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Diffstat (limited to 'example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp')
| -rw-r--r-- | example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp | 172 |
1 files changed, 0 insertions, 172 deletions
diff --git a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp b/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp deleted file mode 100644 index 71fc0802..00000000 --- a/example/Persistent_cohomology/rips_persistence_via_boundary_matrix.cpp +++ /dev/null @@ -1,172 +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): Clément Maria, Marc Glisse - * - * 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/>. - */ - -#include <gudhi/Simplex_tree.h> -#include <gudhi/Persistent_cohomology.h> -#include <gudhi/Rips_complex.h> -#include <gudhi/Hasse_complex.h> -#include <gudhi/Points_off_io.h> -#include <gudhi/distance_functions.h> - -#include <boost/program_options.hpp> - -#ifdef GUDHI_USE_TBB -#include <tbb/task_scheduler_init.h> -#endif - -#include <string> -#include <vector> - -//////////////////////////////////////////////////////////////// -// // -// WARNING: persistence computation itself is not parallel, // -// and this uses more memory than rips_persistence. // -// // -//////////////////////////////////////////////////////////////// - -// Types definition -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 Point = std::vector<double>; -using Points_off_reader = Gudhi::Points_off_reader<Point>; - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string off_file_points; - std::string filediag; - Filtration_value threshold; - int dim_max; - int p; - Filtration_value min_persistence; - - program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence); - - Points_off_reader off_reader(off_file_points); - Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); - - // Construct the Rips complex in a Simplex Tree - Simplex_tree& st = *new Simplex_tree; - rips_complex_from_file.create_complex(st, dim_max); - - std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << st.dimension() << " \n"; - -#ifdef GUDHI_USE_TBB - // Unnecessary, but clarifies which operations are parallel. - tbb::task_scheduler_init ts; -#endif - - // Sort the simplices in the order of the filtration - st.initialize_filtration(); - int count = 0; - for (auto sh : st.filtration_simplex_range()) - st.assign_key(sh, count++); - - // Convert to a more convenient representation. - Gudhi::Hasse_complex<> hcpx(st); - -#ifdef GUDHI_USE_TBB - ts.terminate(); -#endif - - // Free some space. - delete &st; - - // Compute the persistence diagram of the complex - Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::Hasse_complex<>, Field_Zp > pcoh(hcpx); - // 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(); - } -} - -void program_options(int argc, char * argv[] - , std::string & off_file_points - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , 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>(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0), - "Maximal length of an edge for the Rips complex construction.") - ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1), - "Maximal dimension of the Rips complex we want to compute.") - ("field-charac,p", po::value<int>(&p)->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 a Rips 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); - } -} |