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BUG: Write out array dimension_names for OME-Zarr 0.5 #124

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merged 1 commit into from
Dec 6, 2024
Merged

BUG: Write out array dimension_names for OME-Zarr 0.5 #124

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13 changes: 12 additions & 1 deletion ngff_zarr/to_ngff_zarr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ def _numpy_to_zarr_dtype(dtype):


def _write_with_tensorstore(
store_path: str, array, region, chunks, zarr_format
store_path: str, array, region, chunks, zarr_format, dimension_names=None
) -> None:
"""Write array using tensorstore backend"""
import tensorstore as ts
Expand All @@ -131,6 +131,8 @@ def _write_with_tensorstore(
"configuration": {"chunk_shape": chunks},
}
spec["metadata"]["data_type"] = _numpy_to_zarr_dtype(array.dtype)
if dimension_names:
spec["metadata"]["dimension_names"] = dimension_names
else:
raise ValueError(f"Unsupported zarr format: {zarr_format}")
dataset = ts.open(spec, create=True, dtype=array.dtype).result()
Expand Down Expand Up @@ -199,6 +201,10 @@ def to_ngff_zarr(
coordinateTransformations=metadata.coordinateTransformations,
name=metadata.name,
)
dimension_names = tuple([ax.name for ax in metadata.axes])
dimension_names_kwargs = (
{"dimension_names": dimension_names} if version != "0.4" else {}
)

metadata_dict = asdict(metadata)
metadata_dict = _pop_metadata_optionals(metadata_dict)
Expand Down Expand Up @@ -274,6 +280,7 @@ def to_ngff_zarr(
path=path,
mode="a",
**zarr_kwargs,
**dimension_names_kwargs,
)

shape = image.data.shape
Expand Down Expand Up @@ -407,6 +414,7 @@ def to_ngff_zarr(
region,
[c[0] for c in arr_region.chunks],
zarr_format=zarr_format,
dimension_names=dimension_names,
**kwargs,
)
else:
Expand All @@ -419,6 +427,7 @@ def to_ngff_zarr(
compute=True,
return_stored=False,
**zarr_kwargs,
**dimension_names_kwargs,
**kwargs,
)
else:
Expand All @@ -435,6 +444,7 @@ def to_ngff_zarr(
region,
[c[0] for c in arr.chunks],
zarr_format=zarr_format,
dimension_names=dimension_names,
**kwargs,
)
else:
Expand All @@ -447,6 +457,7 @@ def to_ngff_zarr(
compute=True,
return_stored=False,
**zarr_kwargs,
**dimension_names_kwargs,
**kwargs,
)

Expand Down
12 changes: 12 additions & 0 deletions test/test_to_ngff_zarr_rfc2_zarr_v3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,11 @@ def test_gaussian_isotropic_scale_factors(input_images):
# store_new_multiscales(dataset_name, baseline_name, multiscales, version=version)
verify_against_baseline(dataset_name, baseline_name, multiscales, version=version)

array0 = zarr.open_array(store=store, path="scale0/image", mode="r", zarr_format=3)
dimension_names = array0.metadata.dimension_names
for idx, ax in enumerate(multiscales.metadata.axes):
assert ax.name == dimension_names[idx]


def test_gaussian_isotropic_scale_factors_tensorstore(input_images):
pytest.importorskip("tensorstore")
Expand All @@ -48,3 +53,10 @@ def test_gaussian_isotropic_scale_factors_tensorstore(input_images):
verify_against_baseline(
dataset_name, baseline_name, multiscales, version=version
)

array0 = zarr.open_array(
store=tmpdir, path="scale0/image", mode="r", zarr_format=3
)
dimension_names = array0.metadata.dimension_names
for idx, ax in enumerate(multiscales.metadata.axes):
assert ax.name == dimension_names[idx]
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