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Diffstat (limited to 'src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp')
| -rw-r--r-- | src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp | 140 |
1 files changed, 140 insertions, 0 deletions
diff --git a/src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp b/src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp new file mode 100644 index 00000000..ddaafea2 --- /dev/null +++ b/src/Persistent_cohomology/example/rips_persistence_from_alpha_shape_3.cpp @@ -0,0 +1,140 @@ + /* 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): Vincent Rouvreau + * + * Copyright (C) 2014 INRIA Saclay (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 & simplex_tree_file + , std::string & output_file + , int & p + , Filtration_value & min_persistence ); + +int main (int argc, char * argv[]) +{ + std::string simplex_tree_file; + std::string output_file ; + int p ; + Filtration_value min_persistence; + + program_options(argc,argv,simplex_tree_file,output_file,p,min_persistence); + + std::cout << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str() << std::endl; + std::cout << " - p=" << p << " - min_persistence=" << min_persistence << std::endl; + + // Construct the Rips complex in a Simplex Tree + Simplex_tree<> simplex_tree; + + std::ifstream simplex_tree_stream(simplex_tree_file); + simplex_tree_stream >> simplex_tree; + + std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl; + std::cout << " - dimension " << simplex_tree.dimension() << " - filtration " << simplex_tree.filtration() << std::endl; + + /* + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl; + for( auto f_simplex : simplex_tree.filtration_simplex_range() ) + { std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) ) + { std::cout << vertex << " "; } + std::cout << std::endl; + }*/ + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + // Compute the persistence diagram of the complex + Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh( simplex_tree ); + pcoh.init_coefficients( p ); //initilizes the coefficient field for homology + + pcoh.compute_persistent_cohomology( min_persistence ); + + // Output the diagram in output_file + if(output_file.empty()) { pcoh.output_diagram(); } + else { + std::ofstream out(output_file); + pcoh.output_diagram(out); + out.close(); } + + return 0; +} + + + +void program_options( int argc, char * argv[] + , std::string & simplex_tree_file + , std::string & output_file + , 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>(&simplex_tree_file), + "Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1 "); + + po::options_description visible("Allowed options", 100); + visible.add_options() + ("help,h", "produce help message") + ("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()), + "Name of file in which the persistence diagram is written. Default print in std::cout") + ("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(); + } +} |