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cech_persistence.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) 2018 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <gudhi/Cech_complex.h>
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Points_off_io.h>
#include <boost/program_options.hpp>
#include <CGAL/Epeck_d.h> // For EXACT or SAFE version
#include <CGAL/Epick_d.h> // For FAST version
#include <string>
#include <vector>
#include <limits> // infinity
// Types definition
using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = Simplex_tree::Filtration_value;
using Field_Zp = Gudhi::persistent_cohomology::Field_Zp;
using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Field_Zp>;
void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast,
std::string& filediag, Filtration_value& max_radius, int& dim_max, int& p,
Filtration_value& min_persistence);
template<class Kernel>
Simplex_tree create_simplex_tree(const std::string &off_file_points, bool exact_version,
Filtration_value max_radius, int dim_max) {
using Point = typename Kernel::Point_d;
using Points_off_reader = Gudhi::Points_off_reader<Point>;
using Cech_complex = Gudhi::cech_complex::Cech_complex<Kernel, Simplex_tree>;
Simplex_tree stree;
Points_off_reader off_reader(off_file_points);
Cech_complex cech_complex_from_file(off_reader.get_point_cloud(), max_radius, exact_version);
cech_complex_from_file.create_complex(stree, dim_max);
return stree;
}
int main(int argc, char* argv[]) {
std::string off_file_points;
std::string filediag;
bool exact_version = false;
bool fast_version = false;
Filtration_value max_radius;
int dim_max;
int p;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, exact_version, fast_version, filediag, max_radius, dim_max, p,
min_persistence);
if ((exact_version) && (fast_version)) {
std::cerr << "You cannot set the exact and the fast version." << std::endl;
exit(-1);
}
Simplex_tree stree;
if (fast_version) {
// WARNING : CGAL::Epick_d is fast but not safe (unlike CGAL::Epeck_d)
// (i.e. when the points are on a grid)
using Fast_kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>;
stree = create_simplex_tree<Fast_kernel>(off_file_points, exact_version, max_radius, dim_max);
} else {
using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
stree = create_simplex_tree<Kernel>(off_file_points, exact_version, max_radius, dim_max);
}
std::clog << "The complex contains " << stree.num_simplices() << " simplices \n";
std::clog << " and has dimension " << stree.dimension() << " \n";
// Sort the simplices in the order of the filtration
stree.initialize_filtration();
// Compute the persistence diagram of the complex
Persistent_cohomology pcoh(stree);
// 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();
}
return 0;
}
void program_options(int argc, char* argv[], std::string& off_file_points, bool& exact, bool& fast,
std::string& filediag, Filtration_value& max_radius, 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 an OFF file containing a point set.\n");
po::options_description visible("Allowed options", 100);
visible.add_options()("help,h", "produce help message")(
"exact,e", po::bool_switch(&exact),
"To activate exact version of Cech complex (default is false, not available if fast is set)")(
"fast,f", po::bool_switch(&fast),
"To activate fast version of Cech complex (default is false, not available if exact is set)")(
"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 standard output")(
"max-radius,r",
po::value<Filtration_value>(&max_radius)->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal length of an edge for the Cech complex construction.")(
"cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
"Maximal dimension of the Cech 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 Cech complex defined on a set of input points.\n \n";
std::clog << "Different versions of Cech complex computation are available:\n";
std::clog << " * fast: right combinatorics, values can be arbitrarily bad\n";
std::clog << " * safe (default): values can have a relative error at most 1e-5\n";
std::clog << " * exact: true values rounded to double.\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);
}
}
Gudhi::Points_off_reader
OFF file reader implementation in order to read points from an OFF file.
Definition Points_off_io.h:122
Gudhi::Simplex_tree
Simplex Tree data structure for representing simplicial complexes.
Definition Simplex_tree.h:98
Gudhi::Simplex_tree< Gudhi::Simplex_tree_options_fast_persistence >::Filtration_value
Options::Filtration_value Filtration_value
Definition Simplex_tree.h:105
Gudhi::Simplex_tree::initialize_filtration
void initialize_filtration(bool ignore_infinite_values=false) const
Initializes the filtration cache, i.e. sorts the simplices according to their order in the filtration...
Definition Simplex_tree.h:1200
Gudhi::Simplex_tree::num_simplices
size_t num_simplices() const
Returns the number of simplices in the simplex_tree.
Definition Simplex_tree.h:791
Gudhi::cech_complex::Cech_complex
Cech complex class.
Definition Cech_complex.h:44
Gudhi::persistent_cohomology::Field_Zp
Structure representing the coefficient field .
Definition Field_Zp.h:27
Gudhi::persistent_cohomology::Persistent_cohomology
Computes the persistent cohomology of a filtered complex.
Definition Persistent_cohomology.h:54