diff options
Diffstat (limited to 'GudhUI/utils')
| -rw-r--r-- | GudhUI/utils/Bar_code_persistence.h | 113 | ||||
| -rw-r--r-- | GudhUI/utils/Critical_points.h | 133 | ||||
| -rw-r--r-- | GudhUI/utils/Edge_collapsor.h | 97 | ||||
| -rw-r--r-- | GudhUI/utils/Edge_contractor.h | 97 | ||||
| -rw-r--r-- | GudhUI/utils/Furthest_point_epsilon_net.h | 132 | ||||
| -rw-r--r-- | GudhUI/utils/Is_manifold.h | 104 | ||||
| -rw-r--r-- | GudhUI/utils/K_nearest_builder.h | 90 | ||||
| -rw-r--r-- | GudhUI/utils/Lloyd_builder.h | 91 | ||||
| -rw-r--r-- | GudhUI/utils/MClock.h | 70 | ||||
| -rw-r--r-- | GudhUI/utils/Persistence_compute.h | 94 | ||||
| -rw-r--r-- | GudhUI/utils/Rips_builder.h | 69 | ||||
| -rw-r--r-- | GudhUI/utils/UI_utils.h | 45 | ||||
| -rw-r--r-- | GudhUI/utils/Vertex_collapsor.h | 89 |
13 files changed, 0 insertions, 1224 deletions
diff --git a/GudhUI/utils/Bar_code_persistence.h b/GudhUI/utils/Bar_code_persistence.h deleted file mode 100644 index 49c87b3c..00000000 --- a/GudhUI/utils/Bar_code_persistence.h +++ /dev/null @@ -1,113 +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): David Salinas - * - * Copyright (C) 2014 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/>. - * - */ - -#include <math.h> // isfinite - -#include <QtGui/QApplication> - -#include <QGraphicsView> -#include <QGraphicsScene> -#include <QPointF> -#include <QVector> -#include <QGraphicsTextItem> - -#include <iostream> -#include <vector> -#include <limits> // NaN, infinity -#include <utility> // for pair -#include <string> - -#ifndef UTILS_BAR_CODE_PERSISTENCE_H_ -#define UTILS_BAR_CODE_PERSISTENCE_H_ - -class Bar_code_persistence { - private: - typedef std::vector<std::pair<double, double>> Persistence; - Persistence persistence_vector; - double min_birth; - double max_death; - - public: - Bar_code_persistence() - : min_birth(std::numeric_limits<double>::quiet_NaN()), - max_death(std::numeric_limits<double>::quiet_NaN()) { } - - void insert(double birth, double death) { - persistence_vector.push_back(std::make_pair(birth, death)); - if (std::isfinite(birth)) { - if ((birth < min_birth) || (std::isnan(min_birth))) - min_birth = birth; - if ((birth > max_death) || (std::isnan(max_death))) - max_death = birth; - } - if (std::isfinite(death)) - if ((death > max_death) || (std::isnan(max_death))) - max_death = death; - } - - void show(const std::string& window_title) { - // Create a view, put a scene in it - QGraphicsView * view = new QGraphicsView(); - QGraphicsScene * scene = new QGraphicsScene(); - view->setScene(scene); - double ratio = 600.0 / (max_death - min_birth); - // std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl; - - double height = 0.0, birth = 0.0, death = 0.0; - int pers_num = 1; - for (auto& persistence : persistence_vector) { - height = 5.0 * pers_num; - // std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl; - if (std::isfinite(persistence.first)) - birth = ((persistence.first - min_birth) * ratio) + 50.0; - else - birth = 0.0; - - if (std::isfinite(persistence.second)) - death = ((persistence.second - min_birth) * ratio) + 50.0; - else - death = 700.0; - - scene->addLine(birth, height, death, height, QPen(Qt::blue, 2)); - pers_num++; - } - height += 10.0; - // scale line - scene->addLine(0, height, 700.0, height, QPen(Qt::black, 1)); - int modulo = 0; - for (double scale = 50.0; scale < 700.0; scale += 50.0) { - modulo++; - // scale small dash - scene->addLine(scale, height - 3.0, scale, height + 3.0, QPen(Qt::black, 1)); - // scale text - QString scale_value = QString::number(((scale - 50.0) / ratio) + min_birth); - QGraphicsTextItem* dimText = scene->addText(scale_value, QFont("Helvetica", 8)); - dimText->setPos(scale - (3.0 * scale_value.size()), height + 9.0 * (modulo % 2)); - } - view->setWindowTitle(window_title.c_str()); - // Show the view - view->show(); - } -}; - -#endif // UTILS_BAR_CODE_PERSISTENCE_H_ diff --git a/GudhUI/utils/Critical_points.h b/GudhUI/utils/Critical_points.h deleted file mode 100644 index fbd690f8..00000000 --- a/GudhUI/utils/Critical_points.h +++ /dev/null @@ -1,133 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_CRITICAL_POINTS_H_ -#define UTILS_CRITICAL_POINTS_H_ - -#include <deque> -#include <utility> // for pair<> -#include <algorithm> // for sort - -#include "utils/Edge_contractor.h" - -/** - * Iteratively tries to anticollapse smallest edge non added so far. - * If its link is contractible then no topological change and else possible topological change. - * - * todo do a sparsification with some parameter eps while growing - */ -template<typename SkBlComplex> class Critical_points { - private: - SkBlComplex filled_complex_; - const SkBlComplex& input_complex_; - double max_length_; - std::ostream& stream_; - - public: - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - typedef typename SkBlComplex::Edge_handle Edge_handle; - typedef typename std::pair<Vertex_handle, Vertex_handle> Edge; - - /** - * @brief check all pair of points with length smaller than max_length - */ - Critical_points(const SkBlComplex& input_complex, std::ostream& stream, double max_length) : - input_complex_(input_complex), max_length_(max_length), stream_(stream) { - std::deque<Edge> edges; - auto vertices = input_complex.vertex_range(); - for (auto p = vertices.begin(); p != vertices.end(); ++p) { - filled_complex_.add_vertex(input_complex.point(*p)); - for (auto q = p; ++q != vertices.end(); /**/) - if (squared_eucl_distance(input_complex.point(*p), input_complex.point(*q)) < max_length_ * max_length_) - edges.emplace_back(*p, *q); - } - - std::sort(edges.begin(), edges.end(), - [&](Edge e1, Edge e2) { - return squared_edge_length(e1) < squared_edge_length(e2); - }); - - anti_collapse_edges(edges); - } - - private: - double squared_eucl_distance(const Point& p1, const Point& p2) const { - return Geometry_trait::Squared_distance_d()(p1, p2); - } - - void anti_collapse_edges(const std::deque<Edge>& edges) { - unsigned pos = 0; - for (Edge e : edges) { - std::cout << "edge " << pos++ << "/" << edges.size() << "\n"; - auto eh = filled_complex_.add_edge_without_blockers(e.first, e.second); - int is_contractible(is_link_reducible(eh)); - - switch (is_contractible) { - case 0: - stream_ << "alpha=" << std::sqrt(squared_edge_length(e)) << " topological change" << std::endl; - break; - case 2: - stream_ << "alpha=" << std::sqrt(squared_edge_length(e)) << " maybe a topological change" << std::endl; - break; - default: - break; - } - } - } - - // 0 -> not - // 1 -> yes - // 2 -> maybe - - int is_link_reducible(Edge_handle e) { - auto link = filled_complex_.link(e); - - if (link.empty()) - return 0; - - Edge_contractor<Complex> contractor(link, link.num_vertices() - 1); - (void)contractor; - - if (link.num_connected_components() > 1) - // one than more CC -> not contractible - return 0; - - if (link.num_vertices() == 1) - // reduced to one point -> contractible - return 1; - else - // we dont know - return 2; - } - - double squared_edge_length(Edge_handle e) const { - return squared_eucl_distance(input_complex_.point(input_complex_.first_vertex(e)), - input_complex_.point(input_complex_.second_vertex(e))); - } - - double squared_edge_length(Edge e) const { - return squared_eucl_distance(input_complex_.point(e.first), input_complex_.point(e.second)); - } -}; - -#endif // UTILS_CRITICAL_POINTS_H_ diff --git a/GudhUI/utils/Edge_collapsor.h b/GudhUI/utils/Edge_collapsor.h deleted file mode 100644 index b3cc7df7..00000000 --- a/GudhUI/utils/Edge_collapsor.h +++ /dev/null @@ -1,97 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_EDGE_COLLAPSOR_H_ -#define UTILS_EDGE_COLLAPSOR_H_ - -#include <list> -#include "utils/Edge_contractor.h" -#include "utils/UI_utils.h" - -/** - * Iteratively puts every vertex