git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2408 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 324d557360a52e7181d9cf3c7d77c8445a367808

12 files changed, 396 insertions, 137 deletions

diff --git a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
index 0b51e345..44e23983 100644
--- a/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
+++ b/src/Nerve_GIC/doc/Intro_graph_induced_complex.h
@@ -33,9 +33,7 @@ namespace graph_induced_complex {
  * 
  * @{
  * 
- * \section complexes Graph induced complexes (GIC) and Nerves
- * 
- * GIC and Nerves are simplicial complexes built on top of a point cloud P.
+ * \section nerves Nerves
  *
  * \subsection nervedefinition Nerve definition
  *
@@ -46,78 +44,106 @@ namespace graph_induced_complex {
  *
  * \subsection nerveexample Example
  *
- * This example builds the Nerve of a point cloud sampled on a 3D human shape.
- * The cover C comes from the preimages of intervals covering the height function.
+ * This example builds the Nerve of a point cloud sampled on a 3D human shape (human.off).
+ * The cover C comes from the preimages of intervals (10 intervals with gain 0.3)
+ * covering the height function (coordinate 2),
+ * which are then refined into their connected components using the triangulation of the .OFF file.
  * All intervals have the resolution (either the length or the number of the intervals)
  * and gain (overlap percentage).
  *
- * \include
+ * \include Nerve_GIC/Nerve.cpp
  *
  * When launching:
  *
- * \code $>
+ * \code $> ./Nerve ../../../data/points/human.off 2 10 0.3
  * \endcode
  *
  * the program output is:
  *
- * \include
+ * \include Nerve_GIC/Nerve.txt
+ *
+ * \section gic Graph Induced Complexes (GIC)
  *
- * \section gicdefinition GIC definition
+ * \subsection gicdefinition GIC definition
  *
  * Again, assume you are given a cover C of your point cloud P. Moreover, assume
  * you are also given a graph G built on top of P. Then, for any clique in G
  * whose nodes all belong to different elements of C, the GIC includes a corresponding
  * simplex, whose dimension is the number of nodes in the clique minus one.
+ * See <a target="_blank" href="https://arxiv.org/abs/1304.0662"> this article </a>
+ * for more details.
  *
  * \subsection gicexample Example
  *
- * This example builds the GIC of a point cloud sampled on a 3D human shape.
- * The cover C comes from the preimages of intervals covering the height function,
- * and the graph G comes from a Rips complex built with a threshold parameter.
+ * This example builds the GIC of a point cloud sampled on a 3D human shape (human.off).
+ * The cover C comes from the preimages of intervals (with length 0.1 and gain 0)
+ * covering the height function (coordinate 2),
+ * and the graph G comes from a Rips complex built with threshold 0.1.
  * Note that if the gain is too big, the number of cliques increases a lot,
  * which make the computation time much larger.
  *
- * \include
+ * \include Nerve_GIC/GIC.cpp
  *
  * When launching:
  *
- * \code $>
+ * \code $> ./GIC ../../../data/points/human.off 0.1 2 0.1 0
  * \endcode
  *
  * the program output is:
  *
- * \include
+ * \include Nerve_GIC/GIC.txt
  *
  * \subsection mapperdeltadefinition Mapper Delta
  *
  * If one restricts to the cliques in G whose nodes all belong to preimages of consecutive
  * intervals (assuming the cover of the height function is minimal, i.e. no more than
  * two intervals can intersect at a time), the GIC is of dimension one, i.e. a graph.
- * We call this graph the Mapper Delta, since it is related to the usual Mapper (see
- * <a target="_blank" href="https://arxiv.org/abs/1511.05823"> this article </a>).
+ * We call this graph the Mapper Delta, since it is related to the usual Mapper. See
+ * <a target="_blank" href="https://arxiv.org/abs/1511.05823"> this article </a> for more details.
  *
  * \subsection mapperdeltaexample Example
  *
  * Mapper Delta comes with optimal selection for the Rips threshold,
  * the resolution and the gain of the function cover. In this example,
- * we compute the Mapper Delta of a point cloud sampled on a 3D human shape,
+ * we compute the Mapper Delta of a point cloud sampled on a 3D human shape (human.off),
  * where the graph G comes from a Rips complex with optimal threshold,
- * and the cover C comes from the preimages of intervals covering the height function,
+ * and the cover C comes from the preimages of intervals covering the height function (coordinate 2),
  * with optimal resolution and gain. Note that optimal threshold, resolution and gain
  * also exist for the Nerve of this cover.
  *
- * \include
+ * \include Nerve_GIC/MapperDeltaCoord.cpp
  *
  * When launching:
  *
- * \code $>
+ * \code $> ./MapperDeltaCoord ../../../data/points/human.off 2
  * \endcode
  *
  * the program output is:
  *
- * \include
+ * \include MapperDeltaCoord.txt
+ *
+ * We also provide an example on a set of 72 pictures taken around the same object (lucky_cat.off).
+ * The function is now the first eigenfunction given by PCA, whose values
+ * are written in a file (lucky_cat_PCA1). Threshold, resolution and gain are automatically selected as before.
+ *
+ * \include Nerve_GIC/MapperDeltaFunc.cpp
+ *
+ * When launching:
+ *
+ * \code $> ./MapperDeltaFunc ../../../data/points/COIL_database/lucky_cat.off ../../../data/points/COIL_database/lucky_cat_PCA1
+ * \endcode
+ *
+ * the program output is:
+ *
+ * \include MapperDeltaFunc.txt
+ *
+ * If you have python and firefox, all the previous .txt files can then be plotted using
+ * <a target="_blank" href="https://github.com/MLWave/kepler-mapper"> Kepler-Mapper </a>
+ * with the following:
+ *
+ * \code python visu.py && firefox SC_visu.html
+ * \endcode
  *
- * 
  * \copyright GNU General Public License v3.                         
  * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
  */
diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
index e4debf2d..d499613d 100644
--- a/src/Nerve_GIC/example/CMakeLists.txt
+++ b/src/Nerve_GIC/example/CMakeLists.txt
@@ -1,8 +1,21 @@
 cmake_minimum_required(VERSION 2.6)
 project(Nerve_GIC_examples)
 
