usable version of dilatation/erosion during connexion of extensions

brick/component/connection.py

@@ -84,7 +84,7 @@ def ShortestPathFromToN(
     extension: extension_t,
     costs: array_t,
     candidate_points_fct: Callable,
-    all_end_points: tuple = None,
+    all_end_points: list = None,
     extensions: tuple = None,
     max_straight_sq_dist: float = np_.inf,
     erode_path: bool = False,
@@ -114,12 +114,12 @@ def ShortestPathFromToN(
             # -- important for dilatation/erosion process
             for candidate, indx in enumerate(candidate_points):
                 # Verify if end point
-                if candidate not in zip(*all_end_points):
+                if candidate not in all_end_points:
                     # Here  necessary to delete the 2 closest points next to the end points
                     # because if the all extension is candidate there might be a endpoint
                     # that will be polluted by the connection
                     not_allowed = set()
-                    for e_p in zip(*all_end_points):
+                    for e_p in all_end_points:
                         not_allowed_ = set(
                             (e_p[0] + i, e_p[1] + j, e_p[2] + k)
                             for i in (-2, -1, 0, 1, 2)
@@ -177,7 +177,7 @@ def ShortestPathFromToN(
 
 
 def ValidateConnection(
-    glial_cmp: glial_cmp_t, extension: glial_cmp_t, end_point: tuple, dijkstra_path: site_path_h, costs: array_t,
+    glial_cmp: glial_cmp_t, extension: glial_cmp_t, end_point: tuple, dijkstra_path: site_path_h, costs: array_t, all_ep: list,
 ) -> None:
     '''
     Keep the connection path in the glial_cmp.
@@ -200,6 +200,8 @@ def ValidateConnection(
     # restrain the verification to the soma <-> ext step
 
     # Store the new endpoints of the extended extension - TODO update the end point vector
+    all_ep.remove(end_point)
+
     if type(glial_cmp) is soma_t:
         end_point = UpdateEndPointsWithConnexionPath(connection_path, end_point)
         glial_cmp.ext_roots.append((extension.uid, end_point))
@@ -218,28 +220,13 @@ def ValidateConnection(
         extension.sites = tuple(extension.sites)
 
 
+
 def UpdateEndPointsWithConnexionPath(connexion_path: tuple, end_point: tuple) -> tuple:
     #
     if connexion_path is None:
         return end_point
 
     else:
-        # /!\ may yield a bug
-        # Update the end point vector - delete the old endpoint
-        # # reformat to modify them
-        # all_end_points_var = list(all_end_points)
-        # all_end_points = []
-        # for i in all_end_points_var:
-        #     indx = list(i)
-        #     all_end_points.append(indx)
-        # # delete the connected end point
-        # if end_point in zip(*all_end_points):
-        #     idx = list(zip(*all_end_points)).index(end_point)
-        #     for i in range(3):
-        #         all_end_points[i].pop(idx)
-        # else:
-        #     print("WARNING: End point not in the all end points vectors !")
-
         # Search the connection point link to the extension
         connexion_path = tuple(zip(*connexion_path))
 
@@ -251,15 +238,9 @@ def UpdateEndPointsWithConnexionPath(connexion_path: tuple, end_point: tuple) ->
             if i != 0 or j != 0 or k != 0)
 
         if connexion_path[0] in close_end_pt:
-            # for i in range(3):
-            #     all_end_points.append(connexion_path[-1][i])
-            # all_end_points = tuple(all_end_points)
             return connexion_path[-1]
 
         elif connexion_path[-1] in close_end_pt:
-            # for i in range(3):
-            #     all_end_points.append(connexion_path[0][i])
-            # all_end_points = tuple(all_end_points)
             return connexion_path[0]
 
