[FIX] addresses #169, also adds short-term fix for #150

Author: sophiamaedler

src/scportrait/pipeline/_utils/sdata_io.py

@@ -187,49 +187,47 @@ def _write_image_sdata(
         # check if the image is already a multi-scale image
         if isinstance(image, xarray.DataTree):
             # if so only validate the model since this means we are getting the image from a spatialdata object already
-            # image = Image2DModel.validate(image)
-            # this appraoch is currently not functional but an issue was opened at https://github.com/scverse/spatialdata/issues/865
+            # fix until #https://github.com/scverse/spatialdata/issues/528 is resolved
+            Image2DModel().validate(image)
             if scale_factors is not None:
                 Warning("Scale factors are ignored when passing a multi-scale image.")
-            image = image.scale0.image
-
-        if scale_factors is None:
-            scale_factors = [2, 4, 8]
-        if scale_factors is None:
-            scale_factors = [2, 4, 8]
-
-        if isinstance(image, xarray.DataArray):
-            # if so first validate the model since this means we are getting the image from a spatialdata object already
-            # then apply the scales transform
-            # image = Image2DModel.validate(image)
-            # this appraoch is currently not functional but an issue was opened at https://github.com/scverse/spatialdata/issues/865
-
-            if channel_names is not None:
-                Warning(
-                    "Channel names are ignored when passing a single scale image in the DataArray format. Channel names are read directly from the DataArray."
+        else:
+            if scale_factors is None:
+                scale_factors = [2, 4, 8]
+            if scale_factors is None:
+                scale_factors = [2, 4, 8]
+
+            if isinstance(image, xarray.DataArray):
+                # if so first validate the model since this means we are getting the image from a spatialdata object already
+                # fix until #https://github.com/scverse/spatialdata/issues/528 is resolved
+                Image2DModel().validate(image)
+
+                if channel_names is not None:
+                    Warning(
+                        "Channel names are ignored when passing a single scale image in the DataArray format. Channel names are read directly from the DataArray."
+                    )
+
+                image = Image2DModel.parse(
+                    image,
+                    scale_factors=scale_factors,
+                    rgb=False,
                 )
 
-            image = Image2DModel.parse(
-                image,
-                scale_factors=scale_factors,
-                rgb=False,
-            )
-
-        else:
-            if channel_names is None:
-                channel_names = [f"channel_{i}" for i in range(image.shape[0])]
-
-            # transform to spatialdata image model
-            transform_original = Identity()
-            image = Image2DModel.parse(
-                image,
-                dims=["c", "y", "x"],
-                chunks=chunks,
-                c_coords=channel_names,
-                scale_factors=scale_factors,
-                transformations={"global": transform_original},
-                rgb=False,
-            )
+            else:
+                if channel_names is None:
+                    channel_names = [f"channel_{i}" for i in range(image.shape[0])]
+
+                # transform to spatialdata image model
+                transform_original = Identity()
+                image = Image2DModel.parse(
+                    image,
+                    dims=["c", "y", "x"],
+                    chunks=chunks,
+                    c_coords=channel_names,
+                    scale_factors=scale_factors,
+                    transformations={"global": transform_original},
+                    rgb=False,
+                )
 
         if overwrite:
             self._force_delete_object(_sdata, image_name, "images")