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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): David Salinas
+ *
+ * Copyright (C) 2014 INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ * 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 <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));
+ }
+
+
+ Graph_t prox_graph = compute_proximity_graph(points, params.threshold, euclidean_distance<Point_t>);
+ Gudhi::Simplex_tree<> st;
+ st.insert_graph(prox_graph);
+ st.expansion(params.max_dim);
+
+ Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Simplex_tree<>,
+ Gudhi::persistent_cohomology::Field_Zp > 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_