-add_executable ( GIC simple_GIC.cpp )
-target_link_libraries(GIC ${Boost_SYSTEM_LIBRARY})
+add_executable ( Nerve Nerve.cpp )
+target_link_libraries(Nerve  ${Boost_SYSTEM_LIBRARY})
+
+add_executable ( GIC GIC.cpp )
+target_link_libraries(GIC  ${Boost_SYSTEM_LIBRARY})
+
+add_executable ( MapperDeltaCoord MapperDeltaCoord.cpp )
+target_link_libraries(MapperDeltaCoord  ${Boost_SYSTEM_LIBRARY})
+
+add_executable ( MapperDeltaFunc MapperDeltaFunc.cpp )
+target_link_libraries(MapperDeltaFunc  ${Boost_SYSTEM_LIBRARY})
+
 if (TBB_FOUND)
+  target_link_libraries(Nerve ${TBB_LIBRARIES})
   target_link_libraries(GIC ${TBB_LIBRARIES})
+  target_link_libraries(MapperDeltaCoord ${TBB_LIBRARIES})
+  target_link_libraries(MapperDeltaFunc ${TBB_LIBRARIES})
 endif()
\ No newline at end of file
diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp
index 5161a46b..30a485d5 100644
--- a/src/Nerve_GIC/example/GIC.cpp
+++ b/src/Nerve_GIC/example/GIC.cpp
@@ -3,7 +3,7 @@
 void usage(int nbArgs, char * const progName) {
   std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
   std::cerr << "Usage: " << progName << " filename.off threshold coordinate resolution gain\n";
-  std::cerr << "       i.e.: " << progName << " ../../data/points/test.off 1.5 1 10 0.3 \n";
+  std::cerr << "       i.e.: " << progName << " ../../../data/points/human.off 1.5 2 10 0.3 \n";
   exit(-1);  // ----- >>
 }
 
@@ -12,7 +12,6 @@ int main(int argc, char **argv) {
 
   std::string off_file_name(argv[1]);
   double threshold = atof(argv[2]);
-  //std::string func_file_name = argv[3];
   int coord = atoi(argv[3]);
   double resolution = atof(argv[4]);
   double gain = atof(argv[5]);
@@ -30,24 +29,12 @@ int main(int argc, char **argv) {
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
   GIC.set_verbose(verb);
 
