Added things

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@937 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4f0ae39ee1f68d8cce565ad0855edb3bff1e7f3f

4 files changed, 43 insertions, 28 deletions

diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
index 44bf9dbb..0b196f18 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_furthest_point.h
@@ -31,18 +31,22 @@
  *  \ingroup witness_complex
  */
 
-class Landmark_choice_by_random_point {
+class Landmark_choice_by_furthest_point {
 
+public:
+  
 /** 
  *  \brief Landmark choice strategy by iteratively adding the furthest witness from the
- *  current landmark set as the new landmark. It takes a random access range `points` and
+ *  current landmark set as the new landmark. 
+ *  \details It chooses nbL landmarks from a random access range `points` and
  *  writes {witness}*{closest landmarks} matrix in `knn`.
  */
 
     template <typename KNearestNeighbours,
               typename Point_random_access_range>
-    Landmark_choice_by_furthest_points(Point_random_access_range &points,
-                                            KNearestNeighbours &knn)
+    Landmark_choice_by_furthest_point(Point_random_access_range &points,
+                                      int nbL,
+                                      KNearestNeighbours &knn)
     {
       int nb_points = points.end() - points.begin();
       std::vector<std::vector<double>> wit_land_dist(nb_points, std::vector<double>());    // distance matrix witness x landmarks
diff --git a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
index bc3e72d9..fa822591 100644
--- a/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
+++ b/src/Witness_complex/include/gudhi/Landmark_choice_by_random_point.h
@@ -33,18 +33,19 @@
 
 class Landmark_choice_by_random_point {
 
-
+public:
+  
     /** \brief Landmark choice strategy by taking random vertices for landmarks.
-     *  It takes a random access range points and outputs a matrix {witness}*{closest landmarks}
-     *  in knn.
+     *  \details It chooses nbL distinct landmarks from a random access range `points`
+     *  and outputs a matrix {witness}*{closest landmarks} in knn.
      */
     
     template <typename KNearestNeighbours,
               typename Point_random_access_range>                 
-    void landmark_choice_by_random_points(Point_random_access_range &points, KNearestNeighbours &knn)
+    Landmark_choice_by_random_point(Point_random_access_range &points, int nbL, KNearestNeighbours &knn)
     {
       int nbP = points.end() - points.begin();
-      std::set<int> &landmarks;
+      std::set<int> landmarks;
       int current_number_of_landmarks=0;                        // counter for landmarks 
 
       int chosen_landmark = rand()%nbP;
@@ -55,9 +56,10 @@ class Landmark_choice_by_random_point {
           landmarks.insert(chosen_landmark);
         }
 
-      int D = points.begin().size();
+      int dim = points.begin()->size();
       typedef std::pair<double,int> dist_i;
       typedef bool (*comp)(dist_i,dist_i);
+      knn = KNearestNeighbours(nbP);
       for (int points_i = 0; points_i < nbP; points_i++)
         {
           std::priority_queue<dist_i, std::vector<dist_i>, comp> l_heap([&](dist_i j1, dist_i j2){return j1.first > j2.first;});
@@ -68,7 +70,7 @@ class Landmark_choice_by_random_point {
               dist_i dist = std::make_pair(euclidean_distance(points[points_i],points[*landmarks_it]), landmarks_i);
               l_heap.push(dist);
             }
-          for (int i = 0; i < D+1; i++)
+          for (int i = 0; i < dim+1; i++)
             {
               dist_i dist = l_heap.top();
               knn[points_i].push_back(dist.second);
diff --git a/src/Witness_complex/include/gudhi/Witness_complex.h b/src/Witness_complex/include/gudhi/Witness_complex.h
index b218611b..791d0e45 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex.h
@@ -73,10 +73,11 @@ namespace Gudhi {
       
     typedef std::vector< double > Point_t;
     typedef std::vector< Point_t > Point_Vector;
-    
+
+    typedef typename Simplicial_complex::Filtration_value Filtration_value;
     typedef std::vector< Vertex_handle > typeVectorVertex;
     typedef std::pair< typeVectorVertex, Filtration_value> typeSimplex;
-    typedef std::pair< Simplex_tree<>::Simplex_handle, bool > typePairSimplexBool;
+    typedef std::pair< Simplex_handle, bool > typePairSimplexBool;
     
     typedef int Witness_id;
     typedef int Landmark_id;
@@ -204,11 +205,12 @@ namespace Gudhi {
   public:
     
     /**
-     *  \brief Verification if every simplex in the complex is witnessed.
+     *  \brief Verification if every simplex in the complex is witnessed by witnesses in knn.
+     *  \param print_output =true will print the witnesses for each simplex
      *  \remark Added for debugging purposes.
      */
     template< class KNearestNeighbors >
-    bool is_witness_complex(KNearestNeighbors & knn)
+    bool is_witness_complex(KNearestNeighbors & knn, bool print_output)
     {
       //bool final_result = true;
       for (Simplex_handle sh: sc.complex_simplex_range())
@@ -231,19 +233,25 @@ namespace Gudhi {
               if (has_vertices)
                 {
                   is_witnessed = true;
-                  std::cout << "The simplex ";
-                  print_vector(simplex);
-                  std::cout << " is witnessed by the witness ";
-                  print_vector(w);
-                  std::cout << std::endl;
+                  if (print_output)
+                    {
+                      std::cout << "The simplex ";
+                      print_vector(simplex);
+                      std::cout << " is witnessed by the witness ";
+                      print_vector(w);
+                      std::cout << std::endl;
+                    }
                   break;
                 }
             }
           if (!is_witnessed)
             {
-              std::cout << "The following simplex is not witnessed ";
-              print_vector(simplex);
-              std::cout << std::endl;
+              if (print_output)
+                {
+                  std::cout << "The following simplex is not witnessed ";
+                  print_vector(simplex);
+                  std::cout << std::endl;
+                }
               assert(is_witnessed);
               return false;
             }
diff --git a/src/Witness_complex/include/gudhi/Witness_complex_doc.h b/src/Witness_complex/include/gudhi/Witness_complex_doc.h
index 22cfe992..446f0d11 100644
--- a/src/Witness_complex/include/gudhi/Witness_complex_doc.h
+++ b/src/Witness_complex/include/gudhi/Witness_complex_doc.h
@@ -21,14 +21,15 @@
       
    \section Implementation
 
-   Two classes are implemented in this module: Gudhi::Witness_complex and Gudhi::Relaxed_witness_complex.
+   The principal class of this module is Gudhi::Witness_complex.
 
-   While Gudhi::Witness_complex represents the classical witness complex, Gudhi::Relaxed_witness_complex takes an additional positive real parameter \f$ \alpha \f$ and constructs simplices \f$ \sigma \f$, for which
-   there exists \f$ w \in W \f$, such that \f$ d(p,w) < d(q,w) + \alpha \f$ for all \f$ p \in \sigma, q \in L\setminus \sigma \f$.
-
-   In both cases, the constructors take a {witness}x{closest_landmarks} table,
+   In both cases, the constructor for this class takes a {witness}x{closest_landmarks} table,
    which can be constructed by two additional classes Landmark_choice_by_furthest_point and Landmark_choice_by_random_point also included in the module.
 
+   *\image html "bench_Cy8.png" "Running time as function on number of landmarks" width=10cm
+   *\image html "bench_sphere.png" "Running time as function on number of witnesses for |L|=300" width=10cm
+   
+
    \copyright GNU General Public License v3.