ngio 0.5.0a1__py3-none-any.whl → 0.5.0a2__py3-none-any.whl

ngio/common/_pyramid.py

@@ -41,9 +41,19 @@ def _on_disk_dask_zoom(
     source_array = da.from_zarr(source)
     target_array = dask_zoom(source_array, target_shape=target.shape, order=order)
 
-    target_array = target_array.rechunk(target.chunks)  # type: ignore
-    target_array.compute_chunk_sizes()
+    # This is a potential fix for Dask 2025.11
+    # import dask.config
+    # chunk_size_bytes = np.prod(target.chunks) * target_array.dtype.itemsize
+    # current_chunk_size = dask.config.get("array.chunk-size")
+    # Increase the chunk size to avoid dask potentially creating
+    # corrupted chunks when writing chunks that are not multiple of the
+    # target chunk size
+    # dask.config.set({"array.chunk-size": f"{chunk_size_bytes}B"})
+    target_array = target_array.rechunk(target.chunks)
+    target_array = target_array.compute_chunk_sizes()
     target_array.to_zarr(target)
+    # Restore previous chunk size
+    # dask.config.set({"array.chunk-size": current_chunk_size})
 
 
 def _on_disk_coarsen(

ngio/hcs/_plate.py

@@ -40,6 +40,7 @@ from ngio.tables import (
 )
 from ngio.utils import (
     AccessModeLiteral,
+    NgioCache,
     NgioValueError,
     StoreOrGroup,
     ZarrGroupHandler,
@@ -239,6 +240,12 @@ class OmeZarrPlate:
         self._group_handler = group_handler
         self._meta_handler = find_plate_meta_handler(group_handler)
         self._tables_container = table_container
+        self._wells_cache: NgioCache[OmeZarrWell] = NgioCache(
+            use_cache=self._group_handler.use_cache
+        )
+        self._images_cache: NgioCache[OmeZarrContainer] = NgioCache(
+            use_cache=self._group_handler.use_cache
+        )
 
     def __repr__(self) -> str:
         """Return a string representation of the plate."""
@@ -356,6 +363,24 @@ class OmeZarrPlate:
         well = self.get_well(row=row, column=column)
         return well.get_image_acquisition_id(image_path=image_path)
 
+    def _get_well(self, well_path: str) -> OmeZarrWell:
+        """Get a well from the plate by its path.
+
+        Args:
+            well_path (str): The path of the well.
+
+        Returns:
+            OmeZarrWell: The well.
+
+        """
+        cached_well = self._wells_cache.get(well_path)
+        if cached_well is not None:
+            return cached_well
+
+        group_handler = self._group_handler.derive_handler(well_path)
+        self._wells_cache.set(well_path, OmeZarrWell(group_handler))
+        return OmeZarrWell(group_handler)
+
     def get_well(self, row: str, column: int | str) -> OmeZarrWell:
         """Get a well from the plate.
 
@@ -367,8 +392,7 @@ class OmeZarrPlate:
             OmeZarrWell: The well.
         """
         well_path = self._well_path(row=row, column=column)
-        group_handler = self._group_handler.derive_handler(well_path)
-        return OmeZarrWell(group_handler)
+        return self._get_well(well_path=well_path)
 
     async def get_wells_async(self) -> dict[str, OmeZarrWell]:
         """Get all wells in the plate asynchronously.
@@ -380,26 +404,17 @@ class OmeZarrPlate:
             dict[str, OmeZarrWell]: A dictionary of wells, where the key is the well
                 path and the value is the well object.
         """
-        wells = self._group_handler.get_from_cache("wells")
-        if wells is not None:
-            assert isinstance(wells, dict)
-            return wells
-
-        def process_well(well_path):
-            group_handler = self._group_handler.derive_handler(well_path)
-            well = OmeZarrWell(group_handler)
-            return well_path, well
-
         wells, tasks = {}, []
         for well_path in self.wells_paths():
-            task = asyncio.to_thread(process_well, well_path)
+            task = asyncio.to_thread(
+                lambda well_path: (well_path, self._get_well(well_path)), well_path
+            )
             tasks.append(task)
 
         results = await asyncio.gather(*tasks)
         for well_path, well in results:
             wells[well_path] = well
 
-        self._group_handler.add_to_cache("wells", wells)
         return wells
 
     def get_wells(self) -> dict[str, OmeZarrWell]:
@@ -409,24 +424,25 @@ class OmeZarrPlate:
             dict[str, OmeZarrWell]: A dictionary of wells, where the key is the well
                 path and the value is the well object.
         """
-        wells = self._group_handler.get_from_cache("wells")
-        if wells is not None:
-            assert isinstance(wells, dict)
-            return wells
-
-        def process_well(well_path):
-            group_handler = self._group_handler.derive_handler(well_path)
-            well = OmeZarrWell(group_handler)
-            return well_path, well
-
         wells = {}
         for well_path in self.wells_paths():
-            _, well = process_well(well_path)
-            wells[well_path] = well
-
-        self._group_handler.add_to_cache("wells", wells)
+            wells[well_path] = self._get_well(well_path)
         return wells
 
+    def _get_image(self, image_path: str) -> OmeZarrContainer:
+        """Get an image from the plate by its path.
+
+        Args:
+            image_path (str): The path of the image.
+        """
+        cached_image = self._images_cache.get(image_path)
+        if cached_image is not None:
+            return cached_image
+        img_group_handler = self._group_handler.derive_handler(image_path)
+        image = OmeZarrContainer(img_group_handler)
+        self._images_cache.set(image_path, image)
+        return image
+
     async def get_images_async(
         self, acquisition: int | None = None
     ) -> dict[str, OmeZarrContainer]:
@@ -442,30 +458,19 @@ class OmeZarrPlate:
             dict[str, OmeZarrContainer]: A dictionary of images, where the key is the
                 image path and the value is the image object.
         """
-        images = self._group_handler.get_from_cache("images")
-        if images is not None:
-            assert isinstance(images, dict)
-            return images
-
         paths = await self.images_paths_async(acquisition=acquisition)
 
