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Diffstat (limited to 'src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp')
-rw-r--r-- | src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp | 152 |
1 files changed, 152 insertions, 0 deletions
diff --git a/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp new file mode 100644 index 00000000..11ee5871 --- /dev/null +++ b/src/Collapse/utilities/distance_matrix_edge_collapse_rips_persistence.cpp @@ -0,0 +1,152 @@ +/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT. + * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details. + * Author(s): Siddharth Pritam, Vincent Rouvreau + * + * Copyright (C) 2020 Inria + * + * Modification(s): + * - YYYY/MM Author: Description of the modification + */ + +#include <gudhi/Flag_complex_edge_collapser.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <gudhi/reader_utils.h> +#include <gudhi/graph_simplicial_complex.h> + +#include <boost/program_options.hpp> +#include <boost/range/adaptor/transformed.hpp> + +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; +using Vertex_handle = Simplex_tree::Vertex_handle; + +using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>; +using Proximity_graph = Gudhi::Proximity_graph<Simplex_tree>; + +using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; +using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>; +using Distance_matrix = std::vector<std::vector<Filtration_value>>; + +void program_options(int argc, char* argv[], std::string& csv_matrix_file, std::string& filediag, + Filtration_value& threshold, int& dim_max, int& p, int& edge_collapse_iter_nb, + Filtration_value& min_persistence); + +int main(int argc, char* argv[]) { + std::string csv_matrix_file; + std::string filediag; + Filtration_value threshold; + int dim_max = 2; + int p; + int edge_collapse_iter_nb; + Filtration_value min_persistence; + + program_options(argc, argv, csv_matrix_file, filediag, threshold, dim_max, p, edge_collapse_iter_nb, + min_persistence); + + Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); + std::cout << "Read the distance matrix succesfully, of size: " << distances.size() << std::endl; + + Proximity_graph proximity_graph = Gudhi::compute_proximity_graph<Simplex_tree>(boost::irange((size_t)0, + distances.size()), + threshold, + [&distances](size_t i, size_t j) { + return distances[j][i]; + }); + + auto edges_from_graph = boost::adaptors::transform(edges(proximity_graph), [&](auto&&edge){ + return std::make_tuple(source(edge, proximity_graph), + target(edge, proximity_graph), + get(Gudhi::edge_filtration_t(), proximity_graph, edge)); + }); + std::vector<Filtered_edge> edges_list(edges_from_graph.begin(), edges_from_graph.end()); + std::vector<Filtered_edge> remaining_edges; + for (int iter = 0; iter < edge_collapse_iter_nb; iter++) { + auto remaining_edges = Gudhi::collapse::flag_complex_collapse_edges(edges_list); + edges_list = std::move(remaining_edges); + remaining_edges.clear(); + } + + Simplex_tree stree; + for (Vertex_handle vertex = 0; static_cast<std::size_t>(vertex) < distances.size(); vertex++) { + // insert the vertex with a 0. filtration value just like a Rips + stree.insert_simplex({vertex}, 0.); + } + for (auto filtered_edge : edges_list) { + stree.insert_simplex({std::get<0>(filtered_edge), std::get<1>(filtered_edge)}, std::get<2>(filtered_edge)); + } + + stree.expansion(dim_max); + + std::cout << "The complex contains " << stree.num_simplices() << " simplices after collapse. \n"; + std::cout << " and has dimension " << stree.dimension() << " \n"; + + // Sort the simplices in the order of the filtration + stree.initialize_filtration(); + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(stree); + // initializes the coefficient field for homology + pcoh.init_coefficients(3); + + pcoh.compute_persistent_cohomology(min_persistence); + 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& csv_matrix_file, std::string& filediag, + Filtration_value& threshold, int& dim_max, int& p, int& edge_collapse_iter_nb, + Filtration_value& min_persistence) { + namespace po = boost::program_options; + po::options_description hidden("Hidden options"); + hidden.add_options()( + "input-file", po::value<std::string>(&csv_matrix_file), + "Name of file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'."); + + 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(std::numeric_limits<Filtration_value>::infinity()), + "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.")( + "edge-collapse-iterations,i", po::value<int>(&edge_collapse_iter_nb)->default_value(1), + "Number of iterations edge collapse is performed.")( + "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 after edge collapse defined on a set of distance matrix.\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); + } +} |