 
@@ -298,7 +279,7 @@ def Erode(path: Tuple[tuple],
 
     for point in path:
         # find out whether this is a end point or not
-        if point in zip(*all_end_points):
+        if point in all_end_points:
             ErodeEndPoint(point, costs_map, extension, image)
         else:
             # build a new path with no endpoints inside

nutrimorph.py

@@ -205,7 +205,7 @@ def NutriMorph(data_path: str,
     # 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:, 300:]
+    # image = image[:, 800:, 300:]
     img_shape = image.shape
     #
     print(f"IMAGE: s.{img_shape} t.{image.dtype} m.{image.min()} M.{image.max()}")
@@ -351,7 +351,7 @@ def NutriMorph(data_path: str,
 
     # Create global end point map for extensions
     glob_ext_ep_map = xt_.EndPointMap(ext_nfo["lmp"] > 0)
-    all_end_points = glob_ext_ep_map.nonzero()
+    all_end_points = list(zip(*glob_ext_ep_map.nonzero()))  # updated in ValidateConnexion
 
     #
     elapsed_time = tm_.gmtime(tm_.time() - start_time)
@@ -411,7 +411,7 @@ def NutriMorph(data_path: str,
                 # length in pixel and max_weighted_length_c too
                 if length <= max_weighted_length_c:
                     # Validate and update all the fields + dilate again the whole extension
-                    cn_.ValidateConnection(soma, extension, end_point, path, dijkstra_costs)
+                    cn_.ValidateConnection(soma, extension, end_point, path, dijkstra_costs, all_ep=all_end_points)
                     if dilatation_erosion:
                         # Dilate extensions
                         cn_.Dilate(extension.sites, dijkstra_costs)
@@ -495,7 +495,7 @@ def NutriMorph(data_path: str,
                         # If so, returns the extensions containing the path last site.
                         tgt_extenstion = extension_t.ExtensionContainingSite(extensions, path[-1])
                         # Validate connexion: update the glial component objects and store more info in their fields
-                        cn_.ValidateConnection(tgt_extenstion, extension, end_point, path, dijkstra_costs)
+                        cn_.ValidateConnection(tgt_extenstion, extension, end_point, path, dijkstra_costs, all_ep=all_end_points)
                         if dilatation_erosion:
                             # Dilate extensions
                             cn_.Dilate(extension.sites, dijkstra_costs)
@@ -618,7 +618,7 @@ def NutriMorph(data_path: str,
     else:
         features_df.to_csv(f"{name_dir}\\{name_file}.csv")
 
-    #
+
     elapsed_time = tm_.gmtime(tm_.time() - start_time)
     print(f"\nElapsed Time={tm_.strftime('%Hh %Mm %Ss', elapsed_time)}")
     print(f"DONE: {tm_.strftime('%a, %b %d %Y @ %H:%M:%S')}\n")

parameters.ini

@@ -49,7 +49,8 @@ parameter3                  :   None
 ; then your parameter has the value string: 'None', and not None
 
 [Input]
-data_path                   :   .\\data\\DIO_6H_6_1.70bis_2.2_3.tif
+data_path                   :   \\path_to_tif_imgs_or_directories
+#.\\data\\DIO_6H_6_1.70bis_2.2_3.tif
 ; direct data path to the image
 channel                     :   G
 ; Can take the values R, G or B.
@@ -61,10 +62,10 @@ save_images                :    \\path_where_to_save_MIP_and_graphs
 ; if None, no saving. Otherwise, path where to save images (MIP & graphs)
 save_csv                   :    \\path_where_to_save_features_csv
 ; where to save the csv. if None, by default it is in the .tif directory
-dilatation_erosion         :    False
+dilatation_erosion         :    True
 ; Choose whether to perform erosion/dilation on the extensions during the connexion process.
-; For the moment, better results are achieved without it, but doing dilatation_erosion is theoretically more rigorous
-statistical_analysis       :    True
+; Better results are achieved with it, and doing dilatation_erosion is theoretically more rigorous
+statistical_analysis       :    False
 
 [Somas]
 soma_low_c                 :    0.15