-        def process_image(image_path):
-            """Process a single image and return the image path and image object."""
-            img_group_handler = self._group_handler.derive_handler(image_path)
-            image = OmeZarrContainer(img_group_handler)
-            return image_path, image
-
         images, tasks = {}, []
         for image_path in paths:
-            task = asyncio.to_thread(process_image, image_path)
+            task = asyncio.to_thread(
+                lambda image_path: (image_path, self._get_image(image_path)), image_path
+            )
             tasks.append(task)
 
         results = await asyncio.gather(*tasks)
 
         for image_path, image in results:
             images[image_path] = image
-
-        self._group_handler.add_to_cache("images", images)
         return images
 
     def get_images(self, acquisition: int | None = None) -> dict[str, OmeZarrContainer]:
@@ -474,24 +479,11 @@ class OmeZarrPlate:
         Args:
             acquisition: The acquisition id to filter the images.
         """
-        images = self._group_handler.get_from_cache("images")
-        if images is not None:
-            assert isinstance(images, dict)
-            return images
         paths = self.images_paths(acquisition=acquisition)
-
-        def process_image(image_path):
-            """Process a single image and return the image path and image object."""
-            img_group_handler = self._group_handler.derive_handler(image_path)
-            image = OmeZarrContainer(img_group_handler)
-            return image_path, image
-
         images = {}
         for image_path in paths:
-            _, image = process_image(image_path)
-            images[image_path] = image
+            images[image_path] = self._get_image(image_path)
 
-        self._group_handler.add_to_cache("images", images)
         return images
 
     def get_image(
@@ -508,8 +500,7 @@ class OmeZarrPlate:
             OmeZarrContainer: The image.
         """
         image_path = self._image_path(row=row, column=column, path=image_path)
-        group_handler = self._group_handler.derive_handler(image_path)
-        return OmeZarrContainer(group_handler)
+        return self._get_image(image_path)
 
     def get_image_store(
         self, row: str, column: int | str, image_path: str
@@ -785,7 +776,6 @@ class OmeZarrPlate:
         keep_acquisitions: bool = False,
         cache: bool = False,
         overwrite: bool = False,
-        parallel_safe: bool = True,
     ) -> "OmeZarrPlate":
         """Derive a new OME-Zarr plate from an existing one.
 
@@ -796,7 +786,6 @@ class OmeZarrPlate:
             keep_acquisitions (bool): Whether to keep the acquisitions in the new plate.
             cache (bool): Whether to use a cache for the zarr group metadata.
             overwrite (bool): Whether to overwrite the existing plate.
-            parallel_safe (bool): Whether the group handler is parallel safe.
         """
         return derive_ome_zarr_plate(
             ome_zarr_plate=self,
@@ -806,7 +795,6 @@ class OmeZarrPlate:
             keep_acquisitions=keep_acquisitions,
             cache=cache,
             overwrite=overwrite,
-            parallel_safe=parallel_safe,
         )
 
     def _get_tables_container(self) -> TablesContainer | None:
@@ -1143,7 +1131,6 @@ def open_ome_zarr_plate(
     store: StoreOrGroup,
     cache: bool = False,
     mode: AccessModeLiteral = "r+",
-    parallel_safe: bool = True,
 ) -> OmeZarrPlate:
     """Open an OME-Zarr plate.
 
@@ -1152,11 +1139,8 @@ def open_ome_zarr_plate(
         cache (bool): Whether to use a cache for the zarr group metadata.
         mode (AccessModeLiteral): The
             access mode for the image. Defaults to "r+".
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
-    group_handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
-    )
+    group_handler = ZarrGroupHandler(store=store, cache=cache, mode=mode)
     return OmeZarrPlate(group_handler)
 
 
@@ -1168,9 +1152,7 @@ def _create_empty_plate_from_meta(
 ) -> ZarrGroupHandler:
     """Create an empty OME-Zarr plate from metadata."""
     mode = "w" if overwrite else "w-"
-    group_handler = ZarrGroupHandler(
-        store=store, cache=True, mode=mode, parallel_safe=False
-    )
+    group_handler = ZarrGroupHandler(store=store, cache=True, mode=mode)
     meta_handler = get_plate_meta_handler(group_handler, version=version)
     meta_handler.write_meta(meta)
     return group_handler
@@ -1183,9 +1165,18 @@ def create_empty_plate(
     version: NgffVersions = "0.4",
     cache: bool = False,
     overwrite: bool = False,
-    parallel_safe: bool = True,
 ) -> OmeZarrPlate:
-    """Initialize and create an empty OME-Zarr plate."""
+    """Initialize and create an empty OME-Zarr plate.
+
+    Args:
+        store (StoreOrGroup): The Zarr store or group that stores the plate.
+        name (str): The name of the plate.
+        images (list[ImageInWellPath] | None): A list of images to add to the plate.
+            If None, no images are added. Defaults to None.
+        version (NgffVersion): The version of the new plate.
+        cache (bool): Whether to use a cache for the zarr group metadata.
+        overwrite (bool): Whether to overwrite the existing plate.
+    """
     plate_meta = NgioPlateMeta.default_init(
         name=name,
         version=version,
@@ -1211,7 +1202,6 @@ def create_empty_plate(
         store=store,
         cache=cache,
         mode="r+",
-        parallel_safe=parallel_safe,
     )
 
 
@@ -1223,7 +1213,6 @@ def derive_ome_zarr_plate(
     keep_acquisitions: bool = False,
     cache: bool = False,
     overwrite: bool = False,
-    parallel_safe: bool = True,
 ) -> OmeZarrPlate:
     """Derive a new OME-Zarr plate from an existing one.
 
@@ -1235,7 +1224,6 @@ def derive_ome_zarr_plate(
         keep_acquisitions (bool): Whether to keep the acquisitions in the new plate.
         cache (bool): Whether to use a cache for the zarr group metadata.
         overwrite (bool): Whether to overwrite the existing plate.
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
     if plate_name is None:
         plate_name = ome_zarr_plate.meta.plate.name
@@ -1255,7 +1243,6 @@ def derive_ome_zarr_plate(
         store=store,
         cache=cache,
         mode="r+",
-        parallel_safe=parallel_safe,
     )
 
 
@@ -1263,7 +1250,6 @@ def open_ome_zarr_well(
     store: StoreOrGroup,
     cache: bool = False,
     mode: AccessModeLiteral = "r+",
-    parallel_safe: bool = True,
 ) -> OmeZarrWell:
     """Open an OME-Zarr well.
 
