From 599d68cd916f533bdb66dd9e684dd5703233b6bb Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Wed, 25 Sep 2019 14:29:41 +0200 Subject: Delete all files in order to incorporate upstream's move to git. --- .../Witness_complex/strong_witness_persistence.cpp | 156 --------------------- 1 file changed, 156 deletions(-) delete mode 100644 utilities/Witness_complex/strong_witness_persistence.cpp (limited to 'utilities/Witness_complex/strong_witness_persistence.cpp') diff --git a/utilities/Witness_complex/strong_witness_persistence.cpp b/utilities/Witness_complex/strong_witness_persistence.cpp deleted file mode 100644 index f386e992..00000000 --- a/utilities/Witness_complex/strong_witness_persistence.cpp +++ /dev/null @@ -1,156 +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): Siargey Kachanovich - * - * 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 . - */ - -#include -#include -#include -#include -#include -#include - -#include - -#include - -#include -#include -#include // infinity - -using K = CGAL::Epick_d; -using Point_d = K::Point_d; - -using Point_vector = std::vector; -using Strong_witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; -using SimplexTree = Gudhi::Simplex_tree<>; - -using Filtration_value = SimplexTree::Filtration_value; - -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; - -void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag, - Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence); - -int main(int argc, char* argv[]) { - std::string file_name; - std::string filediag; - Filtration_value max_squared_alpha; - int p, nbL, lim_d; - Filtration_value min_persistence; - SimplexTree simplex_tree; - - program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); - - // Extract the points from the file file_name - Point_vector witnesses, landmarks; - Gudhi::Points_off_reader off_reader(file_name); - if (!off_reader.is_valid()) { - std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; - exit(-1); // ----- >> - } - witnesses = Point_vector(off_reader.get_point_cloud()); - std::cout << "Successfully read " << witnesses.size() << " points.\n"; - std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; - - // Choose landmarks (decomment one of the following two lines) - // Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); - Gudhi::subsampling::choose_n_farthest_points(K(), witnesses, nbL, Gudhi::subsampling::random_starting_point, - std::back_inserter(landmarks)); - - // Compute witness complex - Strong_witness_complex strong_witness_complex(landmarks, witnesses); - - strong_witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); - - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - -void program_options(int argc, char* argv[], int& nbL, std::string& file_name, std::string& filediag, - Filtration_value& max_squared_alpha, int& p, int& dim_max, Filtration_value& min_persistence) { - namespace po = boost::program_options; - - po::options_description hidden("Hidden options"); - hidden.add_options()("input-file", po::value(&file_name), - "Name of file containing a point set in off format."); - - po::options_description visible("Allowed options", 100); - Filtration_value default_alpha = std::numeric_limits::infinity(); - visible.add_options()("help,h", "produce help message")("landmarks,l", po::value(&nbL), - "Number of landmarks to choose from the point cloud.")( - "output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout")( - "max-sq-alpha,a", po::value(&max_squared_alpha)->default_value(default_alpha), - "Maximal squared relaxation parameter.")( - "field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.")( - "min-persistence,m", po::value(&min_persistence)->default_value(0), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length " - "intervals")("cpx-dimension,d", po::value(&dim_max)->default_value(std::numeric_limits::max()), - "Maximal dimension of the strong witness complex we want to compute."); - - 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 a Strong witness 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); - } -} -- cgit v1.2.3