Fix crash when no brain detected

FNNDSC · Mar 7, 2024 · 62965d5 · 62965d5
1 parent a74dbf3
commit 62965d5
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/emerald/__init__.py b/emerald/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.2.1'
+__version__ = '0.2.2'
 
 DISPLAY_TITLE = r"""
        _                                     _     _ 

diff --git a/emerald/emerald.py b/emerald/emerald.py
@@ -1,5 +1,6 @@
 from pathlib import Path
 from typing import Optional, List, Tuple
+import logging
 
 import cv2
 import numpy as np
@@ -10,6 +11,8 @@
 
 from emerald.model import Unet
 
+logger = logging.getLogger(__name__)
+
 
 def getImageData(fname):
 
@@ -119,6 +122,11 @@ def emerald(model: Unet, input_path: str, mask_path: Optional[Path], brain_paths
         # jennings to sofia: why np.float32 instead of uint8?
         res = __resizeData(res.astype(np.float32), target = original_shape)
 
+    # some type duct tape
+    if str(res.dtype) == 'bool':
+        logger.warning(f'Brain not found in {input_path}')
+        res = res.astype(np.float32)
+
     #remove extra dimension
     res = np.squeeze(res)