Fix export of masks with multi-theC as multi-channel labels

CHANGELOG.md

@@ -1,8 +1,8 @@
-# 0.6.1 (June 2024)
+# 0.6.1 (June 2025)
 
 - Fix version
 
-# 0.6.0 (June 2024)
+# 0.6.0 (June 2025)
 
 - Support --name_by option ([#147](https://github.com/ome/omero-cli-zarr/pull/147))
 - Fix export of Plate labels ([#173](https://github.com/ome/omero-cli-zarr/pull/173))

src/omero_zarr/masks.py

@@ -293,12 +293,13 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
         # Figure out whether we can flatten some dimensions
         unique_dims: Dict[str, Set[int]] = {
             "T": {unwrap(mask.theT) for shapes in masks for mask in shapes},
+            "C": {unwrap(mask.theC) for shapes in masks for mask in shapes},
             "Z": {unwrap(mask.theZ) for shapes in masks for mask in shapes},
         }
         ignored_dimensions: Set[str] = set()
-        # We always ignore the C dimension
-        ignored_dimensions.add("C")
         print(f"Unique dimensions: {unique_dims}")
+        if unique_dims["C"] == {None} or len(unique_dims["C"]) == 1:
+            ignored_dimensions.add("C")
 
         for d in "TZ":
             if unique_dims[d] == {None}:
@@ -308,8 +309,6 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
 
         # Verify that we are linking this mask to a real ome-zarr
         source_image = self.source_image
-        print(f"source_image ??? needs to be None to use filename: {source_image}")
-        print(f"filename: {filename}", self.output, self.name_by)
         source_image_link = self.source_image
         if source_image is None:
             # Assume that we're using the output directory
@@ -320,11 +319,11 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
             assert self.plate_path, "Need image path within the plate"
             source_image = f"{source_image}/{self.plate_path}"
 
-        print(f"source_image {source_image}")
         image_path = source_image
         if self.output:
             image_path = os.path.join(self.output, source_image)
         src = parse_url(image_path)
+        print(f"Writing labels to image at: {image_path}")
         assert src, f"Source image does not exist at {image_path}"
         input_pyramid = Node(src, [])
         assert input_pyramid.load(Multiscales), "No multiscales metadata found"
@@ -578,7 +577,7 @@ def masks_to_labels(
                                 if check_overlaps:
                                     raise Exception(
                                         f"Shape {shape.roi.id.val} overlaps "
-                                        "with existing labels"
+                                        "with existing labels. Use --overlaps=dtype_max"
                                     )
                                 else:
                                     # set overlapping region to max(dtype)

test/integration/clitest/test_export.py

@@ -192,20 +192,21 @@ def test_export_masks(
         img_id = images[0].id.val
         size_xy = 512
 
-        # Create a mask
+        # Create a mask for each channel
         from skimage.data import binary_blobs
 
-        blobs = binary_blobs(length=size_xy, volume_fraction=0.1, n_dim=2).astype(
-            "int8"
-        )
         red = [255, 0, 0, 255]
-        mask = mask_from_binary_image(blobs, rgba=red, z=0, c=0, t=0)
-
-        roi = RoiI()
-        roi.setImage(images[0])
-        roi.addShape(mask)
-        updateService = self.client.sf.getUpdateService()
-        updateService.saveAndReturnObject(roi)
+        green = [0, 255, 0, 255]
+        for ch, color in enumerate([red, green]):
+            blobs = binary_blobs(length=size_xy, volume_fraction=0.1, n_dim=2).astype(
+                "int8"
+            )
+            mask = mask_from_binary_image(blobs, rgba=color, z=0, c=ch, t=0)
+            roi = RoiI()
+            roi.setImage(images[0])
+            roi.addShape(mask)
+            updateService = self.client.sf.getUpdateService()
+            updateService.saveAndReturnObject(roi)
 
         print("tmp_path", tmp_path)
 
@@ -232,19 +233,22 @@ def test_export_masks(
         all_lines = ", ".join(lines)
         assert "Exporting to" in all_lines
         assert "Finished" in all_lines
-        assert "Found 1 mask shapes in 1 ROIs" in all_lines
+        assert "Found 2 mask shapes in 2 ROIs" in all_lines
 
         labels_text = (tmp_path / zarr_name / "labels" / "0" / ".zattrs").read_text(
             encoding="utf-8"
         )
         labels_json = json.loads(labels_text)
-        assert labels_json["image-label"]["colors"] == [{"label-value": 1, "rgba": red}]
+        assert labels_json["image-label"]["colors"] == [
+            {"label-value": 1, "rgba": red},
+            {"label-value": 2, "rgba": green},
+        ]
 
         arr_text = (tmp_path / zarr_name / "labels" / "0" / "0" / ".zarray").read_text(
             encoding="utf-8"
         )
         arr_json = json.loads(arr_text)
-        assert arr_json["shape"] == [1, 512, 512]
+        assert arr_json["shape"] == [2, 512, 512]
 
     @pytest.mark.parametrize("name_by", ["id", "name"])
     def test_export_plate_polygons(