Improve ODF background image normalization

foa3d/odf.py

@@ -432,14 +432,16 @@ def generate_odf_background(bg_img, bg_mrtrix_mmap, vxl_side):
     # get shape of new downsampled array
     new_shape = bg_mrtrix_mmap.shape[:-1]
 
-    # normalize
+    # image normalization: get global minimum and maximum values
     if bg_img.ndim == 3:
-        bg_img = normalize_image(bg_img)
+        min_glob = np.min(bg_img)
+        max_glob = np.max(bg_img)
 
     # loop over z-slices, and resize them
     for z in range(0, bg_img.shape[0], vxl_side):
         if bg_img.ndim == 3:
-            tmp_slice = np.mean(bg_img[z:z + vxl_side, ...], axis=0)
+            tmp_slice = normalize_image(bg_img[z:z + vxl_side, ...], min_val=min_glob, max_val=max_glob)
+            tmp_slice = np.mean(tmp_slice, axis=0)
         elif bg_img.ndim == 4:
             tmp_slice = 255.0 * np.sum(np.abs(bg_img[z, ...]), axis=-1)
             tmp_slice = np.where(tmp_slice <= 255.0, tmp_slice, 255.0)

foa3d/utils.py

@@ -402,14 +402,20 @@ def normalize_angle(angle, lower=0.0, upper=360.0, dtype=None):
     return norm_angle
 
 
-def normalize_image(img, max_out_val=255.0, dtype=np.uint8):
+def normalize_image(img, min_val=None, max_val=None, max_out_val=255.0, dtype=np.uint8):
     """
     Normalize image data.
 
     Parameters
     ----------
     img: numpy.ndarray
         input image
+        
+    min_val: float
+        minimum input value
+    
+    max_val: float
+        maximum input value
 
     max_out_val: float
         maximum output value
@@ -424,8 +430,10 @@ def normalize_image(img, max_out_val=255.0, dtype=np.uint8):
     """
 
     # get min and max values
-    min_val = np.min(img)
-    max_val = np.max(img)
+    if min_val is None:
+        min_val = np.min(img)
+    if max_val is None:
+        max_val = np.max(img)
 
     # normalize
     if max_val != 0: