git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2424 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 93dd0d2099fce5d2b5b05f2ddc22cfebecac14fc

11 files changed, 300 insertions, 302 deletions

diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
index a2e4efe5..b2c501c3 100644
--- a/src/Nerve_GIC/example/CMakeLists.txt
+++ b/src/Nerve_GIC/example/CMakeLists.txt
@@ -13,6 +13,9 @@ target_link_libraries(MapperDeltaCoord  ${Boost_SYSTEM_LIBRARY})
 add_executable ( MapperDeltaFunc MapperDeltaFunc.cpp )
 target_link_libraries(MapperDeltaFunc  ${Boost_SYSTEM_LIBRARY})
 
+add_executable ( GICvoronoi GICvoronoi.cpp )
+target_link_libraries(MapperDeltaFunc  ${Boost_SYSTEM_LIBRARY})
+
 file(COPY visu.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
 
 if (TBB_FOUND)
diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp
index cae0d55d..1889cb33 100644
--- a/src/Nerve_GIC/example/GIC.cpp
+++ b/src/Nerve_GIC/example/GIC.cpp
@@ -2,8 +2,8 @@
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
-  std::cerr << "Usage: " << progName << " filename.off threshold coordinate resolution gain\n";
-  std::cerr << "       i.e.: " << progName << " ../../../../data/points/human.off 0.075 2 0.075 0 \n";
+  std::cerr << "Usage: " << progName << " filename.off threshold coordinate resolution gain [--v] \n";
+  std::cerr << "       i.e.: " << progName << " ../../../../data/points/human.off 0.075 2 0.075 0 --v \n";
   exit(-1);  // ----- >>
 }
 
diff --git a/src/Nerve_GIC/example/GIC.txt b/src/Nerve_GIC/example/GIC.txt
index 6d9f07f5..79f61e92 100644
--- a/src/Nerve_GIC/example/GIC.txt
+++ b/src/Nerve_GIC/example/GIC.txt
@@ -1,92 +1,89 @@
-../../../../data/points/human.off
-coordinate 2
-coordinate 2
-0.075 0
-44 43
-0 -0.954369 220
-1 -0.954377 220
-2 -0.869559 45
-3 -0.869405 45
-4 -0.794255 25
-5 -0.795222 26
-6 -0.723847 48
-7 -0.722679 48
-8 -0.633796 48
-9 -0.634232 48
-10 -0.564455 48
-11 -0.564428 48
-12 -0.491837 98
-13 -0.491864 98
-14 -0.422733 88
-15 -0.422739 88
-16 -0.343376 74
-17 -0.343367 74
-18 -0.271635 96
-19 -0.190912 96
-20 -0.158869 3
-21 -0.158905 3
-22 -0.114958 97
-23 -0.108561 96
-24 -0.115241 100
-25 -0.0317845 185
-26 -0.041866 50
-27 -0.0429161 51
-28 0.0353033 158
-29 0.0275106 31
-30 0.0252492 30
-31 0.107097 170
-32 0.110226 51
-33 0.110952 50
-34 0.186188 57
-35 0.176564 97
-36 0.186215 57
-37 0.256898 232
-38 0.338811 268
-39 0.406299 273
-40 0.481925 220
-41 0.555454 241
-42 0.632415 198
-43 0.744473 407
-0 3
-1 2
-2 4
-3 5
-4 7
-5 6
-6 9
-7 8
-8 10
-9 11
-10 13
-11 12
-12 14
-13 15
-14 16
-15 17
-16 18
-17 18
-18 19
-19 23
-20 22
-21 24
-22 27
-23 25
-24 26
-25 28
-26 29
-27 30
-28 31
-29 33
-30 32
-31 35
-32 34
-33 36
-34 37
-35 37
-36 37
-37 38
-38 39
-39 40
-40 41
-41 42
-42 43
+Graph induced complex is of dimension 1 - 87 simplices - 44 vertices.
+Iterator on graph induced complex simplices
+0 
+1 
+2 
+2 1 
+3 
+3 0 
+4 
+4 2 
+5 
+5 3 
+6 
+6 5 
+7 
+7 4 
+8 
+8 7 
+9 
+9 6 
+10 
+10 8 
+11 
+11 9 
+12 
+12 11 
+13 
+13 10 
+14 
+14 12 
+15 
+15 13 
+16 
+16 14 
+17 
+17 15 
+18 
+18 16 
+18 17 
+19 
+19 18 
+20 
+21 
+22 
+22 20 
+23 
+23 19 
+24 
+24 21 
+25 
+25 23 
+26 
+26 24 
+27 
+27 22 
+28 
+28 25 
+29 
+29 26 
+30 
+30 27 
+31 
+31 28 
+32 
+32 30 
+33 
+33 29 
+34 
+34 32 
+35 
+35 31 
+36 
+36 33 
+37 
+37 34 
+37 35 
+37 36 
+38 
+38 37 
+39 
+39 38 
+40 
+40 39 
+41 
+41 40 
+42 
+42 41 
+43 
+43 42 
diff --git a/src/Nerve_GIC/example/GICvoronoi.cpp b/src/Nerve_GIC/example/GICvoronoi.cpp
index 141268a5..9bf3de5e 100644
--- a/src/Nerve_GIC/example/GICvoronoi.cpp
+++ b/src/Nerve_GIC/example/GICvoronoi.cpp
@@ -2,18 +2,17 @@
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
-  std::cerr << "Usage: " << progName << " filename.off threshold N\n";
-  std::cerr << "       i.e.: " << progName << " ../../../data/points/human.off 0.075 100 \n";
+  std::cerr << "Usage: " << progName << " filename.off N [--v] \n";
+  std::cerr << "       i.e.: " << progName << " ../../../../data/points/human.off 100 --v \n";
   exit(-1);  // ----- >>
 }
 
