fixes on docs, updated notebooks

CHANGELOG.md

@@ -10,13 +10,15 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.1.2] - 2024-xx-xx
 
+### Minor
 
+-   Made `get_channels()` public.
 
 ## [0.1.1] - 2024-03-28
 
 ### Added
 
--   Added method `update_annotated_regions_metadata() which updates the `region` value automatically from the `region_key` columns
+-   Added method `update_annotated_regions_metadata() which updates the `region`value automatically from the`region_key` columns
 
 ### Changed
 

docs/api.md

@@ -83,6 +83,7 @@ The elements (building-blocks) that consitute `SpatialData`.
     get_spatial_axes
     points_geopandas_to_dask_dataframe
     points_dask_dataframe_to_geopandas
+    get_channels
 ```
 
 ## Transformations

src/spatialdata/_io/_utils.py

@@ -271,36 +271,6 @@ def _get_backing_files(element: DaskArray | DaskDataFrame) -> list[str]:
     return files
 
 
-@singledispatch
-def get_channels(data: Any) -> list[Any]:
-    """Get channels from data.
-
-    Parameters
-    ----------
-    data
-        data to get channels from
-
-    Returns
-    -------
-    List of channels
-    """
-    raise ValueError(f"Cannot get channels from {type(data)}")
-
-
-@get_channels.register
-def _(data: SpatialImage) -> list[Any]:
-    return data.coords["c"].values.tolist()  # type: ignore[no-any-return]
-
-
-@get_channels.register
-def _(data: MultiscaleSpatialImage) -> list[Any]:
-    name = list({list(data[i].data_vars.keys())[0] for i in data})[0]
-    channels = {tuple(data[i][name].coords["c"].values) for i in data}
-    if len(channels) > 1:
-        raise ValueError("TODO")
-    return list(next(iter(channels)))
-
-
 def save_transformations(sdata: SpatialData) -> None:
     """
     Save all the transformations of a SpatialData object to disk.

src/spatialdata/_io/format.py

@@ -7,8 +7,8 @@
 from shapely import GeometryType
 from spatial_image import SpatialImage
 
-from spatialdata._io._utils import get_channels
 from spatialdata.models import PointsModel, ShapesModel
+from spatialdata.models._utils import get_channels
 
 CoordinateTransform_t = list[dict[str, Any]]
 

src/spatialdata/models/__init__.py

@@ -7,6 +7,7 @@
     Y,
     Z,
     get_axes_names,
+    get_channels,
     get_spatial_axes,
     points_dask_dataframe_to_geopandas,
     points_geopandas_to_dask_dataframe,
@@ -48,4 +49,5 @@
     "points_dask_dataframe_to_geopandas",
     "check_target_region_column_symmetry",
     "get_table_keys",
+    "get_channels",
 ]

src/spatialdata/models/_utils.py

@@ -266,3 +266,33 @@ def points_geopandas_to_dask_dataframe(gdf: GeoDataFrame, suppress_z_warning: bo
     else:
         ddf = PointsModel.parse(ddf, coordinates={"x": "x", "y": "y"})
     return ddf
+
+
+@singledispatch
+def get_channels(data: Any) -> list[Any]:
+    """Get channels from data.
+
+    Parameters
+    ----------
+    data
+        data to get channels from
+
+    Returns
+    -------
+    List of channels
+    """
+    raise ValueError(f"Cannot get channels from {type(data)}")
+
+
+@get_channels.register
+def _(data: SpatialImage) -> list[Any]:
+    return data.coords["c"].values.tolist()  # type: ignore[no-any-return]
+
+
+@get_channels.register
+def _(data: MultiscaleSpatialImage) -> list[Any]:
+    name = list({list(data[i].data_vars.keys())[0] for i in data})[0]
+    channels = {tuple(data[i][name].coords["c"].values) for i in data}
+    if len(channels) > 1:
+        raise ValueError("TODO")
+    return list(next(iter(channels)))

src/spatialdata/models/models.py

@@ -120,6 +120,10 @@ def parse(
             Method to use for multiscale.
         chunks
             Chunks to use for dask array.
+        kwargs
+            Additional arguments for :func:`to_spatial_image`. In particular the `c_coords` kwargs argument (an
+            iterable) can be used to set the channel coordinates for image data. `c_coords` is not available for labels
+            data as labels do not have channels.
 
         Returns
         -------