sb_wrapper working

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/toplex_map@3308 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c7400a11583b8b67483974664e410f4c77232fb1

7 files changed, 49 insertions, 20 deletions

diff --git a/src/Rips_complex/example/example_rips_complex_from_fvecs.cpp b/src/Rips_complex/example/example_rips_complex_from_fvecs.cpp
index 5e7667bd..1b683326 100644
--- a/src/Rips_complex/example/example_rips_complex_from_fvecs.cpp
+++ b/src/Rips_complex/example/example_rips_complex_from_fvecs.cpp
@@ -1,10 +1,11 @@
 #include <gudhi/Rips_complex.h>
-// to construct Rips_complex from a fvecs file of points
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Fake_simplex_tree.h>
+#include <gudhi/Sb_wrapper.h>
 #include <gudhi/distance_functions.h>
 #include <gudhi/Points_fvecs_reader.h>
 
+
 #include <CGAL/Epick_d.h>
 
 #include <iostream>
@@ -30,7 +31,8 @@ int main(int argc, char **argv) {
     using K = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
     using Point = typename K::Point_d;
     //using Simplex_tree = Gudhi::Simplex_tree<>;
-    using Simplex_tree = Gudhi::Fake_simplex_tree;
+    //using Simplex_tree = Gudhi::Fake_simplex_tree;
+    using Simplex_tree = Gudhi::Sb_wrapper;
     using Filtration_value = Simplex_tree::Filtration_value;
     using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
     using Point_vector = std::vector<Point>;
@@ -52,7 +54,7 @@ int main(int argc, char **argv) {
     end = clock();
 
     std::cout << "Strong witness complex took "<< static_cast<double>(end - start) / CLOCKS_PER_SEC << " s." << std::endl;
-    std::cout << "Rips complex is of dimension " << stree.dimension() <<  " - " << stree.num_simplices() << " simplices." << std::endl;
+    //std::cout << "Rips complex is of dimension " << stree.dimension() <<  " - " << stree.num_simplices() << " simplices." << std::endl;
 
     return 0;
 }
diff --git a/src/Toplex_map/include/gudhi/Fake_simplex_tree.h b/src/Toplex_map/include/gudhi/Fake_simplex_tree.h
index abd815f9..55955e7b 100644
--- a/src/Toplex_map/include/gudhi/Fake_simplex_tree.h
+++ b/src/Toplex_map/include/gudhi/Fake_simplex_tree.h
@@ -31,9 +31,6 @@ struct Visitor {
 class Fake_simplex_tree : public Filtered_toplex_map {
 
 public:
-    /** The type of the sets of Simplex_ptr.
-     * \ingroup toplex_map   */
-    typedef Toplex_map::Simplex_ptr_set Simplex_ptr_set;
 
     /** Handle type to a vertex contained in the simplicial complex.
      * \ingroup toplex_map   */
@@ -87,6 +84,8 @@ public:
       * \ingroup toplex_map   */
     std::vector<Toplex_map::Simplex> skeleton_simplex_range(int d) const;
 
+    Toplex_map::Vertex contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y);
+
 
 protected:
 
@@ -99,14 +98,14 @@ protected:
 
 template<class OneSkeletonGraph>
 void Fake_simplex_tree::insert_graph(const OneSkeletonGraph& skel_graph){
-    toplex_maps.emplace(nan(""),Toplex_map());
+    toplex_maps.emplace(nan(""), new Toplex_map());
     using vertex_iterator = typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator;
     vertex_iterator vi, vi_end;
     for (std::tie(vi, vi_end) = boost::vertices(skel_graph); vi != vi_end; ++vi) {
         Simplex s; s.insert(*vi);
         insert_simplex_and_subfaces(s);
     }
-    bron_kerbosch_all_cliques(skel_graph, Visitor(&(this->toplex_maps.at(nan("")))));
+    bron_kerbosch_all_cliques(skel_graph, Visitor(this->toplex_maps.at(nan(""))));
 }
 