 int main(int argc, char **argv) {
-  if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1));
+  if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
 
   std::string off_file_name(argv[1]);
-  double threshold = atof(argv[2]);
-  int m = atoi(argv[3]);
-  bool verb = 0; if(argc == 5)  verb = 1;
+  int m = atoi(argv[2]);
+  bool verb = 0; if(argc == 4)  verb = 1;
 
   // ----------------------------------------------------------------------------
   // Init of a graph induced complex from an OFF file
diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.cpp b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
index c4d86caf..9445e988 100644
--- a/src/Nerve_GIC/example/MapperDeltaCoord.cpp
+++ b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
@@ -2,7 +2,7 @@
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
-  std::cerr << "Usage: " << progName << " filename.off coordinate \n";
+  std::cerr << "Usage: " << progName << " filename.off coordinate [--v] \n";
   std::cerr << "       i.e.: " << progName << " ../../../../data/points/human.off 2 --v \n";
   exit(-1);  // ----- >>
 }
diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.txt b/src/Nerve_GIC/example/MapperDeltaCoord.txt
index c1ead814..faf832c7 100644
--- a/src/Nerve_GIC/example/MapperDeltaCoord.txt
+++ b/src/Nerve_GIC/example/MapperDeltaCoord.txt
@@ -1,134 +1,143 @@
-../../../../data/points/human.off
-coordinate 2
-coordinate 2
-0.072934 0.3
-65 64
-0 -0.954816 218
-1 -0.954824 218
-2 -0.903705 57
-3 -0.9035 57
-4 -0.84796 27
-5 -0.847937 27
-6 -0.794255 25
-7 -0.791001 29
-8 -0.73369 36
-9 -0.733071 35
-10 -0.683795 40
-11 -0.682735 40
-12 -0.633796 48
-13 -0.634232 48
-14 -0.585137 64
-15 -0.585197 64
-16 -0.527997 66
-17 -0.528025 66
-18 -0.478646 93
-19 -0.478673 93
-20 -0.43674 99
-21 -0.436761 99
-22 -0.380976 70
-23 -0.380955 70
-24 -0.33528 72
-25 -0.335279 72
-26 -0.277496 112
-27 -0.232679 96
-28 -0.1842 77
-29 -0.149795 16
-30 -0.150304 16
-31 -0.119698 90
-32 -0.122291 74
-33 -0.119626 94
-34 -0.0849586 74
-35 -0.0681724 107
-36 -0.0856915 73
-37 -0.0263688 211
-38 -0.025358 49
-39 -0.025088 50
-40 0.0287585 146
-41 0.022349 34
-42 0.0213867 34
-43 0.0768417 175
-44 0.081987 34
-45 0.0819086 34
-46 0.128047 150
-47 0.129348 53
-48 0.128561 54
-49 0.173705 104
-50 0.180884 53
-51 0.180911 53
-52 0.229553 68
-53 0.233083 77
-54 0.23311 77
-55 0.283572 215
-56 0.338574 266
-57 0.381249 299
-58 0.433627 244
-59 0.485309 214
-60 0.535849 237
-61 0.588559 193
-62 0.638771 196
-63 0.692993 222
-64 0.763344 307
-0 3
-1 2
-2 4
-3 5
-4 6
-5 7
-6 9
-7 8
-8 10
-9 11
-10 13
-11 12
-12 14
-13 15
-14 17
-15 16
-16 18
-17 19
-18 20
-19 21
-20 22
-21 23
-22 24
-23 25
-24 26
-25 26
-26 27
-27 28
-28 32
-29 31
-30 33
-31 34