-  GIC.set_graph_from_automatic_rips(off_file_name);
-  //GIC.set_graph_from_rips(threshold, off_file_name);
-  //GIC.set_graph_from_OFF(off_file_name);
-
+  GIC.set_graph_from_rips(threshold, off_file_name);
   GIC.set_function_from_coordinate(coord, off_file_name);
-  //GIC.set_function_from_file(func_file_name);
-
-  GIC.set_color_from_coordinate(coord, off_file_name);
-  //GIC.set_color_from_file(func_file_name);
-
-  GIC.set_automatic_resolution_for_GICMAP();
-  GIC.set_gain();
+  GIC.set_color_from_coordinate(off_file_name, coord);
+  GIC.set_resolution_double(resolution); GIC.set_gain(gain);
   GIC.set_cover_from_function(1);
-
-  //GIC.find_GIC_simplices();
-  //GIC.find_Nerve_simplices();
-  GIC.find_GICMAP_simplices_with_functional_minimal_cover();
-
+  GIC.find_GIC_simplices();
   GIC.plot_with_KeplerMapper();
 
   Simplex_tree stree; GIC.create_complex(stree);
diff --git a/src/Nerve_GIC/example/GIC.txt b/src/Nerve_GIC/example/GIC.txt
new file mode 100644
index 00000000..9871cf41
--- /dev/null
+++ b/src/Nerve_GIC/example/GIC.txt
@@ -0,0 +1,57 @@
+Cloud
+Function
+0 0
+27 26
+0 -0.949318 240
+1 -0.949346 240
+2 -0.822129 50
+3 -0.822037 51
+4 -0.723847 48
+5 -0.722679 48
+6 -0.625409 57
+7 -0.625771 57
+8 -0.528161 99
+9 -0.528188 99
+10 -0.436343 126
+11 -0.436356 126
+12 -0.330775 194
+13 -0.233638 98
+14 -0.116276 100
+15 -0.129017 144
+16 -0.116513 103
+17 -0.0213554 243
+18 -0.0301512 65
+19 -0.0315443 66
+20 0.0750623 308
+21 0.166778 305
+22 0.270037 307
+23 0.371609 380
+24 0.468078 306
+25 0.567395 312
+26 0.721079 534
+0 3
+1 2
+2 5
+3 4
+4 7
+5 6
+6 9
+7 8
+8 10
+9 11
+10 12
+11 12
+12 13
+13 15
+14 19
+15 17
+16 18
+17 20
+18 20
+19 20
+20 21
+21 22
+22 23
+23 24
+24 25
+25 26
diff --git a/src/Nerve_GIC/example/MapperDelta.cpp b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
index 1f8f1582..aa12afe6 100644
--- a/src/Nerve_GIC/example/MapperDelta.cpp
+++ b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
@@ -3,12 +3,12 @@
 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 << "       i.e.: " << progName << " ../../data/points/human.off 2 --v \n";
+  std::cerr << "       i.e.: " << progName << " ../../../data/points/human.off 2 --v \n";
   exit(-1);  // ----- >>
 }
 
 int main(int argc, char **argv) {
-  if ((argc != 6) && (argc != 7)) usage(argc, (argv[0] - 1));
+  if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
 
   std::string off_file_name(argv[1]);
   int coord = atoi(argv[2]);
@@ -28,9 +28,8 @@ int main(int argc, char **argv) {
 