@@ -1271,10 +1257,11 @@ def open_ome_zarr_well(
         store (StoreOrGroup): The Zarr store or group that stores the plate.
         cache (bool): Whether to use a cache for the zarr group metadata.
         mode (AccessModeLiteral): The access mode for the image. Defaults to "r+".
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
     group_handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
+        store=store,
+        cache=cache,
+        mode=mode,
     )
     return OmeZarrWell(group_handler)
 
@@ -1284,7 +1271,6 @@ def create_empty_well(
     version: NgffVersions = "0.4",
     cache: bool = False,
     overwrite: bool = False,
-    parallel_safe: bool = True,
 ) -> OmeZarrWell:
     """Create an empty OME-Zarr well.
 
@@ -1293,10 +1279,9 @@ def create_empty_well(
         version (NgffVersion): The version of the new well.
         cache (bool): Whether to use a cache for the zarr group metadata.
         overwrite (bool): Whether to overwrite the existing well.
-        parallel_safe (bool): Whether the group handler is parallel safe.
     """
     group_handler = ZarrGroupHandler(
-        store=store, cache=True, mode="w" if overwrite else "w-", parallel_safe=False
+        store=store, cache=True, mode="w" if overwrite else "w-"
     )
     meta_handler = get_well_meta_handler(group_handler, version=version)
     meta = NgioWellMeta.default_init()
@@ -1306,5 +1291,4 @@ def create_empty_well(
         store=store,
         cache=cache,
         mode="r+",
-        parallel_safe=parallel_safe,
     )

ngio/images/_create.py

@@ -40,7 +40,7 @@ def _init_generic_meta(
     space_unit: SpaceUnits | str | None = DefaultSpaceUnit,
     time_unit: TimeUnits | str | None = DefaultTimeUnit,
     name: str | None = None,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> tuple[_image_or_label_meta, list[float]]:
     """Initialize the metadata for an image or label."""
     scaling_factors = []
@@ -75,7 +75,7 @@ def _init_generic_meta(
         axes_names=axes_names,
         pixel_size=pixel_sizes,
         scaling_factors=scaling_factors,
-        version=version,
+        version=ngff_version,
     )
     return meta, scaling_factors
 
@@ -98,7 +98,7 @@ def create_empty_label_container(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
     """Create an empty label with the given shape and metadata.
 
@@ -130,7 +130,7 @@ def create_empty_label_container(
         dtype (str, optional): The data type of the image. Defaults to "uint16".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
+        ngff_version (str, optional): The version of the OME-Zarr specification.
             Defaults to DefaultVersion.
 
     """
@@ -155,14 +155,16 @@ def create_empty_label_container(
         time_unit=time_unit,
         axes_names=axes_names,
         name=name,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     mode = "w" if overwrite else "w-"
     group_handler = ZarrGroupHandler(
         store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
     )
-    image_handler = get_label_meta_handler(version=version, group_handler=group_handler)
+    image_handler = get_label_meta_handler(
+        version=ngff_version, group_handler=group_handler
+    )
     image_handler.write_meta(meta)
 
     init_empty_pyramid(
@@ -199,7 +201,7 @@ def create_empty_image_container(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> ZarrGroupHandler:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -231,7 +233,7 @@ def create_empty_image_container(
         compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
+        ngff_version (str, optional): The version of the OME-Zarr specification.
             Defaults to DefaultVersion.
 
     """
@@ -256,13 +258,15 @@ def create_empty_image_container(
         time_unit=time_unit,
         axes_names=axes_names,
         name=name,
-        version=version,
+        ngff_version=ngff_version,
     )
     mode = "w" if overwrite else "w-"
     group_handler = ZarrGroupHandler(
         store=store, mode=mode, cache=False, zarr_format=meta.zarr_format
     )
-    image_handler = get_image_meta_handler(version=version, group_handler=group_handler)
+    image_handler = get_image_meta_handler(
+        version=ngff_version, group_handler=group_handler
+    )
     image_handler.write_meta(meta)
 
     init_empty_pyramid(

ngio/images/_create_synt_container.py

@@ -40,7 +40,7 @@ def create_synthetic_ome_zarr(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -72,7 +72,7 @@ def create_synthetic_ome_zarr(
         compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (NgffVersion, optional): The version of the OME-Zarr specification.
+        ngff_version (NgffVersion, optional): The version of the OME-Zarr specification.
             Defaults to DefaultNgffVersion.
     """
     if isinstance(reference_sample, str):
@@ -105,7 +105,7 @@ def create_synthetic_ome_zarr(
         overwrite=overwrite,
         dimension_separator=dimension_separator,
         compressors=compressors,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     image = ome_zarr.get_image()

ngio/images/_image.py

@@ -823,7 +823,7 @@ def derive_image_container(
         dimension_separator=dimension_separator,
         compressors=compressors,
         overwrite=overwrite,
-        version=ngff_version,
+        ngff_version=ngff_version,
     )
     image_container = ImagesContainer(handler)
 
@@ -885,7 +885,7 @@ def _parse_str_or_model(
             )
         elif channel_selection.mode == "wavelength_id":
             return image.get_channel_idx(
-                channel_label=str(channel_selection.identifier)
+                wavelength_id=str(channel_selection.identifier)
             )
         elif channel_selection.mode == "index":
             return int(channel_selection.identifier)

ngio/images/_label.py

@@ -329,7 +329,7 @@ def derive_label(
         dimension_separator=dimension_separator,
         compressors=compressors,
         overwrite=overwrite,
-        version=ref_meta.version,
+        ngff_version=ref_meta.version,
         name=name,
     )
     return None

ngio/images/_ome_zarr_container.py

@@ -845,7 +845,7 @@ def create_empty_ome_zarr(
     channel_colors: Sequence[str] | None = None,
     channel_active: Sequence[bool] | None = None,
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
     """Create an empty OME-Zarr image with the given shape and metadata.
 
@@ -885,7 +885,7 @@ def create_empty_ome_zarr(
             active. Defaults to None.
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (NgffVersion, optional): The version of the OME-Zarr specification.
+        ngff_version (NgffVersion, optional): The version of the OME-Zarr specification.
             Defaults to DefaultNgffVersion.
     """
     handler = create_empty_image_container(
@@ -906,7 +906,7 @@ def create_empty_ome_zarr(
         dimension_separator=dimension_separator,
         compressors=compressors,
         overwrite=overwrite,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     ome_zarr = OmeZarrContainer(group_handler=handler)
@@ -942,7 +942,7 @@ def create_ome_zarr_from_array(
     dimension_separator: Literal[".", "/"] = "/",
     compressors: CompressorLike = "auto",
     overwrite: bool = False,
-    version: NgffVersions = DefaultNgffVersion,
+    ngff_version: NgffVersions = DefaultNgffVersion,
 ) -> OmeZarrContainer:
     """Create an OME-Zarr image from a numpy array.
 