at the center of its neighbors - */ -template<typename SkBlComplex> class Edge_collapsor { - private: - SkBlComplex& complex_; - unsigned num_collapses_; - - public: - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - typedef typename SkBlComplex::Edge_handle Edge_handle; - - /** - * @brief Collapse num_collapses edges. If num_collapses<0 then it collapses all possible edges. - * Largest edges are collapsed first. - * - */ - Edge_collapsor(SkBlComplex& complex, unsigned num_collapses) : - complex_(complex), num_collapses_(num_collapses) { - std::list<Edge_handle> edges; - edges.insert(edges.begin(), complex_.edge_range().begin(), complex_.edge_range().end()); - - edges.sort( - [&](Edge_handle e1, Edge_handle e2) { - return squared_edge_length(e1) < squared_edge_length(e2); - }); - - collapse_edges(edges); - } - - private: - void collapse_edges(std::list<Edge_handle>& edges) { - while (!edges.empty() && num_collapses_--) { - Edge_handle current_edge = edges.front(); - edges.pop_front(); - if (is_link_reducible(current_edge)) - complex_.remove_edge(current_edge); - } - } - - bool is_link_reducible(Edge_handle e) { - auto link = complex_.link(e); - - if (link.empty()) - return false; - - if (link.is_cone()) - return true; - - if (link.num_connected_components() > 1) - return false; - - Edge_contractor<SkBlComplex> contractor(link, link.num_vertices() - 1); - - return (link.num_vertices() == 1); - } - - double squared_edge_length(Edge_handle e) const { - return squared_eucl_distance(complex_.point(complex_.first_vertex(e)), complex_.point(complex_.second_vertex(e))); - } - - double squared_eucl_distance(const Point& p1, const Point& p2) const { - return Geometry_trait::Squared_distance_d()(p1, p2); - } -}; - -#endif // UTILS_EDGE_COLLAPSOR_H_ diff --git a/GudhUI/utils/Edge_contractor.h b/GudhUI/utils/Edge_contractor.h deleted file mode 100644 index 090baabe..00000000 --- a/GudhUI/utils/Edge_contractor.h +++ /dev/null @@ -1,97 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_EDGE_CONTRACTOR_H_ -#define UTILS_EDGE_CONTRACTOR_H_ - - -#include <gudhi/Skeleton_blocker_contractor.h> -#include <gudhi/Contraction/Edge_profile.h> -#include <gudhi/Contraction/policies/Cost_policy.h> - -#include <vector> - -/** - * Iteratively puts every vertex at the center of its neighbors - */ -template<typename SkBlComplex> class Edge_contractor { - private: - SkBlComplex& complex_; - unsigned num_contractions_; - - /** - * @brief return a cost corresponding to the squared length of the edge - */ - template< typename EdgeProfile> class Length_cost : public contraction::Cost_policy<EdgeProfile> { - public: - typedef typename contraction::Cost_policy<EdgeProfile>::Cost_type Cost_type; - typedef typename EdgeProfile::Point Point; - - Cost_type operator()(const EdgeProfile& profile, const boost::optional<Point>& placement) const override { - Cost_type res; - if (!placement) - return res; - return Geometry_trait::Squared_distance_d()(profile.p0(), profile.p1()); // not working?? - } - }; - - /** - * @brief return a cost corresponding to the squared length of the edge - */ - template< typename EdgeProfile> class Middle_placement : public contraction::Placement_policy<EdgeProfile> { - public: - typedef typename contraction::Placement_policy<EdgeProfile>::Placement_type Placement_type; - typedef typename EdgeProfile::Point Point; - - Placement_type operator()(const EdgeProfile& profile) const override { - std::vector<double> mid_coords(profile.p0().dimension(), 0); - for (int i = 0; i < profile.p0().dimension(); ++i) { - mid_coords[i] = (profile.p0()[i] + profile.p1()[i]) / 2.; - } - return Point(profile.p0().dimension(), mid_coords.begin(), mid_coords.end()); - } - }; - - public: - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - typedef typename SkBlComplex::Edge_handle Edge_handle; - - /** - * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. - */ - Edge_contractor(SkBlComplex& complex, unsigned num_contractions) : - complex_(complex), num_contractions_(num_contractions) { - typedef typename contraction::Edge_profile<Complex> Profile; - num_contractions = (std::min)(static_cast<int>(num_contractions), static_cast<int>(complex_.num_vertices() - 1)); - typedef typename contraction::Skeleton_blocker_contractor<Complex> Contractor; - Contractor contractor(complex_, - new Length_cost<contraction::Edge_profile < Complex >> (), - new Middle_placement<contraction::Edge_profile < Complex >> (), - contraction::make_link_valid_contraction<Profile>(), - contraction::make_remove_popable_blockers_visitor<Profile>()); - contractor.contract_edges(num_contractions); - } -}; - -#endif // UTILS_EDGE_CONTRACTOR_H_ diff --git a/GudhUI/utils/Furthest_point_epsilon_net.h b/GudhUI/utils/Furthest_point_epsilon_net.h deleted file mode 100644 index dbb6661c..00000000 --- a/GudhUI/utils/Furthest_point_epsilon_net.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): David Salinas - * - * Copyright (C) 2014 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 UTILS_FURTHEST_POINT_EPSILON_NET_H_ -#define UTILS_FURTHEST_POINT_EPSILON_NET_H_ - -#include <vector> -#include <algorithm> // for sort - -#include "utils/UI_utils.h" - -/** - * Computes an epsilon net with furthest point strategy. - */ -template<typename SkBlComplex> class Furthest_point_epsilon_net { - private: - SkBlComplex& complex_; - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - typedef typename SkBlComplex::Edge_handle Edge_handle; - - /** - * Let V be the set of vertices. - * Initially v0 is one arbitrarly vertex and the set V0 is {v0}. - * Then Vk is computed as follows. - * First we compute the vertex pk that is the furthest from Vk - * then Vk = Vk \cup pk. - * The radius of pk is its distance to Vk and its meeting vertex - * is the vertex of Vk for which this distance is achieved. - */ - struct Net_filtration_vertex { - Vertex_handle vertex_handle; - Vertex_handle meeting_vertex; - double radius; - - Net_filtration_vertex(Vertex_handle vertex_handle_, - Vertex_handle meeting_vertex_, - double radius_) : - vertex_handle(vertex_handle_), meeting_vertex(meeting_vertex_), radius(radius_) { } - - bool operator<(const Net_filtration_vertex& other) const { - return radius < other.radius; - } - }; - - public: - std::vector<Net_filtration_vertex> net_filtration_; - - /** - * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. - */ - Furthest_point_epsilon_net(SkBlComplex& complex) : - complex_(complex) { - if (!complex.empty()) { - init_filtration(); - for (std::size_t k = 2; k < net_filtration_.size(); ++k) { - update_radius_value(k); - } - } - } - - // xxx does not work if complex not full - - double radius(Vertex_handle v) { - return net_filtration_[v.vertex].radius; - } - - private: - void init_filtration() { - Vertex_handle v0 = *(complex_.vertex_range().begin()); - net_filtration_.reserve(complex_.num_vertices()); - for (auto v : complex_.vertex_range()) { - if (v != v0) - net_filtration_.push_back(Net_filtration_vertex(v, - Vertex_handle(-1), - squared_eucl_distance(v, v0))); - } - net_filtration_.push_back(Net_filtration_vertex(v0, Vertex_handle(-1), 1e10)); - auto n = net_filtration_.size(); - sort_filtration(n - 1); - } - - void update_radius_value(int k) { - int n = net_filtration_.size(); - int index_to_update = n - k; - for (int i = 0; i < index_to_update; ++i) { - net_filtration_[i].radius = (std::min)(net_filtration_[i].radius, - squared_eucl_distance(net_filtration_[i].vertex_handle, - net_filtration_[index_to_update].vertex_handle)); - } - sort_filtration(n - k); - } - - /** - * sort all i first elements. - */ - void sort_filtration(int i) { - std::sort(net_filtration_.begin(), net_filtration_.begin() + i); - } - - double squared_eucl_distance(Vertex_handle v1, Vertex_handle v2) const { - return std::sqrt(Geometry_trait::Squared_distance_d()(complex_.point(v1), complex_.point(v2))); - } - - void print_filtration() const { - for (auto v : net_filtration_) { - std::cerr << "v=" << v.vertex_handle << "-> d=" << v.radius << std::endl; - } - } -}; - -#endif // UTILS_FURTHEST_POINT_EPSILON_NET_H_ diff --git a/GudhUI/utils/Is_manifold.h b/GudhUI/utils/Is_manifold.h deleted file mode 100644 index 732df607..00000000 --- a/GudhUI/utils/Is_manifold.h +++ /dev/null @@ -1,104 +0,0 @@ -/* - * Is_manifold.h - * Created on: Jan 28, 2015 - * 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): David Salinas - * - * Copyright (C) 2014 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 UTILS_IS_MANIFOLD_H_ -#define UTILS_IS_MANIFOLD_H_ - -#include "utils/UI_utils.h" -#include "utils/Edge_contractor.h" - -/** - * Iteratively tries to anticollapse smallest edge non added so far. - * If its link is contractible then no topological change and else possible topological change. - * - * todo do a sparsification with some parameter eps while growing - */ -template<typename SkBlComplex> class Is_manifold { - private: - const SkBlComplex& input_complex_; - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - - public: - /* - * return dim the maximum dimension around one simplex and res which is true if the complex is a manifold. - * If the complex has dimension <= 3 then if res is false, the complex is not a manifold. - * For d-manifold with d>=4, res may be false while the complex is a manifold. - */ - Is_manifold(const SkBlComplex& input_complex, unsigned& dim, bool & res) : input_complex_(input_complex) { - res = true; - dim = -1; - if (!input_complex_.empty()) { - for (auto v : input_complex_.vertex_range()) { - dim = local_dimension(v); - break; - } - // check that the link of every vertex is a dim-1 sphere - for (auto v : input_complex_.vertex_range()) { - if (!is_k_sphere(v, dim - 1)) { - res = false; - break; - } - } - } - } - - private: - unsigned local_dimension(Vertex_handle v) { - unsigned dim = 0; - for (const auto& s : input_complex_.star_simplex_range(v)) - dim = (std::max)(dim, (unsigned) s.dimension()); - return dim; - } - - bool is_k_sphere(Vertex_handle v, int k) { - auto link = input_complex_.link(v); - Edge_contractor<Complex> contractor(link, link.num_vertices() - 1); - (void)contractor; - return (is_sphere_simplex(link) == k); - } - - // A minimal sphere is a complex that contains vertices v1...vn and all faces - // made upon this set except the face {v1,...,vn} - // return -2 if not a minimal sphere - // and d otherwise if complex is a d minimal sphere - - template<typename SubComplex> - int is_sphere_simplex(const SubComplex& complex) { - if (complex.empty()) return -1; - if (complex.num_blockers() != 1) return -2; - - // necessary and sufficient condition : there exists a unique blocker that passes through all vertices - auto first_blocker = *(complex.const_blocker_range().begin()); - - if (first_blocker->dimension() + 1 != complex.num_vertices()) - return -2; - else - return (first_blocker->dimension() - 1); - } -}; - -#endif // UTILS_IS_MANIFOLD_H_ diff --git a/GudhUI/utils/K_nearest_builder.h b/GudhUI/utils/K_nearest_builder.h deleted file mode 100644 index 14851d96..00000000 --- a/GudhUI/utils/K_nearest_builder.h +++ /dev/null @@ -1,90 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_K_NEAREST_BUILDER_H_ -#define UTILS_K_NEAREST_BUILDER_H_ - -#include <CGAL/Euclidean_distance.h> -#include <CGAL/Orthogonal_k_neighbor_search.h> -#include <CGAL/Search_traits_d.h> -#include <CGAL/Search_traits_adapter.h> -#include <CGAL/property_map.h> - -#include <unordered_map> -#include <list> -#include <utility> - -#include "utils/UI_utils.h" -#include "model/Complex_typedefs.h" - -template<typename SkBlComplex> class K_nearest_builder { - private: - typedef Geometry_trait Kernel; - typedef Point