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diff --git a/include/gudhi/Persistence_graph.h b/include/gudhi/Persistence_graph.h
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-/* 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: Francois Godi
- *
- * 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
- * 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 PERSISTENCE_GRAPH_H_
-#define PERSISTENCE_GRAPH_H_
-
-#include <gudhi/Internal_point.h>
-
-#ifdef GUDHI_USE_TBB
-#include <tbb/parallel_sort.h>
-#endif
-
-#include <vector>
-#include <algorithm>
-#include <limits> // for numeric_limits
-
-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 PersistenceDiagrams (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));
- }
-}
-
-inline bool Persistence_graph::on_the_u_diagonal(int u_point_index) const {
- 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());
-}
-
-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());
-}
-
-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());
-}
-
-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()));
-}
-
-inline int Persistence_graph::size() const {
- return static_cast<int> (u.size() + v.size());
-}
-
-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));
- }
-#ifdef GUDHI_USE_TBB
- tbb::parallel_sort(distances.begin(), distances.end());
-#else
- std::sort(distances.begin(), distances.end());
-#endif
- 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);
-}
-
-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);
-}
-
-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;
-}
-
-} // namespace persistence_diagram
-
-} // namespace Gudhi
-
-#endif // PERSISTENCE_GRAPH_H_