@@ -983,7 +983,7 @@ def create_ome_zarr_from_array(
         compressors (CompressorLike): The compressors to use. Defaults to "auto".
         overwrite (bool, optional): Whether to overwrite an existing image.
             Defaults to True.
-        version (str, optional): The version of the OME-Zarr specification.
+        ngff_version (str, optional): The version of the OME-Zarr specification.
             Defaults to DefaultNgffVersion.
     """
     handler = create_empty_image_container(
@@ -1004,7 +1004,7 @@ def create_ome_zarr_from_array(
         overwrite=overwrite,
         dimension_separator=dimension_separator,
         compressors=compressors,
-        version=version,
+        ngff_version=ngff_version,
     )
 
     ome_zarr = OmeZarrContainer(group_handler=handler)

ngio/tables/_tables_container.py

@@ -359,13 +359,10 @@ ImplementedTables().add_implementation(ConditionTableV1)
 def open_tables_container(
     store: StoreOrGroup,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
-    parallel_safe: bool = False,
+    mode: AccessModeLiteral = "r+",
 ) -> TablesContainer:
     """Open a table handler from a Zarr store."""
-    handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
-    )
+    handler = ZarrGroupHandler(store=store, cache=cache, mode=mode)
     return TablesContainer(handler)
 
 
@@ -373,12 +370,13 @@ def open_table(
     store: StoreOrGroup,
     backend: TableBackend | None = None,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
-    parallel_safe: bool = False,
+    mode: AccessModeLiteral = "r+",
 ) -> Table:
     """Open a table from a Zarr store."""
     handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
+        store=store,
+        cache=cache,
+        mode=mode,
     )
     meta = _get_meta(handler)
     return ImplementedTables().get_table(
@@ -391,12 +389,13 @@ def open_table_as(
     table_cls: type[TableType],
     backend: TableBackend | None = None,
     cache: bool = False,
-    mode: AccessModeLiteral = "a",
-    parallel_safe: bool = False,
+    mode: AccessModeLiteral = "r+",
 ) -> TableType:
     """Open a table from a Zarr store as a specific type."""
     handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
+        store=store,
+        cache=cache,
+        mode=mode,
     )
     return table_cls.from_handler(
         handler=handler,
@@ -410,12 +409,20 @@ def write_table(
     backend: TableBackend = DefaultTableBackend,
     cache: bool = False,
     mode: AccessModeLiteral = "a",
-    parallel_safe: bool = False,
 ) -> None:
-    """Write a table to a Zarr store."""
-    handler = ZarrGroupHandler(
-        store=store, cache=cache, mode=mode, parallel_safe=parallel_safe
-    )
+    """Write a table to a Zarr store.
+
+    A table will be created at the given store location.
+
+    Args:
+        store (StoreOrGroup): The Zarr store or group to write the table to.
+        table (Table): The table to write.
+        backend (TableBackend): The backend to use for writing the table.
+        cache (bool): Whether to use caching for the Zarr group handler.
+        mode (AccessModeLiteral): The access mode to use for the Zarr group handler.
+
+    """
+    handler = ZarrGroupHandler(store=store, cache=cache, mode=mode)
     table.set_backend(
         handler=handler,
         backend=backend,

ngio/tables/v1/_roi_table.py

@@ -86,10 +86,10 @@ def _dataframe_to_rois(
 ) -> dict[str, Roi]:
     """Convert a DataFrame to a WorldCooROI object."""
     # Validate the columns of the DataFrame
-    _required_columns = set(dataframe.columns).intersection(set(required_columns))
-    if len(_required_columns) != len(required_columns):
+    _missing_columns = set(required_columns).difference(set(dataframe.columns))
+    if len(_missing_columns) != 0:
         raise NgioTableValidationError(
-            f"Could not find required columns: {_required_columns} in the table."
+            f"Could not find required columns: {_missing_columns} in the table."
         )
 
     extra_columns = set(dataframe.columns).difference(

ngio/utils/__init__.py

@@ -18,6 +18,7 @@ from ngio.utils._fractal_fsspec_store import fractal_fsspec_store
 from ngio.utils._logger import ngio_logger, ngio_warn, set_logger_level
 from ngio.utils._zarr_utils import (
     AccessModeLiteral,
+    NgioCache,
     StoreOrGroup,
     ZarrGroupHandler,
     open_group_wrapper,
@@ -28,6 +29,7 @@ set_logger_level(os.getenv("NGIO_LOGGER_LEVEL", "WARNING"))
 __all__ = [
     # Zarr
     "AccessModeLiteral",
+    "NgioCache",
     # Errors
     "NgioFileExistsError",
     "NgioFileNotFoundError",

ngio/utils/_cache.py

@@ -0,0 +1,48 @@
+from typing import Generic, TypeVar
+
+T = TypeVar("T")
+
+
+class NgioCache(Generic[T]):
+    """A simple cache for NGIO objects."""
+
+    def __init__(self, use_cache: bool = True):
+        self._cache: dict[str, T] = {}
+        self._use_cache = use_cache
+
+    def _cache_sanity_check(self) -> None:
+        if len(self._cache) > 0:
+            raise RuntimeError(
+                "Cache is disabled, but cache contains items. "
+                "This indicates a logic error."
+            )
+
+    @property
+    def use_cache(self) -> bool:
+        return self._use_cache
+
+    @property
+    def cache(self) -> dict[str, T]:
+        return self._cache
+
+    @property
+    def is_empty(self) -> bool:
+        return len(self._cache) == 0
+
+    def get(self, key: str, default: T | None = None) -> T | None:
+        if not self._use_cache:
+            self._cache_sanity_check()
+            return default
+        return self._cache.get(key, default)
+
+    def set(self, key: str, value: T, overwrite: bool = True) -> None:
+        if not self._use_cache:
+            self._cache_sanity_check()
+            return
+        self._cache[key] = value
+
+    def clear(self) -> None:
+        if not self._use_cache:
+            self._cache_sanity_check()
+            return
+        self._cache.clear()

ngio/utils/_zarr_utils.py

@@ -1,5 +1,6 @@
 """Common utilities for working with Zarr groups in consistent ways."""
 
