/* 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 * * 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 . */ #include #include #include #include #include #include #include #include #include // infinity #include // for pair #include // ---------------------------------------------------------------------------- // rips_persistence_step_by_step is an example of each step that is required to // build a Rips over a Simplex_tree. Please refer to rips_persistence to see // how to do the same thing with the Rips_complex wrapper for less detailed // steps. // ---------------------------------------------------------------------------- // Types definition using Simplex_tree = Gudhi::Simplex_tree; using Vertex_handle = Simplex_tree::Vertex_handle; using Filtration_value = Simplex_tree::Filtration_value; using Proximity_graph = Gudhi::Proximity_graph; using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; using Point = std::vector; using Points_off_reader = Gudhi::Points_off_reader; 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); // Extract the points from the file filepoints Points_off_reader off_reader(off_file_points); // Compute the proximity graph of the points Proximity_graph prox_graph = Gudhi::compute_proximity_graph(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance()); // Construct the Rips complex in a Simplex Tree Simplex_tree st; // insert the proximity graph in the simplex tree st.insert_graph(prox_graph); // expand the graph until dimension dim_max st.expansion(dim_max); std::cout << "The complex contains " << st.num_simplices() << " simplices \n"; std::cout << " and has dimension " << st.dimension() << " \n"; // Sort the simplices in the order of the filtration st.initialize_filtration(); // Compute the persistence diagram of the complex Persistent_cohomology pcoh(st); // 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[] , 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(&off_file_points), "Name of an OFF file containing a point set.\n"); po::options_description visible("Allowed options", 100); visible.add_options() ("help,h", "produce help message") ("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-edge-length,r", po::value(&threshold)->default_value(std::numeric_limits::infinity()), "Maximal length of an edge for the Rips complex construction.") ("cpx-dimension,d", po::value(&dim_max)->default_value(1), "Maximal dimension of the Rips complex we want to compute.") ("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), "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); } }