Move bottleneck_chrono in benchmark

Add test in cmake for basic example
Move CGAL gudhi patches for bottleneck in dedicated directory
Fix cpplint syntax issue


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneck_integration@1920 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 24671facf791de93dc6fd94bb39ca7362bb22959

1 files changed, 94 insertions, 97 deletions

diff --git a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
index 45a4d586..3a4a5fec 100644
--- a/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
+++ b/src/Bottleneck_distance/include/gudhi/Persistence_graph.h
@@ -4,7 +4,7 @@
  *
  *    Author:       Francois Godi
  *
- *    Copyright (C) 2015  INRIA (France)
+ *    Copyright (C) 2015  INRIA
  *
  *    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
@@ -31,147 +31,144 @@ namespace Gudhi {
 
 namespace persistence_diagram {
 
-
 /** \internal \brief Structure representing an euclidean bipartite graph containing
  *  the points from the two persistence diagrams (including the projections).
  *
  * \ingroup bottleneck_distance
  */
 class Persistence_graph {
-public:
-    /** \internal \brief Constructor taking 2 Persistence_Diagrams (concept) as parameters. */
-    template<typename Persistence_diagram1, typename Persistence_diagram2>
-    Persistence_graph(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e);
-    /** \internal \brief Is the given point from U the projection of a point in V ? */
-    bool on_the_u_diagonal(int u_point_index) const;
-    /** \internal \brief Is the given point from V the projection of a point in U ? */
-    bool on_the_v_diagonal(int v_point_index) const;
-    /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */
-    int corresponding_point_in_u(int v_point_index) const;
-    /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */
-    int corresponding_point_in_v(int u_point_index) const;
-    /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */
-    double distance(int u_point_index, int v_point_index) const;
-    /** \internal \brief Returns size = |U| = |V|. */
-    int size() const;
-    /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */
-    double bottleneck_alive() const;
-    /** \internal \brief Returns the O(n^2) sorted distances between the points. */
-    std::vector<double> sorted_distances() const;
-    /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */
-    double diameter_bound() const;
-    /** \internal \brief Returns the corresponding internal point */
-    Internal_point get_u_point(int u_point_index) const;
-    /** \internal \brief Returns the corresponding internal point */
-    Internal_point get_v_point(int v_point_index) const;
-
-private:
-    std::vector<Internal_point> u;
-    std::vector<Internal_point> v;
-    double b_alive;
+ public:
+  /** \internal \brief Constructor taking 2 Persistence_Diagrams (concept) as parameters. */
+  template<typename Persistence_diagram1, typename Persistence_diagram2>
+  Persistence_graph(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e);
+  /** \internal \brief Is the given point from U the projection of a point in V ? */
+  bool on_the_u_diagonal(int u_point_index) const;
+  /** \internal \brief Is the given point from V the projection of a point in U ? */
+  bool on_the_v_diagonal(int v_point_index) const;
+  /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */
+  int corresponding_point_in_u(int v_point_index) const;
+  /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */
+  int corresponding_point_in_v(int u_point_index) const;
+  /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */
+  double distance(int u_point_index, int v_point_index) const;
+  /** \internal \brief Returns size = |U| = |V|. */
+  int size() const;
+  /** \internal \brief Is there as many infinite points (alive components) in both diagrams ? */
+  double bottleneck_alive() const;
+  /** \internal \brief Returns the O(n^2) sorted distances between the points. */
+  std::vector<double> sorted_distances() const;
+  /** \internal \brief Returns an upper bound for the diameter of the convex hull of all non infinite points */
+  double diameter_bound() const;
+  /** \internal \brief Returns the corresponding internal point */
+  Internal_point get_u_point(int u_point_index) const;
+  /** \internal \brief Returns the corresponding internal point */
+  Internal_point get_v_point(int v_point_index) const;
+
+ private:
+  std::vector<Internal_point> u;
+  std::vector<Internal_point> v;
+  double b_alive;
 };
 