Point_d; - typedef std::pair<Point_d, unsigned> Point_d_with_id; - typedef CGAL::Search_traits_d<Kernel> Traits_base; - typedef CGAL::Search_traits_adapter<Point_d_with_id, CGAL::First_of_pair_property_map<Point_d_with_id>, - Traits_base> Traits; - typedef CGAL::Orthogonal_k_neighbor_search<Traits> Neighbor_search; - typedef Neighbor_search::Tree Tree; - typedef Neighbor_search::Distance Distance; - - SkBlComplex& complex_; - - public: - /** - * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. - */ - K_nearest_builder(SkBlComplex& complex, unsigned k) : complex_(complex) { - complex.keep_only_vertices(); - compute_edges(k); - } - - private: - double squared_eucl_distance(const Point& p1, const Point& p2) const { - return Geometry_trait::Squared_distance_d()(p1, p2); - } - - void compute_edges(unsigned k) { - std::list<Point_d_with_id> points_with_id; - for (auto v : complex_.vertex_range()) { - Point_d_with_id point_v(complex_.point(v), v.vertex); - points_with_id.push_back(point_v); - } - - Tree tree(points_with_id.begin(), points_with_id.end()); - - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - for (auto p : complex_.vertex_range()) { - Neighbor_search search(tree, complex_.point(p), k + 1); - for (auto it = ++search.begin(); it != search.end(); ++it) { - Vertex_handle q(std::get<1>(it->first)); - if (p != q && complex_.contains_vertex(p) && complex_.contains_vertex(q)) - complex_.add_edge_without_blockers(p, q); - } - } - } -}; - -#endif // UTILS_K_NEAREST_BUILDER_H_ diff --git a/GudhUI/utils/Lloyd_builder.h b/GudhUI/utils/Lloyd_builder.h deleted file mode 100644 index 67595d33..00000000 --- a/GudhUI/utils/Lloyd_builder.h +++ /dev/null @@ -1,91 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_LLOYD_BUILDER_H_ -#define UTILS_LLOYD_BUILDER_H_ - -#include <vector> -#include <list> - -/** - * Iteratively puts every vertex at the center of its neighbors - */ -template<typename SkBlComplex> class Lloyd_builder { - private: - SkBlComplex& complex_; - int dim; - - public: - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - - /** - * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. - */ - Lloyd_builder(SkBlComplex& complex, unsigned num_iterations) : complex_(complex), dim(-1) { - if (!complex_.empty()) { - dim = get_dimension(); - while (num_iterations--) { - std::list<Point> new_points; - for (auto v : complex.vertex_range()) - new_points.push_back(barycenter_neighbors(v)); - - auto new_points_it = new_points.begin(); - for (auto v : complex.vertex_range()) - complex_.point(v) = *(new_points_it++); - } - } - } - - private: - int get_dimension() { - assert(!complex_.empty()); - for (auto v : complex_.vertex_range()) - return complex_.point(v).dimension(); - return -1; - } - - Point barycenter_neighbors(Vertex_handle v) const { - if (complex_.degree(v) == 0) - return complex_.point(v); - - std::vector<double> res(dim, 0); - unsigned num_points = 0; - for (auto nv : complex_.vertex_range(v)) { - ++num_points; - const Point& point = complex_.point(nv); - assert(point.dimension() == dim); - for (int i = 0; i < point.dimension(); ++i) - res[i] += point[i]; - } - for (auto& x : res) - x /= num_points; - return Point(dim, res.begin(), res.end()); - } - - double squared_eucl_distance(const Point& p1, const Point& p2) const { - return Geometry_trait::Squared_distance_d()(p1, p2); - } -}; - -#endif // UTILS_LLOYD_BUILDER_H_ diff --git a/GudhUI/utils/MClock.h b/GudhUI/utils/MClock.h deleted file mode 100644 index 992f6fa5..00000000 --- a/GudhUI/utils/MClock.h +++ /dev/null @@ -1,70 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_MCLOCK_H_ -#define UTILS_MCLOCK_H_ - -#include <sys/time.h> - -class MClock { - public: - MClock() { - end_called = false; - begin(); - } - - void begin() const { - end_called = false; - gettimeofday(&startTime, NULL); - } - - void end() const { - end_called = true; - gettimeofday(&endTime, NULL); - } - - friend std::ostream& operator<<(std::ostream& stream, const MClock& clock) { - // if(!clock.end_called) clock.end(); - if (!clock.end_called) { - stream << "end not called"; - } else { - long totalTime = (clock.endTime.tv_sec - clock.startTime.tv_sec) * 1000000L; - totalTime += (clock.endTime.tv_usec - clock.startTime.tv_usec); - stream << clock.num_seconds() << "s"; - } - return stream; - } - - double num_seconds() const { - if (!end_called) end(); - long totalTime = (endTime.tv_sec - startTime.tv_sec) * 1000000L; - totalTime += (endTime.tv_usec - startTime.tv_usec); - return (totalTime / 1000L) / static_cast<double>(1000); - } - - private: - mutable struct timeval startTime, endTime; - mutable bool end_called; -}; - -#endif // UTILS_MCLOCK_H_ diff --git a/GudhUI/utils/Persistence_compute.h b/GudhUI/utils/Persistence_compute.h deleted file mode 100644 index c8afded9..00000000 --- a/GudhUI/utils/Persistence_compute.h +++ /dev/null @@ -1,94 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_PERSISTENCE_COMPUTE_H_ -#define UTILS_PERSISTENCE_COMPUTE_H_ - -#include <gudhi/graph_simplicial_complex.h> -#include <gudhi/Simplex_tree.h> -#include <gudhi/distance_functions.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Rips_complex.h> - -#include <vector> - -struct Persistence_params { - int p; - double threshold; - int max_dim; - double min_pers; - - Persistence_params(int p_, double th_, int max_dim_ = 10, double min_pers_ = 0) - : p(p_), threshold(th_), max_dim(max_dim_), min_pers(min_pers_) { } -}; - -/** - * Show persistence into output stream - */ -template<typename SkBlComplex> class Persistence_compute { - public: - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - typedef typename SkBlComplex::Edge_handle Edge_handle; - - /** - * @brief Compute persistence - * parameters : - * unsigned dim_max - * double threshold - * int p for coefficient Z_p - */ - Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) { - // for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an - // initial vector - typedef std::vector<double> Point_t; - std::vector< Point_t > points; - points.reserve(complex.num_vertices()); - for (auto v : complex.vertex_range()) { - const auto & pt = complex.point(v); - Point_t pt_to_add(pt.cartesian_begin(), pt.cartesian_end()); - points.emplace_back(std::move(pt_to_add)); - } - - using Simplex_tree = Gudhi::Simplex_tree<>; - using Filtration_value = Simplex_tree::Filtration_value; - using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>; - using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; - using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; - - Rips_complex rips_complex(points, params.threshold, Euclidean_distance()); - - Simplex_tree st; - rips_complex.create_complex(st, params.max_dim); - Persistent_cohomology pcoh(st); - // initializes the coefficient field for homology - pcoh.init_coefficients(params.p); - // put params.min_pers - pcoh.compute_persistent_cohomology(params.min_pers); - stream << "persistence: \n"; - stream << "p dimension birth death: \n"; - pcoh.output_diagram(stream); - } -}; - -#endif // UTILS_PERSISTENCE_COMPUTE_H_ diff --git a/GudhUI/utils/Rips_builder.h b/GudhUI/utils/Rips_builder.h deleted file mode 100644 index ed62c1c0..00000000 --- a/GudhUI/utils/Rips_builder.h +++ /dev/null @@ -1,69 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_RIPS_BUILDER_H_ -#define UTILS_RIPS_BUILDER_H_ - -#include <boost/iterator/iterator_facade.hpp> - -#include <CGAL/Euclidean_distance.h> -#include <CGAL/Orthogonal_k_neighbor_search.h> -#include <CGAL/Search_traits_d.h> - -#include "utils/UI_utils.h" -#include "model/Complex_typedefs.h" - -template<typename SkBlComplex> class Rips_builder { - private: - SkBlComplex& complex_; - - public: - /** - * @brief Modify complex to be the Rips complex - * of its points with offset