rips_persistence_via_boundary_matrix.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): Clément Maria, Marc Glisse
*
* Copyright (C) 2014 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Rips_complex.h>
#include <gudhi/Hasse_complex.h>
#include <gudhi/Points_off_io.h>
#include <boost/program_options.hpp>
#include <string>
#include <vector>
// //
// WARNING: persistence computation itself is not parallel, //
// and this uses more memory than rips_persistence. //
// //
// Types definition
using Point = std::vector<double>;
void program_options(int argc, char * argv[]
, std::string & off_file_points
, std::string & filediag
, Filtration_value & threshold
, int & dim_max
, int & p
, Filtration_value & min_persistence);
int main(int argc, char * argv[]) {
std::string off_file_points;
std::string filediag;
Filtration_value threshold;
int dim_max;
int p;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, filediag, threshold, dim_max, p, min_persistence);
Points_off_reader off_reader(off_file_points);
Rips_complex rips_complex_from_file(off_reader.get_point_cloud(), threshold, Gudhi::Euclidean_distance());
// Construct the Rips complex in a Simplex Tree
rips_complex_from_file.create_complex(st, dim_max);
std::clog << "The complex contains " << st.num_simplices() << " simplices \n";
std::clog << " and has dimension " << st.dimension() << " \n";
// Sort the simplices in the order of the filtration
int count = 0;
for (auto sh : st.filtration_simplex_range())
st.assign_key(sh, count++);
// Convert to a more convenient representation.
Gudhi::Hasse_complex<> hcpx(st);
// Free some space.
delete &st;
// Compute the persistence diagram of the complex
// 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();
}
}
void program_options(int argc, char * argv[]
, std::string & off_file_points
, 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<std::string>(&off_file_points),
"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<std::string>(&filediag)->default_value(std::string()),
"Name of file in which the persistence diagram is written. Default print in std::clog")
("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.")
("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::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);
}
}
Compute the Euclidean distance between two Points given by a range of coordinates....
Definition: distance_functions.h:32
OFF file reader implementation in order to read points from an OFF file.
Definition: Points_off_io.h:122
Options::Filtration_value Filtration_value
Type for the value of the filtration function.
Definition: Simplex_tree.h:86
Filtration_simplex_range const & filtration_simplex_range(Indexing_tag=Indexing_tag())
Returns a range over the simplices of the simplicial complex, in the order of the filtration.
Definition: Simplex_tree.h:271
void assign_key(Simplex_handle sh, Simplex_key key)
Assign a value 'key' to the key of the simplex represented by the Simplex_handle 'sh'.
Definition: Simplex_tree.h:868
void initialize_filtration()
Initializes the filtration cache, i.e. sorts the simplices according to their order in the filtration...
Definition: Simplex_tree.h:912
int dimension(Simplex_handle sh)
Returns the dimension of a simplex.
Definition: Simplex_tree.h:600
size_t num_simplices()
returns the number of simplices in the simplex_tree.
Definition: Simplex_tree.h:578
Structure representing the coefficient field .
Definition: Field_Zp.h:27
Computes the persistent cohomology of a filtered complex.
Definition: Persistent_cohomology.h:52
Rips complex data structure.
Definition: Rips_complex.h:45
Global distance functions.
Value type for a filtration function on a cell complex.
Definition: FiltrationValue.h:20