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git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/bottleneckDistance@661 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 3316ed6b6f7d865605786547b62ee1e5d9118d19

6 files changed, 0 insertions, 920 deletions

diff --git a/src/Bottleneck/include/gudhi/Graph_matching.h b/src/Bottleneck/include/gudhi/Graph_matching.h
deleted file mode 100644
index 2bcc6a61..00000000
--- a/src/Bottleneck/include/gudhi/Graph_matching.h
+++ /dev/null
@@ -1,216 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Francois Godi
- *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (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
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
-
-#include <deque>
-#include <list>
-#include <vector>
-
-#include "Layered_neighbors_finder.h"
-
-namespace Gudhi {
-
-namespace bottleneck {
-
-/** \brief Function to use in order to compute the Bottleneck distance between two persistence diagrams.
- *
- *
- *
- * \ingroup bottleneck_distance
- */
-template<typename Persistence_diagram1, typename Persistence_diagram2>
-double bottleneck_distance(const Persistence_diagram1& diag1, const Persistence_diagram2& diag2, double e = 0.);
-
-/** \internal \brief Structure representing a graph matching. The graph is a Persistence_diagrams_graph.
- *
- * \ingroup bottleneck_distance
- */
-class Graph_matching {
-public:
-    /** \internal \brief Constructor constructing an empty matching. */
-    explicit Graph_matching();
-    /** \internal \brief Copy operator. */
-    Graph_matching& operator=(const Graph_matching& m);
-    /** \internal \brief Is the matching perfect ? */
-    bool perfect() const;
-    /** \internal \brief Augments the matching with a maximal set of edge-disjoint shortest augmenting paths. */
-    bool multi_augment();
-    /** \internal \brief Sets the maximum length of the edges allowed to be added in the matching, 0 initially. */
-    void set_r(double r);
-
-private:
-    double r;
-    /** \internal \brief Given a point from V, provides its matched point in U, null_point_index() if there isn't. */
-    std::vector<int> v_to_u;
-    /** \internal \brief All the unmatched points in U. */
-    std::list<int> unmatched_in_u;
-
-    /** \internal \brief Provides a Layered_neighbors_finder dividing the graph in layers. Basically a BFS. */
-    std::unique_ptr<Layered_neighbors_finder> layering() const;
-    /** \internal \brief Augments the matching with a simple path no longer than max_depth. Basically a DFS. */
-    bool augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth);
-    /** \internal \brief Update the matching with the simple augmenting path given as parameter. */
-    void update(std::deque<int> & path);
-};
-
-inline Graph_matching::Graph_matching()
-    : r(0.), v_to_u(G::size(), null_point_index()), unmatched_in_u() {
-    for (int u_point_index = 0; u_point_index < G::size(); ++u_point_index)
-        unmatched_in_u.emplace_back(u_point_index);
-}
-
-inline Graph_matching& Graph_matching::operator=(const Graph_matching& m) {
-    r = m.r;
-    v_to_u = m.v_to_u;
-    unmatched_in_u = m.unmatched_in_u;
-    return *this;
-}
-
-inline bool Graph_matching::perfect() const {
-    return unmatched_in_u.empty();
-}
-
-inline bool Graph_matching::multi_augment() {
-    if (perfect())
-        return false;
-    Layered_neighbors_finder layered_nf = *layering();
-    int max_depth = layered_nf.vlayers_number()*2 - 1;
-    double rn = sqrt(G::size());
-    // verification of a necessary criterion in order to shortcut if possible
-    if (max_depth <0 || (unmatched_in_u.size() > rn && max_depth >= rn))
-        return false;
-    bool successful = false;
-    std::list<int> tries(unmatched_in_u);
-    for (auto it = tries.cbegin(); it != tries.cend(); it++)
-        // 'augment' has side-effects which have to be always executed, don't change order
-        successful =  augment(layered_nf, *it, max_depth) || successful;
-    return successful;
-}
-
-inline void Graph_matching::set_r(double r) {
-    this->r = r;
-}
-
-inline bool Graph_matching::augment(Layered_neighbors_finder & layered_nf, int u_start_index, int max_depth) {
-    //V vertices have at most one successor, thus when we backtrack from U we can directly pop_back 2 vertices.
