Merge pull request #21 from angelolab/qupath_24bit_images

Qupath 24bit images

src/nimbus_inference/utils.py

@@ -120,6 +120,9 @@ def handle_qupath_segmentation_map(instance_mask: np.array):
     logging.warning("QuPath RGB segmentation map detected. Converting to instance map by")
     logging.warning("combining the RGB channels into a single channel via the following formula:")
     logging.warning("label = RED*256**2 + GREEN * 256 + BLUE")
+    # move channel axis to last if not already
+    if instance_mask.shape.index(3) == 0:
+        instance_mask = np.moveaxis(instance_mask, 0, -1)
     instance_mask_handled = instance_mask[..., 0] * 256**2 + instance_mask[..., 1] * 256 \
         + instance_mask[..., 2]
     instance_mask_handled = instance_mask_handled.round(0).astype(np.uint64)
@@ -263,10 +266,11 @@ def get_segmentation(self, fov: str):
         fov_path = self.fov_paths[idx]
         instance_path = self.segmentation_naming_convention(fov_path)
         if isinstance(instance_path, str):
-            instance_mask = np.squeeze(io.imread(instance_path))
+            instance_mask = io.imread(instance_path)
         else:
-            instance_mask = np.squeeze(instance_path)
-        if len(instance_mask.shape) == 3 and instance_mask.shape[-1] == 3:
+            instance_mask = instance_path
+        instance_mask = np.squeeze(instance_mask)
+        if len(instance_mask.shape) == 3:
             instance_mask = handle_qupath_segmentation_map(instance_mask)
         instance_mask = instance_mask.astype(np.uint32)
         return instance_mask