   GIC.set_graph_from_automatic_rips(off_file_name);
   GIC.set_function_from_coordinate(coord, off_file_name);
-  GIC.set_color_from_coordinate(coord, off_file_name);
-  GIC.set_automatic_resolution_for_GICMAP();
-  GIC.set_gain();
+  GIC.set_color_from_coordinate(off_file_name, coord);
+  GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
   GIC.set_cover_from_function(1);
   GIC.find_GICMAP_simplices_with_functional_minimal_cover();
   GIC.plot_with_KeplerMapper();
diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.txt b/src/Nerve_GIC/example/MapperDeltaCoord.txt
new file mode 100644
index 00000000..2c2296ea
--- /dev/null
+++ b/src/Nerve_GIC/example/MapperDeltaCoord.txt
@@ -0,0 +1,125 @@
+Cloud
+Function
+0 0
+61 60
+0 -0.954369 220
+1 -0.954377 220
+2 -0.902361 54
+3 -0.901235 55
+4 -0.84796 27
+5 -0.844637 29
+6 -0.777883 37
+7 -0.778882 39
+8 -0.72868 42
+9 -0.72734 42
+10 -0.677728 48
+11 -0.676848 48
+12 -0.633796 48
+13 -0.634232 48
+14 -0.567924 52
+15 -0.567897 52
+16 -0.52287 77
+17 -0.522897 77
+18 -0.467859 105
+19 -0.467886 105
+20 -0.422377 87
+21 -0.422383 87
+22 -0.363537 80
+23 -0.363508 80
+24 -0.312836 126
+25 -0.267775 84
+26 -0.197152 78
+27 -0.149293 96
+28 -0.134636 48
+29 -0.134463 51
+30 -0.104389 93
+31 -0.108561 96
+32 -0.105219 93
+33 -0.0362235 183
+34 -0.0498358 53
+35 -0.050197 51
+36 -0.000444973 187
+37 0.000472738 42
+38 -0.000214643 42
+39 0.0616246 164
+40 0.0590725 29
+41 0.0590271 31
+42 0.108834 170
+43 0.110991 50
+44 0.110952 50
+45 0.158372 129
+46 0.161945 54
+47 0.161972 54
+48 0.210958 76
+49 0.221521 73
+50 0.221548 73
+51 0.263419 220
+52 0.324345 241
+53 0.371963 311
+54 0.422902 272
+55 0.476693 223
+56 0.530461 246
+57 0.58285 217
+58 0.63636 203
+59 0.690953 230
+60 0.76296 309
+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 24
+24 25
+25 26
+26 27
+27 31
+28 30
+29 32
+30 35
+31 33
+32 34
+33 36
+34 37
+35 38
+36 39
+37 41
+38 40
+39 42
+40 43
+41 44
+42 45
+43 46
+44 47
+45 48
+46 49
+47 50
+48 51
+49 51
+50 51
+51 52
+52 53
+53 54
+54 55
+55 56
+56 57
+57 58
+58 59
+59 60
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.cpp b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
new file mode 100644
index 00000000..20924b9c
--- /dev/null
+++ b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
@@ -0,0 +1,61 @@
+#include <gudhi/GIC.h>
+
+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 << "       i.e.: " << progName << " ../../../data/points/human.off 2 --v \n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
+
+  std::string off_file_name(argv[1]);
+  std::string func_file_name = argv[2];
+  bool verb = 0; if(argc == 4)  verb = 1;
+
+  // Type definitions
+  using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,\
+                                          boost::property < vertex_filtration_t, Filtration_value >,\
+                                          boost::property < edge_filtration_t, Filtration_value > >;
+
+  // ---------------------------------------
+  // Init of a Mapper Delta from an OFF file
+  // ---------------------------------------
+
+  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
+  GIC.set_verbose(verb);
+
+  GIC.set_graph_from_automatic_rips(off_file_name);
+  GIC.set_function_from_file(func_file_name);
+  GIC.set_color_from_file(func_file_name);
+  GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
+  GIC.set_cover_from_function(1);
+  GIC.find_GICMAP_simplices_with_functional_minimal_cover();
+  GIC.plot_with_KeplerMapper();
+
+  Simplex_tree stree; GIC.create_complex(stree);
+
+  std::streambuf* streambufffer = std::cout.rdbuf();
+  std::ostream output_stream(streambufffer);
+
+  // ------------------------------------------
+  // Display information about the Mapper Delta
+  // ------------------------------------------
+
+  if(verb){
+    output_stream << "Mapper Delta is of dimension " << stree.dimension() <<
+                   " - " << stree.num_simplices() << " simplices - " <<
+                   stree.num_vertices() << " vertices." << std::endl;
+
+    output_stream << "Iterator on Mapper Delta simplices" << std::endl;
+    for (auto f_simplex : stree.filtration_simplex_range()) {
+      for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+        output_stream << vertex << " ";
+      }
+      output_stream << std::endl;
+    }
+  }
+
+  return 0;
+}
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.txt b/src/Nerve_GIC/example/MapperDeltaFunc.txt
new file mode 100644
index 00000000..046d2278
--- /dev/null
+++ b/src/Nerve_GIC/example/MapperDeltaFunc.txt
@@ -0,0 +1,16 @@
+Cloud
+Function
+0 0
+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
diff --git a/src/Nerve_GIC/example/Nerve.cpp b/src/Nerve_GIC/example/Nerve.cpp
index adcc715d..d4a68c71 100644
--- a/src/Nerve_GIC/example/Nerve.cpp
+++ b/src/Nerve_GIC/example/Nerve.cpp
@@ -3,16 +3,16 @@
 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 << "       i.e.: " << progName << " ../../data/points/human.off 2 1 0.3 --v \n";
+  std::cerr << "       i.e.: " << progName << " ../../../data/points/human.off 2 10 0.3 --v \n";
   exit(-1);  // ----- >>
 }
 
