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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 SIMPLEX_TREE_INTERFACE_H
+#define SIMPLEX_TREE_INTERFACE_H
+
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/distance_functions.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Points_off_io.h>
+
+#include <vector>
+#include <utility> // std::pair
+#include <iostream>
+
+namespace Gudhi {
+
+template<typename SimplexTreeOptions = Simplex_tree_options_full_featured>
+class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> {
+ typedef typename Simplex_tree<SimplexTreeOptions>::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>;
+
+ public:
+
+ bool find_simplex(const Simplex& vh) {
+ return (Simplex_tree<SimplexTreeOptions>::find(vh) != Simplex_tree<SimplexTreeOptions>::null_simplex());
+ }
+
+ bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) {
+ Insertion_result result = Simplex_tree<SimplexTreeOptions>::insert_simplex_and_subfaces(complex, filtration);
+ return (result.second);
+ }
+
+ Filtration_value simplex_filtration(const Simplex& complex) {
+ return Simplex_tree<SimplexTreeOptions>::filtration(Simplex_tree<SimplexTreeOptions>::find(complex));
+ }
+
+ void remove_maximal_simplex(const Simplex& complex) {
+ return Simplex_tree<SimplexTreeOptions>::remove_maximal_simplex(Simplex_tree<SimplexTreeOptions>::find(complex));
+ }
+
+ Complex_tree get_filtered_tree() {
+ Complex_tree filtered_tree;
+ for (auto f_simplex : Simplex_tree<SimplexTreeOptions>::filtration_simplex_range()) {
+ Simplex simplex;
+ for (auto vertex : Simplex_tree<SimplexTreeOptions>::simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ filtered_tree.push_back(std::make_pair(simplex, Simplex_tree<SimplexTreeOptions>::filtration(f_simplex)));
+ }
+ return filtered_tree;
+
+ }
+
+ Complex_tree get_skeleton_tree(int dimension) {
+ Complex_tree skeleton_tree;
+ for (auto f_simplex : Simplex_tree<SimplexTreeOptions>::skeleton_simplex_range(dimension)) {
+ Simplex simplex;
+ for (auto vertex : Simplex_tree<SimplexTreeOptions>::simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ skeleton_tree.push_back(std::make_pair(simplex, Simplex_tree<SimplexTreeOptions>::filtration(f_simplex)));
+ }
+ return skeleton_tree;
+ }
+
+ Complex_tree get_star_tree(const Simplex& complex) {
+ Complex_tree star_tree;
+ for (auto f_simplex : Simplex_tree<SimplexTreeOptions>::star_simplex_range(Simplex_tree<SimplexTreeOptions>::find(complex))) {
+ Simplex simplex;
+ for (auto vertex : Simplex_tree<SimplexTreeOptions>::simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ star_tree.push_back(std::make_pair(simplex, Simplex_tree<SimplexTreeOptions>::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<SimplexTreeOptions>::cofaces_simplex_range(Simplex_tree<SimplexTreeOptions>::find(complex), dimension)) {
+ Simplex simplex;
+ for (auto vertex : Simplex_tree<SimplexTreeOptions>::simplex_vertex_range(f_simplex)) {
+ simplex.insert(simplex.begin(), vertex);
+ }
+ coface_tree.push_back(std::make_pair(simplex, Simplex_tree<SimplexTreeOptions>::filtration(f_simplex)));
+ }
+ return coface_tree;
+ }
+
+ void graph_expansion(std::vector<std::vector<double>>&points, int max_dimension, double max_edge_length) {
+ Graph_t prox_graph = compute_proximity_graph(points, max_edge_length, euclidean_distance<std::vector<double>>);
+ Simplex_tree<SimplexTreeOptions>::insert_graph(prox_graph);
+ Simplex_tree<SimplexTreeOptions>::expansion(max_dimension);
+ Simplex_tree<SimplexTreeOptions>::initialize_filtration();
+ }
+
+ void graph_expansion(std::string& off_file_name, int max_dimension, double max_edge_length, bool from_file=true) {
+ Gudhi::Points_off_reader<std::vector <double>> off_reader(off_file_name);
+ // Check the read operation was correct
+ if (!off_reader.is_valid()) {
+ std::cerr << "Unable to read file " << off_file_name << std::endl;
+ } else {
+ std::vector<std::vector <double>> points = off_reader.get_point_cloud();
+ Graph_t prox_graph = compute_proximity_graph(points, max_edge_length,
+ euclidean_distance<std::vector<double>>);
+ Simplex_tree<SimplexTreeOptions>::insert_graph(prox_graph);
+ Simplex_tree<SimplexTreeOptions>::expansion(max_dimension);
+ Simplex_tree<SimplexTreeOptions>::initialize_filtration();
+ }
+ }
+
+};
+
+struct Simplex_tree_options_mini : Simplex_tree_options_full_featured {
+ // Not doing persistence, so we don't need those
+ static const bool store_key = true;
+ static const bool store_filtration = false;
+ // I have few vertices
+ typedef short Vertex_handle;
+};
+
+} // namespace Gudhi
+
+#endif // SIMPLEX_TREE_INTERFACE_H
+