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Diffstat (limited to 'src/Persistent_cohomology/example/rips_persistence.cpp')
| -rw-r--r-- | src/Persistent_cohomology/example/rips_persistence.cpp | 146 |
1 files changed, 146 insertions, 0 deletions
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp new file mode 100644 index 00000000..d7927223 --- /dev/null +++ b/src/Persistent_cohomology/example/rips_persistence.cpp @@ -0,0 +1,146 @@ + /* 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 Sophia Antipolis-Méditerranée (France) + * + * 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/reader_utils.h" +#include "gudhi/graph_simplicial_complex.h" +#include "gudhi/distance_functions.h" +#include "gudhi/Simplex_tree.h" +#include "gudhi/Persistent_cohomology.h" + +#include <boost/program_options.hpp> + +using namespace Gudhi; + +typedef int Vertex_handle; +typedef double Filtration_value; + +void program_options( int argc, char * argv[] + , std::string & filepoints + , std::string & filediag + , Filtration_value & threshold + , int & dim_max + , int & p + , Filtration_value & min_persistence ); + +int main (int argc, char * argv[]) +{ + std::string filepoints; + std::string filediag ; + Filtration_value threshold ; + int dim_max ; + int p ; + Filtration_value min_persistence; + + program_options(argc,argv,filepoints,filediag,threshold,dim_max,p,min_persistence); + +// Extract the points from the file filepoints + typedef std::vector<double> Point_t; + std::vector< Point_t > points; + read_points( filepoints, points ); + +// Compute the proximity graph of the points + Graph_t prox_graph = compute_proximity_graph( points, threshold + , euclidean_distance<Point_t> ); + +// Construct the Rips complex in a Simplex Tree + Simplex_tree<> st; + st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree + st.expansion( dim_max ); // expand the graph until dimension 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< Simplex_tree<>, Field_Zp > pcoh( st ); + pcoh.init_coefficients( p ); //initilizes the coefficient field for homology + + 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 & filepoints + , 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>(&filepoints), + "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"); + + 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; + std::abort(); + } +} |