 int main(int argc, char **argv) {
-  if ((argc != 6) && (argc != 7)) usage(argc, (argv[0] - 1));
+  if ((argc != 5) && (argc != 6)) usage(argc, (argv[0] - 1));
 
   std::string off_file_name(argv[1]);
   int coord = atoi(argv[2]);
-  double resolution = atof(argv[3]);
+  int resolution = atoi(argv[3]);
   double gain = atof(argv[4]);
   bool verb = 0; if(argc == 6)  verb = 1;
 
@@ -28,11 +28,11 @@ int main(int argc, char **argv) {
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
   GIC.set_verbose(verb);
 
+  GIC.set_graph_from_OFF(off_file_name);
   GIC.set_function_from_coordinate(coord, off_file_name);
-  GIC.set_color_from_coordinate(coord, off_file_name);
-  GIC.set_resolution_double(resolution);
-  GIC.set_gain(gain);
-  GIC.set_cover_from_function(1);
+  GIC.set_color_from_coordinate(off_file_name, --coord);
+  GIC.set_resolution_int(resolution); GIC.set_gain(gain);
+  GIC.set_cover_from_function(0);
   GIC.find_Nerve_simplices();
   GIC.plot_with_KeplerMapper();
 
diff --git a/src/Nerve_GIC/example/Nerve.txt b/src/Nerve_GIC/example/Nerve.txt
new file mode 100644
index 00000000..9ebb2fbb
--- /dev/null
+++ b/src/Nerve_GIC/example/Nerve.txt
@@ -0,0 +1,45 @@
+Cloud
+Function
+0 0
+21 20
+0 -0.0149926 290
+1 -0.0152551 291
+2 -0.0695028 127
+3 -0.0700955 128
+4 -0.0449554 250
+5 -0.045006 251
+6 -0.0130144 247
+7 -0.0131973 247
+8 0.0766414 127
+9 -0.0118972 165
+10 -0.0121551 165
+11 0.0785204 128
+12 0.0559145 183
+13 -0.0298394 542
+14 0.0569878 181
+15 -0.0201742 388
+16 -0.00110905 208
+17 -0.00131087 208
+18 0.0228028 854
+19 0.0181739 764
+20 0.0307483 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
diff --git a/src/Nerve_GIC/example/simple_GIC.cpp b/src/Nerve_GIC/example/simple_GIC.cpp
deleted file mode 100644
index 5161a46b..00000000
--- a/src/Nerve_GIC/example/simple_GIC.cpp
+++ /dev/null
@@ -1,77 +0,0 @@
-#include <gudhi/GIC.h>
-
-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/test.off 1.5 1 10 0.3 \n";
-  exit(-1);  // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if ((argc != 6) && (argc != 7)) usage(argc, (argv[0] - 1));
-
-  std::string off_file_name(argv[1]);
-  double threshold = atof(argv[2]);
-  //std::string func_file_name = argv[3];
-  int coord = atoi(argv[3]);
-  double resolution = atof(argv[4]);
-  double gain = atof(argv[5]);
-  bool verb = 0; if(argc == 7)  verb = 1;
-
-  // Type definitions
-  using Graph_t = boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS,\
-                                          boost::property < vertex_filtration_t, Filtration_value >,\
-                                          boost::property < edge_filtration_t, Filtration_value > >;
-
-  // ----------------------------------------------------------------------------
-  // Init of a graph induced complex from an OFF file
-  // ----------------------------------------------------------------------------
-
-  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
-  GIC.set_verbose(verb);
-
-  GIC.set_graph_from_automatic_rips(off_file_name);
-  //GIC.set_graph_from_rips(threshold, off_file_name);
-  //GIC.set_graph_from_OFF(off_file_name);
-
-  GIC.set_function_from_coordinate(coord, off_file_name);
-  //GIC.set_function_from_file(func_file_name);
-
-  GIC.set_color_from_coordinate(coord, off_file_name);
-  //GIC.set_color_from_file(func_file_name);
-
-  GIC.set_automatic_resolution_for_GICMAP();
-  GIC.set_gain();
-  GIC.set_cover_from_function(1);
-
-  //GIC.find_GIC_simplices();
-  //GIC.find_Nerve_simplices();
-  GIC.find_GICMAP_simplices_with_functional_minimal_cover();
-
-  GIC.plot_with_KeplerMapper();
-
-  Simplex_tree stree; GIC.create_complex(stree);
-
-  std::streambuf* streambufffer = std::cout.rdbuf();
-  std::ostream output_stream(streambufffer);
-
-  // ----------------------------------------------------------------------------
-  // Display information about the graph induced complex
-  // ----------------------------------------------------------------------------
-
-  if(verb){
-    output_stream << "Graph induced complex is of dimension " << stree.dimension() <<
-                   " - " << stree.num_simplices() << " simplices - " <<
-                   stree.num_vertices() << " vertices." << std::endl;
-
-    output_stream << "Iterator on graph induced complex simplices" << std::endl;
-    for (auto f_simplex : stree.filtration_simplex_range()) {
-      for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
-        output_stream << vertex << " ";
-      }
-      output_stream << std::endl;
-    }
-  }
-
-  return 0;
-}
diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h
index abd833e0..c373b25c 100644
--- a/src/Nerve_GIC/include/gudhi/GIC.h
+++ b/src/Nerve_GIC/include/gudhi/GIC.h
@@ -45,6 +45,7 @@
 #include <algorithm>  // for std::max
 #include <cstdint>  // for std::uint32_t
 #include <random>
+#include <cassert>
 