-32 35
-33 36
-34 39
-35 37
-36 38
-37 40
-38 41
-39 42
-40 43
-41 45
-42 44
-43 46
-44 47
-45 48
-46 49
-47 50
-48 51
-49 52
-50 53
-51 54
-52 55
-53 55
-54 55
-55 56
-56 57
-57 58
-58 59
-59 60
-60 61
-61 62
-62 63
-63 64
+Mapper Delta is of dimension 1 - 141 simplices - 71 vertices.
+Iterator on Mapper Delta simplices
+0 
+1 
+2 
+2 1 
+3 
+3 0 
+4 
+4 2 
+5 
+5 3 
+6 
+6 4 
+7 
+7 5 
+8 
+8 6 
+9 
+9 7 
+10 
+10 9 
+11 
+11 8 
+12 
+12 11 
+13 
+13 10 
+14 
+14 12 
+15 
+15 13 
+16 
+16 14 
+17 
+17 15 
+18 
+18 17 
+19 
+19 16 
+20 
+20 18 
+21 
+21 19 
+22 
+22 20 
+23 
+23 21 
+24 
+24 22 
+25 
+25 23 
+26 
+26 24 
+27 
+27 25 
+28 
+28 26 
+28 27 
+29 
+29 28 
+30 
+30 29 
+31 
+32 
+33 
+33 30 
+34 
+34 31 
+35 
+35 32 
+36 
+36 34 
+37 
+37 33 
+38 
+38 35 
+39 
+39 37 
+40 
+40 38 
+41 
+41 36 
+42 
+42 39 
+43 
+43 40 
+44 
+44 41 
+45 
+45 42 
+46 
+46 44 
+47 
+47 43 
+48 
+48 45 
+49 
+49 46 
+50 
+50 47 
+51 
+51 48 
+52 
+52 49 
+53 
+53 50 
+54 
+54 51 
+55 
+55 52 
+56 
+56 53 
+57 
+57 54 
+58 
+58 55 
+59 
+59 56 
+60 
+60 57 
+60 58 
+60 59 
+61 
+61 60 
+62 
+62 61 
+63 
+63 62 
+64 
+64 63 
+65 
+65 64 
+66 
+66 65 
+67 
+67 66 
+68 
+68 67 
+69 
+69 68 
+70 
+70 69 
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.cpp b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
index 1c3a77a5..448323b1 100644
--- a/src/Nerve_GIC/example/MapperDeltaFunc.cpp
+++ b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
@@ -2,7 +2,7 @@
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
-  std::cerr << "Usage: " << progName << " filename.off coordinate \n";
+  std::cerr << "Usage: " << progName << " filename.off function [--v] \n";
   std::cerr << "       i.e.: " << progName << " ../../../../data/points/COIL_database/lucky_cat.off ../../../../data/points/COIL_database/lucky_cat_PCA1 --v \n";
   exit(-1);  // ----- >>
 }
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.txt b/src/Nerve_GIC/example/MapperDeltaFunc.txt
index 01b0fbea..d13d0695 100644
--- a/src/Nerve_GIC/example/MapperDeltaFunc.txt
+++ b/src/Nerve_GIC/example/MapperDeltaFunc.txt
@@ -1,17 +1,10 @@
-../../../../data/points/COIL_database/lucky_cat.off
-../../../../data/points/COIL_database/lucky_cat_PCA1
-../../../../data/points/COIL_database/lucky_cat_PCA1
-2592.99 0.3
-6 6
-0 -1382.24 20
-1 385.162 3
-2 246.455 12
-3 2204.66 4
-4 2238.94 5
-5 5346.1 39
-0 1
-0 2
-1 3
-2 4
-3 5
-4 5
+Mapper Delta is of dimension 1 - 8 simplices - 4 vertices.
+Iterator on Mapper Delta simplices
+0 
+1 
+1 0 
+2 
+2 0 
+3 
+3 1 
+3 2 
diff --git a/src/Nerve_GIC/example/Nerve.cpp b/src/Nerve_GIC/example/Nerve.cpp
index a549f544..84f74625 100644
--- a/src/Nerve_GIC/example/Nerve.cpp
+++ b/src/Nerve_GIC/example/Nerve.cpp
@@ -2,7 +2,7 @@
 
