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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
- *
- * 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_