-    std::deque<int> path;
-    path.emplace_back(u_start_index);
-    do {
-        if (static_cast<int>(path.size()) > max_depth) {
-            path.pop_back();
-            path.pop_back();
-        }
-        if (path.empty())
-            return false;
-        path.emplace_back(layered_nf.pull_near(path.back(), static_cast<int>(path.size())/2));
-        while (path.back() == null_point_index()) {
-            path.pop_back();
-            path.pop_back();
-            if (path.empty())
-                return false;
-            path.pop_back();
-            path.emplace_back(layered_nf.pull_near(path.back(), path.size() / 2));
-        }
-        path.emplace_back(v_to_u.at(path.back()));
-    } while (path.back() != null_point_index());
-    //if v_to_u.at(path.back()) has no successor, path.back() is an exposed vertex
-    path.pop_back();
-    update(path);
-    return true;
-}
-
-inline std::unique_ptr<Layered_neighbors_finder> Graph_matching::layering() const {
-    std::list<int> u_vertices(unmatched_in_u);
-    std::list<int> v_vertices;
-    Neighbors_finder nf(r);
-    for (int v_point_index = 0; v_point_index < G::size(); ++v_point_index)
-        nf.add(v_point_index);
-    std::unique_ptr<Layered_neighbors_finder> layered_nf(new Layered_neighbors_finder(r));
-    for(int layer = 0; !u_vertices.empty(); layer++) {
-        // one layer is one step in the BFS
-        for (auto it = u_vertices.cbegin(); it != u_vertices.cend(); ++it) {
-            std::unique_ptr< std::list<int> > u_succ = std::move(nf.pull_all_near(*it));
-            for (auto it = u_succ->cbegin(); it != u_succ->cend(); ++it) {
-                layered_nf->add(*it, layer);
-                v_vertices.emplace_back(*it);
-            }
-        }
-        // When the above for finishes, we have progress of one half-step (from U to V) in the BFS
-        u_vertices.clear();
-        bool end = false;
-        for (auto it = v_vertices.cbegin(); it != v_vertices.cend(); it++)
-            if (v_to_u.at(*it) == null_point_index())
-                // we stop when a nearest exposed V vertex (from U exposed vertices) has been found
-                end = true;
-            else
-                u_vertices.emplace_back(v_to_u.at(*it));
-        // When the above for finishes, we have progress of one half-step (from V to U) in the BFS
-        if (end)
-            return layered_nf;
-        v_vertices.clear();
-    }
-    return layered_nf;
-}
-
-inline void Graph_matching::update(std::deque<int>& path) {
-    unmatched_in_u.remove(path.front());
-    for (auto it = path.cbegin(); it != path.cend(); ++it) {
-        // Be careful, the iterator is incremented twice each time
-        int tmp = *it;
-        ++it;
-        v_to_u[*it] = tmp;
-    }
-}
-
-template<typename Persistence_diagram1, typename Persistence_diagram2>
-double bottleneck_distance(const Persistence_diagram1 &diag1, const Persistence_diagram2 &diag2, double e) {
-    G::initialize(diag1, diag2, e);
-    std::unique_ptr< std::vector<double> > sd = std::move(G::sorted_distances());
-    int idmin = 0;
-    int idmax = sd->size() - 1;
-    // alpha can be modified, this will change the complexity
-    double alpha = pow(sd->size(), 0.25);
-    Graph_matching m;
-    Graph_matching biggest_unperfect;
-    while (idmin != idmax) {
-        int step = static_cast<int>((idmax - idmin) / alpha);
-        m.set_r(sd->at(idmin + step));
-        while (m.multi_augment());
-        // The above while compute a maximum matching (according to the r setted before)