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
-  std::cerr << "Usage: " << progName << " filename.off coordinate resolution gain --v \n";
+  std::cerr << "Usage: " << progName << " filename.off coordinate resolution gain [--v] \n";
   std::cerr << "       i.e.: " << progName << " ../../../../data/human.off 2 10 0.3 --v \n";
   exit(-1);  // ----- >>
 }
diff --git a/src/Nerve_GIC/example/Nerve.txt b/src/Nerve_GIC/example/Nerve.txt
index a6fad665..2a861c5f 100644
--- a/src/Nerve_GIC/example/Nerve.txt
+++ b/src/Nerve_GIC/example/Nerve.txt
@@ -1,46 +1,43 @@
-../../../../data/points/human.off
-coordinate 2
-coordinate 2
-0 0.3
-21 20
-0 -0.927412 290
-1 -0.927011 291
-2 -0.708477 127
-3 -0.709946 128
-4 -0.513775 250
-5 -0.514319 251
-6 -0.376304 247
-7 -0.376315 247
-8 -0.104886 127
-9 -0.168391 165
-10 -0.16871 165
-11 -0.105984 128
-12 -0.0174106 183
-13 0.0197303 542
-14 -0.0161482 181
-15 0.159925 388
-16 0.204922 208
-17 0.204892 208
-18 0.368798 854
-19 0.542323 764
-20 0.709288 597
-0 2
-1 3
-2 5
-3 4
-4 6
-5 7
-6 9
-7 10
-8 12
-9 13
-10 13
-11 14
-12 16
-13 15
-14 17
-15 18
-16 18
-17 18
-18 19
-19 20
+Nerve is of dimension 1 - 41 simplices - 21 vertices.
+Iterator on Nerve simplices
+0 
+1 
+2 
+2 0 
+3 
+3 1 
+4 
+4 3 
+5 
+5 2 
+6 
+6 4 
+7 
+7 5 
+8 
+9 
+9 6 
+10 
+10 7 
+11 
+12 
+12 8 
+13 
+13 9 
+13 10 
+14 
+14 11 
+15 
+15 13 
+16 
+16 12 
+17 
+17 14 
+18 
+18 15 
+18 16 
+18 17 
+19 
+19 18 
+20 
+20 19 
diff --git a/src/Nerve_GIC/example/km.py b/src/Nerve_GIC/example/km.py
index 881273ad..a1a08156 100755
--- a/src/Nerve_GIC/example/km.py
+++ b/src/Nerve_GIC/example/km.py
@@ -248,9 +248,9 @@ class KeplerMapper(object):
       if custom_tooltips is not None:
         tooltip_s = "<h2>Cluster %s</h2>"%k + " ".join(str(custom_tooltips[complex["nodes"][k][0]]).split(" "))
         if maximum == minimum:
-          tooltip_i = int(30*(custom_tooltips[complex["nodes"][k][0]]-minimum)/(maximum-minimum))
-        else:
           tooltip_i = 0
+        else:
+          tooltip_i = int(30*(custom_tooltips[complex["nodes"][k][0]]-minimum)/(maximum-minimum))
         json_s["nodes"].append({"name": str(k), "tooltip": tooltip_s, "group": 2 * int(np.log(complex["nodes"][k][2])), "color": tooltip_i})
       else:
         tooltip_s = "<h2>Cluster %s</h2>Contains %s members."%(k,len(complex["nodes"][k]))