small corrections

brick/processing/graph_extraction.py

@@ -34,7 +34,6 @@ import numpy as np_
 
 from brick.component.soma import soma_t
 from brick.general.type import array_t
-from sklgraph.skl_graph import skl_graph_t
 from typing import Tuple, Dict, Union, Any
 
 
@@ -75,15 +74,8 @@ def FindGraphsRootWithEdges(soma: soma_t, ext_nfo: Dict[str, Union[array_t, Any]
                     for k in (-1, 0, 1)
                     if i != 0 or j != 0 or k != 0)
 
-                # soma_contour_sites = set(
-                #     (soma.contour_points[0] + i, soma.contour_points[1] + j, soma.contour_points[2] + k)
-                #     for i in (-1, 0, 1)
-                #     for j in (-1, 0, 1)
-                #     for k in (-1, 0, 1)
-                #     if i != 0 or j != 0 or k != 0
-
                 # Find the intersection between the extended root node candidate and the soma contour points
-                intersections = soma_contour_sites.intersection(root_sites)
+                intersections = set(soma.contour_points).intersection(root_sites)
 
                 # if the graph root sites are included in the soma extensions sites (non-nul intersection):
                 if len(intersections) > 0:
@@ -91,10 +83,10 @@ def FindGraphsRootWithEdges(soma: soma_t, ext_nfo: Dict[str, Union[array_t, Any]
                     root_nodes[ext_uid] = root_node
                         ## By construction, only one root node possible for an ext
 
-    return root_nodes
+    return root_nodes  # TODO: find out why there are less root points than extensions !!
 
 
-def FindGraphsRootWithNodes(soma: soma_t) -> list:
+def FindGraphsRootWithNodes(soma: soma_t) -> dict:
     """
     Find the roots of the {extension+connexion} graphs to be lined to the soma.
     Add a key "root" (bool) in the dict of nodes attributes.

nutrimorph.py

@@ -117,7 +117,7 @@ image = in_.ImageVerification(image, channel)
 # iv_.image_verification(image, channel)  # -> PySide2 user interface  # TODO: must return the modified image!
 # /!\ conflicts between some versions of PySide2 and Python3
 
-image = image[:, 800:, 800:]  # 512 # 562 # Just for development
+image = image[:, 512:, 512:]  # 512 # 562 # Just for development
 img_shape = image.shape
 
 #
@@ -344,7 +344,7 @@ 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')
@@ -378,8 +378,8 @@ for soma in somas:
         soma.skl_graph.add_edge(node, soma_node, root=True)
         # print(node, "<->", soma_node,': Done')
 
-    nx_.draw_networkx(soma.skl_graph)
-    pl_.show(block=True)
+    # nx_.draw_networkx(soma.skl_graph)
+    # pl_.show(block=True)
 
     if with_plot:
         nx_.draw_networkx(soma.skl_graph)