+import warnings
 from pathlib import Path
 from typing import Literal
 
@@ -7,12 +8,16 @@ import fsspec
 import zarr
 from filelock import BaseFileLock, FileLock
 from zarr.abc.store import Store
-from zarr.core.array import CompressorLike
 from zarr.errors import ContainsGroupError
 from zarr.storage import FsspecStore, LocalStore, MemoryStore
 
-from ngio.utils import NgioFileExistsError, NgioFileNotFoundError, NgioValueError
-from ngio.utils._errors import NgioError
+from ngio.utils._cache import NgioCache
+from ngio.utils._errors import (
+    NgioError,
+    NgioFileExistsError,
+    NgioFileNotFoundError,
+    NgioValueError,
+)
 
 AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
 # StoreLike is more restrictive than it could be
@@ -27,32 +32,33 @@ StoreOrGroup = GenericStore | zarr.Group
 
 def _check_store(store) -> NgioSupportedStore:
     """Check the store and return a valid store."""
-    if isinstance(store, NgioSupportedStore):
-        return store
-
-    raise NotImplementedError(
-        f"Store type {type(store)} is not supported. "
-        f"Supported types are: {NgioSupportedStore}"
-    )
+    if not isinstance(store, NgioSupportedStore):
+        warnings.warn(
+            f"Store type {type(store)} is not explicitly supported. "
+            f"Supported types are: {NgioSupportedStore}. "
+            "Proceeding, but this may lead to unexpected behavior.",
+            UserWarning,
+            stacklevel=2,
+        )
+    return store
 
 
-def _check_group(group: zarr.Group, mode: AccessModeLiteral) -> zarr.Group:
+def _check_group(
+    group: zarr.Group, mode: AccessModeLiteral | None = None
+) -> zarr.Group:
     """Check the group and return a valid group."""
-    if group.read_only and mode in ["w", "w-"]:
-        raise NgioValueError(
-            "The group is read only. Cannot open in write mode ['w', 'w-']"
-        )
+    if group.read_only and mode not in [None, "r"]:
+        raise NgioValueError(f"The group is read only. Cannot open in mode {mode}.")
 
     if mode == "r" and not group.read_only:
         # let's make sure we don't accidentally write to the group
         group = zarr.open_group(store=group.store, path=group.path, mode="r")
-
     return group
 
 
 def open_group_wrapper(
     store: StoreOrGroup,
-    mode: AccessModeLiteral,
+    mode: AccessModeLiteral | None = None,
     zarr_format: Literal[2, 3] | None = None,
 ) -> zarr.Group:
     """Wrapper around zarr.open_group with some additional checks.
@@ -72,6 +78,7 @@ def open_group_wrapper(
 
     try:
         _check_store(store)
+        mode = mode if mode is not None else "a"
         group = zarr.open_group(store=store, mode=mode, zarr_format=zarr_format)
 
     except FileExistsError as e:
@@ -98,68 +105,32 @@ class ZarrGroupHandler:
         store: StoreOrGroup,
         zarr_format: Literal[2, 3] | None = None,
         cache: bool = False,
-        mode: AccessModeLiteral = "a",
-        parallel_safe: bool = False,
-        parent: "ZarrGroupHandler | None" = None,
+        mode: AccessModeLiteral | None = None,
     ):
         """Initialize the handler.
 
         Args:
             store (StoreOrGroup): The Zarr store or group containing the image data.
             meta_mode (str): The mode of the metadata handler.
-            zarr_format (int): The Zarr format version to use.
+            zarr_format (int | None): The Zarr format version to use.
             cache (bool): Whether to cache the metadata.
-            mode (str): The mode of the store.
-            parallel_safe (bool): If True, the handler will create a lock file to make
-                that can be used to make the handler parallel safe.
-                Be aware that the lock needs to be used manually.
-            parent (ZarrGroupHandler | None): The parent handler.
+            mode (str | None): The mode of the store.
         """
-        if mode not in ["r", "r+", "w", "w-", "a"]:
+        if mode not in ["r", "r+", "w", "w-", "a", None]:
             raise NgioValueError(f"Mode {mode} is not supported.")
 
-        if parallel_safe and cache:
-            raise NgioValueError(
-                "The cache and parallel_safe options are mutually exclusive."
-                "If you want to use the lock mechanism, you should not use the cache."
-            )
-
         group = open_group_wrapper(store=store, mode=mode, zarr_format=zarr_format)
-        _store = group.store
-
-        # Make sure the cache is set in the attrs
-        # in the same way as the cache in the handler
-
-        ## TODO
-        # Figure out how to handle the cache in the new zarr version
-        # group.attrs.cache = cache
-
-        if parallel_safe:
-            if not isinstance(_store, LocalStore):
-                raise NgioValueError(
-                    "The store needs to be a LocalStore to use the lock mechanism. "
-                    f"Instead, got {_store.__class__.__name__}."
-                )
-
-            store_path = _store.root / group.path
-            self._lock_path = store_path.with_suffix(".lock")
-            self._lock = FileLock(self._lock_path, timeout=10)
-
-        else:
-            self._lock_path = None
-            self._lock = None
-
         self._group = group
-        self._mode = mode
         self.use_cache = cache
-        self._parallel_safe = parallel_safe
-        self._cache = {}
-        self._parent = parent
+
+        self._group_cache: NgioCache[zarr.Group] = NgioCache(use_cache=cache)
+        self._array_cache: NgioCache[zarr.Array] = NgioCache(use_cache=cache)
+        self._lock: tuple[Path, BaseFileLock] | None = None
 
     def __repr__(self) -> str:
         """Return a string representation of the handler."""
         return (
-            f"ZarrGroupHandler(full_url={self.full_url}, mode={self.mode}, "
+            f"ZarrGroupHandler(full_url={self.full_url}, read_only={self.read_only}, "
             f"cache={self.use_cache}"
         )
 
@@ -183,35 +154,55 @@ class ZarrGroupHandler:
         return self._group.metadata.zarr_format
 
     @property
-    def mode(self) -> AccessModeLiteral:
-        """Return the mode of the group."""
-        return self._mode  # type: ignore
+    def read_only(self) -> bool:
+        """Return whether the group is read only."""
+        return self._group.read_only
+
+    def _create_lock(self) -> tuple[Path, BaseFileLock]:
+        """Create the lock."""
+        if self._lock is not None:
+            return self._lock
+
+        if self.use_cache is True:
+            raise NgioValueError(
+                "Lock mechanism is not compatible with caching. "
+                "Please set cache=False to use the lock mechanism."
+            )
+
+        if not isinstance(self.store, LocalStore):
+            raise NgioValueError(
+                "The store needs to be a LocalStore to use the lock mechanism. "
+                f"Instead, got {self.store.__class__.__name__}."
+            )
+
+        store_path = Path(self.store.root) / self.group.path
+        _lock_path = store_path.with_suffix(".lock")
+        _lock = FileLock(_lock_path, timeout=10)
+        return _lock_path, _lock
 