-        if (m.perfect()) {
-            idmax = idmin + step;
-            m = biggest_unperfect;
-        } else {
-            biggest_unperfect = m;
-            idmin = idmin + step + 1;
-        }
-    }
-    return sd->at(idmin);
-}
-
-}  // namespace bottleneck
-
-}  // namespace Gudhi
-
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_GRAPH_MATCHING_H_
diff --git a/src/Bottleneck/include/gudhi/Grid_cell.h b/src/Bottleneck/include/gudhi/Grid_cell.h
deleted file mode 100644
index eee938cb..00000000
--- a/src/Bottleneck/include/gudhi/Grid_cell.h
+++ /dev/null
@@ -1,188 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Francois Godi
- *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (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
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_
-
-#include <list>
-#include <set>
-#include <map>
-
-#include "Persistence_diagrams_graph.h"
-
-namespace Gudhi {
-
-namespace bottleneck {
-
-/** \internal \brief TODO
- *
- * \ingroup bottleneck_distance
- */
-class Grid_cell {
-public:
-    Grid_cell(double r);
-    void add(int v_point_index);
-    void remove(int v_point_index);
-    bool contains(int v_point_index) const;
-    int pull_center();
-    int pull_xi(int u_point_index);
-    int pull_xd(int u_point_index);
-    int pull_yi(int u_point_index);
-    int pull_yd(int u_point_index);
-    int pull_xi_yi(int u_point_index);
-    int pull_xi_yd(int u_point_index);
-    int pull_xd_yi(int u_point_index);
-    int pull_xd_yd(int u_point_index);
-
-private:
-    double r;
-    std::set<int, G::Compare_x> xi_order;
-    std::set<int, G::Compare_y> yi_order;
-    struct Hidden_points_tree{int point; std::list<Hidden_points_tree> hidden;};
-    typedef std::map<int, std::list<Hidden_points_tree>, G::Compare_x> Corner_tree;
-    Corner_tree xi_yi_order;
-    Corner_tree xi_yd_order;
-    Corner_tree xd_yi_order;
-    Corner_tree xd_yd_order;
-    void remove_aux(Corner_tree t, int v_point_index);
-    void build_xi_yi();
-    void build_xi_yd();
-    void build_xd_yi();
-    void build_xd_yd();
-};
-
-
-inline Grid_cell::Grid_cell(double r)
-    : r(r), xi_order(G::Compare_x(r)), yi_order(G::Compare_y(r)), xi_yi_order(G::Compare_x(r)),
-      xi_yd_order(G::Compare_x(r)), xd_yi_order(G::Compare_x(r)), xd_yd_order(G::Compare_x(r)) {}
-
-inline void Grid_cell::add(int v_point_index){
-    xi_order.emplace(v_point_index);
-}
-
-inline bool Grid_cell::contains(int v_point_index) const{
-    return (xi_order.count(v_point_index) > 0);
-}
-
-inline void Grid_cell::remove_aux(Corner_tree t, int v_point_index){
-    if(t.empty())
-        return;
-    std::list<Hidden_points_tree> hidden_points = t.at(v_point_index);
-    t.erase(v_point_index);
-    for(auto it = hidden_points.begin(); it != hidden_points.end(); ++it)
-        t.emplace(it->point,it->hidden);
-
-}
-
-inline void Grid_cell::remove(int v_point_index){
-    xi_order.erase(v_point_index);
-    yi_order.erase(v_point_index);
-    remove_aux(xi_yi_order,v_point_index);
-    remove_aux(xi_yd_order,v_point_index);
-    remove_aux(xd_yi_order,v_point_index);
-    remove_aux(xd_yd_order,v_point_index);
-}
-
-//factorization needed \/ \/ \/
-
-inline int Grid_cell::pull_center(){
-    if(xi_order.empty())
-        return null_point_index();
-    int v_point_index = *xi_order.begin();
-    remove(v_point_index);
-    return v_point_index;
-}
-
-inline int Grid_cell::pull_xi(int u_point_index){
-    if(xi_order.empty())
-        return null_point_index();
-    int v_point_index = *xi_order.begin(); //!
