Add distance matrix read from csv files

Distance template instead of Point_d for distance matrices


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/distance_matrix_in_rips_module@1762 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 695bead714228c57e1be1650048125aa0b841683

1 files changed, 53 insertions, 36 deletions

diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
index da755b7c..6f947f41 100644
--- a/src/Rips_complex/include/gudhi/Rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -2,7 +2,7 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Clément Maria, Vincent Rouvreau
+ *    Author(s):       Clément Maria, Pawel Dlotko, Vincent Rouvreau
  *
  *    Copyright (C) 2016  INRIA
  *
@@ -58,12 +58,13 @@ template<typename Filtration_value>
 class Rips_complex {
  private:
   typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
-      , boost::property < vertex_filtration_t, Filtration_value >
-      , boost::property < edge_filtration_t, Filtration_value >> Graph_t;
-  
+  , boost::property < vertex_filtration_t, Filtration_value >
+  , boost::property < edge_filtration_t, Filtration_value >> Graph_t;
+
   typedef int Vertex_handle;
-  
+
  public:
+
   /** \brief Rips_complex constructor from a list of points.
    *
    * @param[in] points Range of points.
@@ -72,9 +73,51 @@ class Rips_complex {
    * 
    * The type InputPointRange must be a range for which std::begin and std::end return input iterators on a point.
    */
-  template<typename InputPointRange, typename Point_d >
-  Rips_complex(const InputPointRange& points, Filtration_value threshold,
-               Filtration_value distance(const Point_d& p1,const Point_d& p2)) {
+  template<typename InputPointRange, typename Distance >
+  Rips_complex(const InputPointRange& points, Filtration_value threshold, Distance distance) {
+    compute_proximity_graph<InputPointRange, Distance >(points, threshold, distance);
+  }
+
+  /** \brief Initializes the simplicial complex from the 1-skeleton graph and expands it until a given maximal
+   * dimension.
+   *
+   * \tparam SimplicialComplexForRips must meet `SimplicialComplexForRips` concept.
+   * 
+   * @param[in] complex SimplicialComplexForRips to be created.
+   * @param[in] dim_max graph expansion for rips until this given maximal dimension.
+   * 
+   * @return true if creation succeeds, false otherwise.
+   * 
+   */
+  template <typename SimplicialComplexForRips>
+  bool create_complex(SimplicialComplexForRips& complex, int dim_max) {
+    if (complex.num_vertices() > 0) {
+      std::cerr << "Rips_complex create_complex - complex is not empty\n";
+      return false; // ----- >>
+    }
+
+    // insert the proximity graph in the simplicial complex
+    complex.insert_graph(rips_skeleton_graph_);
+    // expand the graph until dimension dim_max
+    complex.expansion(dim_max);
+
+    // --------------------------------------------------------------------------------------------
+    return true;
+  }
+
+ public:
+  /** \brief Output the proximity graph of the points.
+   *
+   * If points contains n elements, the proximity graph is the graph 
+   * with n vertices, and an edge [u,v] iff the distance function between 
+   * points u and v is smaller than threshold.
+   *
+   * The type PointCloud furnishes .begin() and .end() methods, that return
+   * iterators with value_type Point.
+   */
+  template< typename InputPointRange, typename Distance >
+  void compute_proximity_graph(const InputPointRange& points, Filtration_value threshold,
+               Distance distance) {
     std::vector< std::pair< Vertex_handle, Vertex_handle > > edges;
     std::vector< Filtration_value > edges_fil;
     std::map< Vertex_handle, Filtration_value > vertices;
@@ -102,7 +145,7 @@ class Rips_complex {
     // --------------------------------------------------------------------------------------------
     // Creates the proximity graph from edges and sets the property with the filtration value.
     // Number of points is labeled from 0 to idx_u-1
-    rips_skeleton_graph_ = Graph_t(edges.begin() , edges.end() , edges_fil.begin() , idx_u);
+    rips_skeleton_graph_ = Graph_t(edges.begin(), edges.end(), edges_fil.begin(), idx_u);
 
     auto vertex_prop = boost::get(vertex_filtration_t(), rips_skeleton_graph_);
 
@@ -112,37 +155,11 @@ class Rips_complex {
          vi != vi_end; ++vi) {
       boost::put(vertex_prop, *vi, 0.);
     }
-
   }
 
-  /** \brief Initializes the simplicial complex from the 1-skeleton graph and expands it until a given maximal
-   * dimension.
-   *
-   * \tparam SimplicialComplexForRips must meet `SimplicialComplexForRips` concept.
-   * 
-   * @param[in] complex SimplicialComplexForRips to be created.
-   * @param[in] dim_max graph expansion for rips until this given maximal dimension.
-   * 
-   * @return true if creation succeeds, false otherwise.
-   * 
-   */
-  template <typename SimplicialComplexForRips>
-  bool create_complex(SimplicialComplexForRips& complex, int dim_max) {
-    if (complex.num_vertices() > 0) {
-      std::cerr << "Rips_complex create_complex - complex is not empty\n";
-      return false; // ----- >>
-    }
-
-    // insert the proximity graph in the simplicial complex
-    complex.insert_graph(rips_skeleton_graph_);
-    // expand the graph until dimension dim_max
-    complex.expansion(dim_max);
-
-    // --------------------------------------------------------------------------------------------
-    return true;
-  }
  private:
   Graph_t rips_skeleton_graph_;
+
 };
 
 } // namespace rips_complex