POC validation of NGFF with pydantic_ome_ngff

.isort.cfg

@@ -1,5 +1,5 @@
 [settings]
-known_third_party = dask,numcodecs,numpy,pytest,scipy,setuptools,skimage,zarr
+known_third_party = dask,numcodecs,numpy,pydantic_ome_ngff,pytest,scipy,setuptools,skimage,zarr
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0

ome_zarr/reader.py

@@ -8,6 +8,7 @@
 import dask.array as da
 import numpy as np
 from dask import delayed
+from pydantic_ome_ngff.v04.multiscales import Multiscale
 
 from .axes import Axes
 from .format import format_from_version
@@ -296,6 +297,11 @@ def __init__(self, node: Node) -> None:
             node.metadata["coordinateTransformations"] = transformations
         LOGGER.info("datasets %s", datasets)
 
+        for multi in multiscales:
+            # raises Exception if can't be parsed. Only v0.4 supported
+            if multi.get("version") == "0.4":
+                Multiscale.parse_obj(multi)
+
         for resolution in self.datasets:
             data: da.core.Array = self.array(resolution, version)
             chunk_sizes = [

setup.py

@@ -25,6 +25,7 @@ def read(fname):
 install_requires += (["requests"],)
 install_requires += (["scikit-image"],)
 install_requires += (["toolz"],)
+install_requires += (["pydantic-ome-ngff"],)
 
 
 setup(

tests/test_reader.py

@@ -1,3 +1,5 @@
+import random
+
 import pytest
 import zarr
 from numpy import zeros
@@ -50,6 +52,32 @@ def test_invalid_version(self):
             assert len(list(reader())) == 2
         assert str(exe.value) == "Version invalid not recognized"
 
+    @pytest.mark.parametrize(
+        "axes",
+        [
+            [{"type": "space", "name": "x"}, {"type": "space", "name": "x"}],
+            [{"type": "time", "name": "t"}, {"type": "space", "name": "x"}],
+            [
+                {"type": "time", "name": "t"},
+                {"type": "time", "name": "time"},
+                {"type": "space", "name": "y"},
+                {"type": "space", "name": "x"},
+            ],
+        ],
+    )
+    def test_invalid_axes(self, tmpdir, axes):
+        # new dir each time - otherwise repeated read gives different node count
+        tmp_dir = tmpdir.mkdir(str(random.random()))
+        grp = create_zarr(str(tmp_dir))
+        attrs = grp.attrs.asdict()
+        attrs["multiscales"][0]["axes"] = axes
+        grp.attrs.put(attrs)
+        # should raise exception
+        with pytest.raises(ValueError):
+            reader = Reader(parse_url(str(tmp_dir)))
+            nodes = list(reader())
+            assert len(nodes) == 3
+
 
 class TestHCSReader:
     @pytest.fixture(autouse=True)