diff options
Diffstat (limited to 'src/Alpha_complex/utilities/alpha_complex_persistence.cpp')
| -rw-r--r-- | src/Alpha_complex/utilities/alpha_complex_persistence.cpp | 107 |
1 files changed, 66 insertions, 41 deletions
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp index fab7bd30..486347cc 100644 --- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -24,63 +24,84 @@ 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 &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; + 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, 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); + if ((exact_version) && (fast_version)) { + std::cerr << "You cannot set the exact and the fast version." << std::endl; + exit(-1); + } 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(); + 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>; + + // Init of an alpha complex from an OFF file + Gudhi::alpha_complex::Alpha_complex<Fast_kernel> alpha_complex_from_file(off_file_points); + + if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value)) { + std::cerr << "Fast Alpha complex simplicial complex creation failed." << std::endl; + exit(-1); } - } + } else { + using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>; + // Init of an alpha complex from an OFF file + Gudhi::alpha_complex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points); + + if (!alpha_complex_from_file.create_complex(simplex, alpha_square_max_value, exact_version)) { + std::cerr << "Alpha complex simplicial complex creation failed." << std::endl; + exit(-1); + } + } + // ---------------------------------------------------------------------------- + // 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) { +void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &fast, + 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), @@ -88,6 +109,10 @@ 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)")( "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) |