diff options
Diffstat (limited to 'src/Alpha_complex/utilities/alpha_complex_persistence.cpp')
| -rw-r--r-- | src/Alpha_complex/utilities/alpha_complex_persistence.cpp | 182 |
1 files changed, 128 insertions, 54 deletions
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index fab7bd30..29edbd8e 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -11,76 +11,144 @@ #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> 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); +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, output_file_diag, alpha_square_max_value, coeff_field_characteristic, - 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); + } // ---------------------------------------------------------------------------- - // Init of an alpha complex from an OFF file + // Display information about the alpha complex // ---------------------------------------------------------------------------- - 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(); - } + 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 + Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh( + 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, std::string &output_file_diag, - Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, - Filtration_value &min_persistence) { +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), @@ -88,8 +156,14 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std:: 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::cout")( + "Name of file in which the persistence diagram is written. Default print in standard output")( "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.")( @@ -110,17 +184,17 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std:: 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::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); } } |