/* 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 .
*/
#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
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 & p
, Filtration_value & min_persistence );
int main (int argc, char * argv[])
{
std::string filepoints;
std::string filediag ;
Filtration_value threshold ;
int dim_max ;
int p ;
Filtration_value min_persistence;
program_options(argc,argv,filepoints,filediag,threshold,dim_max,p,min_persistence);
// Extract the points from the file filepoints
typedef std::vector 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 );
// Construct the Rips complex in a Simplex Tree
Simplex_tree<> st;
st.insert_graph(prox_graph); // insert the proximity graph in the simplex tree
st.expansion( dim_max ); // expand the graph until dimension dim_max
std::cout << "The complex contains " << st.num_simplices() << " simplices \n";
std::cout << " and has dimension " << st.dimension() << " \n";
// Sort the simplices in the order of the filtration
st.initialize_filtration();
// Compute the persistence diagram of the complex
persistent_cohomology::Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(st);
pcoh.init_coefficients( p ); //initilizes the coefficient field for homology
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 & p
, Filtration_value & min_persistence )
{
namespace po = boost::program_options;
po::options_description hidden("Hidden options");
hidden.add_options()
("input-file", po::value(&filepoints),
"Name of file containing a point set. Format is one point per line: X1 ... Xd ");
po::options_description visible("Allowed options", 100);
visible.add_options()
("help,h", "produce help message")
("output-file,o", po::value(&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(&threshold)->default_value(0),
"Maximal length of an edge for the Rips complex construction.")
("cpx-dimension,d", po::value(&dim_max)->default_value(1),
"Maximal dimension of the Rips complex we want to compute.")
("field-charac,p", po::value(&p)->default_value(11),
"Characteristic p of the coefficient field Z/pZ for computing homology.")
("min-persistence,m", po::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 coefficient field Z/pZ \n";
std::cout << "of a Rips complex defined on a set of input points.\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;
std::abort();
}
}