-    if(G::distance(u_point_index,v_point_index)<=r){
-        remove(v_point_index);
-        return v_point_index;
-    }
-    return null_point_index();
-}
-
-inline int Grid_cell::pull_xd(int u_point_index){
-    if(xi_order.empty())
-        return null_point_index();
-    int v_point_index = *xi_order.rbegin(); //!
-    if(G::distance(u_point_index,v_point_index)<=r){
-        remove(v_point_index);
-        return v_point_index;
-    }
-    return null_point_index();
-}
-
-inline int Grid_cell::pull_yi(int u_point_index){
-    if(xi_order.empty())
-        return null_point_index();
-    if(yi_order.empty())
-        for(auto it = xi_order.begin(); it!= xi_order.end(); ++it)
-            yi_order.emplace(*it);
-    int v_point_index = *yi_order.begin(); //!
-    if(G::distance(u_point_index,v_point_index)<=r){
-        remove(v_point_index);
-        return v_point_index;
-    }
-    return null_point_index();
-}
-
-inline int Grid_cell::pull_yd(int u_point_index){
-    if(xi_order.empty())
-        return null_point_index();
-    if(yi_order.empty())
-        for(auto it = xi_order.begin(); it!= xi_order.end(); ++it)
-            yi_order.emplace(*it);
-    int v_point_index = *yi_order.rbegin(); //!
-    if(G::distance(u_point_index,v_point_index)<=r){
-        remove(v_point_index);
-        return v_point_index;
-    }
-    return null_point_index();
-}
-
-inline int Grid_cell::pull_xi_yi(int u_point_index){
-    if(xi_order.empty())
-        return null_point_index();
-    if(xi_yi_order.empty())
-        build_xi_yi();
-    auto it = xi_yi_order.upper_bound(u_point_index+G::size());
-    if(it==xi_yi_order.cbegin()) //!
-        return null_point_index();
-    it--; //!
-    int v_point_index = it->first;
-    for(auto it2=it->second.begin();it2!=it->second.end();it2++)
-        xi_yi_order.emplace(it2->point,it2->hidden);
-    if(G::distance(u_point_index,v_point_index)<=r){
-        remove(v_point_index);
-        return v_point_index;
-    }
-    return null_point_index();
-}
-
-}  // namespace bottleneck
-
-}  // namespace Gudhi
-
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_GRID_CELL_H_
diff --git a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h b/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h
deleted file mode 100644
index 58805b86..00000000
--- a/src/Bottleneck/include/gudhi/Layered_neighbors_finder.h
+++ /dev/null
@@ -1,80 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Francois Godi
- *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (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
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_
-
-#include <vector>
-
-#include "Neighbors_finder.h"
-
-namespace Gudhi {
-
-namespace bottleneck {
-
-/** \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.
- *
- * \ingroup bottleneck_distance
- */
-class Layered_neighbors_finder {
-public:
-    /** \internal \brief Constructor taking the near distance definition as parameter. */
-    Layered_neighbors_finder(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 double r;
-    std::vector<Neighbors_finder> neighbors_finder;
-};
-
-inline Layered_neighbors_finder::Layered_neighbors_finder(double r) :
-    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(Neighbors_finder(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);
-}
-
-inline int Layered_neighbors_finder::vlayers_number() const {
-    return static_cast<int>(neighbors_finder.size());
-}
-
-}  // namespace bottleneck
-
-}  // namespace Gudhi
-
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_LAYERED_NEIGHBORS_FINDER_H_
diff --git a/src/Bottleneck/include/gudhi/Neighbors_finder.h b/src/Bottleneck/include/gudhi/Neighbors_finder.h
deleted file mode 100644
index be81877a..00000000
--- a/src/Bottleneck/include/gudhi/Neighbors_finder.h
+++ /dev/null
@@ -1,114 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Francois Godi
- *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (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
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_
-
-#include <unordered_set>
-#include <list>
-
-#include "Planar_neighbors_finder.h"
-
-namespace Gudhi {
-
-namespace bottleneck {
-
-/** \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.
