Persistent_cohomology/rips_multifield_persistence.cpp

/*    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();
  }
}