feat: add OME-Zarr (ngff-zarr) and DICOM dataset I/O backends - #3
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feat: add OME-Zarr (ngff-zarr) and DICOM dataset I/O backends#3vboussot wants to merge 1 commit into
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Superseded: the disjoint per-theme split couldn't pass CI (shared ruff/build config + cross-theme tests). Replaced by a stacked set: a core base PR (tooling+perf, verified green) with thin imaging/model/docs PRs stacked on it. |
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Jun 29, 2026
- AGENTS.md (303 -> 93 lines): a shorter, more general guide. Keeps the load-bearing parts -- the three design pillars, the extension model (subclass + classpath), the do-not-break invariants, and the coding/commit/ agent conventions -- and drops the verbose config-key catalogues, per-subsystem deep-dives, env-var/optional-dep tables, and the end-to-end run trace, which belong in docs/ and examples/. - AUDIT.md (206 -> 64 lines): rewritten to the current state after PR #10. It records concisely what is fixed (modernization #6-#9 + audit follow-up #1, #2, #10, #14-#19, DICOM hardening, os.environ device fix) versus what remains -- the audit does NOT claim everything is resolved: ~9 confirmed bugs are still a clearly-listed backlog (#3 VAE noise, #4 EMA early-stop score, #5 explicit Standardize, #6 Rotate deg->rad, #7 CLI tensorboard, #8 Unsqueeze, #9 ResampleToShape, #12 Select, #13 ITK) plus the deferred cross-cutting refactors.
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Description
Add DICOM and OME-Zarr as first-class dataset I/O backends, alongside SimpleITK and HDF5.
pydicom): series discovery, position-based slice ordering, geometry (origin/spacing/direction), HU rescale, lazy per-slice patch reads, write. Geometry round-trips byte-identically to SimpleITK's GDCM reader.ngff-zarr(no hand-rolled NGFF parsing) — lazy chunked reads, write, interoperable output.omezarr@<level>(e.g../Dataset:a:omezarr@2), independent of any transform; level 0 by default.dicom,ome-zarr,zarr) and end-to-end + interop tests.Testing
pixi run --environment dev python -m pytest tests/unit/test_imaging_formats.py tests/unit/test_imaging_roundtrip.py— green.