wip: allow reading v0.5 images

Author: ziw-liu

iohub/ngff/nodes.py

@@ -571,12 +571,13 @@ def _set_meta(
             )
             example_image: ImageArray = self[
                 self.metadata.multiscales[0].datasets[0].path
-            ].channels
+            ]
             self._channel_names = list(range(example_image.channels))
 
     def _parse_meta(self):
-        multiscales = self.zattrs.get("multiscales")
-        omero = self.zattrs.get("omero")
+        attrs = self.zattrs.get("ome") or self.zattrs
+        multiscales = attrs.get("multiscales")
+        omero = attrs.get("omero")
         if multiscales:
             try:
                 self._set_meta(multiscales=multiscales, omero=omero)
@@ -1925,6 +1926,49 @@ def rename_well(self, old: str, new: str):
         self.dump_meta()
 
 
+def _check_file_mode(
+    store_path: Path,
+    mode: Literal["r", "r+", "a", "w", "w-"],
+    disable_path_checking: bool,
+) -> bool:
+    if mode == "a":
+        mode = ("w-", "r+")[int(store_path.exists())]
+    parse_meta = False
+    if mode in ("r", "r+"):
+        parse_meta = True
+    elif mode == "w-":
+        if store_path.exists():
+            raise FileExistsError(store_path)
+    elif mode == "w":
+        if store_path.exists():
+            if (
+                ".zarr" not in str(store_path.resolve())
+                and not disable_path_checking
+            ):
+                raise ValueError(
+                    "Cannot overwrite a path that does not contain '.zarr', "
+                    "use `disable_path_checking=True` if you are sure that "
+                    f"{store_path} should be overwritten."
+                )
+            _logger.warning(f"Overwriting data at {store_path}")
+    else:
+        raise ValueError(f"Invalid persistence mode '{mode}'.")
+    return parse_meta
+
+
+def _detect_layout(meta_keys: list[str]) -> Literal["fov", "hcs"]:
+    if "plate" in meta_keys:
+        return "hcs"
+    elif "multiscales" in meta_keys:
+        return "fov"
+    else:
+        raise KeyError(
+            "Dataset metadata keys ('plate'/'multiscales') not in "
+            f"the found store metadata keys: {meta_keys}. "
+            "Is this a valid OME-Zarr dataset?"
+        )
+
+
 def open_ome_zarr(
     store_path: StrOrBytesPath | Path,
     layout: Literal["auto", "fov", "hcs", "tiled"] = "auto",
@@ -1998,42 +2042,16 @@ def open_ome_zarr(
         or :py:class:`iohub.ngff.TiledPosition`)
     """
     store_path = Path(store_path)
-    if mode == "a":
-        mode = ("w-", "r+")[int(store_path.exists())]
-    parse_meta = False
-    if mode in ("r", "r+"):
-        parse_meta = True
-    elif mode == "w-":
-        if store_path.exists():
-            raise FileExistsError(store_path)
-    elif mode == "w":
-        if store_path.exists():
-            if (
-                ".zarr" not in str(store_path.resolve())
-                and not disable_path_checking
-            ):
-                raise ValueError(
-                    "Cannot overwrite a path that does not contain '.zarr', "
-                    "use `disable_path_checking=True` if you are sure that "
-                    f"{store_path} should be overwritten."
-                )
-            _logger.warning(f"Overwriting data at {store_path}")
-    else:
-        raise ValueError(f"Invalid persistence mode '{mode}'.")
+    parse_meta = _check_file_mode(
+        store_path, mode, disable_path_checking=disable_path_checking
+    )
     root = _open_store(store_path, mode, version)
     meta_keys = root.attrs.keys() if parse_meta else []
+    if "ome" in meta_keys:
+        meta_keys = root.attrs["ome"].keys()
     if layout == "auto":
         if parse_meta:
-            if "plate" in meta_keys:
-                layout = "hcs"
-            elif "multiscales" in meta_keys:
-                layout = "fov"
-            else:
-                raise KeyError(
-                    "Dataset metadata keys ('plate'/'multiscales') not in "
-                    f"the found store metadata keys: {meta_keys}. "
-                    "Is this a valid OME-Zarr dataset?"
-                )
+            layout = _detect_layout(meta_keys)
         else:
             raise ValueError(
                 "Store layout must be specified when creating a new dataset."
@@ -2054,5 +2072,6 @@ def open_ome_zarr(
         parse_meta=parse_meta,
         channel_names=channel_names,
         axes=axes,
+        version=version,
         **kwargs,
     )