bugs 7701c38 fix(roi): LR::get_ram_footprint_estimate(_3D) underflow at n_rois==0 eb5f7bf chore(io): drop machine-specific paths and planning labels from tests a6a575a fix(ome): parse OME physical sizes without floating-point from_chars 904519b docs(readme): document native OME 3D input and physical voxel spacing 9545836 fix(build): require the zstd header, not just the library, before WITH_ZSTD bebb43f fix(tests): pick a ram_limit the host can actually grant e97228b Fix GCC link error: make OutOfRamVoxelCloud::BLK_RECORDS constexpr db0f981 refactor(io,3d): remove dead code, dedupe Zarr loaders + histogram, speed up OOC paths daeb1c0 refactor(comments): drop FIX-prefixed bug narration from loader dispatch and 3D intensity comments
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Part 4 of 4 (final) of the native OME IO series. Stacked on
main-io-reorg-3.Closes out the series:
mainafter an earlier rebaseconstexprlink errorram_limit), dead-code removal, Zarr-loader dedupStandalone build/test verified green (C++ gtest 852/852 +
pytest tests/python/96 passed/1 skipped). This PR's tip is content-identical to the originalmain-iobranch.