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persistence_from_file.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): Vincent Rouvreau
*
* Copyright (C) 2014 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <gudhi/reader_utils.h>
#include <gudhi/graph_simplicial_complex.h>
#include <gudhi/distance_functions.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <boost/program_options.hpp>
#include <string>
using namespace Gudhi;
using namespace Gudhi::persistent_cohomology;
typedef double Filtration_value;
void program_options(int argc, char * argv[]
, std::string & simplex_tree_file
, std::string & output_file
, int & p
, Filtration_value & min_persistence);
int main(int argc, char * argv[]) {
std::string simplex_tree_file;
std::string output_file;
int p;
Filtration_value min_persistence;
program_options(argc, argv, simplex_tree_file, output_file, p, min_persistence);
std::clog << "Simplex_tree from file=" << simplex_tree_file.c_str() << " - output_file=" << output_file.c_str()
<< std::endl;
std::clog << " - p=" << p << " - min_persistence=" << min_persistence << std::endl;
// Read the list of simplices from a file.
Simplex_tree<> simplex_tree;
std::ifstream simplex_tree_stream(simplex_tree_file);
simplex_tree_stream >> simplex_tree;
std::clog << "The complex contains " << simplex_tree.num_simplices() << " simplices" << std::endl;
std::clog << " - dimension " << simplex_tree.dimension() << std::endl;
/*
std::clog << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
for( auto f_simplex : simplex_tree.filtration_simplex_range() )
{ std::clog << " " << "[" << simplex_tree.filtration(f_simplex) << "] ";
for( auto vertex : simplex_tree.simplex_vertex_range(f_simplex) )
{ std::clog << vertex << " "; }
std::clog << std::endl;
}*/
// Compute the persistence diagram of the complex
Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree);
// initializes the coefficient field for homology
pcoh.init_coefficients(p);
pcoh.compute_persistent_cohomology(min_persistence);
// Output the diagram in output_file
if (output_file.empty()) {
pcoh.output_diagram();
} else {
std::ofstream out(output_file);
pcoh.output_diagram(out);
out.close();
}
return 0;
}
void program_options(int argc, char * argv[]
, std::string & simplex_tree_file
, std::string & output_file
, 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>(&simplex_tree_file),
"Name of file containing a simplex set. Format is one simplex per line (cf. reader_utils.h - read_simplex): Dim1 X11 X12 ... X1d Fil1 ");
po::options_description visible("Allowed options", 100);
visible.add_options()
("help,h", "produce help message")
("output-file,o", po::value<std::string>(&output_file)->default_value(std::string()),
"Name of file in which the persistence diagram is written. Default print in standard output")
("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");
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::clog << std::endl;
std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
std::clog << "of a Rips complex defined on a set of input points.\n \n";
std::clog << "The output diagram contains one bar per line, written with the convention: \n";
std::clog << " p dim b d \n";
std::clog << "where dim is the dimension of the homological feature,\n";
std::clog << "b and d are respectively the birth and death of the feature and \n";
std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
std::clog << visible << std::endl;
exit(-1);
}
}
distance_functions.h
Global distance functions.
graph_simplicial_complex.h
Graph simplicial complex methods.
Gudhi
Gudhi namespace.
Definition SimplicialComplexForAlpha.h:14
reader_utils.h
This file includes common file reader for GUDHI.