 #define CONSTANT 10
 #define ETA 0.001
@@ -549,7 +550,7 @@ class Graph_induced_complex {
     * @param[in] off_file_name name of the input .OFF file.
     *
     */
-   void set_color_from_coordinate(int k = 0, const std::string& off_file_name){
+   void set_color_from_coordinate(const std::string& off_file_name, int k = 0){
      Points_off_reader<Point> off_reader(off_file_name);
      int numpts = off_reader.get_point_cloud().size();
      for(int i = 0; i < numpts; i++)  func_color.insert(std::pair<int,double>(i,off_reader.get_point_cloud()[i][k]));
@@ -569,7 +570,7 @@ class Graph_induced_complex {
    /** \brief Creates a .dot file for neato once the simplicial complex is computed to get a .pdf output.
     */
    void plot_with_neato(){
-     char mapp[11] = "mapper.dot";   std::ofstream graphic(mapp); graphic << "graph Mapper {" << std::endl;
+     char mapp[11] = "SC.dot";   std::ofstream graphic(mapp); graphic << "graph Mapper {" << std::endl;
      double maxv, minv; maxv = std::numeric_limits<double>::min(); minv = std::numeric_limits<double>::max();
      for (std::map<Cover_t,std::pair<int,double> >::iterator iit = cover_color.begin(); iit != cover_color.end(); iit++){
        maxv = std::max(maxv, iit->second.second);  minv = std::min(minv, iit->second.second);
@@ -598,7 +599,7 @@ class Graph_induced_complex {
    void plot_with_KeplerMapper(){
 
      int num_simplices = simplices.size(); int num_edges = 0;
-     char mapp[11] = "mapper.txt";  std::ofstream graphic(mapp);
+     char mapp[11] = "SC.txt";  std::ofstream graphic(mapp);
      for (int i = 0; i < num_simplices; i++)
        if (simplices[i].size() == 2)
          if (cover_color[simplices[i][0]].first > MASK && cover_color[simplices[i][1]].first > MASK)
@@ -711,11 +712,17 @@ class Graph_induced_complex {
    }
 
  public:
-   /** \brief Computes the simplices in the Mapper Delta.
+   /** \brief Computes the simplices in the Mapper Delta by looking at all the edges of the graph
+    * and adding the corresponding edges in the Mapper Delta if the images of the endpoints belong
+    * to consecutive intervals.
+    *
+    * \remark WARNING: the output of this function is correct ONLY if the cover is minimal, i.e.
+    * the gain is less than 0.5!!!
+    *
     */
    void find_GICMAP_simplices_with_functional_minimal_cover(){
 
-     int v1, v2;
+     int v1, v2; assert(gain < 0.5);
 
      // Loop on all points.
      for(std::map<int,std::vector<Cover_t> >::iterator it = cover.begin(); it != cover.end(); it++){