add dimensio separator and derive to new version of ngff

Author: lorenzocerrone

src/ngio/common/_pyramid.py

@@ -203,6 +203,7 @@ def init_empty_pyramid(
     paths: list[str],
     ref_shape: Sequence[int],
     scaling_factors: Sequence[float],
+    axes: Sequence[str],
     chunks: Sequence[int] | Literal["auto"] = "auto",
     dtype: str = "uint16",
     mode: AccessModeLiteral = "a",
@@ -248,6 +249,7 @@ def init_empty_pyramid(
             "name": "default",
             "separator": dimension_separator,
         }
+        array_static_kwargs["dimension_names"] = axes
 
     for path in paths:
         if any(s < 1 for s in ref_shape):

src/ngio/images/_create.py

@@ -171,6 +171,7 @@ def create_empty_label_container(
         scaling_factors=scaling_factors,
         ref_shape=shape,
         chunks=chunks,
+        axes=axes_names,
         dtype=dtype,
         mode="a",
         dimension_separator=dimension_separator,
@@ -270,6 +271,7 @@ def create_empty_image_container(
         scaling_factors=scaling_factors,
         ref_shape=shape,
         chunks=chunks,
+        axes=axes_names,
         dtype=dtype,
         mode="a",
         dimension_separator=dimension_separator,

src/ngio/images/_image.py

@@ -32,6 +32,7 @@
     ChannelVisualisation,
     DefaultSpaceUnit,
     DefaultTimeUnit,
+    NgffVersions,
     SpaceUnits,
     TimeUnits,
 )
@@ -607,6 +608,7 @@ def derive(
         dtype: str | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
         compressors: CompressorLike | None = None,
+        ngff_version: NgffVersions | None = None,
         overwrite: bool = False,
     ) -> "ImagesContainer":
         """Create an empty OME-Zarr image from an existing image.
@@ -626,6 +628,7 @@ def derive(
             compressors: The compressor to use. If None it will use
                 the same as the reference image.
             dtype (str | None): The data type of the new image.
+            ngff_version (NgffVersions): The NGFF version to use.
             overwrite (bool): Whether to overwrite an existing image.
 
         Returns:
@@ -644,6 +647,7 @@ def derive(
             dtype=dtype,
             dimension_separator=dimension_separator,
             compressors=compressors,
+            ngff_version=ngff_version,
             overwrite=overwrite,
         )
 
@@ -728,6 +732,7 @@ def derive_image_container(
     dtype: str | None = None,
     dimension_separator: Literal[".", "/"] | None = None,
     compressors: CompressorLike | None = None,
+    ngff_version: NgffVersions | None = None,
     overwrite: bool = False,
 ) -> ImagesContainer:
     """Create an empty OME-Zarr image from an existing image.
@@ -746,6 +751,7 @@ def derive_image_container(
             dimensions. If None it will use the same as the reference image.
         compressors (CompressorLike | None): The compressors to use. If None it will use
             the same as the reference image.
+        ngff_version (NgffVersions): The NGFF version to use.
         dtype (str | None): The data type of the new image.
         overwrite (bool): Whether to overwrite an existing image.
 
@@ -796,6 +802,9 @@ def derive_image_container(
     if compressors is None:
         compressors = ref_image.zarr_array.compressors  # type: ignore
 
+    if ngff_version is None:
+        ngff_version = ref_meta.version
+
     handler = create_empty_image_container(
         store=store,
         shape=shape,
@@ -814,7 +823,7 @@ def derive_image_container(
         dimension_separator=dimension_separator,
         compressors=compressors,
         overwrite=overwrite,
-        version=ref_meta.version,
+        version=ngff_version,
     )
     image_container = ImagesContainer(handler)
 

src/ngio/images/_ome_zarr_container.py

@@ -414,6 +414,7 @@ def derive_image(
         compressors: CompressorLike | None = None,
         copy_labels: bool = False,
         copy_tables: bool = False,
+        ngff_version: NgffVersions | None = None,
         overwrite: bool = False,
     ) -> "OmeZarrContainer":
         """Create an empty OME-Zarr container from an existing image.
@@ -436,13 +437,14 @@ def derive_image(
                 the compressors of the reference image will be used.
             copy_labels (bool): Whether to copy the labels from the reference image.
             copy_tables (bool): Whether to copy the tables from the reference image.
+            ngff_version (NgffVersions): The NGFF version to use.
             overwrite (bool): Whether to overwrite an existing image.
 
         Returns:
             OmeZarrContainer: The new image container.
 
         """
-        _ = self._images_container.derive(
+        new_container = self._images_container.derive(
             store=store,
             ref_path=ref_path,
             shape=shape,
@@ -454,18 +456,12 @@ def derive_image(
             dtype=dtype,
             dimension_separator=dimension_separator,
             compressors=compressors,
+            ngff_version=ngff_version,
             overwrite=overwrite,
         )
 
-        handler = ZarrGroupHandler(
-            store,
-            cache=self._group_handler.use_cache,
-            mode=self._group_handler.mode,
-            zarr_format=self._group_handler.zarr_format,
-        )
-
         new_ome_zarr = OmeZarrContainer(
-            group_handler=handler,
+            group_handler=new_container._group_handler,
             validate_paths=False,
         )