alpha_complex_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) 2016 Inria
*
* Modification(s):
* - YYYY/MM Author: Description of the modification
*/
#include <boost/program_options.hpp>
#include <CGAL/Epick_d.h>
#include <CGAL/Epeck_d.h>
#include <gudhi/Alpha_complex.h>
#include <gudhi/Persistent_cohomology.h>
// to construct a simplex_tree from alpha complex
#include <gudhi/Simplex_tree.h>
#include <gudhi/Points_off_io.h>
#include <iostream>
#include <string>
#include <limits> // for numeric_limits
#include <vector>
#include <fstream>
void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast,
std::string &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value,
int &coeff_field_characteristic, Filtration_value &min_persistence);
template<class Point_d>
std::vector<Point_d> read_off(const std::string &off_file_points) {
Gudhi::Points_off_reader<Point_d> off_reader(off_file_points);
if (!off_reader.is_valid()) {
std::cerr << "Alpha_complex - Unable to read file " << off_file_points << "\n";
exit(-1); // ----- >>
}
return off_reader.get_point_cloud();
}
std::vector<double> read_weight_file(const std::string &weight_file) {
std::vector<double> weights;
// Read weights information from file
std::ifstream weights_ifstr(weight_file);
if (weights_ifstr.good()) {
double weight = 0.0;
// Attempt read the weight in a double format, return false if it fails
while (weights_ifstr >> weight) {
weights.push_back(weight);
}
} else {
std::cerr << "Unable to read weights file " << weight_file << std::endl;
exit(-1);
}
return weights;
}
template<class Kernel>
Simplex_tree create_simplex_tree(const std::string &off_file_points, const std::string &weight_file,
bool exact_version, Filtration_value alpha_square_max_value) {
Simplex_tree stree;
auto points = read_off<typename Kernel::Point_d>(off_file_points);
if (weight_file != std::string()) {
std::vector<double> weights = read_weight_file(weight_file);
if (points.size() != weights.size()) {
std::cerr << "Alpha_complex - Inconsistency between number of points (" << points.size()
<< ") and number of weights (" << weights.size() << ")" << "\n";
exit(-1); // ----- >>
}
// Init of an alpha complex from an OFF file
Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex_from_file(points, weights);
if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) {
std::cerr << "Alpha complex simplicial complex creation failed." << std::endl;
exit(-1);
}
} else {
// Init of an alpha complex from an OFF file
Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(points);
if (!alpha_complex_from_file.create_complex(stree, alpha_square_max_value, exact_version)) {
std::cerr << "Alpha complex simplicial complex creation failed." << std::endl;
exit(-1);
}
}
return stree;
}
int main(int argc, char **argv) {
std::string weight_file;
std::string off_file_points;
std::string output_file_diag;
bool exact_version = false;
bool fast_version = false;
Filtration_value alpha_square_max_value;
int coeff_field_characteristic;
Filtration_value min_persistence;
program_options(argc, argv, off_file_points, exact_version, fast_version, weight_file, output_file_diag,
alpha_square_max_value, coeff_field_characteristic, 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, weight_file, exact_version, alpha_square_max_value);
} else {
using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>;
stree = create_simplex_tree<Kernel>(off_file_points, weight_file, exact_version, alpha_square_max_value);
}
// ----------------------------------------------------------------------------
// Display information about the alpha complex
// ----------------------------------------------------------------------------
std::clog << "Simplicial complex is of dimension " << stree.dimension() << " - " << stree.num_simplices()
<< " simplices - " << stree.num_vertices() << " vertices." << std::endl;
std::clog << "Simplex_tree dim: " << stree.dimension() << std::endl;
// Compute the persistence diagram of the complex
stree);
// initializes the coefficient field for homology
pcoh.init_coefficients(coeff_field_characteristic);
pcoh.compute_persistent_cohomology(min_persistence);
// Output the diagram in filediag
if (output_file_diag.empty()) {
pcoh.output_diagram();
} else {
std::clog << "Result in file: " << output_file_diag << std::endl;
std::ofstream out(output_file_diag);
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 &weight_file, std::string &output_file_diag, Filtration_value &alpha_square_max_value,
int &coeff_field_characteristic, 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")(
"exact,e", po::bool_switch(&exact),
"To activate exact version of Alpha complex (default is false, not available if fast is set)")(
"fast,f", po::bool_switch(&fast),
"To activate fast version of Alpha complex (default is false, not available if exact is set)")(
"weight-file,w", po::value<std::string>(&weight_file)->default_value(std::string()),
"Name of file containing a point weights. Format is one weight per line:\n W1\n ...\n Wn ")(
"output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
"Name of file in which the persistence diagram is written. Default print in std::clog")(
"max-alpha-square-value,r", po::value<Filtration_value>(&alpha_square_max_value)
->default_value(std::numeric_limits<Filtration_value>::infinity()),
"Maximal alpha square value for the Alpha complex construction.")(
"field-charac,p", po::value<int>(&coeff_field_characteristic)->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 an Alpha 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);
}
}
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
size_t num_vertices() const
Returns the number of vertices in the complex.
Definition: Simplex_tree.h:572
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
Alpha complex data structure.
Definition: Alpha_complex.h:103
Computes the persistent cohomology of a filtered complex.
Definition: Persistent_cohomology.h:52
Value type for a filtration function on a cell complex.
Definition: FiltrationValue.h:20