update omero exlcuding it from labels

scverse · Feb 20, 2023 · f65151e · f65151e
1 parent 4214abc
commit f65151e
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Showing 3 changed files with 10 additions and 13 deletions.
diff --git a/spatialdata/_io/read.py b/spatialdata/_io/read.py
@@ -155,8 +155,10 @@ def _read_multiscale(
     encoded_ngff_transformations = multiscales[0]["coordinateTransformations"]
     transformations = _get_transformations_from_ngff_dict(encoded_ngff_transformations)
     node.metadata["name"]
-    omero = multiscales[0]["omero"]
-    channels = fmt.channels_from_metadata(omero)
+    # if image, read channels metadata
+    if raster_type == "image":
+        omero = multiscales[0]["omero"]
+        channels = fmt.channels_from_metadata(omero)
     axes = [i["name"] for i in node.metadata["axes"]]
     if len(datasets) > 1:
         multiscale_image = {}
@@ -168,7 +170,7 @@ def _read_multiscale(
                 name="image",
                 # name=name,
                 dims=axes,
-                coords={"c": channels},
+                coords={"c": channels} if raster_type == "image" else {},
                 # attrs={"transform": t},
             )
         msi = MultiscaleSpatialImage.from_dict(multiscale_image)
@@ -182,7 +184,7 @@ def _read_multiscale(
             name="image",
             # name=name,
             dims=axes,
-            coords={"c": channels},
+            coords={"c": channels} if raster_type == "image" else {},
             # attrs={TRANSFORM_KEY: t},
         )
         _set_transformations(si, transformations)

diff --git a/spatialdata/_io/write.py b/spatialdata/_io/write.py
@@ -144,7 +144,8 @@ def _get_group_for_writing_transformations() -> zarr.Group:
             return group["labels"][name]
 
     # convert channel names to channel metadata
-    metadata["omero"] = fmt.channels_to_metadata(raster_data, channels_metadata)
+    if raster_type == "image":
+        metadata["omero"] = fmt.channels_to_metadata(raster_data, channels_metadata)
 
     if isinstance(raster_data, SpatialImage):
         data = raster_data.data

diff --git a/tests/_io/test_readwrite.py b/tests/_io/test_readwrite.py
@@ -26,10 +26,7 @@ def test_images(self, tmp_path: str, images: SpatialData) -> None:
         sdata = SpatialData.read(tmpdir)
         assert images.images.keys() == sdata.images.keys()
         for k in images.images.keys():
-            if isinstance(sdata.images[k], SpatialImage):
-                assert images.images[k].equals(sdata.images[k])
-            elif isinstance(images.images[k], MultiscaleSpatialImage):
-                assert images.images[k].equals(sdata.images[k])
+            assert images.images[k].equals(sdata.images[k])
 
     def test_labels(self, tmp_path: str, labels: SpatialData) -> None:
         """Test read/write."""
@@ -38,10 +35,7 @@ def test_labels(self, tmp_path: str, labels: SpatialData) -> None:
         sdata = SpatialData.read(tmpdir)
         assert labels.labels.keys() == sdata.labels.keys()
         for k in labels.labels.keys():
-            if isinstance(sdata.labels[k], SpatialImage):
-                assert labels.labels[k].equals(sdata.labels[k])
-            elif isinstance(sdata.labels[k], MultiscaleSpatialImage):
-                assert labels.labels[k].equals(sdata.labels[k])
+            assert labels.labels[k].equals(sdata.labels[k])
 
     def test_shapes(self, tmp_path: str, shapes: SpatialData) -> None:
         """Test read/write."""