fix: adding ome-zarr v0.4 back#398
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Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
TensorStore's zarr2 driver requires fill_value to be a boolean for bool dtype arrays, not an integer 0. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…to zarr-python, keeping TensorStore solely for array I/O. Route array access through impl.open_array() in the node layer. Also unblocks OME-Zarr v0.4 store creation and adds a sharding guard for Zarr v2 Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
ieivanov
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Apr 9, 2026
| ) | ||
| _ = dataset.create_position(row_name=row, col_name=col, pos_name=pos) | ||
| ome = dataset.zgroup.attrs["ome"] | ||
| ome = dict(dataset.zgroup.attrs) if version == "0.4" else dataset.zgroup.attrs["ome"] |
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Did the location of ome metadata chance between v0.4 and v0.5? Do we not have a convenience method to extra this metadata, independent on ngff version?
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Yeah it did change.
- v0.4: flat in
.zattrs->{"multiscales": [...], "omero": {...}} - v0.5: wrapped under
"ome"key inzarr.json->{"attributes": {"ome": {"multiscales": [...], "omero": {...}}}}
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Thanks Sri. Could you create a pypi release once that's merged? |
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I realized that for TensorStore, we can take Zarr-Python's implementation of Zarr groups and leave the actual Array I/O to TensorStore instead of writing shims for TensorStore.
yes |
… OME metadata access Replace inline v0.4/v0.5 metadata branching with get_ome_attrs() from core.compat. Used in NGFFNode.maybe_wrapped_ome_attrs, Plate.first_position, and tests. Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
…iteral["0.4",-"0.5"]): Replace version: Literal["0.5"] | None = None with version: Literal["0.4", "0.5"] on ImagesMeta and LabelImageMeta. Simplify creation code from "0.5" if self.version == "0.5" else None to self.version Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
… and LabelImage _parse_meta Old v0.4 stores often omit the root version field (SHOULD, not MUST in the spec). Align Position and LabelImage _parse_meta with the Well and Plate pattern of injecting self.version before model_validate. Signed-off-by: Sricharan Reddy Varra <sricharan.varra@biohub.org>
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Allows writing to OME-Zarr v0.4.