ENH: Add NGFF 0.4 JSON Schema validation test

pyproject.toml

@@ -21,6 +21,7 @@ requires = [
 [tool.flit.metadata.requires-extra]
 test = [
     "itk-filtering",
+    "jsonschema",
     "pytest",
     "pytest-mypy",
     "fsspec",

test/test_ngff_validation.py

@@ -0,0 +1,73 @@
+from audioop import mul
+import json
+from typing import Dict
+import urllib.request
+
+from jsonschema import RefResolver, Draft202012Validator
+from jsonschema.exceptions import ValidationError
+
+from jsonschema import validate, RefResolver
+
+from spatial_image_multiscale import to_multiscale, MultiscaleSpatialImage
+from spatial_image import to_spatial_image
+import numpy as np
+import zarr
+
+def load_schema(version: str = '0.4', strict: bool = False) -> Dict:
+    strict_str = ''
+    if strict:
+        strict_str = 'strict_'
+    # Needs: https://github.com/ome/ngff/pull/113
+    # with urllib.request.urlopen(f"https://ngff.openmicroscopy.org/{version}/schemas/{strict_str}image.schema") as url:
+    with urllib.request.urlopen(f"https://raw.githubusercontent.com/ome/ngff/main/{version}/schemas/{strict_str}image.schema") as url:
+        schema = json.loads(url.read().decode())
+    return schema
+
+def check_valid_ngff(multiscale: MultiscaleSpatialImage):
+    store = zarr.storage.MemoryStore(dimension_separator='/')
+    multiscale.to_zarr(store)
+    zarr.convenience.consolidate_metadata(store)
+    metadata = json.loads(store.get('.zmetadata'))['metadata']
+    ngff = metadata['.zattrs']
+
+    image_schema = load_schema(version='0.4', strict=False)
+    strict_image_schema = load_schema(version='0.4', strict=True)
+    schema_store = {
+        image_schema['$id']: image_schema,
+        strict_image_schema['$id']: strict_image_schema,
+    }
+    resolver = RefResolver.from_schema(image_schema, store=schema_store)
+    validator = Draft202012Validator(image_schema, resolver=resolver)
+    strict_validator = Draft202012Validator(strict_image_schema, resolver=resolver)
+
+    validator.validate(ngff)
+    # Need to add NGFF metadata property
+    # strict_validator.validate(ngff)
+
+def test_y_x_valid_ngff():
+    array = np.random.random((32,16))
+    image = to_spatial_image(array)
+    multiscale = to_multiscale(image, [2,4])
+
+    check_valid_ngff(multiscale)
+
+def test_z_y_x_valid_ngff():
+    array = np.random.random((32, 32, 16))
+    image = to_spatial_image(array)
+    multiscale = to_multiscale(image, [2,4])
+
+    check_valid_ngff(multiscale)
+
+def test_z_y_x_c_valid_ngff():
+    array = np.random.random((32, 32, 16, 3))
+    image = to_spatial_image(array)
+    multiscale = to_multiscale(image, [2,4])
+
+    check_valid_ngff(multiscale)
+
+def test_t_z_y_x_c_valid_ngff():
+    array = np.random.random((2, 32, 32, 16, 3))
+    image = to_spatial_image(array)
+    multiscale = to_multiscale(image, [2,4])
+
+    check_valid_ngff(multiscale)