diff options
Diffstat (limited to 'src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp')
| -rw-r--r-- | src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp | 368 |
1 files changed, 207 insertions, 161 deletions
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp index 6e603155..09c84eb3 100644 --- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp @@ -20,188 +20,219 @@ * along with this program. If not, see <http://www.gnu.org/licenses/>. */ -#include <boost/version.hpp> #include <boost/program_options.hpp> #include <boost/variant.hpp> -#if BOOST_VERSION >= 105400 -#include <boost/container/static_vector.hpp> -#endif - +#include <gudhi/Alpha_complex_3d.h> #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #include <gudhi/Points_3D_off_io.h> -#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> -#include <CGAL/Delaunay_triangulation_3.h> -#include <CGAL/Alpha_shape_3.h> -#include <CGAL/Alpha_shape_cell_base_3.h> -#include <CGAL/Alpha_shape_vertex_base_3.h> -#include <CGAL/iterator.h> - #include <fstream> -#include <cmath> #include <string> -#include <tuple> -#include <map> -#include <utility> #include <vector> -#include <cstdlib> - -#include "alpha_complex_3d_helper.h" - -// Alpha_shape_3 templates type definitions -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel>; -using Fb = CGAL::Alpha_shape_cell_base_3<Kernel>; -using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>; -using Triangulation_3 = CGAL::Delaunay_triangulation_3<Kernel, Tds>; -using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>; - -// From file type definition -using Point_3 = Kernel::Point_3; - -// filtration with alpha values needed type definition -using Alpha_value_type = Alpha_shape_3::FT; -using Object = CGAL::Object; -using Dispatch = - CGAL::Dispatch_output_iterator<CGAL::cpp11::tuple<Object, Alpha_value_type>, - CGAL::cpp11::tuple<std::back_insert_iterator<std::vector<Object> >, - std::back_insert_iterator<std::vector<Alpha_value_type> > > >; -using Cell_handle = Alpha_shape_3::Cell_handle; -using Facet = Alpha_shape_3::Facet; -using Edge_3 = Alpha_shape_3::Edge; -using Vertex_handle = Alpha_shape_3::Vertex_handle; - -#if BOOST_VERSION >= 105400 -using Vertex_list = boost::container::static_vector<Alpha_shape_3::Vertex_handle, 4>; -#else -using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>; -#endif +#include <limits> // for numeric_limits<> // gudhi type definition -using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; -using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - int &coeff_field_characteristic, Filtration_value &min_persistence); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string output_file_diag; - int coeff_field_characteristic; - Filtration_value min_persistence; + Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>; + +void program_options(int argc, char *argv[], std::string &off_file_points, bool &exact, bool &safe, + std::string &weight_file, std::string &cuboid_file, std::string &output_file_diag, + Filtration_value &alpha_square_max_value, int &coeff_field_characteristic, + Filtration_value &min_persistence); + +bool 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 { + return false; + } + return true; +} - program_options(argc, argv, off_file_points, output_file_diag, coeff_field_characteristic, min_persistence); +bool read_cuboid_file(const std::string &cuboid_file, double &x_min, double &y_min, double &z_min, double &x_max, + double &y_max, double &z_max) { + // Read weights information from file + std::ifstream iso_cuboid_str(cuboid_file); + if (iso_cuboid_str.is_open()) { + if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) { + return false; + } + } else { + return false; + } + return true; +} +template <typename AlphaComplex3d> +std::vector<typename AlphaComplex3d::Point_3> read_off(const std::string &off_file_points) { // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader<Point_3> off_reader(off_file_points); + Gudhi::Points_3D_off_reader<typename AlphaComplex3d::Point_3> off_reader(off_file_points); // Check the read operation was correct if (!off_reader.is_valid()) { - std::cerr << "Unable to read file " << off_file_points << std::endl; + std::cerr << "Unable to read OFF file " << off_file_points << std::endl; exit(-1); } + return off_reader.get_point_cloud(); +} - // Retrieve the points - std::vector<Point_3> lp = off_reader.get_point_cloud(); - - // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. - Alpha_shape_3 as(lp.begin(), lp.end(), 0, Alpha_shape_3::GENERAL); -#ifdef DEBUG_TRACES - std::cout << "Alpha shape computed in GENERAL mode" << std::endl; -#endif // DEBUG_TRACES - - // filtration with alpha values from alpha shape - std::vector<Object> the_objects; - std::vector<Alpha_value_type> the_alpha_values; - - Dispatch disp = CGAL::dispatch_output<Object, Alpha_value_type>(std::back_inserter(the_objects), - std::back_inserter(the_alpha_values)); - - as.filtration_with_alpha_values(disp); -#ifdef DEBUG_TRACES - std::cout << "filtration_with_alpha_values returns : " << the_objects.size() << " objects" << std::endl; -#endif // DEBUG_TRACES - - Alpha_shape_3::size_type count_vertices = 0; - Alpha_shape_3::size_type count_edges = 0; - Alpha_shape_3::size_type count_facets = 0; - Alpha_shape_3::size_type count_cells = 0; - - // Loop on objects vector - Vertex_list vertex_list; - ST simplex_tree; - Alpha_shape_simplex_tree_map map_cgal_simplex_tree; - std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin(); - for (auto object_iterator : the_objects) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { - vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); - count_cells++; - } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from_facet<Vertex_list, Facet>(*facet); - count_facets++; - } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from_edge<Vertex_list, Edge_3>(*edge); - count_edges++; - } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex); - } - // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex - Simplex_tree_vector_vertex the_simplex; - for (auto the_alpha_shape_vertex : vertex_list) { - Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex); - if (the_map_iterator == map_cgal_simplex_tree.end()) { - // alpha shape not found - Simplex_tree_vertex vertex = map_cgal_simplex_tree.size(); -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex); - } else { - // alpha shape found - Simplex_tree_vertex vertex = the_map_iterator->second; -#ifdef DEBUG_TRACES - std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl; -#endif // DEBUG_TRACES - the_simplex.push_back(vertex); - } +int main(int argc, char **argv) { + std::string off_file_points; + std::string weight_file; + std::string