diff options
author | skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-12-07 14:45:43 +0000 |
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committer | skachano <skachano@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2015-12-07 14:45:43 +0000 |
commit | c4078affdbf6fac7150c10ade96fcb72270ac013 (patch) | |
tree | 1ad197bb90078a56036a49c6ee3766a032f85e63 /src/Persistent_cohomology/example/rips_persistence.cpp | |
parent | f70e386fc98f1dbd8287d1cb7cc715710a8f751b (diff) | |
parent | 061e43a2a48525bc5a69482a1ea80f20ff505e55 (diff) |
Merged with trunk and removed unnecessary files
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/witness@934 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: d0ec52d222d22c102e9fe57590882cd0024c82d5
Diffstat (limited to 'src/Persistent_cohomology/example/rips_persistence.cpp')
-rw-r--r-- | src/Persistent_cohomology/example/rips_persistence.cpp | 222 |
1 files changed, 113 insertions, 109 deletions
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp index 4253def9..9b1ef42f 100644 --- a/src/Persistent_cohomology/example/rips_persistence.cpp +++ b/src/Persistent_cohomology/example/rips_persistence.cpp @@ -1,147 +1,151 @@ - /* 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" +/* 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> +#include <string> +#include <vector> + using namespace Gudhi; using namespace Gudhi::persistent_cohomology; -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 ; +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); + program_options(argc, argv, filepoints, filediag, threshold, dim_max, p, min_persistence); -// Extract the points from the file filepoints + // Extract the points from the file filepoints typedef std::vector<double> Point_t; std::vector< Point_t > points; - read_points( filepoints, 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> ); + // 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 + // 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 + // Sort the simplices in the order of the filtration st.initialize_filtration(); -// Compute the persistence diagram of the complex + // Compute the persistence diagram of the complex persistent_cohomology::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(); } + // 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 & filepoints - , std::string & filediag - , Filtration_value & threshold - , int & dim_max - , int & p - , Filtration_value & min_persistence ) -{ +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"); + 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 "); - + ("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. Enter a negative value to see zero length intervals"); + ("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::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); + 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(); + 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(); } } |