 void Fake_simplex_tree::expansion(int max_dim){}
@@ -150,7 +149,7 @@ Toplex_map::Simplex Fake_simplex_tree::simplex_vertex_range(const Simplex& s) co
 std::vector<Toplex_map::Simplex> Fake_simplex_tree::max_simplices() const{
     std::vector<Toplex_map::Simplex> max_s;
     for(auto kv : toplex_maps)
-        for(const Toplex_map::Simplex_ptr& sptr : kv.second.maximal_cofaces(Simplex()))
+        for(const Toplex_map::Simplex_ptr& sptr : kv.second->maximal_cofaces(Simplex()))
             max_s.emplace_back(*sptr);
     return max_s;
 }
@@ -178,6 +177,12 @@ std::vector<Toplex_map::Simplex> Fake_simplex_tree::skeleton_simplex_range(int d
     return filtration_simplex_range(d);
 }
 
+Toplex_map::Vertex Fake_simplex_tree::contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y){
+    for(auto kv : toplex_maps)
+        kv.second->contraction(x,y,true);
+    return y;
+}
+
 } //namespace Gudhi
 
 #endif /* FAKE_SIMPLEX_TREE_H */
diff --git a/src/Toplex_map/include/gudhi/Filtered_toplex_map.h b/src/Toplex_map/include/gudhi/Filtered_toplex_map.h
index 379c65dd..a3653acd 100644
--- a/src/Toplex_map/include/gudhi/Filtered_toplex_map.h
+++ b/src/Toplex_map/include/gudhi/Filtered_toplex_map.h
@@ -50,15 +50,15 @@ public:
     bool membership(const Input_vertex_range &vertex_range) const;
 
 protected:
-    std::map<Filtration_value, Toplex_map> toplex_maps;
+    std::map<Filtration_value, Toplex_map*> toplex_maps;
 };
 
 template <typename Input_vertex_range>
 std::pair<Toplex_map::Simplex, bool> Filtered_toplex_map::insert_simplex_and_subfaces(const Input_vertex_range &vertex_range, Filtration_value f){
     Simplex s(vertex_range.begin(),vertex_range.end());
     if(membership(s)) return make_pair(s,false);
-    if(!toplex_maps.count(f)) toplex_maps.emplace(f,Toplex_map());
-    toplex_maps.at(f).insert_simplex(vertex_range);
+    if(!toplex_maps.count(f)) toplex_maps.emplace(f,new Toplex_map());
+    toplex_maps.at(f)->insert_simplex(vertex_range);
     return make_pair(s,true);
 }
 
@@ -66,7 +66,7 @@ std::pair<Toplex_map::Simplex, bool> Filtered_toplex_map::insert_simplex_and_sub
 template <typename Input_vertex_range>
 Filtered_toplex_map::Filtration_value Filtered_toplex_map::filtration(const Input_vertex_range &vertex_range) const{
     for(auto kv : toplex_maps)
-        if(kv.second.membership(vertex_range))
+        if(kv.second->membership(vertex_range))
             return kv.first; //min only because a map is ordered
     return nan("");
 }
@@ -74,7 +74,7 @@ Filtered_toplex_map::Filtration_value Filtered_toplex_map::filtration(const Inpu
 template <typename Input_vertex_range>
 bool Filtered_toplex_map::membership(const Input_vertex_range &vertex_range) const{
     for(auto kv : toplex_maps)
-        if(kv.second.membership(vertex_range))
+        if(kv.second->membership(vertex_range))
             return true;
     return false;
 }
diff --git a/src/Toplex_map/include/gudhi/Toplex_map.h b/src/Toplex_map/include/gudhi/Toplex_map.h
index 00127baf..ccea34d5 100644
--- a/src/Toplex_map/include/gudhi/Toplex_map.h
+++ b/src/Toplex_map/include/gudhi/Toplex_map.h
@@ -69,7 +69,7 @@ public:
      * The edge has to verify the link condition if you want to preserve topology.
      * Returns the remaining vertex.
      * \ingroup toplex_map   */
-    Toplex_map::Vertex contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y);
+    Toplex_map::Vertex contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y, bool force=false);
 
     /** Adds the given simplex to the complex.
      * The simplex must not have neither maximal face nor coface in the complex.
@@ -196,17 +196,18 @@ Toplex_map::Simplex_ptr_set Toplex_map::maximal_cofaces(const Input_vertex_range
     return cofaces;
 }
 
