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, 87 insertions, 85 deletions

diff --git a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
index 792925b7..96ece360 100644
--- a/src/Bottleneck_distance/include/gudhi/Neighbors_finder.h
+++ b/src/Bottleneck_distance/include/gudhi/Neighbors_finder.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
@@ -24,10 +24,9 @@
 #define NEIGHBORS_FINDER_H_
 
 // Inclusion order is important for CGAL patch
-#include "CGAL/Kd_tree_node.h"
-#include "CGAL/Kd_tree.h"
-#include "CGAL/Orthogonal_k_neighbor_search.h"
-
+#include <CGAL/Kd_tree.h>
+#include <CGAL/Kd_tree_node.h>
+#include <CGAL/Orthogonal_k_neighbor_search.h>
 #include <CGAL/Weighted_Minkowski_distance.h>
 #include <CGAL/Search_traits.h>
 
@@ -43,123 +42,126 @@ namespace persistence_diagram {
 /** \internal \brief data structure used to find any point (including projections) in V near to a query point from U
  * (which can be a projection).
  *
- * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed.
+ * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically
+ * removed.
  *
  * \ingroup bottleneck_distance
  */
 class Neighbors_finder {
-
-    typedef CGAL::Dimension_tag<2> D;
-    typedef CGAL::Search_traits<double, Internal_point, const double*, Construct_coord_iterator, D> Traits;
-    typedef CGAL::Weighted_Minkowski_distance<Traits> Distance;
-    typedef CGAL::Orthogonal_k_neighbor_search<Traits, Distance> K_neighbor_search;
-    typedef K_neighbor_search::Tree Kd_tree;
-
-public:
-    /** \internal \brief Constructor taking the near distance definition as parameter. */
-    Neighbors_finder(const Persistence_graph& g, double r);
-    /** \internal \brief A point added will be possibly pulled. */
-    void add(int v_point_index);
-    /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */
-    int pull_near(int u_point_index);
-    /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */
-    std::vector<int> pull_all_near(int u_point_index);
-
-private:
-    const Persistence_graph& g;
-    const double r;
-    Kd_tree kd_t;
-    std::unordered_set<int> projections_f;
+  typedef CGAL::Dimension_tag<2> D;
+  typedef CGAL::Search_traits<double, Internal_point, const double*, Construct_coord_iterator, D> Traits;
+  typedef CGAL::Weighted_Minkowski_distance<Traits> Distance;
+  typedef CGAL::Orthogonal_k_neighbor_search<Traits, Distance> K_neighbor_search;
+  typedef K_neighbor_search::Tree Kd_tree;
+
+ public:
+  /** \internal \brief Constructor taking the near distance definition as parameter. */
+  Neighbors_finder(const Persistence_graph& g, double r);
+  /** \internal \brief A point added will be possibly pulled. */
+  void add(int v_point_index);
+  /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if
+   * there isn't such a point. */
+  int pull_near(int u_point_index);
+  /** \internal \brief Returns and remove all the V points near to the U point given as parameter. */
+  std::vector<int> pull_all_near(int u_point_index);
+
+ private:
+  const Persistence_graph& g;
+  const double r;
+  Kd_tree kd_t;
+  std::unordered_set<int> projections_f;
 };
 
 /** \internal \brief data structure used to find any point (including projections) in V near to a query point from U
  * (which can be a projection) in a layered graph layer given as parmeter.
  *
- * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically removed.
+ * V points have to be added manually using their index and before the first pull. A neighbor pulled is automatically
+ * removed.
  *
  * \ingroup bottleneck_distance
  */
 class Layered_neighbors_finder {
-public:
-    /** \internal \brief Constructor taking the near distance definition as parameter. */
-    Layered_neighbors_finder(const Persistence_graph& g, double r);
-    /** \internal \brief A point added will be possibly pulled. */
-    void add(int v_point_index, int vlayer);
-    /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if there isn't such a point. */
-    int pull_near(int u_point_index, int vlayer);
-    /** \internal \brief Returns the number of layers. */
-    int vlayers_number() const;
-
-private:
-    const Persistence_graph& g;
-    const double r;
-    std::vector<std::unique_ptr<Neighbors_finder>> neighbors_finder;
+ public:
+  /** \internal \brief Constructor taking the near distance definition as parameter. */
+  Layered_neighbors_finder(const Persistence_graph& g, double r);
+  /** \internal \brief A point added will be possibly pulled. */
+  void add(int v_point_index, int vlayer);
+  /** \internal \brief Returns and remove a V point near to the U point given as parameter, null_point_index() if
+   * there isn't such a point. */
+  int pull_near(int u_point_index, int vlayer);
+  /** \internal \brief Returns the number of layers. */
+  int vlayers_number() const;
+
+ private:
+  const Persistence_graph& g;
+  const double r;
+  std::vector<std::unique_ptr<Neighbors_finder>> neighbors_finder;
 };
 
