git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@2771 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: cd87a5b72b67d27b21f765fac822ea69f9496019

6 files changed, 45 insertions, 47 deletions

diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt
index ea504c11..871e46a6 100644
--- a/src/Nerve_GIC/example/CMakeLists.txt
+++ b/src/Nerve_GIC/example/CMakeLists.txt
@@ -4,24 +4,20 @@ project(Nerve_GIC_examples)
 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 ( CoordGIC CoordGIC.cpp )
+target_link_libraries(CoordGIC  ${Boost_SYSTEM_LIBRARY})
 
-add_executable ( MapperDeltaCoord MapperDeltaCoord.cpp )
-target_link_libraries(MapperDeltaCoord  ${Boost_SYSTEM_LIBRARY})
+add_executable ( FuncGIC FuncGIC.cpp )
+target_link_libraries(FuncGIC  ${Boost_SYSTEM_LIBRARY})
 
-add_executable ( MapperDeltaFunc MapperDeltaFunc.cpp )
-target_link_libraries(MapperDeltaFunc  ${Boost_SYSTEM_LIBRARY})
+add_executable ( VoronoiGIC VoronoiGIC.cpp )
+target_link_libraries(VoronoiGIC  ${Boost_SYSTEM_LIBRARY})
 
-add_executable ( GICvoronoi GICvoronoi.cpp )
-target_link_libraries(MapperDeltaFunc  ${Boost_SYSTEM_LIBRARY})
-
-file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+#[[file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)]]
 
 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})
-  target_link_libraries(GICvoronoi ${TBB_LIBRARIES})
+  target_link_libraries(CoordGIC ${TBB_LIBRARIES})
+  target_link_libraries(FuncGIC ${TBB_LIBRARIES})
+  target_link_libraries(VoronoiGIC ${TBB_LIBRARIES})
 endif()
\ No newline at end of file
diff --git a/src/Nerve_GIC/example/MapperDeltaCoord.cpp b/src/Nerve_GIC/example/CoordGIC.cpp
index 382649e8..89b0f9a4 100644
--- a/src/Nerve_GIC/example/MapperDeltaCoord.cpp
+++ b/src/Nerve_GIC/example/CoordGIC.cpp
@@ -38,12 +38,12 @@ int main(int argc, char **argv) {
   int coord = atoi(argv[2]);
   bool verb = 0; if(argc == 4)  verb = 1;
 
-  // ---------------------------------------
-  // Init of a Mapper Delta from an OFF file
-  // ---------------------------------------
+  // -----------------------------------------
+  // Init of a functional GIC from an OFF file
+  // -----------------------------------------
 
   Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
-  GIC.set_verbose(verb); GIC.set_mask(); GIC.set_subsampling();
+  GIC.set_verbose(verb);
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -55,25 +55,25 @@ int main(int argc, char **argv) {
 
     GIC.set_graph_from_automatic_rips(Gudhi::Euclidean_distance());
 
-    GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
+    GIC.set_automatic_resolution_for_GIC(); GIC.set_gain();
     GIC.set_cover_from_function();
 
-    GIC.find_GICMAP_simplices_with_functional_minimal_cover();
+    GIC.find_GIC_simplices_with_functional_minimal_cover();
 
-    GIC.plot_DOT_for_neato();
+    GIC.plot_DOT();
 
-    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::Simplex_tree<> stree; GIC.create_complex(stree);
 
-    // ------------------------------------------
-    // Display information about the Mapper Delta
-    // ------------------------------------------
+    // --------------------------------------------
+    // Display information about the functional GIC
+    // --------------------------------------------
 
     if(verb){
-      std::cout << "Mapper Delta is of dimension " << stree.dimension() <<
+      std::cout << "Functional GIC is of dimension " << stree.dimension() <<
                      " - " << stree.num_simplices() << " simplices - " <<
                      stree.num_vertices() << " vertices." << std::endl;
 
-      std::cout << "Iterator on Mapper Delta simplices" << std::endl;
+      std::cout << "Iterator on functional GIC simplices" << std::endl;
       for (auto f_simplex : stree.filtration_simplex_range()) {
         for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
           std::cout << vertex << " ";
diff --git a/src/Nerve_GIC/example/MapperDeltaFunc.cpp b/src/Nerve_GIC/example/FuncGIC.cpp
index 586b733c..56c97b7f 100644
--- a/src/Nerve_GIC/example/MapperDeltaFunc.cpp
+++ b/src/Nerve_GIC/example/FuncGIC.cpp
@@ -38,12 +38,12 @@ int main(int argc, char **argv) {
   std::string func_file_name = argv[2];
   bool verb = 0; if(argc == 4)  verb = 1;
 
-  // ---------------------------------------
-  // Init of a Mapper Delta from an OFF file
-  // ---------------------------------------
+  // -----------------------------------------
+  // Init of a functional GIC from an OFF file
+  // -----------------------------------------
 
   Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
-  GIC.set_verbose(verb); GIC.set_mask(); GIC.set_subsampling();
+  GIC.set_verbose(verb);
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -55,25 +55,25 @@ int main(int argc, char **argv) {
 
     GIC.set_graph_from_automatic_rips(Gudhi::Euclidean_distance());
 
-    GIC.set_automatic_resolution_for_GICMAP(); GIC.set_gain();
+    GIC.set_automatic_resolution_for_GIC(); GIC.set_gain();
     GIC.set_cover_from_function();
 
-    GIC.find_GICMAP_simplices_with_functional_minimal_cover();
+    GIC.find_GIC_simplices_with_functional_minimal_cover();
 
-    GIC.plot_DOT_for_neato();
+    GIC.plot_DOT();
 
-    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::Simplex_tree<> stree; GIC.create_complex(stree);
 
-    // ------------------------------------------
-    // Display information about the Mapper Delta
-    // ------------------------------------------
+    // --------------------------------------------
+    // Display information about the functional GIC
+    // --------------------------------------------
 
     if(verb){
-      std::cout << "Mapper Delta is of dimension " << stree.dimension() <<
+      std::cout << "Functional GIC is of dimension " << stree.dimension() <<
                      " - " << stree.num_simplices() << " simplices - " <<
                      stree.num_vertices() << " vertices." << std::endl;
 
-      std::cout << "Iterator on Mapper Delta simplices" << std::endl;
+      std::cout << "Iterator on functional GIC simplices" << std::endl;
       for (auto f_simplex : stree.filtration_simplex_range()) {
         for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
           std::cout << vertex << " ";
diff --git a/src/Nerve_GIC/example/GIC.cpp b/src/Nerve_GIC/example/GIC.cpp
index 6e5c5ca7..b8b5cd05 100644
--- a/src/Nerve_GIC/example/GIC.cpp
+++ b/src/Nerve_GIC/example/GIC.cpp
@@ -46,7 +46,7 @@ int main(int argc, char **argv) {
   // ----------------------------------------------------------------------------
 
   Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
-  GIC.set_verbose(verb); GIC.set_mask();
+  GIC.set_verbose(verb);
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -65,7 +65,7 @@ int main(int argc, char **argv) {
 
     GIC.plot_TXT_for_KeplerMapper();
 
-    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::Simplex_tree<> stree; GIC.create_complex(stree);
 
     // ----------------------------------------------------------------------------
     // Display information about the graph induced complex
diff --git a/src/Nerve_GIC/example/Nerve.cpp b/src/Nerve_GIC/example/Nerve.cpp
index e47982c4..e863b48b 100644
--- a/src/Nerve_GIC/example/Nerve.cpp
+++ b/src/Nerve_GIC/example/Nerve.cpp
@@ -39,13 +39,14 @@ int main(int argc, char **argv) {
   int resolution = atoi(argv[3]);
   double gain = atof(argv[4]);
   bool verb = 0; if(argc == 6)  verb = 1;
+  //int mask = 0;
 
   // --------------------------------
   // Init of a Nerve from an OFF file
   // --------------------------------
 
   Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
-  GIC.set_verbose(verb); GIC.set_mask();
+  GIC.set_verbose(verb);
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -62,9 +63,9 @@ int main(int argc, char **argv) {
 
     GIC.find_Nerve_simplices();
 
-    GIC.plot_TXT_for_KeplerMapper();
+    GIC.plot_TXT();
 
-    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::Simplex_tree<> stree; GIC.create_complex(stree);
 
     // ----------------------------------------------------------------------------
     // Display information about the graph induced complex
diff --git a/src/Nerve_GIC/example/GICvoronoi.cpp b/src/Nerve_GIC/example/VoronoiGIC.cpp
index 2c4f5acf..f000c263 100644
--- a/src/Nerve_GIC/example/GICvoronoi.cpp
+++ b/src/Nerve_GIC/example/VoronoiGIC.cpp
@@ -37,13 +37,14 @@ int main(int argc, char **argv) {
   std::string off_file_name(argv[1]);
   int m = atoi(argv[2]);
   bool verb = 0; if(argc == 4)  verb = 1;
+  //int mask = 0;
 
   // ----------------------------------------------------------------------------
   // Init of a graph induced complex from an OFF file
   // ----------------------------------------------------------------------------
 
   Gudhi::graph_induced_complex::Graph_induced_complex<Point> GIC;
-  GIC.set_verbose(verb); GIC.set_mask();
+  GIC.set_verbose(verb);
 
   bool check = GIC.read_point_cloud(off_file_name);
 
@@ -60,7 +61,7 @@ int main(int argc, char **argv) {
 
     GIC.plot_OFF();
 
-    Gudhi::graph_induced_complex::Simplex_tree stree; GIC.create_complex(stree);
+    Gudhi::Simplex_tree<> stree; GIC.create_complex(stree);
 
     // ----------------------------------------------------------------------------
     // Display information about the graph induced complex