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Diffstat (limited to 'include/gudhi/Neighbors_finder.h')
-rw-r--r-- | include/gudhi/Neighbors_finder.h | 193 |
1 files changed, 0 insertions, 193 deletions
diff --git a/include/gudhi/Neighbors_finder.h b/include/gudhi/Neighbors_finder.h deleted file mode 100644 index 36a63ea0..00000000 --- a/include/gudhi/Neighbors_finder.h +++ /dev/null @@ -1,193 +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: 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 NEIGHBORS_FINDER_H_ -#define NEIGHBORS_FINDER_H_ - -// Inclusion order is important for CGAL patch -#include <CGAL/Kd_tree.h> -#include <CGAL/Search_traits.h> - -#include <gudhi/Persistence_graph.h> -#include <gudhi/Internal_point.h> - -#include <unordered_set> -#include <vector> -#include <algorithm> // for std::max - -namespace Gudhi { - -namespace persistence_diagram { - -/** \internal \brief Variant of CGAL::Fuzzy_iso_box to ensure that the box ic closed. It isn't clear how necessary that is. - */ -struct Square_query { - typedef CGAL::Dimension_tag<2> D; - typedef Internal_point Point_d; - typedef double FT; - bool contains(Point_d p) const { - return std::max(std::abs(p.x()-c.x()), std::abs(p.y()-c.y())) <= size; - } - bool inner_range_intersects(CGAL::Kd_tree_rectangle<FT, D> const&r) const { - return - r.max_coord(0) >= c.x() - size && - r.min_coord(0) <= c.x() + size && - r.max_coord(1) >= c.y() - size && - r.min_coord(1) <= c.y() + size; - } - bool outer_range_contains(CGAL::Kd_tree_rectangle<FT, D> const&r) const { - return - r.min_coord(0) >= c.x() - size && - r.max_coord(0) <= c.x() + size && - r.min_coord(1) >= c.y() - size && - r.max_coord(1) <= c.y() + size; - } - Point_d c; - FT size; -}; - -/** \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 { - typedef CGAL::Dimension_tag<2> D; - typedef CGAL::Search_traits<double, Internal_point, const double*, Construct_coord_iterator, D> Traits; - typedef CGAL::Kd_tree<Traits> 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. - * - * \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; -}; - -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)); -} - -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); - auto neighbor = kd_t.search_any_point(Square_query{u_point, r}); - if (!neighbor) - return null_point_index(); - tmp = neighbor->point_index; - auto point = g.get_v_point(tmp); - int idx = point.point_index; - kd_t.remove(point, [idx](Internal_point const&p){return p.point_index == idx;}); - } - 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; -} - -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); -} - -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 persistence_diagram - -} // namespace Gudhi - -#endif // NEIGHBORS_FINDER_H_ |