cuboid_file; + std::string output_file_diag; + Filtration_value alpha_square_max_value = 0.; + int coeff_field_characteristic = 0; + Filtration_value min_persistence = 0.; + bool exact_version = false; + bool fast_version = false; + bool weighted_version = false; + bool periodic_version = false; + + program_options(argc, argv, off_file_points, exact_version, fast_version, weight_file, cuboid_file, output_file_diag, + alpha_square_max_value, coeff_field_characteristic, min_persistence); + + std::vector<double> weights; + if (weight_file != std::string()) { + if (!read_weight_file(weight_file, weights)) { + std::cerr << "Unable to read weights file " << weight_file << std::endl; + exit(-1); } - // Construction of the simplex_tree - Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - simplex_tree.insert_simplex(the_simplex, filtr); - GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); - ++the_alpha_value_iterator; + weighted_version = true; } -#ifdef DEBUG_TRACES - std::cout << "vertices \t\t" << count_vertices << std::endl; - std::cout << "edges \t\t" << count_edges << std::endl; - std::cout << "facets \t\t" << count_facets << std::endl; - std::cout << "cells \t\t" << count_cells << std::endl; + double x_min = 0., y_min = 0., z_min = 0., x_max = 0., y_max = 0., z_max = 0.; + std::ifstream iso_cuboid_str(argv[3]); + if (cuboid_file != std::string()) { + if (!read_cuboid_file(cuboid_file, x_min, y_min, z_min, x_max, y_max, z_max)) { + std::cerr << "Unable to read cuboid file " << cuboid_file << std::endl; + exit(-1); + } + periodic_version = true; + } - std::cout << "Information of the Simplex Tree: " << std::endl; - std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; - std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; - std::cout << " Dimension = " << simplex_tree.dimension() << " "; -#endif // DEBUG_TRACES + Gudhi::alpha_complex::complexity complexity = Gudhi::alpha_complex::complexity::SAFE; + if (exact_version) { + if (fast_version) { + std::cerr << "You cannot set the exact and the fast version." << std::endl; + exit(-1); + } + complexity = Gudhi::alpha_complex::complexity::EXACT; + } + if (fast_version) { + complexity = Gudhi::alpha_complex::complexity::FAST; + } -#ifdef DEBUG_TRACES - std::cout << "Iterator on vertices: " << std::endl; - for (auto vertex : simplex_tree.complex_vertex_range()) { - std::cout << vertex << " "; + Simplex_tree simplex_tree; + + switch (complexity) { + case Gudhi::alpha_complex::complexity::FAST: + if (weighted_version) { + if (periodic_version) { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, true>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } else { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, true, false>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, weights); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } + } else { + if (periodic_version) { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, true>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } else { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::FAST, false, false>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } + } + break; + case Gudhi::alpha_complex::complexity::EXACT: + if (weighted_version) { + if (periodic_version) { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, true>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } else { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, true, false>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, weights); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } + } else { + if (periodic_version) { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, true>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } else { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::EXACT, false, false>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } + } + break; + case Gudhi::alpha_complex::complexity::SAFE: + if (weighted_version) { + if (periodic_version) { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, true>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, weights, x_min, y_min, z_min, x_max, y_max, z_max); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } else { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, true, false>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, weights); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } + } else { + if (periodic_version) { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, true>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points, x_min, y_min, z_min, x_max, y_max, z_max); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } else { + using Alpha_complex_3d = + Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::complexity::SAFE, false, false>; + auto points = read_off<Alpha_complex_3d>(off_file_points); + Alpha_complex_3d alpha_complex(points); + alpha_complex.create_complex(simplex_tree, alpha_square_max_value); + } + } + break; + default: + std::cerr << "Unknown complexity value " << std::endl; + exit(-1); + break; } -#endif // DEBUG_TRACES // Sort the simplices in the order of the filtration simplex_tree.initialize_filtration(); @@ -227,8 +258,10 @@ int main(int argc, char **argv) { return 0; } -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag, - 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 &cuboid_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), @@ -236,8 +269,20 @@ 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 3d (default is false, not available if fast is set)")( + "fast,f", po::bool_switch(&fast), + "To activate fast version of Alpha complex 3d (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 ")( + "cuboid-file,c", po::value<std::string>(&cuboid_file), + "Name of file describing the periodic domain. Format is:\n min_hx min_hy min_hz\n max_hx max_hy max_hz")( "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), @@ -254,17 +299,18 @@ void program_options(int argc, char *argv[], std::string &off_file_points, std:: 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")) { + if (vm.count("help") || !vm.count("input-file") || !vm.count("weight-file")) { std::cout << std::endl; std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a 3D Alpha complex defined on a set of input points.\n \n"; + std::cout << "of a 3D Alpha complex defined on a set of input points.\n"; + std::cout << "3D Alpha complex can be safe (by default) exact or fast, weighted and/or periodic\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 << "p is the characteristic of the field Z/pZ used for homology coefficients.\n\n"; - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; + std::cout << "Usage: " << argv[0] << " [options] input-file weight-file\n\n"; std::cout << visible << std::endl; exit(-1); } |