     @property
     def lock(self) -> BaseFileLock:
         """Return the lock."""
         if self._lock is None:
-            raise NgioValueError(
-                "The handler is not parallel safe. "
-                "Reopen the handler with parallel_safe=True."
-            )
-        return self._lock
+            self._lock = self._create_lock()
+        return self._lock[1]
 
     @property
-    def parent(self) -> "ZarrGroupHandler | None":
-        """Return the parent handler."""
-        return self._parent
+    def lock_path(self) -> Path:
+        """Return the lock path."""
+        if self._lock is None:
+            self._lock = self._create_lock()
+        return self._lock[0]
 
     def remove_lock(self) -> None:
         """Return the lock."""
-        if self._lock is None or self._lock_path is None:
+        if self._lock is None:
             return None
 
-        lock_path = Path(self._lock_path)
-        if lock_path.exists() and self._lock.lock_counter == 0:
+        lock_path, lock = self._lock
+        if lock_path.exists() and lock.lock_counter == 0:
             lock_path.unlink()
             self._lock = None
-            self._lock_path = None
             return None
 
         raise NgioValueError("The lock is still in use. Cannot remove it.")
@@ -222,10 +213,7 @@ class ZarrGroupHandler:
         This is useful when the group has been modified
         outside of the handler.
         """
-        if self.mode == "r":
-            mode = "r"
-        else:
-            mode = "r+"
+        mode = "r" if self.read_only else "r+"
         return zarr.open_group(
             store=self._group.store,
             path=self._group.path,
@@ -233,72 +221,57 @@ class ZarrGroupHandler:
             zarr_format=self._group.metadata.zarr_format,
         )
 
+    def reopen_handler(self) -> "ZarrGroupHandler":
+        """Reopen the handler.
+
+        This is useful when the group has been modified
+        outside of the handler.
+        """
+        mode = "r" if self.read_only else "r+"
+        group = self.reopen_group()
+        return ZarrGroupHandler(
+            store=group,
+            zarr_format=group.metadata.zarr_format,
+            cache=self.use_cache,
+            mode=mode,
+        )
+
+    def clean_cache(self) -> None:
+        """Clear the cached metadata."""
+        group = self.reopen_group()
+        self.__init__(
+            store=group,
+            zarr_format=group.metadata.zarr_format,
+            cache=self.use_cache,
+            mode="r" if self.read_only else "r+",
+        )
+
     @property
     def group(self) -> zarr.Group:
         """Return the group."""
-        if self._parallel_safe:
-            # If we are parallel safe, we need to reopen the group
+        if self.use_cache is False:
+            # If we are not using cache, we need to reopen the group
             # to make sure that the attributes are up to date
             return self.reopen_group()
         return self._group
 
-    def add_to_cache(self, key: str, value: object) -> None:
-        """Add an object to the cache."""
-        if not self.use_cache:
-            return None
-        self._cache[key] = value
-
-    def get_from_cache(self, key: str) -> object | None:
-        """Get an object from the cache."""
-        if not self.use_cache:
-            return None
-        return self._cache.get(key, None)
-
-    def clean_cache(self) -> None:
-        """Clear the cached metadata."""
-        self._cache = {}
-
     def load_attrs(self) -> dict:
         """Load the attributes of the group."""
-        attrs = self.get_from_cache("attrs")
-        if attrs is not None and isinstance(attrs, dict):
-            return attrs
-
-        attrs = dict(self.group.attrs)
-
-        self.add_to_cache("attrs", attrs)
-        return attrs
-
-    def _write_attrs(self, attrs: dict, overwrite: bool = False) -> None:
-        """Write the metadata to the store."""
-        if self.group.read_only:
-            raise NgioValueError("The group is read only. Cannot write metadata.")
-
-        # we need to invalidate the current attrs cache
-        self.add_to_cache("attrs", None)
-        if overwrite:
-            self.group.attrs.clear()
-
-        self.group.attrs.update(attrs)
+        return self.reopen_group().attrs.asdict()
 
     def write_attrs(self, attrs: dict, overwrite: bool = False) -> None:
         """Write the metadata to the store."""
         # Maybe we should use the lock here
-        self._write_attrs(attrs, overwrite)
-
-    def _obj_get(self, path: str):
-        """Get a group from the group."""
-        group_or_array = self.get_from_cache(path)
-        if group_or_array is not None:
-            return group_or_array
-
-        group_or_array = self.group.get(path, None)
-        self.add_to_cache(path, group_or_array)
-        return group_or_array
+        if self.read_only:
+            raise NgioValueError("The group is read only. Cannot write metadata.")
+        group = self.reopen_group()
+        if overwrite:
+            group.attrs.clear()
+        group.attrs.update(attrs)
 
     def create_group(self, path: str, overwrite: bool = False) -> zarr.Group:
         """Create a group in the group."""
-        if self.mode == "r":
+        if self.group.read_only:
             raise NgioValueError("Cannot create a group in read only mode.")
 
         try:
@@ -308,7 +281,7 @@ class ZarrGroupHandler:
                 f"A Zarr group already exists at {path}, "
                 "consider setting overwrite=True."
             ) from e
-        self.add_to_cache(path, group)
+        self._group_cache.set(path, group, overwrite=overwrite)
         return group
 
     def get_group(
@@ -334,18 +307,22 @@ class ZarrGroupHandler:
         if overwrite:
             return self.create_group(path, overwrite=overwrite)
 
-        group = self._obj_get(path)
+        group = self._group_cache.get(path)
         if isinstance(group, zarr.Group):
             return group
 
-        if group is not None:
-            raise NgioValueError(
-                f"The object at {path} is not a group, but a {type(group)}"
-            )
+        group = self.group.get(path, default=None)
+        if isinstance(group, zarr.Group):
+            self._group_cache.set(path, group, overwrite=overwrite)
+            return group
+
+        if isinstance(group, zarr.Array):
+            raise NgioValueError(f"The object at {path} is not a group, but an array.")
 
