ENH: Add validate kwarg to from_ngff_zarr

Author: thewtex

ngff_zarr/from_ngff_zarr.py

@@ -9,17 +9,21 @@
 from .ngff_image import NgffImage
 from .to_multiscales import Multiscales
 from .zarr_metadata import Axis, Dataset, Metadata, Scale, Translation
+from .validate import validate as validate_ngff
 
 
 def from_ngff_zarr(
     store: Union[MutableMapping, str, Path, BaseStore],
+    validate: bool = False,
 ) -> Multiscales:
     """
     Read an OME-Zarr NGFF Multiscales data structure from a Zarr store.
 
     store : MutableMapping, str or Path, zarr.storage.BaseStore
         Store or path to directory in file system.
 
+    validate : bool
+        If True, validate the NGFF metadata against the schema.
 
     Returns
     -------
@@ -29,6 +33,8 @@ def from_ngff_zarr(
     """
 
     root = zarr.open_group(store, mode="r")
+    if validate:
+        validate_ngff(root.attrs.asdict())
     metadata = root.attrs["multiscales"][0]
 
     dims = [a["name"] for a in metadata["axes"]]

test/test_ngff_validation.py

@@ -1,22 +1,26 @@
-import json
-
 import numpy as np
 import zarr
-from ngff_zarr import Multiscales, to_multiscales, to_ngff_zarr, validate
+from ngff_zarr import (
+    Multiscales,
+    to_multiscales,
+    to_ngff_zarr,
+    validate,
+    from_ngff_zarr,
+)
 
 
 def check_valid_ngff(multiscale: Multiscales):
     store = zarr.storage.MemoryStore(dimension_separator="/")
     store = zarr.storage.DirectoryStore("/tmp/test.zarr", dimension_separator="/")
     to_ngff_zarr(store, multiscale)
-    zarr.convenience.consolidate_metadata(store)
-    metadata = json.loads(store.get(".zmetadata"))["metadata"]
-    ngff = metadata[".zattrs"]
+    root = zarr.open_group(store, mode="r")
 
-    validate(ngff)
+    validate(root.attrs.asdict())
     # Need to add NGFF metadata property
     # validate(ngff, strict=True)
 
+    from_ngff_zarr(store, validate=True)
+
 
 def test_y_x_valid_ngff():
     array = np.random.random((32, 16))