- *
- * \ingroup bottleneck_distance
- */
-class Neighbors_finder {
-public:
-    /** \internal \brief Constructor taking the near distance definition as parameter. */
-    Neighbors_finder(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::unique_ptr< std::list<int> > pull_all_near(int u_point_index);
-
-private:
-    const double r;
-    Planar_neighbors_finder planar_neighbors_f;
-    std::unordered_set<int> projections_f;
-    void remove(int v_point_index);
-    bool contains(int v_point_index);
-};
-
-inline Neighbors_finder::Neighbors_finder(double r) :
-    r(r), planar_neighbors_f(r), 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
-        planar_neighbors_f.add(v_point_index);
-}
-
-inline void Neighbors_finder::remove(int v_point_index) {
-    if(v_point_index == null_point_index())
-        return;
-    if (G::on_the_v_diagonal(v_point_index))
-        projections_f.erase(v_point_index);
-    else
-        planar_neighbors_f.remove(v_point_index);
-}
-
-inline bool Neighbors_finder::contains(int v_point_index) {
-    return planar_neighbors_f.contains(v_point_index) || (projections_f.count(v_point_index)>0);
-}
-
-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())
-        //All projections are at distance 0
-        tmp = *projections_f.cbegin();
-    else if (contains(c) && (G::distance(u_point_index, c) <= r))
-        //Is the query point near to its projection ?
-        tmp = c;
-    else
-        //Is the query point near to a V point in the plane ?
-        tmp = planar_neighbors_f.pull_near(u_point_index);
-    remove(tmp);
-    return tmp;
-}
-
-inline std::unique_ptr< std::list<int> > Neighbors_finder::pull_all_near(int u_point_index) {
-    std::unique_ptr< std::list<int> > all_pull = std::move(planar_neighbors_f.pull_all_near(u_point_index));
-    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;
-}
-
-}  // namespace bottleneck
-
-}  // namespace Gudhi
-
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_NEIGHBORS_FINDER_H_
diff --git a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h b/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h
deleted file mode 100644
index aed328e2..00000000
--- a/src/Bottleneck/include/gudhi/Persistence_diagrams_graph.h
+++ /dev/null
@@ -1,190 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Francois Godi
- *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (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
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_
-
-#include <vector>
-#include <set>
-#include <cmath>
-#include <utility>
-#include <algorithm>
-#include <math.h>
-
-namespace Gudhi {
-
-namespace bottleneck {
-
-/** \internal \brief Returns the used index for encoding none of the points */
-int null_point_index();
-
-/** \internal \brief Structure representing an euclidean bipartite graph containing
- *  the points from the two persistence diagrams (including the projections).
- *
- * \ingroup bottleneck_distance
- */
-class Persistence_diagrams_graph {
-public:
-    /** \internal \brief Initializer taking 2 Point (concept) ranges as parameters. */
-    template<typename Persistence_diagram1, typename Persistence_diagram2>
-    static void initialize(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 ? */
-    static bool on_the_u_diagonal(int u_point_index);
-    /** \internal \brief Is the given point from V the projection of a point in U ? */
-    static bool on_the_v_diagonal(int v_point_index);
-    /** \internal \brief Given a point from V, returns the corresponding (projection or projector) point in U. */
-    static int corresponding_point_in_u(int v_point_index);
-    /** \internal \brief Given a point from U, returns the corresponding (projection or projector) point in V. */
-    static int corresponding_point_in_v(int u_point_index);
-    /** \internal \brief Given a point from U and a point from V, returns the distance between those points. */
-    static double distance(int u_point_index, int v_point_index);
-    /** \internal \brief Returns size = |U| = |V|. */
-    static int size();
-    /** \internal \brief Returns the O(n^2) sorted distances between the points. */
-    static std::unique_ptr< std::vector<double> > sorted_distances();
-    /** \internal \brief Compare points regarding x%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points.  */
-    struct Compare_x{double r; Compare_x(double r); bool operator()(const int point_index_1, const int point_index_2) const;};
-    /** \internal \brief Compare points regarding y%r coordinate. Use v_point_index for V points and u_point_index + G::size() for U points. */
-    struct Compare_y{double r; Compare_y(double r);bool operator()(const int point_index_1, const int point_index_2) const;};
-
-private:
-    /** \internal \typedef \brief Internal_point is the internal points representation, indexes used outside. */