         if not create_mode:
             raise NgioFileNotFoundError(f"No group found at {path}")
         group = self.create_group(path)
+        self._group_cache.set(path, group, overwrite=overwrite)
         return group
 
     def safe_get_group(
@@ -369,56 +346,17 @@ class ZarrGroupHandler:
 
     def get_array(self, path: str) -> zarr.Array:
         """Get an array from the group."""
-        array = self._obj_get(path)
-        if array is None:
-            raise NgioFileNotFoundError(f"No array found at {path}")
-        if not isinstance(array, zarr.Array):
-            raise NgioValueError(
-                f"The object at {path} is not an array, but a {type(array)}"
-            )
-        return array
-
-    def create_array(
-        self,
-        path: str,
-        shape: tuple[int, ...],
-        dtype: str,
-        chunks: tuple[int, ...] | Literal["auto"] = "auto",
-        compressors: CompressorLike = "auto",
-        separator: Literal[".", "/"] = "/",
-        overwrite: bool = False,
-    ) -> zarr.Array:
-        if self.mode == "r":
-            raise NgioValueError("Cannot create an array in read only mode.")
-
-        if self.zarr_format == 2:
-            chunks_encoding = {
-                "name": "v2",
-                "separator": separator,
-            }
-        else:
-            chunks_encoding = {
-                "name": "default",
-                "separator": separator,
-            }
-
-        try:
-            return self.group.create_array(
-                name=path,
-                shape=shape,
-                dtype=dtype,
-                chunks=chunks,
-                chunk_key_encoding=chunks_encoding,
-                overwrite=overwrite,
-                compressors=compressors,
-            )
-        except ContainsGroupError as e:
-            raise NgioFileExistsError(
-                f"A Zarr array already exists at {path}, "
-                "consider setting overwrite=True."
-            ) from e
-        except Exception as e:
-            raise NgioValueError(f"Error creating array at {path}") from e
+        array = self._array_cache.get(path)
+        if isinstance(array, zarr.Array):
+            return array
+        array = self.group.get(path, default=None)
+        if isinstance(array, zarr.Array):
+            self._array_cache.set(path, array)
+            return array
+
+        if isinstance(array, zarr.Group):
+            raise NgioValueError(f"The object at {path} is not an array, but a group.")
+        raise NgioFileNotFoundError(f"No array found at {path}")
 
     def derive_handler(
         self,
@@ -433,12 +371,7 @@ class ZarrGroupHandler:
         """
         group = self.get_group(path, create_mode=True, overwrite=overwrite)
         return ZarrGroupHandler(
-            store=group,
-            zarr_format=self.zarr_format,
-            cache=self.use_cache,
-            mode=self.mode,
-            parallel_safe=self._parallel_safe,
-            parent=self,
+            store=group, zarr_format=self.zarr_format, cache=self.use_cache, mode="r+"
         )
 
     def safe_derive_handler(

{ngio-0.5.0a1.dist-info → ngio-0.5.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0a1
+Version: 0.5.0a2
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -17,8 +17,8 @@ Classifier: Typing :: Typed
 Requires-Python: <3.14,>=3.11
 Requires-Dist: aiohttp
 Requires-Dist: anndata
-Requires-Dist: dask[array]
-Requires-Dist: dask[distributed]
+Requires-Dist: dask[array]<2025.11.0
+Requires-Dist: dask[distributed]<2025.11.0
 Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models

