From 73efba37dfcab3f9b8589cb3b0b80f6d7dd7bd0b Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 4 Oct 2017 10:24:04 +0000 Subject: Document utilies in README files using Markdown + move/rename some utilities Only missing doc for now: Garland_heckbert git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8 --- .../utilities/alpha_complex_persistence.cpp | 125 +++++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 src/Alpha_complex/utilities/alpha_complex_persistence.cpp (limited to 'src/Alpha_complex/utilities/alpha_complex_persistence.cpp') diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp new file mode 100644 index 00000000..9e84e91f --- /dev/null +++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp @@ -0,0 +1,125 @@ +#include + +#include + +#include +#include +// to construct a simplex_tree from alpha complex +#include + +#include +#include +#include // 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 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(&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(&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(&alpha_square_max_value)->default_value(std::numeric_limits::infinity()), + "Maximal alpha square value for the Alpha complex construction.") + ("field-charac,p", po::value(&coeff_field_characteristic)->default_value(11), + "Characteristic p of the coefficient field Z/pZ for computing homology.") + ("min-persistence,m", po::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(); + } +} -- cgit v1.2.3