copyrigths

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1783 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: c045f59d4f2810aa2193add84ac97a2632888dc4

7 files changed, 26 insertions, 92 deletions

diff --git a/src/Bottleneck_distance/include/gudhi/Bottleneck.h b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
index 71845e25..bb0a13d2 100644
--- a/src/Bottleneck_distance/include/gudhi/Bottleneck.h
+++ b/src/Bottleneck_distance/include/gudhi/Bottleneck.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Francois Godi
+ *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *    Copyright (C) 2015  INRIA (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -65,7 +65,7 @@ double compute(const Persistence_diagram1 &diag1, const Persistence_diagram2 &di
     if(e == 0.)
         return compute_exactly(diag1, diag2);
     G::initialize(diag1, diag2, e);
-    int in = G::diameter()/e;
+    int in = G::diameter()/e + 1;
     int idmin = 0;
     int idmax = in;
     // alpha can be modified, this will change the complexity
diff --git a/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h b/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h
index 278b7955..0959dd03 100644
--- a/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h
+++ b/src/Bottleneck_distance/include/gudhi/Construct_coord_iterator.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Francois Godi
+ *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *    Copyright (C) 2015  INRIA (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
diff --git a/src/Bottleneck_distance/include/gudhi/Graph_matching.h b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
index c50c3a9e..fa20b2a2 100644
--- a/src/Bottleneck_distance/include/gudhi/Graph_matching.h
+++ b/src/Bottleneck_distance/include/gudhi/Graph_matching.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Francois Godi
+ *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *    Copyright (C) 2015  INRIA (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
diff --git a/src/Bottleneck_distance/include/gudhi/Internal_point.h b/src/Bottleneck_distance/include/gudhi/Internal_point.h
index 90b5dd14..78aad470 100644
--- a/src/Bottleneck_distance/include/gudhi/Internal_point.h
+++ b/src/Bottleneck_distance/include/gudhi/Internal_point.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Francois Godi
+ *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *    Copyright (C) 2015  INRIA (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
index e8560559..20b47d0b 100644
--- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Francois Godi
+ *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *    Copyright (C) 2015  INRIA (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h
index 7d37b9e0..8242ce2b 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_diagrams_graph.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Francois Godi
+ *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *    Copyright (C) 2015  INRIA (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -65,8 +65,7 @@ private:
     static Internal_point get_u_point(int u_point_index);
     static Internal_point get_v_point(int v_point_index);
 
-    friend class Naive_pnf;
-    friend class Cgal_pnf;
+    friend class Planar_neighbors_finder;
 };
 
 /** \internal \typedef \brief Shorter alias */
diff --git a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h
index f574231e..c1f4d908 100644
--- a/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Planar_neighbors_finder.h
@@ -2,9 +2,9 @@
  *    (Geometric Understanding in Higher Dimensions) is a generic C++
  *    library for computational topology.
  *
- *    Author(s):       Francois Godi
+ *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (France)
+ *    Copyright (C) 2015  INRIA (France)
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -67,7 +67,7 @@ private:
     std::multimap<std::pair<int,int>,int> grid;
 };
 
-class Cgal_pnf {
+class Planar_neighbors_finder {
 
     typedef CGAL::Dimension_tag<2> D;
     typedef CGAL::Search_traits<double, Internal_point, const double*, CGAL::Construct_coord_iterator, D> Traits;
@@ -78,7 +78,7 @@ class Cgal_pnf {
 
 public:
     /** \internal \brief Constructor taking the near distance definition as parameter. */
-    Cgal_pnf(double r_);
+    Planar_neighbors_finder(double r_);
     /** \internal \brief A point added will be possibly pulled. */
     void add(int v_point_index);
     /** \internal \brief A point manually removed will no longer be possibly pulled. */
@@ -96,79 +96,14 @@ private:
     Kd_tree kd_t;
 };
 
