ngio 0.5.0b5__tar.gz → 0.5.0b6__tar.gz

{ngio-0.5.0b5 → ngio-0.5.0b6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0b5
+Version: 0.5.0b6
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio

{ngio-0.5.0b5 → ngio-0.5.0b6}/src/ngio/common/_roi.py

@@ -1,6 +1,6 @@
 """Region of interest (ROI) metadata.
 
-These are the interfaces bwteen the ROI tables / masking ROI tables and
+These are the interfaces between the ROI tables / masking ROI tables and
     the ImageLikeHandler.
 """
 

{ngio-0.5.0b5 → ngio-0.5.0b6}/src/ngio/images/_abstract_image.py

@@ -822,7 +822,6 @@ def abstract_derive(
         pixelsize (float | tuple[float, float] | None): The pixel size of the new image.
         z_spacing (float | None): The z spacing of the new image.
         time_spacing (float | None): The time spacing of the new image.
-        axes_names (Sequence[str] | None): The axes names of the new image.
         name (str | None): The name of the new image.
         channels_policy (Literal["squeeze", "same", "singleton"] | int):
             Possible policies:
@@ -837,7 +836,7 @@ def abstract_derive(
         chunks (ChunksLike | None): The chunk shape of the new image.
         shards (ShardsLike | None): The shard shape of the new image.
         dtype (str | None): The data type of the new image.
-        dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+        dimension_separator (Literal[".", "/"] | None): The separator to use for
             dimensions.
         compressors (CompressorLike | None): The compressors to use.
         extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to

{ngio-0.5.0b5 → ngio-0.5.0b6}/src/ngio/images/_image.py

@@ -656,7 +656,7 @@ class ImagesContainer:
             chunks (ChunksLike | None): The chunk shape of the new image.
             shards (ShardsLike | None): The shard shape of the new image.
             dtype (str | None): The data type of the new image.
-            dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+            dimension_separator (Literal[".", "/"] | None): The separator to use for
                 dimensions.
             compressors (CompressorLike | None): The compressors to use.
             extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to

{ngio-0.5.0b5 → ngio-0.5.0b6}/src/ngio/images/_label.py

@@ -232,24 +232,18 @@ class LabelsContainer:
         labels: Sequence[str] | None = None,
         pixel_size: PixelSize | None = None,
     ) -> "Label":
-        """Create an empty OME-Zarr image from an existing image.
+        """Create an empty OME-Zarr label from an existing image or label.
 
         If a kwarg is not provided, the value from the reference image will be used.
 
         Args:
-            store (StoreOrGroup): The Zarr store or group to create the image in.
-            ref_image (Image | Label): The reference image to derive the new image from.
-            shape (Sequence[int] | None): The shape of the new image.
+            name (str): The name of the new label.
+            ref_image (Image | Label): The reference image to derive the new label from.
+            shape (Sequence[int] | None): The shape of the new label.
             pixelsize (float | tuple[float, float] | None): The pixel size of the new
-                image.
-            z_spacing (float | None): The z spacing of the new image.
-            time_spacing (float | None): The time spacing of the new image.
-            scaling_factors (Sequence[float] | Literal["auto"] | None): The scaling
-                factors of the new image.
-            axes_names (Sequence[str] | None): The axes names of the new image.
-            name (str | None): The name of the new image.
-            channels_meta (Sequence[str | Channel] | None): The channels metadata
-                of the new image.
+                label.
+            z_spacing (float | None): The z spacing of the new label.
+            time_spacing (float | None): The time spacing of the new label.
             channels_policy (Literal["squeeze", "same", "singleton"] | int):
                 Possible policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
@@ -258,19 +252,19 @@ class LabelsContainer:
                 - If an integer is provided, the channels axis will be changed to have
                     that size.
             ngff_version (NgffVersions | None): The NGFF version to use.
-            chunks (ChunksLike | None): The chunk shape of the new image.
-            shards (ShardsLike | None): The shard shape of the new image.
-            dtype (str | None): The data type of the new image.
-            dimension_separator (DIMENSION_SEPARATOR | None): The separator to use for
+            chunks (ChunksLike | None): The chunk shape of the new label.
+            shards (ShardsLike | None): The shard shape of the new label.
+            dtype (str | None): The data type of the new label.
+            dimension_separator (Literal[".", "/"] | None): The separator to use for
                 dimensions.
             compressors (CompressorLike | None): The compressors to use.
             extra_array_kwargs (Mapping[str, Any] | None): Extra arguments to pass to
                 the zarr array creation.
-            overwrite (bool): Whether to overwrite an existing image.
-            labels (Sequence[str] | None): The labels of the new image.
-                This argument is deprecated please use channels_meta instead.
-            pixel_size (PixelSize | None): The pixel size of the new image.
-                This argument is deprecated please use pixelsize, z_spacing,
+            overwrite (bool): Whether to overwrite an existing label.
+            labels (Sequence[str] | None): Deprecated. This argument is deprecated,
+                please use channels_meta instead.
+            pixel_size (PixelSize | None): Deprecated. The pixel size of the new label.
+                This argument is deprecated, please use pixelsize, z_spacing,
                 and time_spacing instead.
 
         Returns:

{ngio-0.5.0b5 → ngio-0.5.0b6}/src/ngio/images/_ome_zarr_container.py

@@ -266,8 +266,8 @@ class OmeZarrContainer:
 
     def set_channel_meta(
         self,
-        labels: Sequence[str] | int | None = None,
-        wavelength_id: Sequence[str] | None = None,
+        labels: Sequence[str | None] | int | None = None,
+        wavelength_id: Sequence[str | None] | None = None,
         percentiles: tuple[float, float] | None = None,
         colors: Sequence[str] | None = None,
         active: Sequence[bool] | None = None,
@@ -462,7 +462,8 @@ class OmeZarrContainer:
             z_spacing (float | None): The z spacing of the new image.
             time_spacing (float | None): The time spacing of the new image.
             name (str | None): The name of the new image.
-            channels_policy (Literal["squeeze", "same"] | int): Possible policies:
+            channels_policy (Literal["squeeze", "same", "singleton"] | int): Possible
+                policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
                 - If "same", the channels axis will be kept as is (if it exists).
                 - If "singleton", the channels axis will be set to size 1.
@@ -814,7 +815,8 @@ class OmeZarrContainer:
                 label.
             z_spacing (float | None): The z spacing of the new label.
             time_spacing (float | None): The time spacing of the new label.
-            channels_policy (Literal["same", "squeeze"] | int): Possible policies:
+            channels_policy (Literal["same", "squeeze", "singleton"] | int): Possible
+                policies:
                 - If "squeeze", the channels axis will be removed (no matter its size).
                 - If "same", the channels axis will be kept as is (if it exists).
                 - If "singleton", the channels axis will be set to size 1.

{ngio-0.5.0b5 → ngio-0.5.0b6}/src/ngio/ome_zarr_meta/__init__.py

@@ -15,6 +15,9 @@ from ngio.ome_zarr_meta._meta_handlers import (
 )
 from ngio.ome_zarr_meta.ngio_specs import (
     AxesHandler,
+    Channel,
+    ChannelsMeta,
+    ChannelVisualisation,
     Dataset,
     DefaultNgffVersion,
     ImageInWellPath,
@@ -31,6 +34,9 @@ from ngio.ome_zarr_meta.ngio_specs import (
 
 __all__ = [
     "AxesHandler",
+    "Channel",
+    "ChannelVisualisation",
+    "ChannelsMeta",
     "Dataset",
     "DefaultNgffVersion",
     "ImageInWellPath",