-    typedef std::pair<double, double> Internal_point;
-    static std::vector<Internal_point> u;
-    static std::vector<Internal_point> v;
-    static Internal_point get_u_point(int u_point_index);
-    static Internal_point get_v_point(int v_point_index);
-};
-
-/** \internal \typedef \brief Shorter alias */
-typedef Persistence_diagrams_graph G;
-
-// static initialization, seems to work but strange
-std::vector<G::Internal_point> G::u = [] {return std::vector<G::Internal_point>();}();
-std::vector<G::Internal_point> G::v = [] {return std::vector<G::Internal_point>();}();
-
-inline int null_point_index() {
-    return -1;
-}
-
-template<typename Persistence_diagram1, typename Persistence_diagram2>
-inline void G::initialize(const Persistence_diagram1 &diag1,
-                          const Persistence_diagram2 &diag2, double e){
-    u.clear();
-    v.clear();
-    for (auto it = diag1.cbegin(); it != diag1.cend(); ++it)
-        if (it->second - it->first > e)
-            u.emplace_back(*it);
-    for (auto it = diag2.cbegin(); it != diag2.cend(); ++it)
-        if (it->second - it->first > e)
-            v.emplace_back(*it);
-    if (u.size() < v.size())
-        swap(u, v);
-}
-
-inline bool G::on_the_u_diagonal(int u_point_index) {
-    return u_point_index >= static_cast<int> (u.size());
-}
-
-inline bool G::on_the_v_diagonal(int v_point_index) {
-    return v_point_index >= static_cast<int> (v.size());
-}
-
-inline int G::corresponding_point_in_u(int v_point_index) {
-    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 G::corresponding_point_in_v(int u_point_index) {
-    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 G::distance(int u_point_index, int v_point_index) {
-    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.first - p_v.first), std::fabs(p_u.second - p_v.second));
-}
-
-inline int G::size() {
-    return static_cast<int> (u.size() + v.size());
-}
-
-inline std::unique_ptr< std::vector<double> > G::sorted_distances() {
-    // could be optimized
-    std::set<double> sorted_distances;
-    for (int u_point_index = 0; u_point_index < size(); ++u_point_index)
-        for (int v_point_index = 0; v_point_index < size(); ++v_point_index)
-            sorted_distances.emplace(distance(u_point_index, v_point_index));
-    std::unique_ptr< std::vector<double> > sd_up(new std::vector<double>(sorted_distances.cbegin(), sorted_distances.cend()));
-    return sd_up;
-}
-
-inline G::Internal_point G::get_u_point(int 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 x = (projector.first + projector.second) / 2;
-    return Internal_point(x, x);
-}
-
-inline G::Internal_point G::get_v_point(int 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 x = (projector.first + projector.second) / 2;
-    return Internal_point(x, x);
-}
-
-G::Compare_x::Compare_x(double r)
-    : r(r){ }
-
-G::Compare_y::Compare_y(double r)
-    : r(r){ }
-
-inline bool G::Compare_x::operator()(const int point_index_1, const int point_index_2) const{
-    G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size());
-    G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size());
-    double x1 = fmod(p1.first,r);
-    double x2 = fmod(p2.first,r);
-    if(x1 == x2)
-        return point_index_1 > point_index_2;
-    return x1 < x2;
-}
-
-inline bool G::Compare_y::operator()(const int point_index_1, const int point_index_2) const{
-    G::Internal_point p1 = point_index_1 < G::size() ? G::get_v_point(point_index_1) : G::get_u_point(point_index_1 - G::size());
-    G::Internal_point p2 = point_index_2 < G::size() ? G::get_v_point(point_index_2) : G::get_u_point(point_index_2 - G::size());
-    double y1 = fmod(p1.second,r);
-    double y2 = fmod(p2.second,r);
-    if(y1 == y2)
-        return  point_index_1 > point_index_2;
-    return y1 < y2;
-}
-
-}  // namespace bottleneck
-
-}  // namespace Gudhi
-
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_PERSISTENCE_DIAGRAMS_GRAPH_H_
diff --git a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h b/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h
deleted file mode 100644
index e403735c..00000000
--- a/src/Bottleneck/include/gudhi/Planar_neighbors_finder.h
+++ /dev/null
@@ -1,132 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Francois Godi
- *
- *    Copyright (C) 2015  INRIA Sophia-Antipolis (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
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_
-#define SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_
-
-#include <list>
-#include <set>
-
-#include "Persistence_diagrams_graph.h"
-#include "Grid_cell.h"
-
-namespace Gudhi {
-
-namespace bottleneck {
-
-/** \internal \brief Structure used to find any point in V near (according to the planar distance) to a query point from U.
