From 445f2be86554f71f2d106586f1f995e17996b2f1 Mon Sep 17 00:00:00 2001
From: DEBREUVE Eric <eric.debreuve@inria.fr>
Date: Sun, 8 Mar 2020 20:01:25 +0100
Subject: [PATCH] refactoring
---
.gitignore | 2 ++
brick/component/connection.py | 4 ++--
brick/component/extension.py | 2 +-
brick/component/glial_cmp.py | 2 --
brick/processing/map_labeling.py | 5 ++---
nutrimorph.py | 2 +-
parameters.py | 1 +
7 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/.gitignore b/.gitignore
index e3375c6..1fde90e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,8 @@ __material__/
__runtime__/
__version__/
+__when__.txt
+
data/
mprofile_*.dat
diff --git a/brick/component/connection.py b/brick/component/connection.py
index 3679293..83c482c 100644
--- a/brick/component/connection.py
+++ b/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
diff --git a/brick/component/extension.py b/brick/component/extension.py
index a10a0d6..14fd1a9 100644
--- a/brick/component/extension.py
+++ b/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]:
#
diff --git a/brick/component/glial_cmp.py b/brick/component/glial_cmp.py
index b7327e0..ee5aec2 100644
--- a/brick/component/glial_cmp.py
+++ b/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:
#
diff --git a/brick/processing/map_labeling.py b/brick/processing/map_labeling.py
index d3550d0..478de0b 100644
--- a/brick/processing/map_labeling.py
+++ b/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:
diff --git a/nutrimorph.py b/nutrimorph.py
index 73ce4bf..53e4d50 100644
--- a/nutrimorph.py
+++ b/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")
diff --git a/parameters.py b/parameters.py
index 9b5e81d..67c8e73 100644
--- a/parameters.py
+++ b/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
--
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