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Diffstat (limited to 'GudhUI/utils/Persistence_compute.h')
-rw-r--r-- | GudhUI/utils/Persistence_compute.h | 94 |
1 files changed, 0 insertions, 94 deletions
diff --git a/GudhUI/utils/Persistence_compute.h b/GudhUI/utils/Persistence_compute.h deleted file mode 100644 index c8afded9..00000000 --- a/GudhUI/utils/Persistence_compute.h +++ /dev/null @@ -1,94 +0,0 @@ -/* 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_ |