OME metadata support

dacapo/experiments/datasplits/datasets/arrays/zarr_array_config.py

@@ -3,7 +3,7 @@
 from .array_config import ArrayConfig
 
 from funlib.geometry import Coordinate
-from funlib.persistence import open_ds
+from funlib.persistence import open_ds, open_ome_ds
 
 from upath import UPath as Path
 
@@ -56,9 +56,15 @@ class ZarrArrayConfig(ArrayConfig):
     mode: Optional[str] = attr.ib(
         default="a", metadata={"help_text": "The access mode!"}
     )
+    ome_metadata: bool = attr.ib(
+        default=False, metadata={"help_text": "Whether to expect OME metadata"}
+    )
 
     def array(self, mode="r"):
-        return open_ds(f"{self.file_name}/{self.dataset}", mode=mode)
+        if self.ome_metadata:
+            return open_ome_ds(f"{self.file_name}/{self.dataset}", mode=mode)
+        else:
+            return open_ds(f"{self.file_name}/{self.dataset}", mode=mode)
 
     def verify(self) -> Tuple[bool, str]:
         """

pyproject.toml

@@ -47,7 +47,6 @@ dependencies = [
         "funlib.geometry>=0.2",
         "mwatershed>=0.5.2",
         "cellmap-models",
-        "funlib.persistence>=0.5.3",
         "gunpowder>=1.4",
         "lsds",
         "xarray",
@@ -59,6 +58,7 @@ dependencies = [
         "upath",
         "boto3",
         "matplotlib",
+        "funlib.persistence @ git+https://github.com/funkelab/funlib.persistence.git@ome-ngff"
         ]
 
 # extras