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example_rips_complex_from_csv_distance_matrix_file.cpp
#include <gudhi/Rips_complex.h>
// to construct Rips_complex from a csv file representing a distance matrix
#include <gudhi/reader_utils.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/distance_functions.h>
#include <iostream>
#include <string>
#include <vector>
void usage(int nbArgs, char * const progName) {
std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
std::cerr << "Usage: " << progName << " filename.csv threshold dim_max [ouput_file.txt]\n";
std::cerr << " i.e.: " << progName << " ../../data/distance_matrix/full_square_distance_matrix.csv 1.0 3\n";
exit(-1); // ----- >>
}
int main(int argc, char **argv) {
if ((argc != 4) && (argc != 5)) usage(argc, (argv[0] - 1));
std::string csv_file_name(argv[1]);
double threshold = atof(argv[2]);
int dim_max = atoi(argv[3]);
// Type definitions
using Simplex_tree = Gudhi::Simplex_tree<>;
using Filtration_value = Simplex_tree::Filtration_value;
using Rips_complex = Gudhi::rips_complex::Rips_complex<Filtration_value>;
using Distance_matrix = std::vector<std::vector<Filtration_value>>;
// ----------------------------------------------------------------------------
// Init of a Rips complex from a distance matrix in a csv file
// Default separator is ';'
// ----------------------------------------------------------------------------
Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_file_name);
Rips_complex rips_complex_from_file(distances, threshold);
std::streambuf* streambuffer;
std::ofstream ouput_file_stream;
if (argc == 5) {
ouput_file_stream.open(std::string(argv[4]));
streambuffer = ouput_file_stream.rdbuf();
} else {
streambuffer = std::clog.rdbuf();
}
Simplex_tree stree;
rips_complex_from_file.create_complex(stree, dim_max);
std::ostream output_stream(streambuffer);
// ----------------------------------------------------------------------------
// Display information about the Rips complex
// ----------------------------------------------------------------------------
output_stream << "Rips complex is of dimension " << stree.dimension() <<
" - " << stree.num_simplices() << " simplices - " <<
stree.num_vertices() << " vertices." << std::endl;
output_stream << "Iterator on Rips complex simplices in the filtration order, with [filtration value]:" <<
std::endl;
for (auto f_simplex : stree.filtration_simplex_range()) {
output_stream << " ( ";
for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
output_stream << vertex << " ";
}
output_stream << ") -> " << "[" << stree.filtration(f_simplex) << "] ";
output_stream << std::endl;
}
ouput_file_stream.close();
return 0;
}
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::simplex_vertex_range
Simplex_vertex_range simplex_vertex_range(Simplex_handle sh) const
Returns a range over the vertices of a simplex.
Definition Simplex_tree.h:369
Gudhi::Simplex_tree::filtration
static Filtration_value filtration(Simplex_handle sh)
Returns the filtration value of a simplex.
Definition Simplex_tree.h:727
Gudhi::Simplex_tree::filtration_simplex_range
Filtration_simplex_range const & filtration_simplex_range(Indexing_tag=Indexing_tag()) const
Returns a range over the simplices of the simplicial complex, in the order of the filtration.
Definition Simplex_tree.h:358
Gudhi::Simplex_tree::num_vertices
size_t num_vertices() const
Returns the number of vertices in the complex.
Definition Simplex_tree.h:778
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::rips_complex::Rips_complex
Rips complex data structure.
Definition Rips_complex.h:45
distance_functions.h
Global distance functions.
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.