- *
- * V points have to be added manually using their index and before the first remove/pull. A neighbor pulled is automatically removed. but we can also
- * remove points manually using their index.
- *
- * \ingroup bottleneck_distance
- */
-class Abstract_planar_neighbors_finder {
-public:
-    /** \internal \brief Constructor TODO. */
-    Abstract_planar_neighbors_finder(double r);
-    virtual ~Abstract_planar_neighbors_finder() = 0;
-    /** \internal \brief A point added will be possibly pulled. */
-    virtual void add(int v_point_index) = 0;
-    /** \internal \brief A point manually removed will no longer be possibly pulled. */
-    virtual void remove(int v_point_index) = 0;
-    /** \internal \brief Can the point given as parameter be returned ? */
-    virtual bool contains(int v_point_index) const = 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. */
-    virtual int pull_near(int u_point_index) = 0;
-    /** \internal \brief Provide and remove all the V points near to the U point given as parameter. */
-    virtual std::unique_ptr< std::list<int> > pull_all_near(int u_point_index);
-
-protected:
-    const double r;
-};
-
-/** \internal \brief Naive_pnf is an naïve Abstract_planar_neighbors_finder implementation
- *
- * \ingroup bottleneck_distance
- */
-class Naive_pnf : public Abstract_planar_neighbors_finder {
-public:
-    /** \internal \brief Constructor taking the near distance definition as parameter. */
-    Naive_pnf(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. */
-    void remove(int v_point_index);
-    /** \internal \brief Can the point given as parameter be returned ? */
-    bool contains(int v_point_index) const;
-    /** \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. */
-    int pull_near(int u_point_index);
-
-private:
-    std::set<int> candidates;
-};
-
-/** \internal \typedef \brief Planar_neighbors_finder is the used Abstract_planar_neighbors_finder's implementation. */
-typedef Naive_pnf Planar_neighbors_finder;
-
-
-inline Abstract_planar_neighbors_finder::Abstract_planar_neighbors_finder(double r) :
-    r(r) { }
-
-inline Abstract_planar_neighbors_finder::~Abstract_planar_neighbors_finder() {}
-
-inline std::unique_ptr< std::list<int> > Abstract_planar_neighbors_finder::pull_all_near(int u_point_index) {
-    std::unique_ptr< std::list<int> > all_pull(new std::list<int>);
-    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 Naive_pnf::Naive_pnf(double r) :
-    Abstract_planar_neighbors_finder(r), candidates() { }
-
-inline void Naive_pnf::add(int v_point_index) {
-    candidates.emplace(v_point_index);
-}
-
-inline void Naive_pnf::remove(int v_point_index) {
-    candidates.erase(v_point_index);
-}
-
-inline bool Naive_pnf::contains(int v_point_index) const {
-    return (candidates.count(v_point_index) > 0);
-}
-
-inline int Naive_pnf::pull_near(int u_point_index) {
-    for (auto it = candidates.begin(); it != candidates.end(); ++it)
-        if (G::distance(u_point_index, *it) <= r) {
-            int tmp = *it;
-            candidates.erase(it);
-            return tmp;
-        }
-    return null_point_index();
-}
-
-}  // namespace bottleneck
-
-}  // namespace Gudhi
-
-#endif  // SRC_BOTTLENECK_INCLUDE_GUDHI_PLANAR_NEIGHBORS_FINDER_H_