{ngio-0.5.0a1.dist-info → ngio-0.5.0a2.dist-info}/RECORD

@@ -2,7 +2,7 @@ ngio/__init__.py,sha256=rEgnXuU6TCejUUGsxt4eKmjMhxjYh0fYBxWF4o5YjbE,1435
 ngio/common/__init__.py,sha256=aPSuUbdGryrxbnlWrsVNe3LZoBAWC4GijR1BNH1UwuU,612
 ngio/common/_dimensions.py,sha256=w8PYgyWxA8hgJETjFbw5CXf7WrasCL5FbzgfL1in86M,11361
 ngio/common/_masking_roi.py,sha256=ZZTXordEZoq_ADk0OzADvq-5dPOwUBSuNobzFR8fpTw,5697
-ngio/common/_pyramid.py,sha256=186eQSCxP_x2heYKmMP_Edl4Aml9Eo1bBmIHlwslqy8,8699
+ngio/common/_pyramid.py,sha256=loQbtoGWs0g5Ke2s1tSBDsvos0235F-ElhFspsMsIr0,9238
 ngio/common/_roi.py,sha256=9fKFTHoUiP0xmxvQiFkNmIuwWg3bFuRaAx-froCSqvA,11487
 ngio/common/_synt_images_utils.py,sha256=B6uYOW1NyrM06YMR-csca3_YnAAkPRTbvnbLdy9tk9E,3188
 ngio/common/_zoom.py,sha256=U01c-vqXjzZkrpd9Yvs24frVfTls_xPJeeaFCGmUwYI,6727
@@ -15,15 +15,15 @@ ngio/experimental/iterators/_mappers.py,sha256=VVVsjems57wJUnWeufUFcgqa23k7VPeFL
 ngio/experimental/iterators/_rois_utils.py,sha256=Q-8lQ26neYn63h_RvfypYqvrq2UUN2O3xqVe57k_ufU,4363
 ngio/experimental/iterators/_segmentation.py,sha256=xzotGvTn04HPeMeXZ_URnQqWco6d2lH6Ng6vkCUh9NM,9153
 ngio/hcs/__init__.py,sha256=G8j9vD-liLeB_UeGtKYIgshWvJnUA6ks9GwjvWBLdHs,357
-ngio/hcs/_plate.py,sha256=qfRwbCKaoz_AWTi8RDFFwOxy5geSknfJrPcqFVno9zI,44288
+ngio/hcs/_plate.py,sha256=9kvvI_qu946xbRqWeY9q1bp45duREyOx-3a-QeKkrGU,43376
 ngio/images/__init__.py,sha256=9Whvt7GTiCgT_vXaEEqGnDaY1-UsRk3dhLTv091F_g4,1211
 ngio/images/_abstract_image.py,sha256=hrB9xn4MFRxnxE1d7HKnM8SXVPUGhMD9u32yBHTsFiU,18517
-ngio/images/_create.py,sha256=OirIKg843CCSiwy_oUolX2UHlROR_iO4rN_IK47jDWc,10448
-ngio/images/_create_synt_container.py,sha256=D3SkjYN_AZ5fSefjEX0iQ3ZGEuBTWZvuPQIwHc6l-CU,5519
-ngio/images/_image.py,sha256=JWN7qmNVZxAzm9zmaImYseDt8xzYtOw-N0olR6VQo_8,33483
-ngio/images/_label.py,sha256=sJUB8of7t1YErZRu3t7jzGjlRn3KAAs0EL5nFrbvvlc,11921
+ngio/images/_create.py,sha256=IIdX0vER9J3c3aJYZRB7bDGMGv_kv0CbaJjGJM7yjyY,10536
+ngio/images/_create_synt_container.py,sha256=HeRscNNWYHY3rJTO-oKDr5mMuQD6RHWThrv9Rc9yZdg,5539
+ngio/images/_image.py,sha256=LP_XZrL0OLSasPTxaySldKSysyMZvznhFm-E3YLN5Tg,33488
+ngio/images/_label.py,sha256=o7dFDfn-vAgBA80g-vR54M64av_tNebduQqtnG0AkIw,11926
 ngio/images/_masked_image.py,sha256=YhbBzgPZMav6rX0WYue1BaxAzEIsfaQrxUIOK6ZWZcw,18848
-ngio/images/_ome_zarr_container.py,sha256=tfG40PLNfyfaR2pVAmGINlkKJRoQ4W0L0melFotMcP8,38737
+ngio/images/_ome_zarr_container.py,sha256=IlXZojr9HDnfGboLAWD0TlV5Bv7J5fvzKqYc8U43WdU,38777
 ngio/images/_table_ops.py,sha256=jFv_AMqoB4JBpoWsMtZppZVW7dAOC_u-JpfNm8b33kY,15292
 ngio/io_pipes/__init__.py,sha256=arW_7GWzZs82kPNKdm_6B1sIDFV0lWwp-ZaORr9Q1FQ,2412
 ngio/io_pipes/_io_pipes.py,sha256=KuwMYofE11EKx0iplWXBQZ-eE1A9YpGDprWh98cUlAI,10710
@@ -58,7 +58,7 @@ ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/nuclei.png,sha
 ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/raw.jpg,sha256=82lejQAIokj5w9g-qqhysDTWpHtNvJTkdURG_BjqIxQ,37743
 ngio/tables/__init__.py,sha256=_BV3sclNMLITu_J8_3DkkUrCB6Kro0HzeWLDCD1ivKM,877
 ngio/tables/_abstract_table.py,sha256=rwGa47TzbFmosucBWVfFq6JEXtgGvOdUVtU9DIelV88,8204
-ngio/tables/_tables_container.py,sha256=3xmpREaN671l40MPprnl1BD-VoOb6xfjECb5mNoMW0w,12173
+ngio/tables/_tables_container.py,sha256=BfwnCsJ3RGnQGRnRXO2XjdaYniL9sxO4HLiJYVgHkOs,12361
 ngio/tables/backends/__init__.py,sha256=MwSRXNF1rWQBFOTDA_vT3oGoNZpviVgytsL5Txnu08I,1619
 ngio/tables/backends/_abstract_backend.py,sha256=M1ogsBpWBiQMV65YweZhA845PAtkzG2BsZCPN_7Xp8U,7613
 ngio/tables/backends/_anndata.py,sha256=KBzXVxaXstVx3ofcLYYFm8ECVFDaHxfUWcKdg5vQPqY,2992
@@ -73,16 +73,17 @@ ngio/tables/v1/__init__.py,sha256=Wr1_9RZFpaN8FYMTnxT9Yjkw4AS7y9FMWailmB_uj5g,61
 ngio/tables/v1/_condition_table.py,sha256=T0Uq5BKkmMoEspt_Rx0U99Ow6S9GAMZDHqvUO5obCAM,1780
 ngio/tables/v1/_feature_table.py,sha256=n9uMHwoBh-_dlOhUXCFbmAjXFVXncNCR3SjE2qzXI68,3821
 ngio/tables/v1/_generic_table.py,sha256=1ktJHeuv7U1g5Z8PFUuTkCjOzcYMQd8xegKHKUedJB8,1240
-ngio/tables/v1/_roi_table.py,sha256=g7UpMmpf3uAfaG59WYRnimUBgiB_T1qUJRwMZpMt9cI,17099
+ngio/tables/v1/_roi_table.py,sha256=b7lwjsdCSUOCMT6Lx4hwAqGBKC25Q5bdzoK3DQWnAQM,17074
 ngio/transforms/__init__.py,sha256=JA0-Ui7skbXkm9ofN-AEhU1FTLutkMkwTdVD-310frQ,113
 ngio/transforms/_zoom.py,sha256=otyE-vxFnywUJ8U4mHjat-bNG_7_jv62ckTpqDMxyVQ,550
-ngio/utils/__init__.py,sha256=XPYh8ehC7uXNU2cFFXZAw-S3DpWpX1Yq2xGkffZv5vI,1142
+ngio/utils/__init__.py,sha256=w_v3BaphrlsVlZF3tZHlyp6dOfRdRHaauBmdwGsjaCE,1174
+ngio/utils/_cache.py,sha256=Ey9fgc_BTdMyqg6c80C0CuGDhOafln8-3e_1MQ0MFzw,1283
 ngio/utils/_datasets.py,sha256=6GtxfPkjutNaeg5BHuJDBP0GudvQXHLU6mmHp_o0bGA,5650
 ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
 ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
 ngio/utils/_logger.py,sha256=N5W0a_xwze4blS1MolidBkTMbjTbg8GPguJZNun3mAE,1392
-ngio/utils/_zarr_utils.py,sha256=ATehiEALPI__eNQSWdSW5PpJLmI2FECrexA9jTZAI2s,16103
-ngio-0.5.0a1.dist-info/METADATA,sha256=AT0kbnHlYkhiL0_AmZpOm8DagaEPGCkI1xze_cJy3w8,6104
-ngio-0.5.0a1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ngio-0.5.0a1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
-ngio-0.5.0a1.dist-info/RECORD,,
+ngio/utils/_zarr_utils.py,sha256=Ak3M07hxI9-5W1mG2jxZE8rUrSZnidJ-nEQenKuCqls,14114
+ngio-0.5.0a2.dist-info/METADATA,sha256=Skm_1lG1u3unJ7Ij9mnIYm8RVyU0P-AFISHvl-HEz2M,6124
+ngio-0.5.0a2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ngio-0.5.0a2.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.5.0a2.dist-info/RECORD,,