added licence

.gitignore

@@ -2,4 +2,6 @@
 .mypy_cache/
 
 __pycache__/
-__version__/
+
+data/
+runtime/

__COPYRIGHT__.txt

+Copyright CNRS/Inria/UNS
+Contributor(s): Eric Debreuve (since 2019)
+
+eric.debreuve@cnrs.fr
+
+This software is being developed by Eric Debreuve, a CNRS employee and member of team Morpheme.
+Team Morpheme is a joint team between Inria, the CNRS, and UNS (member of UCA).
+It is hosted by Inria Sophia Antipolis Méditerranée, Laboratory I3S, and Laboratory iBV.
+
+CNRS: http://www.cnrs.fr/index.html
+Team Morpheme: http://team.inria.fr/morpheme/
+Inria: http://www.inria.fr/en/
+Inria Sophia Antipolis Méditerranée: http://www.inria.fr/en/centre/sophia
+UNS: http://unice.fr/en
+UCA: http://univ-cotedazur.fr/en
+I3S: http://www.i3s.unice.fr/en
+iBV: http://ibv.unice.fr/EN/index.php

connection.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.
+
 import dijkstra_1_to_n as dk_
 from extension import extension_t
 from soma import soma_t

extension.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 __future__ import annotations
 
 import frangi_3d as fg_
@@ -111,15 +142,15 @@ class extension_t(glial_cmp_t):
         image: array_t, in_parallel: bool = False
     ) -> Tuple[array_t, array_t]:
         #
-        import os.path as ph_
-
-        if ph_.exists("./frangi.npz"):
-            print("/!\\ Reading from precomputed data file")
-            loaded = np_.load("./frangi.npz")
-            enhanced_img = loaded["enhanced_img"]
-            scale_map = loaded["scale_map"]
+        # import os.path as ph_
 
-            return enhanced_img, scale_map
+        # if ph_.exists("./frangi.npz"):
+        #     print("/!\\ Reading from precomputed data file")
+        #     loaded = np_.load("./frangi.npz")
+        #     enhanced_img = loaded["enhanced_img"]
+        #     scale_map = loaded["scale_map"]
+        #
+        #     return enhanced_img, scale_map
 
         preprocessed_img = im_.morphology.white_tophat(
             image, size=2, mode="constant", cval=0.0, origin=0
@@ -136,9 +167,9 @@ class extension_t(glial_cmp_t):
             in_parallel=in_parallel,
         )
 
-        np_.savez_compressed(
-            "./frangi.npz", enhanced_img=enhanced_img, scale_map=scale_map
-        )
+        # np_.savez_compressed(
+        #     "./runtime/frangi.npz", enhanced_img=enhanced_img, scale_map=scale_map
+        # )
 
         return enhanced_img, scale_map
 

features_ext.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.
+
 import numpy as np
 from skimage import measure
 

features_soma.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.
+
 import numpy as np_
 import skimage.measure as ms_
 import sklearn.decomposition as dc_

feedback.py

 from extension import extension_t
+# 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.
+
 import plot as ot_
 from soma import soma_t
 

frangi_3d.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 type import array_t
 
 import multiprocessing as pl_

glial_cmp.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 __future__ import annotations
 
 from type import array_t, np_array_picker_h, py_array_picker_h, site_path_h

main.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.
+
 import connection as cn_
 import extension as xt_
 import feedback as fb_

main_prm.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.
+
 import skimage.morphology as mp_
 
 
-data_path = "./DIO_6H_6_1.70bis_2.2_3.tif"
+data_path = "./data/DIO_6H_6_1.70bis_2.2_3.tif"
 with_plot = False
 
 soma_low_c = 0.15

map_labeling.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 type import array_t
 
 import numpy as np_

plot.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.
+
 import dijkstra_1_to_n as dk_
 from extension import extension_t
 from soma import soma_t

ref_result_nutrimorph.txt

-/usr/bin/python3.7 /home/eric/Code/project/mno/nutrimorph/amina/main.py
-STARTED: Wed, Sep 18 2019 @ 17:28:28
-
---- Soma Detection
-    n = 14
-
---- Extension Detection
-/!\ Reading from precomputed data file
-    n = 64
-
---- Soma <-> Extension
-    Soma.1 <-?-> Ext.9(0): Made
-    Soma.1 <-?-> Ext.21(0): Made
-    Soma.1 <-?-> Ext.31(0): Made
-    Soma.1 <-?-> Ext.32(0): Made
-    Soma.1 <-?-> Ext.35(1): Made
-    Soma.1 <-?-> Ext.38(0): Made
-    Soma.2 <-?-> Ext.1(1): Made
-    Soma.2 <-?-> Ext.10(1): Made
-    Soma.2 <-?-> Ext.18(1): Made
-    Soma.2 <-?-> Ext.19(1): Made
-    Soma.2 <-?-> Ext.23(0): Made
-    Soma.2 <-?-> Ext.25(1): Made
-    Soma.2 <-?-> Ext.27(1): Made
-    Soma.2 <-?-> Ext.30(0): Made
-    Soma.2 <-?-> Ext.34(0): Made
-    Soma.2 <-?-> Ext.36(1): Made
-    Soma.2 <-?-> Ext.37(0): Made
-    Soma.2 <-?-> Ext.41(1): Made
-    Soma.2 <-?-> Ext.43(1): Made
-    Soma.2 <-?-> Ext.44(0): Made
-    Soma.2 <-?-> Ext.46(0): Made
-    Soma.2 <-?-> Ext.47(0): Made
-    Soma.2 <-?-> Ext.50(0): Made
-    Soma.4 <-?-> Ext.2(0): Made
-    Soma.4 <-?-> Ext.4(0): Made
-    Soma.4 <-?-> Ext.5(0): Made
-    Soma.4 <-?-> Ext.6(0): Made
-    Soma.4 <-?-> Ext.7(0): Made
-    Soma.4 <-?-> Ext.11(0): Made
-    Soma.4 <-?-> Ext.12(1): Made
-    Soma.4 <-?-> Ext.15(0): Made
-    Soma.4 <-?-> Ext.17(0): Made
-    Soma.4 <-?-> Ext.20(1): Made
-    Soma.13 <-?-> Ext.64(0): Made
-    Soma.14 <-?-> Ext.33(1): Made
-    Soma.14 <-?-> Ext.48(1): Made
-    Soma.14 <-?-> Ext.58(0): Made
-    Soma.14 <-?-> Ext.59(0): Made
-    Soma.1 <-?-> Ext.26(0): Made
-    Soma.4 <-?-> Ext.14(1): Made
-    Soma.14 <-?-> Ext.39(1): Made
-    Soma.4 <-?-> Ext.13(0): Made
-    Soma.9 <-?-> Ext.57(0): Made
-    Soma.9 <-?-> Ext.55(1)
-    Soma.9 <-?-> Ext.55(0)
-    Connected Ext = 43/64
-    (1, 2, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 43, 44, 46, 47, 48, 50, 57, 58, 59, 64)
-
---- Extension <-> Extension
-    Soma.9 <-?-> Ext.55(1)
-    Soma.9 <-?-> Ext.55(0)
-
-
-
-Elapsed Time=00h 03m 53s
-DONE: Wed, Sep 18 2019 @ 17:32:22
-
-Process finished with exit code 0

soma.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 __future__ import annotations
 
 from glial_cmp import glial_cmp_t