refactoring

.gitignore

@@ -7,6 +7,8 @@ __material__/
 __runtime__/
 __version__/
 
+__when__.txt
+
 data/
 
 mprofile_*.dat

brick/component/connection.py

@@ -68,8 +68,8 @@ def ShortestPathFromToN(
     point: site_h,
     costs: array_t,
     candidate_points_fct: Callable,
-    max_straight_sq_dist: cy_.double = np_.inf,
-) -> Tuple[site_path_h, cy_.double]:
+    max_straight_sq_dist: float = np_.inf,
+) -> Tuple[site_path_h, float]:
     #
     candidate_points, candidate_indexing = candidate_points_fct(
         point, max_straight_sq_dist

brick/component/extension.py

@@ -126,7 +126,7 @@ class extension_t(glial_cmp_t):
         )
 
     @staticmethod
-    def ExtensionWithSite(
+    def ExtensionContainingSite(
         extensions: Sequence[extension_t], site: site_h
     ) -> Optional[extension_t]:
         #

brick/component/glial_cmp.py

@@ -36,8 +36,6 @@ from brick.general.type import array_t, np_array_picker_h, py_array_picker_h, si
 from abc import abstractmethod
 from typing import Dict, List, Optional, Tuple
 
-import numpy as np_
-
 
 class glial_cmp_t:
     #

brick/processing/map_labeling.py

@@ -34,9 +34,6 @@ from brick.general.type import array_t
 import numpy as np_
 
 
-invalid_n_neighbors_c = 27  # Must be positive and higher (strictly) than
-# the max number of neighbors in a skeleton
-
 shifts_of_26_neighbors_c = tuple(
     (i, j, k)
     for i in (-1, 0, 1)
@@ -44,6 +41,8 @@ shifts_of_26_neighbors_c = tuple(
     for k in (-1, 0, 1)
     if i != 0 or j != 0 or k != 0   # take every direct neighbors except itself
 )
+# Must be positive and higher (strictly) than the max number of neighbors
+invalid_n_neighbors_c = shifts_of_26_neighbors_c.__len__() + 1
 
 
 def PartLMap(map_: array_t) -> array_t:

nutrimorph.py

@@ -235,7 +235,7 @@ while should_look_for_connections:
                 max_straight_sq_dist=max_straight_sq_dist_c,
             )
             if length <= max_weighted_length_c:
-                tgt_extenstion = extension_t.ExtensionWithSite(extensions, path[-1])
+                tgt_extenstion = extension_t.ExtensionContainingSite(extensions, path[-1])
                 cn_.ValidateConnection(tgt_extenstion, extension, path, dijkstra_costs)
                 should_look_for_connections = True
                 print(": Made")

parameters.py

@@ -33,6 +33,7 @@ import skimage.morphology as mp_
 
 
 data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
+channel = 1
 with_plot = True
 
 soma_low_c = 0.15