Bring omezarr/smartspim ports into parity with NDR-matlab main - #30
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NDR-matlab now owns a Blosc container codec at +ndr/+format/+blosc, backed by numcodecs.Blosc in a private subprocess venv (sonpipe pattern; ndr.util.blosc.setup manages the venv, MATLAB's pyenv is never touched). There is no Python mirror and none is planned: Python callers should use numcodecs.Blosc directly, and any MATLAB wrapper on top would just be a rename over the same subprocess call. The new bridge yaml records the four MATLAB functions (encode, decode, isBlosc, header) with status: matlab_only so the mirror inventory stays honest. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01N67xH9BejMzZp4GNAq8m7w
…r-ndi-viewer-djp5vk
Follow-up to VH-Lab/NDR-matlab#139 (merged there): the probe/reduce helpers and the omezarr/smartspim reader classes were already ported; this commit adds the pytest coverage that was missing on the Python side and bumps the four bridge entries that had drifted. Tests mirror the MATLAB unit tests function-for-function: - tests/test_omezarr_probe.py mirrors TestOMEZarrProbe.m: ok / n_pyramids / pyramid_names / axes_order / level0_* on the shared programmatic fixture, plus the not-ok paths (missing dir, empty dir). - tests/test_omezarr_reduce.py mirrors TestOMEZarrReduce.m: mean/max, dtype (max preserves, mean promotes to float64), per-axis factor vector, trailing partial block kept, arity + reduction validation, factor-1 pass-through. - tests/test_omezarr_reader.py mirrors TestOMEZarrReader.m: pinned / unpinned / unknown / sidecar resolveepoch, all metadata methods, single-frame / multi-frame / Level>1 pixel reads against ground truth, and mean-vs-max routing proof at level 2. - tests/test_smartspim_reader.py mirrors TestSmartSPIMReader.m: pinned / unpinned-channel / unpinned-tile / sidecar resolveepoch, all metadata methods, single-frame / multi-frame / cross-channel reads against the synthetic fixture, out-of-range error. Programmatic fixtures mirror ndr.test.format.{omezarr,smartspim} .makeExampleFixture.m: dual-pyramid Zarr v2 store with a shared level-0 array (uncompressed C-order chunks are enough since the read path is zarr.open); a synthetic SmartSPIM tree with real TIFF slices whose pixels encode (channelIndex, z) so cross-channel routing has a byte-for-byte proof. Bridge yaml updates (all drift picked up by test_matlab_bridge_completeness.py): - +ndr/+format/+blosc/encode.m 9a87c0a -> aa89463 - +ndr/+format/+blosc/decode.m 9a87c0a -> aa89463 - +ndr/+format/+omezarr/readArray.m a847431 -> 8bea2d2 - +ndr/+format/+omezarr/private/ decompressBlosc.m a847431 -> 5a44303 Every one is MATLAB-side blosc plumbing (batch API, persistent server, MEX preference, hand-rolled codec dispatch replaced with one-line delegation). Python has always used numcodecs.Blosc through zarr directly, so all four are hash-bump-only per the decision_log notes. +ndr/+util/+blosc/* MEX bootstrapping stays deliberately unported (numcodecs.Blosc on the Python side; see the matlab_only entries in src/ndr/format/blosc/ndr_matlab_python_bridge.yaml). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01UdLHfApBhntCz64BatnwY5
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Follow-up to VH-Lab/NDR-matlab#139 (merged there). The Python-side ports of
ndr.format.omezarr.{probe,reduce}andndr.reader.{omezarr,smartspim}were already onmain; this PR adds the pytest coverage that was missing on the Python side and bumps the four bridge entries that had drifted after the recent MATLAB blosc work.Summary
tests/test_omezarr_probe.pymirrorsTestOMEZarrProbe.m(ok / n_pyramids / pyramid_names / axes_order / level0_* plus the not-ok paths).tests/test_omezarr_reduce.pymirrorsTestOMEZarrReduce.m(mean/max, dtype behaviour, per-axis factor, trailing partial block, arity + reduction validation).tests/test_omezarr_reader.pymirrorsTestOMEZarrReader.m(pinned / unpinned / unknown / sidecar resolveepoch, all metadata methods, single- and multi-frame pixel reads against ground truth,Level>1 reads, and the mean-vs-max routing proof at level 2).tests/test_smartspim_reader.pymirrorsTestSmartSPIMReader.m(pinned / unpinned-channel / unpinned-tile / sidecar resolveepoch, metadata, cross-channel reads against a synthetic TIFF fixture whose pixels encode(channelIndex, z)).tests/_omezarr_fixture.pyandtests/_smartspim_fixture.pymirrorndr.test.format.{omezarr,smartspim}.makeExampleFixture(dual-pyramid Zarr v2 store with a shared level-0 array; SmartSPIM tree with real TIFF slices). Zarr chunks are uncompressed here becausezarr.openreads them through the same path as any other codec — no zstd binary ornumcodecs.Bloscneeded to exercise the read side.test_matlab_bridge_completeness.py. Each entry now records the current MATLAB commit and adecision_lognote explaining why the MATLAB change is a no-op on the Python side:+ndr/+format/+blosc/encode.m9a87c0a→aa89463+ndr/+format/+blosc/decode.m9a87c0a→aa89463+ndr/+format/+omezarr/readArray.ma847431→8bea2d2+ndr/+format/+omezarr/private/decompressBlosc.ma847431→5a44303Every one is MATLAB-side blosc plumbing (batch API + persistent server, blosc-matlab MEX preference, hand-rolled codec dispatch replaced with a one-line delegation to
ndr.format.blosc.decode). Python has always usednumcodecs.Bloscthroughzarrdirectly, so all four are hash-bump-only.Intentionally not ported
+ndr/+util/+blosc/*MEX bootstrapping (blosc-matlab pinning, ensureMex, persistent Python server, venv setup) stays MATLAB-only — see thematlab_onlyentries insrc/ndr/format/blosc/ndr_matlab_python_bridge.yaml. The Python side reads and writes Blosc containers throughnumcodecs.Bloscdirectly, so there is nothing to port.Test plan
NDR_MATLAB_PATH=../ndr-matlab pytest tests/ --ignore=tests/symmetry— 613 passed, 3 skipped.NDR_BRIDGE_CHECK_STRICT=1 NDR_MATLAB_PATH=../ndr-matlab pytest tests/test_matlab_bridge_completeness.py tests/test_matlab_bridge_conventions.py— 191 passed, drift check green.test_omezarr_reader.pyandtest_smartspim_reader.py) verify pixel-level correctness against ground truth, including the pyramid-routing invariant that mean and max reads return different pixels at the same coordinates.🤖 Generated with Claude Code
https://claude.ai/code/session_01UdLHfApBhntCz64BatnwY5
Generated by Claude Code