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author | Gard Spreemann <gspreemann@gmail.com> | 2018-02-02 13:51:45 +0100 |
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committer | Gard Spreemann <gspreemann@gmail.com> | 2018-02-02 13:51:45 +0100 |
commit | 9899ae167f281d10b1684dfcd02c6838c5bf28df (patch) | |
tree | ceda62a40a9a8f731298832b1b4ab44ab0dd3a10 /utilities/Alpha_complex/alpha_complex_persistence.cpp | |
parent | 866f6ce614e9c09c97fed12c8c0c2c9fb84fad3f (diff) |
GUDHI 2.1.0 as released by upstream in a tarball.upstream/2.1.0
Diffstat (limited to 'utilities/Alpha_complex/alpha_complex_persistence.cpp')
-rw-r--r-- | utilities/Alpha_complex/alpha_complex_persistence.cpp | 116 |
1 files changed, 116 insertions, 0 deletions
diff --git a/utilities/Alpha_complex/alpha_complex_persistence.cpp b/utilities/Alpha_complex/alpha_complex_persistence.cpp new file mode 100644 index 00000000..2105220a --- /dev/null +++ b/utilities/Alpha_complex/alpha_complex_persistence.cpp @@ -0,0 +1,116 @@ +#include <boost/program_options.hpp> + +#include <CGAL/Epick_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 <iostream> +#include <string> +#include <limits> // for numeric_limits + +using Simplex_tree = Gudhi::Simplex_tree<>; +using Filtration_value = Simplex_tree::Filtration_value; + +void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence); + +int main(int argc, char **argv) { + std::string off_file_points; + std::string output_file_diag; + Filtration_value alpha_square_max_value; + int coeff_field_characteristic; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value, coeff_field_characteristic, + min_persistence); + + // ---------------------------------------------------------------------------- + // Init of an alpha complex from an OFF file + // ---------------------------------------------------------------------------- + using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; + Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points); + + Simplex_tree simplex; + if (alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + // ---------------------------------------------------------------------------- + // Display information about the alpha complex + // ---------------------------------------------------------------------------- + std::cout << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices() + << " simplices - " << simplex.num_vertices() << " vertices." << std::endl; + + // Sort the simplices in the order of the filtration + simplex.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl; + // Compute the persistence diagram of the complex + Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh( + simplex); + // 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::cout << "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, 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")( + "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::cout")( + "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::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of an Alpha 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(); + } +} |