dealt with hysteresis pb + added features:

* ellipsoid axes sorted in croissant order
* other parameters adjusted

nutrimorph.py

@@ -123,7 +123,7 @@ 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[:, 512:, 512:]  # 512 # 562 # Just for development
+image = image[:, 800:, 800:]  # 512 # 562 # Just for development
 img_shape = image.shape
 
 #

parameters.ini

@@ -70,7 +70,7 @@ soma_min_area_c            :    (0.24050024 ** 2) * 1000
 [Extensions]
 ; for hysteresis
 ext_low_c                  :    1e-20
-ext_high_c                 :    0.1
+ext_high_c                 :    0.15
 ; for morphological cleaning
 ext_selem_micron_c         :    0.24050024 * 1
 ext_min_area_c             :    (0.24050024 ** 2) * 100

sklgraph/brick/edge.py

@@ -95,14 +95,16 @@ class edge_t:
 
         self.widths = widths[self.sites]
 
-    def SetLengths(self, size_voxel: list, widths: array_t = None, check_validity: bool = False) -> None:
+    def SetLengths(self, size_voxel: array_t, widths: array_t = None, check_validity: bool = False) -> None:
         #
         if self.node_uids.__len__() != 2:
             raise ValueError("Edge: Missing sites from adjacent nodes")
 
         sites_as_array = np_.array(self.sites)
         segments = np_.diff(sites_as_array, axis=1)
-        sq_lengths = (segments.transpose() * np_.diag(size_voxel) * segments).sum(axis=0) # TODO add param size_voxel everyzhere
+        # segmentsT = segments.transpose()
+        # sq_lengths = (segmentsT.dot(np_.diag(size_voxel)).dot(segments)).sum(axis=0)
+        sq_lengths = (segments ** 2).sum(axis=0)
         lengths = np_.sqrt(sq_lengths)
         length = lengths.sum().item()
 

sklgraph/skl_graph.py

@@ -72,7 +72,7 @@ class skl_graph_t(nx_.MultiGraph):
 
     @classmethod
     def FromSkeleton(
-        cls, skeleton: , size_voxel: list) -> skl_graph_t:
+        cls, skeleton: skl_map_t, size_voxel: array_t) -> skl_graph_t:
         #
         instance = cls()
 
@@ -95,7 +95,7 @@ class skl_graph_t(nx_.MultiGraph):
         instance.add_nodes_from((node.uid, dict(as_node_t=node)) for node in e_nodes)
         instance.add_nodes_from((node.uid, dict(as_node_t=node)) for node in b_nodes)
         for edge in edges:
-            edge.SetLengths(skeleton.widths, size_voxel=size_voxel)
+            edge.SetLengths(widths=skeleton.widths, size_voxel=size_voxel)
             instance.AddEdge(edge)
 
         instance.n_e_nodes = e_nodes.__len__()