version 0.1 to 0.3 #112
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version 0.1 to 0.3 #112
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thewtex
commented
Nov 29, 2024
thewtex
commented
- ENH: Support reading and validating OME-Zarr v0.1
- ENH: Support reading and validating OME-Zarr v0.2
- ENH: Support reading and validating OME-Zarr v0.3
- ENH: Update test data hashes
Includes OME-Zarr v0.1-v0.3 input test datasets from the IDR: https://idr.github.io/ome-ngff-samples/
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Copilot reviewed 4 out of 21 changed files in this pull request and generated 1 suggestion.
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- ngff_zarr/spec/0.1/copyright.include: Language not supported
- ngff_zarr/spec/0.1/schemas/image.schema: Language not supported
- ngff_zarr/spec/0.1/schemas/plate.schema: Language not supported
- ngff_zarr/spec/0.1/schemas/strict_image.schema: Language not supported
- ngff_zarr/spec/0.1/schemas/well.schema: Language not supported
- ngff_zarr/spec/0.2/copyright.include: Language not supported
- ngff_zarr/spec/0.2/schemas/image.schema: Language not supported
- ngff_zarr/spec/0.2/schemas/plate.schema: Language not supported
- ngff_zarr/spec/0.2/schemas/well.schema: Language not supported
- ngff_zarr/spec/0.3/copyright.include: Language not supported
- ngff_zarr/spec/0.3/schemas/image.schema: Language not supported
- ngff_zarr/spec/0.3/schemas/jsonld/context.json: Language not supported
- ngff_zarr/spec/0.3/schemas/jsonld/frame.json: Language not supported
- ngff_zarr/spec/0.3/schemas/jsonld/shacl.ttl: Language not supported
- ngff_zarr/spec/0.3/schemas/plate.schema: Language not supported
- ngff_zarr/spec/0.3/schemas/strict_image.schema: Language not supported
- ngff_zarr/spec/0.3/schemas/well.schema: Language not supported
Comments skipped due to low confidence (1)
ngff_zarr/from_ngff_zarr.py:78
- The line 'dims = [a["name"] if "name" in a else a for a in metadata["axes"]]' could lead to inconsistent naming if the axes are not uniformly structured. Consider ensuring that all axes have a 'name' attribute.
dims = [a["name"] if "name" in a else a for a in metadata["axes"]]
| "y": "space", | ||
| "x": "space", | ||
| } | ||
| axes = [Axis(name=axis, type=type_dict[axis]) for axis in metadata["axes"]] |
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The line 'axes = [Axis(name=axis, type=type_dict[axis]) for axis in metadata["axes"]]' assumes that the keys will always be one of "t", "c", "z", "y", or "x". Consider adding a default case or error handling for unexpected keys.
Suggested change
| axes = [Axis(name=axis, type=type_dict[axis]) for axis in metadata["axes"]] | |
| axes = [Axis(name=axis, type=type_dict.get(axis, 'unknown')) for axis in metadata['axes']] |
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