fix: renumbering in __compute_flow_from_masks (it was by batch, it became by batch and channels)

core/segmentator.py

@@ -1772,16 +1772,18 @@ class CellSegmentator:
             # shape (batch, H, W) -> (batch, 1, H, W)
             _true_masks = _true_masks[:, np.newaxis, :, :]
 
-        batch_size, *_ = _true_masks.shape
+        batch_size, num_channels, *_ = _true_masks.shape
         
         # Renumber labels to ensure uniqueness
-        renumbered: np.ndarray = np.stack([fastremap.renumber(_true_masks[i], in_place=True)[0]
-                                        for i in range(batch_size)])
+        for b in range(batch_size):
+            for c in range(num_channels):
+                fastremap.renumber(_true_masks[b, c], in_place=True)
+        
         # Compute vector flows per image
-        flow_vectors = np.stack([self.__compute_flow_from_mask(renumbered[i])
+        flow_vectors = np.stack([self.__compute_flow_from_mask(_true_masks[i])
                         for i in range(batch_size)])
         
-        return np.concatenate((flow_vectors, renumbered), axis=1).astype(np.float32)
+        return np.concatenate((flow_vectors, _true_masks), axis=1).astype(np.float32)
     
     
     def __compute_flow_from_mask(