git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2406 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2d857904595833667d469db97c746bbd8696eac4

4 files changed, 219 insertions, 23 deletions

diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp
new file mode 100644
index 00000000..5161a46b
--- /dev/null
+++ b/src/Nerve_GIC/example/GIC.cpp
@@ -0,0 +1,77 @@
+#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/example/MapperDelta.cpp b/src/Nerve_GIC/example/MapperDelta.cpp
new file mode 100644
index 00000000..1f8f1582
--- /dev/null
+++ b/src/Nerve_GIC/example/MapperDelta.cpp
@@ -0,0 +1,62 @@
+#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 != 6) && (argc != 7)) usage(argc, (argv[0] - 1));
+
+  std::string off_file_name(argv[1]);
+  int coord = atoi(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_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_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/Nerve.cpp b/src/Nerve_GIC/example/Nerve.cpp
new file mode 100644
index 00000000..adcc715d
--- /dev/null
+++ b/src/Nerve_GIC/example/Nerve.cpp
@@ -0,0 +1,63 @@
+#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/points/human.off 2 1 0.3 --v \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]);
+  int coord = atoi(argv[2]);
+  double resolution = atof(argv[3]);
+  double gain = atof(argv[4]);
+  bool verb = 0; if(argc == 6)  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 Nerve from an OFF file
+  // --------------------------------
+
+  Gudhi::graph_induced_complex::Graph_induced_complex GIC;
+  GIC.set_verbose(verb);
+
+  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.find_Nerve_simplices();
+  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 << "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 << std::endl;
+    }
+  }
+
+  return 0;
+}
diff --git a/src/Nerve_GIC/example/simple_GIC.cpp b/src/Nerve_GIC/example/simple_GIC.cpp
index 8b3aecb8..5161a46b 100644
--- a/src/Nerve_GIC/example/simple_GIC.cpp
+++ b/src/Nerve_GIC/example/simple_GIC.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 threshold coordinate resolution gain [ouput_file.txt]\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);  // ----- >>
 }
@@ -16,6 +16,7 @@ int main(int argc, char **argv) {
   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,\
@@ -27,8 +28,9 @@ int main(int argc, char **argv) {
   // ----------------------------------------------------------------------------
 
   Gudhi::graph_induced_complex::Graph_induced_complex GIC;
+  GIC.set_verbose(verb);
 
-  GIC.set_graph_from_automatic_rips(100, off_file_name);
+  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);
 
@@ -38,9 +40,9 @@ int main(int argc, char **argv) {
   GIC.set_color_from_coordinate(coord, off_file_name);
   //GIC.set_color_from_file(func_file_name);
 
-  resolution = GIC.set_automatic_resolution_for_GICMAP();
-
-  GIC.set_cover_from_function(resolution,gain,1);
+  GIC.set_automatic_resolution_for_GICMAP();
+  GIC.set_gain();
+  GIC.set_cover_from_function(1);
 
   //GIC.find_GIC_simplices();
   //GIC.find_Nerve_simplices();
@@ -50,34 +52,26 @@ int main(int argc, char **argv) {
 
   Simplex_tree stree; GIC.create_complex(stree);
 
-  std::streambuf* streambufffer;
-  std::ofstream ouput_file_stream;
-
-  if (argc == 7) {
-    ouput_file_stream.open(std::string(argv[4]));
-    streambufffer = ouput_file_stream.rdbuf();
-  } else {
-    streambufffer = std::cout.rdbuf();
-  }
-
+  std::streambuf* streambufffer = std::cout.rdbuf();
   std::ostream output_stream(streambufffer);
 
   // ----------------------------------------------------------------------------
   // Display information about the graph induced complex
   // ----------------------------------------------------------------------------
-  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;
   }
 
-  ouput_file_stream.close();
-
   return 0;
 }