diff options
author | Gard Spreemann <gspreemann@gmail.com> | 2017-02-07 17:33:01 +0100 |
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committer | Gard Spreemann <gspreemann@gmail.com> | 2017-02-07 17:33:01 +0100 |
commit | 55c7181126aa7defce38c9b82872d14223d4c1dd (patch) | |
tree | 7c683f014709459f066fd87a21da7f74cfc31a53 /GudhUI/utils/Persistence_compute.h |
Initial import of upstream's 1.3.1.upstream/1.3.1
Diffstat (limited to 'GudhUI/utils/Persistence_compute.h')
-rw-r--r-- | GudhUI/utils/Persistence_compute.h | 91 |
1 files changed, 91 insertions, 0 deletions
diff --git a/GudhUI/utils/Persistence_compute.h b/GudhUI/utils/Persistence_compute.h new file mode 100644 index 00000000..97165490 --- /dev/null +++ b/GudhUI/utils/Persistence_compute.h @@ -0,0 +1,91 @@ +/* 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_ |