alpha. - */ - Rips_builder(SkBlComplex& complex, double alpha) : complex_(complex) { - complex.keep_only_vertices(); - if (alpha <= 0) return; - compute_edges(alpha); - } - - private: - double squared_eucl_distance(const Point& p1, const Point& p2) const { - return Geometry_trait::Squared_distance_d()(p1, p2); - } - - void compute_edges(double alpha) { - auto vertices = complex_.vertex_range(); - for (auto p = vertices.begin(); p != vertices.end(); ++p) { - std::cout << *p << " "; - std::cout.flush(); - for (auto q = p; ++q != vertices.end(); /**/) - if (squared_eucl_distance(complex_.point(*p), complex_.point(*q)) < 4 * alpha * alpha) - complex_.add_edge_without_blockers(*p, *q); - } - std::cout << std::endl; - } -}; - -#endif // UTILS_RIPS_BUILDER_H_ diff --git a/GudhUI/utils/UI_utils.h b/GudhUI/utils/UI_utils.h deleted file mode 100644 index 67a02869..00000000 --- a/GudhUI/utils/UI_utils.h +++ /dev/null @@ -1,45 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_UI_UTILS_H_ -#define UTILS_UI_UTILS_H_ - -#define UIDBG_VERBOSE - -#ifdef UIDBG_VERBOSE -#define UIDBG(a) std::cerr << "UIDBG: " << (a) << std::endl -#define UIDBGMSG(a, b) std::cerr << "UIDBG: " << a << b << std::endl -#define UIDBGVALUE(a) std::cerr << "UIDBG: " << #a << ": " << a << std::endl -#define UIDBGCONT(a) std::cerr << "UIDBG: container " << #a << " -> "; for (auto x : a) std::cerr << x << ","; std::cerr << std::endl } -#else -// #define DBG(a) a -// #define DBGMSG(a, b) b -// #define DBGVALUE(a) a -// #define DBGCONT(a) a -#define UIDBG(a) -#define UIDBGMSG(a, b) -#define UIDBGVALUE(a) -#define UIDBGCONT(a) -#endif - -#endif // UTILS_UI_UTILS_H_ diff --git a/GudhUI/utils/Vertex_collapsor.h b/GudhUI/utils/Vertex_collapsor.h deleted file mode 100644 index fca57f7d..00000000 --- a/GudhUI/utils/Vertex_collapsor.h +++ /dev/null @@ -1,89 +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): David Salinas - * - * Copyright (C) 2014 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 UTILS_VERTEX_COLLAPSOR_H_ -#define UTILS_VERTEX_COLLAPSOR_H_ - -#include <list> - -#include "utils/Edge_contractor.h" -#include "utils/Furthest_point_epsilon_net.h" -#include "utils/UI_utils.h" - -/** - * Iteratively puts every vertex at the center of its neighbors - */ -template<typename SkBlComplex> class Vertex_collapsor { - private: - SkBlComplex& complex_; - size_t num_collapses_; - - public: - typedef typename SkBlComplex::Vertex_handle Vertex_handle; - typedef typename SkBlComplex::Edge_handle Edge_handle; - - /** - * @brief Modify complex to be the expansion of the k-nearest neighbor - * symetric graph. - */ - Vertex_collapsor(SkBlComplex& complex, size_t num_collapses) : - complex_(complex), num_collapses_(num_collapses) { - // std::list<Vertex_handle> vertices; - // vertices.insert(vertices.begin(),complex_.vertex_range().begin(),complex_.vertex_range().end()); - // UIDBG("Collapse vertices"); - // collapse_vertices(vertices); - - std::list<Vertex_handle> vertices; - - UIDBG("Compute eps net"); - Furthest_point_epsilon_net<Complex> eps_net(complex_); - - for (auto vh : eps_net.net_filtration_) - vertices.push_back(vh.vertex_handle); - - UIDBG("Collapse vertices"); - collapse_vertices(vertices); - } - - private: - void collapse_vertices(std::list<Vertex_handle>& vertices) { - while (!vertices.empty() && num_collapses_--) { - Vertex_handle current_vertex = vertices.front(); - vertices.pop_front(); - if (is_link_reducible(current_vertex)) - complex_.remove_vertex(current_vertex); - } - } - - bool is_link_reducible(Vertex_handle v) { - auto link = complex_.link(v); - if (link.empty()) return false; - if (link.is_cone()) return true; - if (link.num_connected_components() > 1) return false; - Edge_contractor<Complex> contractor(link, link.num_vertices() - 1); - (void)contractor; - return (link.num_vertices() == 1); - } -}; - -#endif // UTILS_VERTEX_COLLAPSOR_H_ |