Created
March 19, 2019 08:02
-
-
Save VincentRouvreau/4d3f7951fafd4847cd62443a084070e5 to your computer and use it in GitHub Desktop.
sparse_rips_distance_matrix_persistence.cpp
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
/* 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): Marc Glisse, Clément Maria | |
* | |
* Modification(s): | |
* VR - March 2019: Use distance matrix constructor for Sparse rips | |
* | |
* Copyright (C) 2018 Inria | |
* | |
* 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/Sparse_rips_complex.h> | |
#include <gudhi/Simplex_tree.h> | |
#include <gudhi/Persistent_cohomology.h> | |
#include <gudhi/reader_utils.h> | |
#include <boost/program_options.hpp> | |
#include <string> | |
#include <vector> | |
// Types definition | |
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; | |
using Filtration_value = Simplex_tree::Filtration_value; | |
using Sparse_rips = Gudhi::rips_complex::Sparse_rips_complex<Filtration_value>; | |
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, double& epsilon, | |
int& dim_max, int& p, Filtration_value& min_persistence); | |
int main(int argc, char* argv[]) { | |
std::string csv_matrix_file; | |
std::string filediag; | |
double epsilon; | |
int dim_max; | |
int p; | |
Filtration_value min_persistence; | |
program_options(argc, argv, csv_matrix_file, filediag, epsilon, dim_max, p, min_persistence); | |
Distance_matrix distances = Gudhi::read_lower_triangular_matrix_from_csv_file<Filtration_value>(csv_matrix_file); | |
Sparse_rips sparse_rips(distances, epsilon); | |
// Construct the Rips complex in a Simplex Tree | |
Simplex_tree simplex_tree; | |
sparse_rips.create_complex(simplex_tree, dim_max); | |
std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; | |
std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; | |
// Sort the simplices in the order of the filtration | |
simplex_tree.initialize_filtration(); | |
// Compute the persistence diagram of the complex | |
Persistent_cohomology pcoh(simplex_tree); | |
// initializes the coefficient field for homology | |
pcoh.init_coefficients(p); | |
pcoh.compute_persistent_cohomology(min_persistence); | |
// Output the diagram in filediag | |
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, double& epsilon, | |
int& dim_max, 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>(&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")( | |
"approximation,e", po::value<double>(&epsilon)->default_value(.5), | |
"Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex.")( | |
"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.")( | |
"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 sparse (1+epsilon)-approximation of the Rips complex \n"; | |
std::cout << "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); | |
} | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment