git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2462 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b158f4e6fab11aae7ee9927324829aa0b4c18026

7 files changed, 252 insertions, 122 deletions

diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp
index 1889cb33..0f50f712 100644
--- a/src/Nerve_GIC/example/GIC.cpp
+++ b/src/Nerve_GIC/example/GIC.cpp
@@ -1,3 +1,25 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Mathieu Carrière
+ *
+ *    Copyright (C) 2017  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 #include <gudhi/GIC.h>
 
 void usage(int nbArgs, char * const progName) {
@@ -24,40 +46,44 @@ int main(int argc, char **argv) {
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
   GIC.set_verbose(verb);
 
-  GIC.read_point_cloud(off_file_name);
+  bool check = GIC.read_point_cloud(off_file_name);
 
-  GIC.set_color_from_coordinate(coord);
-  GIC.set_function_from_coordinate(coord);
+  if(!check)  std::cout << "Incorrect OFF file." << std::endl;
+  else{
 
-  GIC.set_graph_from_rips(threshold);
+    GIC.set_color_from_coordinate(coord);
+    GIC.set_function_from_coordinate(coord);
 
-  GIC.set_resolution_double(resolution); GIC.set_gain(gain);
-  GIC.set_cover_from_function(1);
+    GIC.set_graph_from_rips(threshold);
 
-  GIC.find_GIC_simplices();
+    GIC.set_resolution_double(resolution); GIC.set_gain(gain);
+    GIC.set_cover_from_function(1);
 
-  GIC.plot_with_KeplerMapper();
+    GIC.find_GIC_simplices();
 
-  Simplex_tree stree; GIC.create_complex(stree);
+    GIC.plot_txt();
 
-  std::streambuf* streambufffer = std::cout.rdbuf();
-  std::ostream output_stream(streambufffer);
+    Simplex_tree stree; GIC.create_complex(stree);
 
-  // ----------------------------------------------------------------------------
-  // Display information about the graph induced complex
-  // ----------------------------------------------------------------------------
+    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() <<
+    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 << "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;
       }
-      output_stream << std::endl;
     }
   }
 
diff --git a/src/Nerve_GIC/example/GICvoronoi.cpp b/src/Nerve_GIC/example/GICvoronoi.cpp
index 9bf3de5e..8061c42d 100644
--- a/src/Nerve_GIC/example/GICvoronoi.cpp
+++ b/src/Nerve_GIC/example/GICvoronoi.cpp
@@ -1,3 +1,25 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Mathieu Carrière
+ *
+ *    Copyright (C) 2017  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 #include <gudhi/GIC.h>
 
 void usage(int nbArgs, char * const progName) {
@@ -21,38 +43,42 @@ int main(int argc, char **argv) {
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
   GIC.set_verbose(verb);
 
-  GIC.read_point_cloud(off_file_name);
+  bool check = GIC.read_point_cloud(off_file_name);
 
-  GIC.set_color_from_coordinate();
+  if(!check)  std::cout << "Incorrect OFF file." << std::endl;
+  else{
 
-  GIC.set_graph_from_OFF(off_file_name);
+    GIC.set_color_from_coordinate();
 
-  GIC.set_cover_from_Voronoi(m);
+    GIC.set_graph_from_OFF(off_file_name);
 
-  GIC.find_GIC_simplices();
+    GIC.set_cover_from_Voronoi(m);
 
-  GIC.plot_with_Geomview();
+    GIC.find_GIC_simplices();
 
-  Simplex_tree stree; GIC.create_complex(stree);
+    GIC.plot_OFF();
 
-  std::streambuf* streambufffer = std::cout.rdbuf();
-  std::ostream output_stream(streambufffer);
+    Simplex_tree stree; GIC.create_complex(stree);
 
-  // ----------------------------------------------------------------------------
-  // Display information about the graph induced complex
-  // ----------------------------------------------------------------------------
+    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;
+    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 << "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;
       }
-      output_stream << std::endl;
     }
   }
 
diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.cpp b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
index 9445e988..84a25bad 100644
--- a/src/Nerve_GIC/example/MapperDeltaCoord.cpp
+++ b/src/Nerve_GIC/example/MapperDeltaCoord.cpp
@@ -1,3 +1,25 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Mathieu Carrière
+ *
+ *    Copyright (C) 2017  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 #include <gudhi/GIC.h>
 
 void usage(int nbArgs, char * const progName) {
@@ -21,40 +43,44 @@ int main(int argc, char **argv) {
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
   GIC.set_verbose(verb);
 
-  GIC.read_point_cloud(off_file_name);
+  bool check = GIC.read_point_cloud(off_file_name);
+
+  if(!check)  std::cout << "Incorrect OFF file." << std::endl;
+  else{
 
-  GIC.set_color_from_coordinate(coord);
-  GIC.set_function_from_coordinate(coord);
+    GIC.set_color_from_coordinate(coord);
+    GIC.set_function_from_coordinate(coord);
 
-  GIC.set_graph_from_automatic_rips();
+    GIC.set_graph_from_automatic_rips();
 
-  GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
-  GIC.set_cover_from_function(1);
+    GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
+    GIC.set_cover_from_function(1);
 
-  GIC.find_GICMAP_simplices_with_functional_minimal_cover();
+    GIC.find_GICMAP_simplices_with_functional_minimal_cover();
 
-  GIC.plot_with_KeplerMapper();
+    GIC.plot_txt();
 
-  Simplex_tree stree; GIC.create_complex(stree);
+    Simplex_tree stree; GIC.create_complex(stree);
 
-  std::streambuf* streambufffer = std::cout.rdbuf();
-  std::ostream output_stream(streambufffer);
+    std::streambuf* streambufffer = std::cout.rdbuf();
+    std::ostream output_stream(streambufffer);
 
-  // ------------------------------------------
-  // Display information about the Mapper Delta
-  // ------------------------------------------
+    // ------------------------------------------
+    // 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;
+    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 << "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;
       }
-      output_stream << std::endl;
     }
   }
 
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.cpp b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
index 448323b1..fa95ca58 100644
--- a/src/Nerve_GIC/example/MapperDeltaFunc.cpp
+++ b/src/Nerve_GIC/example/MapperDeltaFunc.cpp
@@ -1,3 +1,25 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Mathieu Carrière
+ *
+ *    Copyright (C) 2017  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 #include <gudhi/GIC.h>
 
 void usage(int nbArgs, char * const progName) {
@@ -21,40 +43,44 @@ int main(int argc, char **argv) {
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
   GIC.set_verbose(verb);
 
-  GIC.read_point_cloud(off_file_name);
+  bool check = GIC.read_point_cloud(off_file_name);
+
+  if(!check)  std::cout << "Incorrect OFF file." << std::endl;
+  else{
 
-  GIC.set_color_from_file(func_file_name);
-  GIC.set_function_from_file(func_file_name);
+    GIC.set_color_from_file(func_file_name);
+    GIC.set_function_from_file(func_file_name);
 
-  GIC.set_graph_from_automatic_rips();
+    GIC.set_graph_from_automatic_rips();
 
-  GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
-  GIC.set_cover_from_function(1);
+    GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
+    GIC.set_cover_from_function(1);
 
-  GIC.find_GICMAP_simplices_with_functional_minimal_cover();
+    GIC.find_GICMAP_simplices_with_functional_minimal_cover();
 
-  GIC.plot_with_KeplerMapper();
+    GIC.plot_pdf();
 
-  Simplex_tree stree; GIC.create_complex(stree);
+    Simplex_tree stree; GIC.create_complex(stree);
 
-  std::streambuf* streambufffer = std::cout.rdbuf();
-  std::ostream output_stream(streambufffer);
+    std::streambuf* streambufffer = std::cout.rdbuf();
+    std::ostream output_stream(streambufffer);
 
-  // ------------------------------------------
-  // Display information about the Mapper Delta
-  // ------------------------------------------
+    // ------------------------------------------
+    // 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;
+    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 << "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;
       }
-      output_stream << std::endl;
     }
   }
 
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.dot b/src/Nerve_GIC/example/MapperDeltaFunc.dot
new file mode 100644
index 00000000..beafa7f1
--- /dev/null
+++ b/src/Nerve_GIC/example/MapperDeltaFunc.dot
@@ -0,0 +1,10 @@
+graph Mapper {
+0[shape=circle fontcolor=black color=black label="0:26" style=filled fillcolor="0, 1, 1"]
+1[shape=circle fontcolor=black color=black label="1:4" style=filled fillcolor="0.240095, 1, 1"]
+2[shape=circle fontcolor=black color=black label="2:11" style=filled fillcolor="0.209621, 1, 1"]
+3[shape=circle fontcolor=black color=black label="3:42" style=filled fillcolor="0.6, 1, 1"]
+  0 -- 1 [weight=15];
+  0 -- 2 [weight=15];
+  1 -- 3 [weight=15];
+  2 -- 3 [weight=15];
+}
\ No newline at end of file
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.txt b/src/Nerve_GIC/example/MapperDeltaFunc.txt
deleted file mode 100644
index d13d0695..00000000
--- a/src/Nerve_GIC/example/MapperDeltaFunc.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-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 84f74625..8f8037d4 100644
--- a/src/Nerve_GIC/example/Nerve.cpp
+++ b/src/Nerve_GIC/example/Nerve.cpp
@@ -1,9 +1,31 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       Mathieu Carrière
+ *
+ *    Copyright (C) 2017  INRIA Saclay (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
 #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 resolution gain [--v] \n";
-  std::cerr << "       i.e.: " << progName << " ../../../../data/human.off 2 10 0.3 --v \n";
+  std::cerr << "       i.e.: " << progName << " ../../../../data/points/human.off 2 10 0.3 --v \n";
   exit(-1);  // ----- >>
 }
 
@@ -23,40 +45,44 @@ int main(int argc, char **argv) {
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
   GIC.set_verbose(verb);
 
-  GIC.read_point_cloud(off_file_name);
+  bool check = GIC.read_point_cloud(off_file_name);
+
+  if(!check)  std::cout << "Incorrect OFF file." << std::endl;
+  else{
 
-  GIC.set_color_from_coordinate(coord);
-  GIC.set_function_from_coordinate(coord);
+    GIC.set_color_from_coordinate(coord);
+    GIC.set_function_from_coordinate(coord);
 
-  GIC.set_graph_from_OFF(off_file_name);
+    GIC.set_graph_from_OFF(off_file_name);
 
-  GIC.set_resolution_int(resolution); GIC.set_gain(gain);
-  GIC.set_cover_from_function(0);
+    GIC.set_resolution_int(resolution); GIC.set_gain(gain);
+    GIC.set_cover_from_function(0);
 
-  GIC.find_Nerve_simplices();
+    GIC.find_Nerve_simplices();
 
-  GIC.plot_with_KeplerMapper();
+    GIC.plot_txt();
 
-  Simplex_tree stree; GIC.create_complex(stree);
+    Simplex_tree stree; GIC.create_complex(stree);
 
-  std::streambuf* streambufffer = std::cout.rdbuf();
-  std::ostream output_stream(streambufffer);
+    std::streambuf* streambufffer = std::cout.rdbuf();
+    std::ostream output_stream(streambufffer);
 
-  // ----------------------------------------------------------------------------
-  // Display information about the graph induced complex
-  // ----------------------------------------------------------------------------
+    // ----------------------------------------------------------------------------
+    // Display information about the graph induced complex
+    // ----------------------------------------------------------------------------
 
-  if(verb){
-    output_stream << "Nerve is of dimension " << stree.dimension() <<
-                   " - " << stree.num_simplices() << " simplices - " <<
-                   stree.num_vertices() << " vertices." << std::endl;
+    if(verb){
+      output_stream << "Nerve is of dimension " << stree.dimension() <<
+                     " - " << stree.num_simplices() << " simplices - " <<
+                     stree.num_vertices() << " vertices." << std::endl;
 
-    output_stream << "Iterator on Nerve 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 << "Iterator on Nerve 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;
       }
-      output_stream << std::endl;
     }
   }