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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(s): Vincent Rouvreau
+ *
+ * Copyright (C) 2016 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 ALPHA_COMPLEX_INTERFACE_H
+#define ALPHA_COMPLEX_INTERFACE_H
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Alpha_complex.h>
+#include <CGAL/Epick_d.h>
+
+#include "Persistent_cohomology_interface.h"
+
+#include <vector>
+#include <utility> // std::pair
+#include <iostream>
+
+namespace Gudhi {
+
+namespace alpha_complex {
+
+class Alpha_complex_interface {
+ using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >;
+ using Point_d = Dynamic_kernel::Point_d;
+ typedef typename Simplex_tree<>::Simplex_handle Simplex_handle;
+ typedef typename std::pair<Simplex_handle, bool> Insertion_result;
+ using Simplex = std::vector<Vertex_handle>;
+ using Filtered_complex = std::pair<Simplex, Filtration_value>;
+ using Complex_tree = std::vector<Filtered_complex>;
+
+ typedef typename Simplex_tree<>::Simplex_key Simplex_key;
+
+ public:
+ Alpha_complex_interface(std::vector<std::vector<double>>&points, double max_alpha_square)
+ : pcoh_(nullptr) {
+ alpha_complex_ = new Alpha_complex<Dynamic_kernel>(points);
+ alpha_complex_->create_complex(simplex_tree_, max_alpha_square);
+ simplex_tree_.initialize_filtration();
+ }
+
+ Alpha_complex_interface(std::string off_file_name, double max_alpha_square, bool from_file = true)
+ : pcoh_(nullptr) {
+ alpha_complex_ = new Alpha_complex<Dynamic_kernel>(off_file_name);
+ alpha_complex_->create_complex(simplex_tree_, max_alpha_square);
+ simplex_tree_.initialize_filtration();
+ }
+
+ bool find_simplex(const Simplex& vh) {
+ return (simplex_tree_.find(vh) != simplex_tree_.null_simplex());
+ }
+
+ bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) {
+ Insertion_result result = simplex_tree_.insert_simplex_and_subfaces(complex, filtration);
+ return (result.second);
+ }
+
+ Filtration_value simplex_filtration(const Simplex& complex) {
+ return simplex_tree_.filtration(simplex_tree_.find(complex));
+ }
+
+ void remove_maximal_simplex(const Simplex& complex) {
+ return simplex_tree_.remove_maximal_simplex(simplex_tree_.find(complex));
+ }
+
+ Complex_tree get_filtered_tree() {
+ Complex_tree filtered_tree;
+ for (auto f_simplex : simplex_tree_.filtration_simplex_range()) {
+ Simplex simplex;
+ for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ filtered_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+ }
+ return filtered_tree;
+
+ }
+
+ Complex_tree get_skeleton_tree(int dimension) {
+ Complex_tree skeleton_tree;
+ for (auto f_simplex : simplex_tree_.skeleton_simplex_range(dimension)) {
+ Simplex simplex;
+ for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ skeleton_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+ }
+ return skeleton_tree;
+ }
+
+ Complex_tree get_star_tree(const Simplex& complex) {
+ Complex_tree star_tree;
+ for (auto f_simplex : simplex_tree_.star_simplex_range(simplex_tree_.find(complex))) {
+ Simplex simplex;
+ for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ star_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+ }
+ return star_tree;
+ }
+
+ Complex_tree get_coface_tree(const Simplex& complex, int dimension) {
+ Complex_tree coface_tree;
+ for (auto f_simplex : simplex_tree_.cofaces_simplex_range(simplex_tree_.find(complex), dimension)) {
+ Simplex simplex;
+ for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ coface_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex)));
+ }
+ return coface_tree;
+ }
+
+ // Specific to Witness complex because no inheritance
+ Filtration_value filtration() const {
+ return simplex_tree_.filtration();
+ }
+
+ void set_filtration(Filtration_value fil) {
+ simplex_tree_.set_filtration(fil);
+ }
+
+ void initialize_filtration() {
+ simplex_tree_.initialize_filtration();
+ }
+
+ size_t num_vertices() const {
+ return simplex_tree_.num_vertices();
+ }
+
+ size_t num_simplices() {
+ return simplex_tree_.num_simplices();
+ }
+
+ int dimension() const {
+ return simplex_tree_.dimension();
+ }
+
+ void set_dimension(int dimension) {
+ simplex_tree_.set_dimension(dimension);
+ }
+
+ std::vector<double> get_point(int vh) {
+ std::vector<double> vd;
+ try {
+ Point_d ph = alpha_complex_->get_point(vh);
+ for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++)
+ vd.push_back(*coord);
+ } catch (std::out_of_range outofrange) {
+ // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown
+ }
+ return vd;
+ }
+
+ std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) {
+ if (pcoh_ != nullptr) {
+ delete pcoh_;
+ }
+ pcoh_ = new Persistent_cohomology_interface<Simplex_tree<>>(&simplex_tree_);
+ return pcoh_->get_persistence(homology_coeff_field, min_persistence);
+ }
+
+ std::vector<int> get_betti_numbers() const {
+ if (pcoh_ != nullptr) {
+ return pcoh_->betti_numbers();
+ }
+ std::vector<int> betti_numbers;
+ return betti_numbers;
+ }
+
+ std::vector<int> get_persistent_betti_numbers(Filtration_value from, Filtration_value to) const {
+ if (pcoh_ != nullptr) {
+ return pcoh_->persistent_betti_numbers(from, to);
+ }
+ std::vector<int> persistent_betti_numbers;
+ return persistent_betti_numbers;
+ }
+
+ private:
+ Simplex_tree<> simplex_tree_;
+ Persistent_cohomology_interface<Simplex_tree<>>* pcoh_;
+ Alpha_complex<Dynamic_kernel>* alpha_complex_;
+};
+
+} // namespace alpha_complex
+
+} // namespace Gudhi
+
+#endif // ALPHA_COMPLEX_INTERFACE_H
+