-/** \internal \typedef \brief Planar_neighbors_finder is the used implementation. */
-typedef Cgal_pnf Planar_neighbors_finder;
-
-inline Naive_pnf::Naive_pnf(double r_) :
-    r(r_), grid() { }
-
-
-inline std::pair<int,int> Naive_pnf::get_v_key(int v_point_index) const{
-    Internal_point v_point = G::get_v_point(v_point_index);
-    return std::make_pair(static_cast<int>(v_point.x()/r), static_cast<int>(v_point.y()/r));
-}
-
-inline void Naive_pnf::add(int v_point_index) {
-    grid.emplace(get_v_key(v_point_index),v_point_index);
-}
-
-inline void Naive_pnf::remove(int v_point_index) {
-    if(v_point_index != null_point_index())
-        for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++)
-            if(it->second==v_point_index){
-                grid.erase(it);
-                return;
-            }
-}
-
-inline bool Naive_pnf::contains(int v_point_index) const {
-    if(v_point_index == null_point_index())
-        return false;
-    for(auto it = grid.find(get_v_key(v_point_index)); it!=grid.end(); it++)
-        if(it->second==v_point_index)
-            return true;
-    return false;
-}
-
-inline int Naive_pnf::pull_near(int u_point_index) {
-    Internal_point u_point = G::get_u_point(u_point_index);
-    int i0 = static_cast<int>(u_point.x()/r);
-    int j0 = static_cast<int>(u_point.y()/r);
-    for(int i = 1; i<= 3; i++)
-        for(int j = 1; j<= 3; j++)
-            for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end(); it++)
-                if (G::distance(u_point_index, it->second) <= r) {
-                    int tmp = it->second;
-                    grid.erase(it);
-                    return tmp;
-                }
-    return null_point_index();
-}
-
-inline std::vector<int> Naive_pnf::pull_all_near(int u_point_index) {
-    std::vector<int> all_pull;
-    Internal_point u_point = G::get_u_point(u_point_index);
-    int i0 = static_cast<int>(u_point.x()/r);
-    int j0 = static_cast<int>(u_point.y()/r);
-    for(int i = 1; i<= 3; i++)
-        for(int j = 1; j<= 3; j++)
-            for(auto it = grid.find(std::make_pair(i0 +(i%3)-1, j0+(j%3)-1)); it!=grid.end();)
-                if (G::distance(u_point_index, it->second) <= r) {
-                    all_pull.emplace_back(it->second);
-                    it = grid.erase(it);
-                }
-                else it++;
-    return all_pull;
-}
-
 
 /** \internal \brief Constructor taking the near distance definition as parameter. */
-inline Cgal_pnf::Cgal_pnf(double r_)
+inline Planar_neighbors_finder::Planar_neighbors_finder(double r_)
     : r(r_), contents(), kd_t() {}
 
 
 /** \internal \brief A point added will be possibly pulled. */
-inline void Cgal_pnf::add(int v_point_index){
+inline void Planar_neighbors_finder::add(int v_point_index){
     if(v_point_index == null_point_index())
         return;
     contents.insert(v_point_index);
@@ -176,22 +111,20 @@ inline void Cgal_pnf::add(int v_point_index){
 }
 
 /** \internal \brief A point manually removed will no longer be possibly pulled. */
-inline void Cgal_pnf::remove(int v_point_index){
-    if(contains(v_point_index)){
+inline void Planar_neighbors_finder::remove(int v_point_index){
         contents.erase(v_point_index);
         kd_t.remove(G::get_v_point(v_point_index));
-    }
 }
 
 /** \internal \brief Can the point given as parameter be returned ? */
-inline bool Cgal_pnf::contains(int v_point_index) const{
+inline bool Planar_neighbors_finder::contains(int v_point_index) const{
     if(v_point_index == null_point_index())
         return false;
     return contents.count(v_point_index)>0;
 }
 
 /** \internal \brief Provide and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */
-inline int Cgal_pnf::pull_near(int u_point_index){
+inline int Planar_neighbors_finder::pull_near(int u_point_index){
     Internal_point u_point = G::get_u_point(u_point_index);
     std::vector<double> w = {1., 1.};
     K_neighbor_search search(kd_t, u_point, 0., true, Distance(0, 2, w));
@@ -199,11 +132,13 @@ inline int Cgal_pnf::pull_near(int u_point_index){
     if(it==search.end() || G::distance(u_point_index, it->first.point_index) > r)
         return null_point_index();
     int tmp = it->first.point_index;
+    if(!contains(tmp))
+        std::cout << "!! A kd_tree returns a point (Point_index:" << tmp << ") previously removed !!" << std::endl;
     remove(tmp);
     return tmp;
 }
 
-inline std::vector<int> Cgal_pnf::pull_all_near(int u_point_index) {
+inline std::vector<int> Planar_neighbors_finder::pull_all_near(int u_point_index) {
     std::vector<int> all_pull;
     int last_pull = pull_near(u_point_index);
     while (last_pull != null_point_index()) {