 template<typename Persistence_diagram1, typename Persistence_diagram2>
 Persistence_graph::Persistence_graph(const Persistence_diagram1 &diag1,
                                      const Persistence_diagram2 &diag2, double e)
-    : u(), v(), b_alive(0.)
-{
-    std::vector<double> u_alive;
-    std::vector<double> v_alive;
-    for (auto it = std::begin(diag1); it != std::end(diag1); ++it){
-        if(std::get<1>(*it) == std::numeric_limits<double>::infinity())
-            u_alive.push_back(std::get<0>(*it));
-        else if (std::get<1>(*it) - std::get<0>(*it) > e)
-            u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size()));
-    }
-    for (auto it = std::begin(diag2); it != std::end(diag2); ++it){
-        if(std::get<1>(*it) == std::numeric_limits<double>::infinity())
-            v_alive.push_back(std::get<0>(*it));
-        else if (std::get<1>(*it) - std::get<0>(*it) > e)
-            v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size()));
-    }
-    if (u.size() < v.size())
-        swap(u, v);
-    std::sort(u_alive.begin(), u_alive.end());
-    std::sort(v_alive.begin(), v_alive.end());
-    if(u_alive.size() != v_alive.size())
-        b_alive = std::numeric_limits<double>::infinity();
-    else for(auto it_u=u_alive.cbegin(), it_v=v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v)
-        b_alive = std::max(b_alive, std::fabs(*it_u - *it_v));
+    : u(), v(), b_alive(0.) {
+  std::vector<double> u_alive;
+  std::vector<double> v_alive;
+  for (auto it = std::begin(diag1); it != std::end(diag1); ++it) {
+    if (std::get<1>(*it) == std::numeric_limits<double>::infinity())
+      u_alive.push_back(std::get<0>(*it));
+    else if (std::get<1>(*it) - std::get<0>(*it) > e)
+      u.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), u.size()));
+  }
+  for (auto it = std::begin(diag2); it != std::end(diag2); ++it) {
+    if (std::get<1>(*it) == std::numeric_limits<double>::infinity())
+      v_alive.push_back(std::get<0>(*it));
+    else if (std::get<1>(*it) - std::get<0>(*it) > e)
+      v.push_back(Internal_point(std::get<0>(*it), std::get<1>(*it), v.size()));
+  }
+  if (u.size() < v.size())
+    swap(u, v);
+  std::sort(u_alive.begin(), u_alive.end());
+  std::sort(v_alive.begin(), v_alive.end());
+  if (u_alive.size() != v_alive.size())
+    b_alive = std::numeric_limits<double>::infinity();
+  else for (auto it_u = u_alive.cbegin(), it_v = v_alive.cbegin(); it_u != u_alive.cend(); ++it_u, ++it_v)
+      b_alive = std::max(b_alive, std::fabs(*it_u - *it_v));
 }
 
 inline bool Persistence_graph::on_the_u_diagonal(int u_point_index) const {
-    return u_point_index >= static_cast<int> (u.size());
+  return u_point_index >= static_cast<int> (u.size());
 }
 
 inline bool Persistence_graph::on_the_v_diagonal(int v_point_index) const {
-    return v_point_index >= static_cast<int> (v.size());
+  return v_point_index >= static_cast<int> (v.size());
 }
 
 inline int Persistence_graph::corresponding_point_in_u(int v_point_index) const {
-    return on_the_v_diagonal(v_point_index) ?
-                v_point_index - static_cast<int> (v.size()) : v_point_index + static_cast<int> (u.size());
+  return on_the_v_diagonal(v_point_index) ?
+      v_point_index - static_cast<int> (v.size()) : v_point_index + static_cast<int> (u.size());
 }
 
 inline int Persistence_graph::corresponding_point_in_v(int u_point_index) const {
-    return on_the_u_diagonal(u_point_index) ?
-                u_point_index - static_cast<int> (u.size()) : u_point_index + static_cast<int> (v.size());
+  return on_the_u_diagonal(u_point_index) ?
+      u_point_index - static_cast<int> (u.size()) : u_point_index + static_cast<int> (v.size());
 }
 
 inline double Persistence_graph::distance(int u_point_index, int v_point_index) const {
-    if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index))
-        return 0.;
-    Internal_point p_u = get_u_point(u_point_index);
-    Internal_point p_v = get_v_point(v_point_index);
-    return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y()));
+  if (on_the_u_diagonal(u_point_index) && on_the_v_diagonal(v_point_index))
+    return 0.;
+  Internal_point p_u = get_u_point(u_point_index);
+  Internal_point p_v = get_v_point(v_point_index);
+  return std::max(std::fabs(p_u.x() - p_v.x()), std::fabs(p_u.y() - p_v.y()));
 }
 
 inline int Persistence_graph::size() const {
-    return static_cast<int> (u.size() + v.size());
+  return static_cast<int> (u.size() + v.size());
 }
 
-inline double Persistence_graph::bottleneck_alive() const{
-    return b_alive;
+inline double Persistence_graph::bottleneck_alive() const {
+  return b_alive;
 }
 
 inline std::vector<double> Persistence_graph::sorted_distances() const {
-    std::vector<double> distances;
-    distances.push_back(0.); //for empty diagrams
-    for (int u_point_index = 0; u_point_index < size(); ++u_point_index){
-        distances.push_back(distance(u_point_index, corresponding_point_in_v(u_point_index)));
-        for (int v_point_index = 0; v_point_index < size(); ++v_point_index)
-            distances.push_back(distance(u_point_index, v_point_index));
-    }
-    std::sort(distances.begin(), distances.end());
-    return distances;
+  std::vector<double> distances;
+  distances.push_back(0.);  // for empty diagrams
+  for (int u_point_index = 0; u_point_index < size(); ++u_point_index) {
+    distances.push_back(distance(u_point_index, corresponding_point_in_v(u_point_index)));
+    for (int v_point_index = 0; v_point_index < size(); ++v_point_index)
+      distances.push_back(distance(u_point_index, v_point_index));
+  }
+  std::sort(distances.begin(), distances.end());
+  return distances;
 }
 
 inline Internal_point Persistence_graph::get_u_point(int u_point_index) const {
-    if (!on_the_u_diagonal(u_point_index))
-        return u.at(u_point_index);
-    Internal_point projector = v.at(corresponding_point_in_v(u_point_index));
-    double m = (projector.x() + projector.y()) / 2.;
-    return Internal_point(m,m,u_point_index);
+  if (!on_the_u_diagonal(u_point_index))
+    return u.at(u_point_index);
+  Internal_point projector = v.at(corresponding_point_in_v(u_point_index));
+  double m = (projector.x() + projector.y()) / 2.;
+  return Internal_point(m, m, u_point_index);
 }
 
 inline Internal_point Persistence_graph::get_v_point(int v_point_index) const {
-    if (!on_the_v_diagonal(v_point_index))
-        return v.at(v_point_index);
-    Internal_point projector = u.at(corresponding_point_in_u(v_point_index));
-    double m = (projector.x() + projector.y()) / 2.;
-    return Internal_point(m,m,v_point_index);
+  if (!on_the_v_diagonal(v_point_index))
+    return v.at(v_point_index);
+  Internal_point projector = u.at(corresponding_point_in_u(v_point_index));
+  double m = (projector.x() + projector.y()) / 2.;
+  return Internal_point(m, m, v_point_index);
 }
 
 inline double Persistence_graph::diameter_bound() const {
-    double max = 0.;
-    for(auto it = u.cbegin(); it != u.cend(); it++)
-        max = std::max(max, it->y());
-    for(auto it = v.cbegin(); it != v.cend(); it++)
-        max = std::max(max, it->y());
-    return max;
+  double max = 0.;
+  for (auto it = u.cbegin(); it != u.cend(); it++)
+    max = std::max(max, it->y());
+  for (auto it = v.cbegin(); it != v.cend(); it++)
+    max = std::max(max, it->y());
+  return max;
 }
 
-
 }  // namespace persistence_diagram
 
 }  // namespace Gudhi