consistently use uint32 in candidate detection

brainglobe · Feb 16, 2024 · bb44066 · bb44066
1 parent 749af84
commit bb44066
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/cellfinder/core/detect/detect.py b/cellfinder/core/detect/detect.py
@@ -117,6 +117,7 @@ def main(
     if end_plane == -1:
         end_plane = len(signal_array)
     signal_array = signal_array[start_plane:end_plane]
+    signal_array = signal_array.astype(np.uint32)
 
     callback = callback or (lambda *args, **kwargs: None)
 

diff --git a/cellfinder/core/detect/filters/volume/structure_splitting.py b/cellfinder/core/detect/filters/volume/structure_splitting.py
@@ -71,10 +71,10 @@ def ball_filter_imgs(
     )
 
     # FIXME: hard coded type
-    ball_filtered_volume = np.zeros(volume.shape, dtype=np.uint16)
+    ball_filtered_volume = np.zeros(volume.shape, dtype=np.uint32)
     previous_plane = None
     for z in range(volume.shape[2]):
-        bf.append(volume[:, :, z].astype(np.uint16), good_tiles_mask[:, :, z])
+        bf.append(volume[:, :, z].astype(np.uint32), good_tiles_mask[:, :, z])
         if bf.ready:
             bf.walk()
             middle_plane = bf.get_middle_plane()
@@ -92,8 +92,8 @@ def iterative_ball_filter(
     ns = []
     centres = []
 
-    threshold_value = 65534
-    soma_centre_value = 65535
+    threshold_value = np.iinfo(volume.dtype).max() - 1
+    soma_centre_value = np.iinfo(volume.dtype).max()
 
     vol = volume.copy()  # TODO: check if required