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author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-11-23 11:49:15 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-11-23 11:49:15 +0000 |
commit | f843ef3f8e4ab4ce94a28ded6d8cafd37f2b2311 (patch) | |
tree | 7d053afbeb51a16916da07f932deecc364c7eb42 /src/cython/include/Tangential_complex_interface.h | |
parent | 8d656e33138ef8b3a7d86a7375c92646efc29511 (diff) |
Add tangential complex
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1773 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: b47285aafaa430c883c8fe5432ac667d6cedaf37
Diffstat (limited to 'src/cython/include/Tangential_complex_interface.h')
-rw-r--r-- | src/cython/include/Tangential_complex_interface.h | 220 |
1 files changed, 220 insertions, 0 deletions
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h new file mode 100644 index 00000000..645aad72 --- /dev/null +++ b/src/cython/include/Tangential_complex_interface.h @@ -0,0 +1,220 @@ +/* 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): Vincent Rouvreau + * + * Copyright (C) 2016 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 TANGENTIAL_COMPLEX_INTERFACE_H +#define TANGENTIAL_COMPLEX_INTERFACE_H + +#include <gudhi/Simplex_tree.h> +#include <gudhi/Tangential_complex.h> +#include <gudhi/Points_off_io.h> +#include <CGAL/Epick_d.h> + +#include "Persistent_cohomology_interface.h" + +#include <vector> +#include <utility> // std::pair +#include <iostream> + +namespace Gudhi { + +namespace tangential_complex { + +class Tangential_complex_interface { + using Dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; + using Point_d = Dynamic_kernel::Point_d; + typedef typename Simplex_tree<>::Simplex_handle Simplex_handle; + typedef typename std::pair<Simplex_handle, bool> Insertion_result; + using Simplex = std::vector<Vertex_handle>; + using Filtered_complex = std::pair<Simplex, Filtration_value>; + using Complex_tree = std::vector<Filtered_complex>; + using TC = Tangential_complex<Dynamic_kernel, CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>; + + public: + Tangential_complex_interface(std::vector<std::vector<double>>&points, double max_alpha_square) + : pcoh_(nullptr) { + Dynamic_kernel k; + unsigned intrisic_dim = 0; + if (points.size() > 0) + intrisic_dim = points[0].size(); + + tangential_complex_ = new TC(points, intrisic_dim, k); + tangential_complex_->create_complex(simplex_tree_, max_alpha_square); + simplex_tree_.initialize_filtration(); + } + + Tangential_complex_interface(std::string off_file_name, double max_alpha_square, bool from_file = true) + : pcoh_(nullptr) { + Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); + Dynamic_kernel k; + unsigned intrisic_dim = 0; + std::vector<Point_d> points = off_reader.get_point_cloud(); + if (points.size() > 0) + intrisic_dim = points[0].size(); + + tangential_complex_ = new TC(points, intrisic_dim, k); + tangential_complex_->create_complex(simplex_tree_, max_alpha_square); + simplex_tree_.initialize_filtration(); + } + + bool find_simplex(const Simplex& vh) { + return (simplex_tree_.find(vh) != simplex_tree_.null_simplex()); + } + + bool insert_simplex_and_subfaces(const Simplex& complex, Filtration_value filtration = 0) { + Insertion_result result = simplex_tree_.insert_simplex_and_subfaces(complex, filtration); + return (result.second); + } + + Filtration_value simplex_filtration(const Simplex& complex) { + return simplex_tree_.filtration(simplex_tree_.find(complex)); + } + + void remove_maximal_simplex(const Simplex& complex) { + return simplex_tree_.remove_maximal_simplex(simplex_tree_.find(complex)); + } + + Complex_tree get_filtered_tree() { + Complex_tree filtered_tree; + for (auto f_simplex : simplex_tree_.filtration_simplex_range()) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + filtered_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return filtered_tree; + + } + + Complex_tree get_skeleton_tree(int dimension) { + Complex_tree skeleton_tree; + for (auto f_simplex : simplex_tree_.skeleton_simplex_range(dimension)) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + skeleton_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return skeleton_tree; + } + + Complex_tree get_star_tree(const Simplex& complex) { + Complex_tree star_tree; + for (auto f_simplex : simplex_tree_.star_simplex_range(simplex_tree_.find(complex))) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + star_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return star_tree; + } + + Complex_tree get_coface_tree(const Simplex& complex, int dimension) { + Complex_tree coface_tree; + for (auto f_simplex : simplex_tree_.cofaces_simplex_range(simplex_tree_.find(complex), dimension)) { + Simplex simplex; + for (auto vertex : simplex_tree_.simplex_vertex_range(f_simplex)) { + simplex.insert(simplex.begin(), vertex); + } + coface_tree.push_back(std::make_pair(simplex, simplex_tree_.filtration(f_simplex))); + } + return coface_tree; + } + + // Specific to Witness complex because no inheritance + Filtration_value filtration() const { + return simplex_tree_.filtration(); + } + + void set_filtration(Filtration_value fil) { + simplex_tree_.set_filtration(fil); + } + + void initialize_filtration() { + simplex_tree_.initialize_filtration(); + } + + size_t num_vertices() const { + return simplex_tree_.num_vertices(); + } + + size_t num_simplices() { + return simplex_tree_.num_simplices(); + } + + int dimension() const { + return simplex_tree_.dimension(); + } + + void set_dimension(int dimension) { + simplex_tree_.set_dimension(dimension); + } + + std::vector<double> get_point(int vh) { + std::vector<double> vd; + try { + Point_d ph = tangential_complex_->get_point(vh); + for (auto coord = ph.cartesian_begin(); coord < ph.cartesian_end(); coord++) + vd.push_back(*coord); + } catch (std::out_of_range outofrange) { + // std::out_of_range is thrown in case not found. Other exceptions must be re-thrown + } + return vd; + } + + std::vector<std::pair<int, std::pair<double, double>>> get_persistence(int homology_coeff_field, double min_persistence) { + if (pcoh_ != nullptr) { + delete pcoh_; + } + pcoh_ = new Persistent_cohomology_interface<Simplex_tree<>>(&simplex_tree_); + return pcoh_->get_persistence(homology_coeff_field, min_persistence); + } + + std::vector<int> get_betti_numbers() const { + if (pcoh_ != nullptr) { + return pcoh_->betti_numbers(); + } + std::vector<int> betti_numbers; + return betti_numbers; + } + + std::vector<int> get_persistent_betti_numbers(Filtration_value from, Filtration_value to) const { + if (pcoh_ != nullptr) { + return pcoh_->persistent_betti_numbers(from, to); + } + std::vector<int> persistent_betti_numbers; + return persistent_betti_numbers; + } + + private: + Simplex_tree<> simplex_tree_; + Persistent_cohomology_interface<Simplex_tree<>>* pcoh_; + TC* tangential_complex_; +}; + +} // namespace tangential_complex + +} // namespace Gudhi + +#endif // TANGENTIAL_COMPLEX_INTERFACE_H + |