some refactoring

brick/component/extension.py

@@ -52,13 +52,13 @@ class extension_t(glial_cmp_t):
     #
     # soma_uid: connected to a soma somewhere upstream
     #
-    __slots__ = ("scales", "end_points", "soma_uid", "__cache__")
+    __slots__ = ("end_points", "scales", "soma_uid", "__cache__")
 
     def __init__(self):
         #
         super().__init__()
-        self.scales = None
         self.end_points = None
+        self.scales = None
         self.soma_uid = None
         self.__cache__ = None
 
@@ -69,7 +69,7 @@ class extension_t(glial_cmp_t):
 
         bmp = lmp == uid
         instance.InitializeFromMap(bmp, uid)
-        end_point_map = extension_t.EndPointMap(bmp)
+        end_point_map = cls.EndPointMap(bmp)
         end_point_lmp = end_point_map * lmp
         instance.end_points = (end_point_lmp == uid).nonzero()
         instance.scales = scales[instance.sites]

brick/component/glial_cmp.py

@@ -91,17 +91,3 @@ class glial_cmp_t:
     def BackReferenceSoma(self, glial_cmp: glial_cmp_t) -> None:
         #
         raise NotImplementedError
-
-
-def NormalizedImage(image: array_t) -> array_t:
-    #
-    print("This normalization does not bring anything; left as is for now to avoid the need for changing prms")
-    nonextreme_values = image[np_.logical_and(image > 0.0, image < image.max())]
-
-    if nonextreme_values.size > 0:
-        nonextreme_avg = nonextreme_values.mean()
-        result = image.astype(np_.float32) / nonextreme_avg
-    else:
-        result = image.astype(np_.float32)
-
-    return result

brick/component/soma.py

@@ -65,7 +65,7 @@ class soma_t(glial_cmp_t):
 
         bmp = lmp == uid
         instance.InitializeFromMap(bmp, uid)
-        contour_map = soma_t.ContourMap(bmp)
+        contour_map = cls.ContourMap(bmp)
         contour_lmp = contour_map * lmp
         instance.contour_points = tuple(zip(*(contour_lmp == uid).nonzero()))
 

brick/processing/normalization.py

+# Copyright CNRS/Inria/UNS
+# Contributor(s): Eric Debreuve (since 2019)
+#
+# eric.debreuve@cnrs.fr
+#
+# This software is governed by the CeCILL  license under French law and
+# abiding by the rules of distribution of free software.  You can  use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# As a counterpart to the access to the source code and  rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty  and the software's author,  the holder of the
+# economic rights,  and the successive licensors  have only  limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading,  using,  modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean  that it is complicated to manipulate,  and  that  also
+# therefore means  that it is reserved for developers  and  experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and,  more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+
+from brick.general.type import array_t
+
+import numpy as np_
+
+
+def NormalizedImage(image: array_t) -> array_t:
+    #
+    print("This normalization does not bring anything; left as is for now to avoid the need for changing prms")
+    nonextreme_values = image[np_.logical_and(image > 0.0, image < image.max())]
+
+    if nonextreme_values.size > 0:
+        nonextreme_avg = nonextreme_values.mean()
+        result = image.astype(np_.float32) / nonextreme_avg
+    else:
+        result = image.astype(np_.float32)
+
+    return result

nutrimorph.py

@@ -39,9 +39,9 @@
 
 import brick.component.connection as cn_
 import brick.component.extension as xt_
-import brick.component.glial_cmp as gl_
 import brick.component.soma as sm_
 import brick.general.feedback as fb_
+import brick.processing.normalization as nm_
 # from main_prm import *
 
 import os as os_
@@ -98,8 +98,8 @@ img_shape = image.shape
 #
 print(f"IMAGE: s.{img_shape} t.{image.dtype} m.{image.min()} M.{image.max()}")
 
-image_for_soma = gl_.NormalizedImage(image)
-image_for_ext = gl_.NormalizedImage(image)
+image_for_soma = nm_.NormalizedImage(image)
+image_for_ext = nm_.NormalizedImage(image)
 costs = 1.0 / (image + 1.0)
 print(f"NRM-IMG: t.{image_for_soma.dtype} m.{image_for_soma.min():.2f} M.{image_for_soma.max():.2f}")