Fix combine_masks function: Handle numpy arrays properly to prevent ValueError

- Fix ambiguous truth value error when masks is a numpy array
- Add proper type checking for numpy arrays vs lists
- Handle edge cases (scalar arrays, empty arrays, multi-dimensional arrays)
- Improve error handling and logging

utils.py

@@ -131,17 +131,39 @@ def group_images_by_subject(image_files: List[str]) -> Dict[str, Dict[str, Any]]
     return subject_groups
 
 
-def combine_masks(masks: List[np.ndarray]) -> Optional[np.ndarray]:
+def combine_masks(masks) -> Optional[np.ndarray]:
     """
     Combine multiple mask arrays into a single mask.
     
     Args:
-        masks: List of mask arrays
+        masks: List of mask arrays, or numpy array, or None
     
     Returns:
         Combined mask array or None if no valid masks
     """
-    if not masks:
+    if masks is None:
+        return None
+    
+    # Handle numpy array input (convert to list)
+    if isinstance(masks, np.ndarray):
+        if masks.ndim == 0:  # Scalar
+            return None
+        elif masks.ndim == 1:  # 1D array - might be empty
+            if len(masks) == 0:
+                return None
+            masks = [masks]  # Convert to list
+        else:  # Multi-dimensional array - treat as single mask
+            return masks
+    
+    # Handle list/tuple input
+    if not isinstance(masks, (list, tuple)):
+        # Try to convert to list
+        try:
+            masks = list(masks)
+        except Exception:
+            return None
+    
+    if len(masks) == 0:
         return None
     
     mask_arrays = []
@@ -152,17 +174,22 @@ def combine_masks(masks: List[np.ndarray]) -> Optional[np.ndarray]:
             # Try to convert to numpy
             try:
                 mask_np = np.array(mask)
-                mask_arrays.append(mask_np)
+                if mask_np.size > 0:  # Only add non-empty arrays
+                    mask_arrays.append(mask_np)
             except Exception as e:
-                logger.warning(f"Could not convert mask to numpy: {e}")
+                logger.debug(f"Could not convert mask to numpy: {e}")
                 continue
     
-    if not mask_arrays:
+    if len(mask_arrays) == 0:
         return None
     
     # Combine all masks using logical OR
-    combined_mask = np.any(mask_arrays, axis=0)
-    return combined_mask
+    try:
+        combined_mask = np.any(mask_arrays, axis=0)
+        return combined_mask
+    except Exception as e:
+        logger.error(f"Error combining masks: {e}", exc_info=True)
+        return None
 
 
 def create_output_image(