Rips_complex/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/Simplex_tree.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 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* streambufffer;
std::ofstream ouput_file_stream;
if (argc == 5) {
ouput_file_stream.open(std::string(argv[4]));
streambufffer = ouput_file_stream.rdbuf();
} else {
streambufffer = std::cout.rdbuf();
}
Simplex_tree stree;
rips_complex_from_file.create_complex(stree, dim_max);
std::ostream output_stream(streambufffer);
// ----------------------------------------------------------------------------
// 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  Version 2.3.0  - C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding.  - Copyright : GPL v3 Generated on Tue Sep 4 2018 14:32:59 for GUDHI by Doxygen 1.8.13