Merge pull request #121 from thewtex/convert-ome-version

ENH: OME-Zarr format version conversion

docs/python.md

@@ -214,6 +214,24 @@ pip install "ngff-zarr[tensorstore]"
 nz.to_ngff_zarr('cthead1.ome.zarr', multiscales, use_tensorstore=True)
 ```
 
+## Convert OME-Zarr versions
+
+To convert from OME-Zarr version 0.4, which uses the Zarr Format Specification
+2, to 0.5, which uses the Zarr Format Specification 3, or vice version, specify
+the desired version when writing.
+
+```python
+# Convert from 0.4 to 0.5
+multiscales = from_ngff_zarr('cthead1.ome.zarr')
+to_ngff_zarr('cthead1_zarr3.ome.zarr', multiscales, version='0.5')
+```
+
+```python
+# Convert from 0.5 to 0.4
+multiscales = from_ngff_zarr('cthead1.ome.zarr')
+to_ngff_zarr('cthead1_zarr2.ome.zarr', multiscales, version='0.4')
+```
+
 [dataclass]: https://docs.python.org/3/library/dataclasses.html
 [dataclasses]: https://docs.python.org/3/library/dataclasses.html
 [Dask arrays]: https://docs.dask.org/en/stable/array.html

ngff_zarr/from_ngff_zarr.py

@@ -2,6 +2,7 @@
 from pathlib import Path
 from typing import Union, Optional
 import packaging.version
+import sys
 
 import dask.array
 import zarr
@@ -91,6 +92,11 @@ def from_ngff_zarr(
     datasets = []
     for dataset in metadata["datasets"]:
         data = dask.array.from_zarr(store, component=dataset["path"])
+        # Convert endianness to native if needed
+        if (sys.byteorder == "little" and data.dtype.byteorder == ">") or (
+            sys.byteorder == "big" and data.dtype.byteorder == "<"
+        ):
+            data = data.astype(data.dtype.newbyteorder())
 
         scale = {d: 1.0 for d in dims}
         translation = {d: 0.0 for d in dims}

ngff_zarr/to_ngff_zarr.py

@@ -17,6 +17,8 @@
 import zarr
 import zarr.storage
 from ._zarr_open_array import open_array
+from .v04.zarr_metadata import Metadata as Metadata_v04
+from .v05.zarr_metadata import Metadata as Metadata_v05
 
 # Zarr Python 3
 if hasattr(zarr.storage, "StoreLike"):
@@ -182,7 +184,23 @@ def to_ngff_zarr(
     if version != "0.4" and version != "0.5":
         raise ValueError(f"Unsupported version: {version}")
 
-    metadata_dict = asdict(multiscales.metadata)
+    metadata = multiscales.metadata
+    if version == "0.4" and isinstance(metadata, Metadata_v05):
+        metadata = Metadata_v04(
+            axes=metadata.axes,
+            datasets=metadata.datasets,
+            coordinateTransformations=metadata.coordinateTransformations,
+            name=metadata.name,
+        )
+    if version == "0.5" and isinstance(metadata, Metadata_v04):
+        metadata = Metadata_v05(
+            axes=metadata.axes,
+            datasets=metadata.datasets,
+            coordinateTransformations=metadata.coordinateTransformations,
+            name=metadata.name,
+        )
+
+    metadata_dict = asdict(metadata)
     metadata_dict = _pop_metadata_optionals(metadata_dict)
     metadata_dict["@type"] = "ngff:Image"
     zarr_format = 2 if version == "0.4" else 3
@@ -224,7 +242,7 @@ def to_ngff_zarr(
             progress.update_multiscales_task_completed(index + 1)
         image = next_image
         arr = image.data
-        path = multiscales.metadata.datasets[index].path
+        path = metadata.datasets[index].path
         parent = str(PurePosixPath(path).parent)
         if parent not in (".", "/"):
             array_dims_group = root.create_group(parent)

ngff_zarr/validate.py

@@ -1,6 +1,7 @@
 from typing import Dict
 from pathlib import Path
 import json
+from packaging import version as packaging_version
 
 from importlib_resources import files as file_resources
 
@@ -40,5 +41,10 @@ def validate(
     registry = Registry().with_resource(
         NGFF_URI, resource=Resource.from_contents(schema)
     )
+    if packaging_version.parse(version) >= packaging_version.parse("0.5"):
+        version_schema = load_schema(version=version, model="_version")
+        registry = registry.with_resource(
+            NGFF_URI, resource=Resource.from_contents(version_schema)
+        )
     validator = Draft202012Validator(schema, registry=registry)
     validator.validate(ngff_dict)

test/_data.py

@@ -14,8 +14,8 @@
 from zarr.storage import MemoryStore
 from deepdiff import DeepDiff
 
-test_data_ipfs_cid = "bafybeiccqqioflsdnpna3kewhskyjcitqdk6n3yrzhnhj5qzpjk5edc2be"
-test_data_sha256 = "4921b0e38b09ea480d377a89f1b4074f8e783b5703a651c60ef1e495c877f716"
+test_data_ipfs_cid = "bafybeib2s7ls6yscm2uqxby5vbhbfsyxn3ev7soewi3hji4uiki7v6cbiy"
+test_data_sha256 = "58c0219f194cd976acee1ebd19ea78b03aada3f96a54302c8fb8515a349d9613"
 
 test_dir = Path(__file__).resolve().parent
 extract_dir = "data"