tests frangi3d skimage + python

brick/processing/frangi3.py

@@ -44,6 +44,7 @@ from typing import Callable, Optional, Tuple
 import numpy as np_
 from multiprocessing.sharedctypes import Array as shared_array_t
 from scipy import ndimage as im_
+import skimage.filters as fl_
 
 _folder, _ = ph_.split(ph_.realpath(__file__))
 if _folder.__len__() == 0:
@@ -201,6 +202,15 @@ def _EnhancementWSequentialScales(
     enhanced = None
     scale_map = None
 
+    # local_enhanced = fl_.frangi(
+    #     img,
+    #     sigmas=scales,
+    #     alpha=alpha,
+    #     beta=beta,
+    #     gamma=frangi_c,
+    #     black_ridges=not bright_on_dark,
+    # )
+
     for s_idx, scale in enumerate(scales):
         local_enhanced = method_fct(
             img,
@@ -212,6 +222,8 @@ def _EnhancementWSequentialScales(
             bright_on_dark=bright_on_dark,
         )
 
+        # print(f"scale={scale}")
+
         if s_idx > 0:
             larger_map = local_enhanced > enhanced
             enhanced[larger_map] = local_enhanced[larger_map]

nutrimorph.py

@@ -348,7 +348,7 @@ if with_plot:
     pl_.show()
 
 po_.MaximumIntensityProjectionZ(som_nfo['soma_w_ext_lmp'])
-# po_.MaximumIntensityProjectionZ(ext_nfo['lmp_soma'])
+po_.MaximumIntensityProjectionZ(ext_nfo['lmp_soma'])
 
 # --- Extract all the extensions of all somas as a graph
 print('\n--- Graph extraction')