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…is and series metadata - getLabels() reads attributes.ome.labels for zarr v3 labels groups (spec 0.5/0.6), falling back to the legacy attributes.labels; fix the v0.5 labels fixture to the spec layout. - Axis serializes longName (spec) and still accepts long_name on read. - displacements/coordinates transforms keep their interpolation field. - Model labels, image-label and series in the v0.5 and v0.6 OmeMetadata (new shared ImageLabel type; unknown keys in colors/properties are kept). createScaleLevel no longer drops ome fields in v0.5. - Add the projectAxis transform (droppedInputs/createdOutputs). - byDimension items use inputAxes/outputAxes, accepting the snake_case aliases on read. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
OME-NGFF 0.6 requires the input/output of coordinate transformations to be
JSON objects {"name": ..., "path": ...}. The v0.6 model stored them as
strings, squashing objects into "path#name" on read and writing strings
back, so reading a conformant file and saving it corrupted it. Scale levels
created via createScaleLevel also lacked the mandatory dataset input/output.
- Add CoordinateSystemRef (name/path, NON_NULL) and use it for input/output
on all v0.6 transformations; factory methods take CoordinateSystemRef and
gain ref-less scale/translation and a sequence factory.
- Legacy pre-release string refs are still read: a bare string is a name,
except for the input of a dataset transformation, which is the dataset
path; "<path>#<name>" strings from earlier zarr-java are split. Writing
always emits the object form.
- createScaleLevel writes input {"path": <level>} and output
{"name": <intrinsic>} (from existing datasets, else first coordinate
system; ZarrException if neither). Multiple transformations are wrapped in
a sequence whose nested transformations carry no refs; getMultiscaleNode
flattens such sequences back to [scale, translation].
- Scene graph resolution works on CoordinateSystemRef.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…s as {name, path} objects)
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Resolves the conflicts between the two PRs: the projectAxis transform and the convenience constructors of displacements/coordinates from zarr-developers#109 now take CoordinateSystemRef like every other v0.6 transform after zarr-developers#110, and the zarr-developers#109 test for createScaleLevel expects the single sequence zarr-developers#110 writes. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Every OME-Zarr 0.6 metadata document we have test data for is now read and written back, and the result must equal the original: the RFC-5 examples (bumped to their final 0.6 state), the valid cases of the official ngff-spec conformance suite (new submodule at tag 0.6) and our scene fixtures, which are moved from 0.6.dev3 to final 0.6. The round trip found what was still lost on write: - members zarr-java does not model on ome, multiscales entries and omero channels (@id, @type, wavelength_id) are kept as extra fields - unknown transformation types were written as a nested "raw" object - the axes of an image came from the first coordinate system instead of the intrinsic one the datasets map into Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Resolves the conflicts with the move of OME-Zarr to dev.zarr.conventions.ome (zarr-developers#78). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Builds on #109 and #110 and contains both, merged together; only the last commit is new. The merge commit resolves the conflicts between the two:
projectAxisand the displacements/coordinates constructors from #109 still took String refs, which #110 replaces withCoordinateSystemRef, and a #109 test expected two dataset transformations where #110 writes onesequence.To check that we actually write 0.6 correctly, every 0.6 metadata document we have test data for is now read, written back and compared to the original: the RFC-5 examples (bumped to their final 0.6 state), the valid cases of the official ngff-spec conformance suite (new submodule at tag
0.6) and our scene fixtures, moved from 0.6.dev3 to final 0.6.With #109 and #110 that passes for almost everything. What was still lost on write:
@id/@typeor the omerowavelength_id, are now kept as extra fields, the same wayv3.GroupMetadatadoes it{"type": "vendorWarp", "strength": 3.5}came back as{"type": "vendorWarp", "raw": {"strength": 3.5}}[c, z, y, x]for a 2D imageThe legacy test from #110 read the string form from the RFC-5 examples, which no longer have it, so it now uses a small dev3 fixture of its own.
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