-Toplex_map::Vertex Toplex_map::contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y){
+Toplex_map::Vertex Toplex_map::contraction(const Toplex_map::Vertex x, const Toplex_map::Vertex y, bool force){
     if(!t0.count(x)) return y;
     if(!t0.count(y)) return x;
     int k, d;
-    if(t0.at(x).size() > t0.at(y).size())
+    if(force || (t0.at(x).size() > t0.at(y).size()))
         k=x, d=y;
     else
         k=y, d=x;
     for(const Toplex_map::Simplex_ptr& sptr : Simplex_ptr_set(t0.at(d))){
         //Copy constructor needed because the set is modified
         Simplex sigma(*sptr);
+        Simplex s; s.insert(2);
         erase_maximal(sptr);
         sigma.erase(d);
         sigma.insert(k);
diff --git a/src/Toplex_map/test/toplex_map_unit_test.cpp b/src/Toplex_map/test/toplex_map_unit_test.cpp
index b7a9251c..b714cd2a 100644
--- a/src/Toplex_map/test/toplex_map_unit_test.cpp
+++ b/src/Toplex_map/test/toplex_map_unit_test.cpp
@@ -1,6 +1,8 @@
 #include <iostream>
 #include <gudhi/Filtered_toplex_map.h>
 #include <gudhi/Fake_simplex_tree.h>
+#include <gudhi/Sb_wrapper.h>
+
 
 #define BOOST_TEST_DYN_LINK
 #define BOOST_TEST_MODULE "toplex map"
diff --git a/src/Witness_complex/example/example_strong_witness_complex_fvecs.cpp b/src/Witness_complex/example/example_strong_witness_complex_fvecs.cpp
index a8e16fb0..9f5b32c4 100644
--- a/src/Witness_complex/example/example_strong_witness_complex_fvecs.cpp
+++ b/src/Witness_complex/example/example_strong_witness_complex_fvecs.cpp
@@ -22,6 +22,7 @@
 
 #include <gudhi/Simplex_tree.h>
 #include <gudhi/Fake_simplex_tree.h>
+#include <gudhi/Sb_wrapper.h>
 #include <gudhi/Euclidean_strong_witness_complex.h>
 #include <gudhi/pick_n_random_points.h>
 #include <gudhi/Points_fvecs_reader.h>
@@ -51,7 +52,8 @@ int main(int argc, char * const argv[]) {
   double alpha2 = atof(argv[3]);
   clock_t start, end;
   //Gudhi::Simplex_tree<> simplex_tree;
-  Gudhi::Fake_simplex_tree simplex_tree;
+  //Gudhi::Fake_simplex_tree simplex_tree;
+  Gudhi::Sb_wrapper simplex_tree;
 
   // Read the point file
   Point_vector point_vector, landmarks;
@@ -73,7 +75,7 @@ int main(int argc, char * const argv[]) {
   end = clock();
   std::cout << "Strong witness complex took "
       << static_cast<double>(end - start) / CLOCKS_PER_SEC << " s. \n";
-  std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << std::endl;
-  std::cout << "Max dimension is : " << simplex_tree.dimension() << std::endl;
+//  std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << std::endl;
+  // std::cout << "Max dimension is : " << simplex_tree.dimension() << std::endl;
 
 }
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index d6569f0c..71655824 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -133,6 +133,23 @@
     </td>
  </tr>
 </table>
+ \subsection ToplexMapDataStructure Toplex Map
+ \image html "map.png" "Toplex map representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Fran&ccedil;ois Godi<br>
+      <b>Introduced in:</b> GUDHI 2.1.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    The Toplex map data structure is composed firstly of a raw storage of toplices (the maximal simplices)
+    and secondly of a map which associate any vertex to a set of pointers toward all toplices
+    containing this vertex.
+    <b>User manual:</b> \ref toplex_map - <b>Reference manual:</b> Gudhi::Toplex_map
+    </td>
+ </tr>
+
  \subsection WitnessComplexDataStructure Witness complex
  \image html "Witness_complex_representation.png" "Witness complex representation"
 <table border="0">