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/* 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): Clément Maria
*
* Copyright (C) 2014 INRIA Sophia Antipolis-Méditerranée (France)
*
* 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/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 <gudhi/Persistent_cohomology/Multi_field.h>
#include <boost/program_options.hpp>
#include <string>
#include <vector>
using namespace Gudhi;
using namespace Gudhi::persistent_cohomology;
typedef int Vertex_handle;
typedef double Filtration_value;
void program_options(int argc, char * argv[]
, std::string & filepoints
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
, int & min_p
, int & max_p
, Filtration_value & min_persistence);
int main(int argc, char * argv[]) {
std::string filepoints;
std::string filediag;
Filtration_value threshold;
int dim_max;
int min_p;
int max_p;
Filtration_value min_persistence;
program_options(argc, argv, filepoints, filediag, threshold, dim_max, min_p, max_p, min_persistence);
// Extract the points from the file filepoints
typedef std::vector<double> Point_t;
std::vector< Point_t > points;
read_points(filepoints, points);
// Compute the proximity graph of the points
Graph_t prox_graph = compute_proximity_graph(points, threshold
, euclidean_distance<Point_t>);
// Construct the Rips complex in a Simplex Tree
typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
ST st;
// insert the proximity graph in the simplex tree
st.insert_graph(prox_graph);
// expand the graph until dimension dim_max
st.expansion(dim_max);
// Sort the simplices in the order of the filtration
st.initialize_filtration();
// Compute the persistence diagram of the complex
Persistent_cohomology<ST, Multi_field > pcoh(st);
// initializes the coefficient field for homology
pcoh.init_coefficients(min_p, max_p);
// compute persistent homology, disgarding persistent features of life shorter than min_persistence
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 & filepoints
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
, int & min_p
, int & max_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>(&filepoints),
"Name of file containing a point set. Format is one point per line: X1 ... Xd \n");
po::options_description visible("Allowed options");
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")
("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
"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.")
("min-field-charac,p", po::value<int>(&min_p)->default_value(2),
"Minimal characteristic p of the coefficient field Z/pZ.")
("max-field-charac,q", po::value<int>(&max_p)->default_value(1223),
"Minimial characteristic q of the coefficient field Z/pZ.")
("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::cout << std::endl;
std::cout << "Compute the persistent homology with various coefficient fields \n";
std::cout << "of a Rips complex defined on a set of input points. The coefficient \n";
std::cout << "fields are all the Z/rZ for a prime number r contained in the \n";
std::cout << "specified range [p,q]\n \n";
std::cout << "The output diagram contains one bar per line, written with the convention: \n";
std::cout << " p1*...*pr 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 << "p1*...*pr is the product of prime numbers pi such that the homology \n";
std::cout << "feature exists in homology with Z/piZ coefficients." << std::endl << std::endl;
std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
std::cout << visible << std::endl;
std::abort();
}
}
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