 inline Neighbors_finder::Neighbors_finder(const Persistence_graph& g, double r) :
     g(g), r(r), kd_t(), projections_f() { }
 
 inline void Neighbors_finder::add(int v_point_index) {
-    if (g.on_the_v_diagonal(v_point_index))
-        projections_f.emplace(v_point_index);
-    else
-        kd_t.insert(g.get_v_point(v_point_index));
+  if (g.on_the_v_diagonal(v_point_index))
+    projections_f.emplace(v_point_index);
+  else
+    kd_t.insert(g.get_v_point(v_point_index));
 }
 
 inline int Neighbors_finder::pull_near(int u_point_index) {
-    int tmp;
-    int c = g.corresponding_point_in_v(u_point_index);
-    if (g.on_the_u_diagonal(u_point_index) && !projections_f.empty()){
-        //Any pair of projection is at distance 0
-        tmp = *projections_f.cbegin();
-        projections_f.erase(tmp);
-    }
-    else if (projections_f.count(c) && (g.distance(u_point_index, c) <= r)){
-        //Is the query point near to its projection ?
-        tmp = c;
-        projections_f.erase(tmp);
-    }
-    else{
-        //Is the query point near to a V point in the plane ?
-        Internal_point u_point = g.get_u_point(u_point_index);
-        std::array<double, 2> w = { {1., 1.} };
-         K_neighbor_search search(kd_t, u_point, 1, 0., true, Distance(0, 2, w.begin(), w.end()));
-        auto it = search.begin();
-        if(it==search.end() || g.distance(u_point_index, it->first.point_index) > r)
-            return null_point_index();
-        tmp = it->first.point_index;
-        kd_t.remove(g.get_v_point(tmp));
-    }
-    return tmp;
+  int tmp;
+  int c = g.corresponding_point_in_v(u_point_index);
+  if (g.on_the_u_diagonal(u_point_index) && !projections_f.empty()) {
+    // Any pair of projection is at distance 0
+    tmp = *projections_f.cbegin();
+    projections_f.erase(tmp);
+  } else if (projections_f.count(c) && (g.distance(u_point_index, c) <= r)) {
+    // Is the query point near to its projection ?
+    tmp = c;
+    projections_f.erase(tmp);
+  } else {
+    // Is the query point near to a V point in the plane ?
+    Internal_point u_point = g.get_u_point(u_point_index);
+    std::array<double, 2> w = {
+      {1., 1.}
+    };
+    K_neighbor_search search(kd_t, u_point, 1, 0., true, Distance(0, 2, w.begin(), w.end()));
+    auto it = search.begin();
+    if (it == search.end() || g.distance(u_point_index, it->first.point_index) > r)
+      return null_point_index();
+    tmp = it->first.point_index;
+    kd_t.remove(g.get_v_point(tmp));
+  }
+  return tmp;
 }
 
 inline std::vector<int> 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()) {
-        all_pull.emplace_back(last_pull);
-        last_pull = pull_near(u_point_index);
-    }
-    return all_pull;
+  std::vector<int> all_pull;
+  int last_pull = pull_near(u_point_index);
+  while (last_pull != null_point_index()) {
+    all_pull.emplace_back(last_pull);
+    last_pull = pull_near(u_point_index);
+  }
+  return all_pull;
 }
 
 inline Layered_neighbors_finder::Layered_neighbors_finder(const Persistence_graph& g, double r) :
     g(g), r(r), neighbors_finder() { }
 
 inline void Layered_neighbors_finder::add(int v_point_index, int vlayer) {
-    for (int l = neighbors_finder.size(); l <= vlayer; l++)
-        neighbors_finder.emplace_back(std::unique_ptr<Neighbors_finder>(new Neighbors_finder(g, r)));
-    neighbors_finder.at(vlayer)->add(v_point_index);
+  for (int l = neighbors_finder.size(); l <= vlayer; l++)
+    neighbors_finder.emplace_back(std::unique_ptr<Neighbors_finder>(new Neighbors_finder(g, r)));
+  neighbors_finder.at(vlayer)->add(v_point_index);
 }
 
 inline int Layered_neighbors_finder::pull_near(int u_point_index, int vlayer) {
-    if (static_cast<int> (neighbors_finder.size()) <= vlayer)
-        return null_point_index();
-    return neighbors_finder.at(vlayer)->pull_near(u_point_index);
+  if (static_cast<int> (neighbors_finder.size()) <= vlayer)
+    return null_point_index();
+  return neighbors_finder.at(vlayer)->pull_near(u_point_index);
 }
 
 inline int Layered_neighbors_finder::vlayers_number() const {
-    return static_cast<int>(neighbors_finder.size());
+  return static_cast<int> (neighbors_finder.size());
 }
 
 }  // namespace persistence_diagram