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Diffstat (limited to 'utilities/Alpha_complex/alpha_complex_persistence.cpp')
-rw-r--r-- | utilities/Alpha_complex/alpha_complex_persistence.cpp | 138 |
1 files changed, 0 insertions, 138 deletions
diff --git a/utilities/Alpha_complex/alpha_complex_persistence.cpp b/utilities/Alpha_complex/alpha_complex_persistence.cpp deleted file mode 100644 index 8e6c40b7..00000000 --- a/utilities/Alpha_complex/alpha_complex_persistence.cpp +++ /dev/null @@ -1,138 +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): 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/>. - */ - -#include <boost/program_options.hpp> - -#include <CGAL/Epick_d.h> - -#include <gudhi/Alpha_complex.h> -#include <gudhi/Persistent_cohomology.h> -// to construct a simplex_tree from alpha complex -#include <gudhi/Simplex_tree.h> - -#include <iostream> -#include <string> -#include <limits> // for numeric_limits - -using Simplex_tree = Gudhi::Simplex_tree<>; -using Filtration_value = Simplex_tree::Filtration_value; - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, - Filtration_value &min_persistence); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string output_file_diag; - Filtration_value alpha_square_max_value; - int coeff_field_characteristic; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic, - min_persistence); - - // ---------------------------------------------------------------------------- - // Init of an alpha complex from an OFF file - // ---------------------------------------------------------------------------- - using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; - Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points); - - Simplex_tree simplex; - if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - std::cout << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() - << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; - - // Sort the simplices in the order of the filtration - simplex.initialize_filtration(); - - std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; - // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh( - simplex); - // initializes the coefficient field for homology - pcoh.init_coefficients(coeff_field_characteristic); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (output_file_diag.empty()) { - pcoh.output_diagram(); - } else { - std::cout << "Result in file: " << output_file_diag << std::endl; - std::ofstream out(output_file_diag); - pcoh.output_diagram(out); - out.close(); - } - } - - return 0; -} - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, - Filtration_value &min_persistence) { - namespace po = boost::program_options; - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value<std::string>(&off_file_points), - "Name of file containing a point set. Format is one point per line: X1 ... Xd "); - - po::options_description visible("Allowed options", 100); - visible.add_options()("help,h", "produce help message")( - "output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout")( - "max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value) - ->default_value(std::numeric_limits<Filtration_value>::infinity()), - "Maximal alpha square value for the Alpha complex construction.")( - "field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value<Filtration_value>(&min_persistence), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " - "intervals"); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - - po::variables_map vm; - po::store(po::command_line_parser(argc, argv).options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of an Alpha complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - exit(-1); - } -} |