Refactor zarrv3

src/spatialdata/_core/spatialdata.py

@@ -1698,15 +1698,14 @@ def write_metadata(
             check_valid_name(element_name)
             if element_name not in self:
                 raise ValueError(f"Element with name {element_name} not found in SpatialData object.")
+        if write_attrs:
+            self.write_attrs(sdata_format=sdata_format)
 
         self.write_transformations(element_name)
         self.write_channel_names(element_name)
         # TODO: write .uns['spatialdata_attrs'] metadata for AnnData.
         # TODO: write .attrs['spatialdata_attrs'] metadata for DaskDataFrame.
 
-        if write_attrs:
-            self.write_attrs(sdata_format=sdata_format)
-
         if self.has_consolidated_metadata():
             consolidate_metadata = True
         if consolidate_metadata:

src/spatialdata/_io/io_points.py

@@ -46,6 +46,11 @@ def _read_points(
     return points
 
 
+class PointsReader:
+    def __call__(self, store: str | Path | MutableMapping[str, object] | zarr.Group) -> DaskDataFrame:
+        return _read_points(store)
+
+
 def write_points(
     points: DaskDataFrame,
     group: zarr.Group,

src/spatialdata/_io/io_raster.py

@@ -35,33 +35,6 @@
 )
 
 
-def _get_multiscale_nodes(image_nodes: list[Node], nodes: list[Node]) -> list[Node]:
-    """Get nodes with Multiscales spec from a list of nodes.
-
-    The nodes with the Multiscales spec are the nodes used for reading in image and label data. We only have to check
-    the multiscales now, while before we also had to check the label spec. In the new ome-zarr-py though labels can have
-    the Label spec, these do not contain the multiscales anymore used to read the data. They can contain label specific
-    metadata though.
-
-    Parameters
-    ----------
-    image_nodes
-        List of nodes returned from the ome-zarr-py Reader.
-    nodes
-        List to append the nodes with the multiscales spec to.
-
-    Returns
-    -------
-    List of nodes with the multiscales spec.
-    """
-    if len(image_nodes):
-        for node in image_nodes:
-            # Labels are now also Multiscales in newer version of ome-zarr-py
-            if np.any([isinstance(spec, Multiscales) for spec in node.specs]):
-                nodes.append(node)
-    return nodes
-
-
 def _read_multiscale(
     store: str | Path, raster_type: Literal["image", "labels"], reader_format: Format
 ) -> DataArray | DataTree:
@@ -134,6 +107,7 @@ def _read_multiscale(
         msi = DataTree.from_dict(multiscale_image)
         _set_transformations(msi, transformations)
         return compute_coordinates(msi)
+
     data = node.load(Multiscales).array(resolution=datasets[0])
     si = DataArray(
         data,
@@ -145,6 +119,40 @@ def _read_multiscale(
     return compute_coordinates(si)
 
 
+def _get_multiscale_nodes(image_nodes: list[Node], nodes: list[Node]) -> list[Node]:
+    """Get nodes with Multiscales spec from a list of nodes.
+
+    The nodes with the Multiscales spec are the nodes used for reading in image and label data. We only have to check
+    the multiscales now, while before we also had to check the label spec. In the new ome-zarr-py though labels can have
+    the Label spec, these do not contain the multiscales anymore used to read the data. They can contain label specific
+    metadata though.
+
+    Parameters
+    ----------
+    image_nodes
+        List of nodes returned from the ome-zarr-py Reader.
+    nodes
+        List to append the nodes with the multiscales spec to.
+
+    Returns
+    -------
+    List of nodes with the multiscales spec.
+    """
+    if len(image_nodes):
+        for node in image_nodes:
+            # Labels are now also Multiscales in newer version of ome-zarr-py
+            if np.any([isinstance(spec, Multiscales) for spec in node.specs]):
+                nodes.append(node)
+    return nodes
+
+
+class MultiscaleReader:
+    def __call__(
+        self, path: str | Path, raster_type: Literal["image", "labels"], reader_format: Format
+    ) -> DataArray | DataTree:
+        return _read_multiscale(path, raster_type, reader_format)
+
+
 def _write_raster(
     raster_type: Literal["image", "labels"],
     raster_data: DataArray | DataTree,

src/spatialdata/_io/io_shapes.py

@@ -30,7 +30,7 @@
 
 
 def _read_shapes(
-    store: str | Path | MutableMapping | zarr.Group,  # type: ignore[type-arg]
+    store: str | Path | MutableMapping[str, object] | zarr.Group,
 ) -> GeoDataFrame:
     """Read shapes from a zarr store."""
     assert isinstance(store, str | Path)
@@ -67,6 +67,11 @@ def _read_shapes(
     return geo_df
 
 
+class ShapesReader:
+    def __call__(self, store: str | Path | MutableMapping[str, object] | zarr.Group) -> GeoDataFrame:
+        return _read_shapes(store)
+
+
 def write_shapes(
     shapes: GeoDataFrame,
     group: zarr.Group,

src/spatialdata/_io/io_table.py

@@ -21,7 +21,7 @@ def _read_table(
     group: zarr.Group,
     tables: dict[str, AnnData],
     on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN] = BadFileHandleMethod.ERROR,
-) -> dict[str, AnnData]:
+) -> None:
     """
     Read in tables in the tables Zarr.group of a SpatialData Zarr store.
 
@@ -85,7 +85,17 @@ def _read_table(
             count += 1
 
     logger.debug(f"Found {count} elements in {group}")
-    return tables
+
+
+class TablesReader:
+    def __call__(
+        self,
+        path: str,
+        group: zarr.Group,
+        container: dict[str, AnnData],
+        on_bad_files: Literal[BadFileHandleMethod.ERROR, BadFileHandleMethod.WARN],
+    ) -> None:
+        return _read_table(path, group, container, on_bad_files)
 
 
 def write_table(