Loading...
Searching...
No Matches
distance_matrix_edge_collapse_rips_persistence.cpp
/* 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 successfully, 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 standard output")(
"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);
}
}
Gudhi::Simplex_tree
Simplex Tree data structure for representing simplicial complexes.
Definition Simplex_tree.h:98
Gudhi::Simplex_tree< Gudhi::Simplex_tree_options_fast_persistence >::Filtration_value
Options::Filtration_value Filtration_value
Definition Simplex_tree.h:105
Gudhi::Simplex_tree::initialize_filtration
void initialize_filtration(bool ignore_infinite_values=false) const
Initializes the filtration cache, i.e. sorts the simplices according to their order in the filtration...
Definition Simplex_tree.h:1200
Gudhi::Simplex_tree::insert_simplex
std::pair< Simplex_handle, bool > insert_simplex(const InputVertexRange &simplex, Filtration_value filtration=0)
Insert a simplex, represented by a range of Vertex_handles, in the simplicial complex.
Definition Simplex_tree.h:1045
Gudhi::Simplex_tree< Gudhi::Simplex_tree_options_fast_persistence >::Vertex_handle
Options::Vertex_handle Vertex_handle
Definition Simplex_tree.h:119
Gudhi::Simplex_tree::expansion
void expansion(int max_dim)
Expands the Simplex_tree containing only its one skeleton until dimension max_dim.
Definition Simplex_tree.h:1512
Gudhi::Simplex_tree::num_simplices
size_t num_simplices() const
Returns the number of simplices in the simplex_tree.
Definition Simplex_tree.h:791
Gudhi::persistent_cohomology::Field_Zp
Structure representing the coefficient field .
Definition Field_Zp.h:27
Gudhi::persistent_cohomology::Persistent_cohomology
Computes the persistent cohomology of a filtered complex.
Definition Persistent_cohomology.h:54
graph_simplicial_complex.h
Graph simplicial complex methods.
std::get
constexpr auto & get(Gudhi::persistence_matrix::Persistence_interval< Dimension, Event_value > &i) noexcept
Partial specialization of get for Gudhi::persistence_matrix::Persistence_interval.
Definition persistence_interval.h:199
Gudhi::Proximity_graph
typename boost::adjacency_list< boost::vecS, boost::vecS, boost::directedS, boost::property< vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >, boost::property< edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value > > Proximity_graph
Proximity_graph contains the vertices and edges with their filtration values in order to store the re...
Definition graph_simplicial_complex.h:43
Gudhi::compute_proximity_graph
Proximity_graph< SimplicialComplexForProximityGraph > compute_proximity_graph(const ForwardPointRange &points, typename SimplicialComplexForProximityGraph::Filtration_value threshold, Distance distance)
Computes the proximity graph of the points.
Definition graph_simplicial_complex.h:62
Gudhi::read_lower_triangular_matrix_from_csv_file
std::vector< std::vector< Filtration_value > > read_lower_triangular_matrix_from_csv_file(const std::string &filename, const char separator=';')
Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole (squ...
Definition reader_utils.h:220
reader_utils.h
This file includes common file reader for GUDHI.