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Diffstat (limited to 'src/GudhUI/utils/Persistence_compute.h')
-rw-r--r-- | src/GudhUI/utils/Persistence_compute.h | 81 |
1 files changed, 81 insertions, 0 deletions
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h new file mode 100644 index 00000000..874f31cf --- /dev/null +++ b/src/GudhUI/utils/Persistence_compute.h @@ -0,0 +1,81 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): David Salinas + * + * Copyright (C) 2014 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + + +#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_ |