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Diffstat (limited to 'utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp')
| -rw-r--r-- | utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp | 300 |
1 files changed, 300 insertions, 0 deletions
diff --git a/utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp new file mode 100644 index 00000000..188cf604 --- /dev/null +++ b/utilities/Alpha_complex/periodic_alpha_complex_3d_persistence.cpp @@ -0,0 +1,300 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Vincent Rouvreau + * Pawel Dlotko - 2017 - Swansea University, UK + * + * Copyright (C) 2014 INRIA + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <boost/program_options.hpp> +#include <boost/variant.hpp> + +#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/Periodic_3_Delaunay_triangulation_traits_3.h> +#include <CGAL/Periodic_3_Delaunay_triangulation_3.h> +#include <CGAL/Alpha_shape_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" + +// Traits +using K = CGAL::Exact_predicates_inexact_constructions_kernel; +using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>; +// Vertex type +using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; +using Vb = CGAL::Triangulation_vertex_base_3<PK, DsVb>; +using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>; +// Cell type +using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; +using Cb = CGAL::Triangulation_cell_base_3<PK, DsCb>; +using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>; +using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>; +using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK, Tds>; +using Alpha_shape_3 = CGAL::Alpha_shape_3<P3DT3>; +using Point_3 = PK::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; +using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>; + +// 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 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 &cuboid_file, + 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 cuboid_file; + std::string output_file_diag; + int coeff_field_characteristic; + Filtration_value min_persistence; + + program_options(argc, argv, off_file_points, cuboid_file, output_file_diag, coeff_field_characteristic, + min_persistence); + + // 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); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read OFF file " << off_file_points << std::endl; + exit(-1); + } + + // Read iso_cuboid_3 information from file + std::ifstream iso_cuboid_str(cuboid_file); + double x_min, y_min, z_min, x_max, y_max, z_max; + if (iso_cuboid_str.good()) { + iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max; + } else { + std::cerr << "Unable to read file " << cuboid_file << std::endl; + exit(-1); + } + // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it. + if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) { + std::cerr << "The size of the cuboid in every directions is not the same." << std::endl; + exit(-1); + } + + // Retrieve the points + std::vector<Point_3> lp = off_reader.get_point_cloud(); + + // Define the periodic cube + P3DT3 pdt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + // Heuristic for inserting large point sets (if pts is reasonably large) + pdt.insert(lp.begin(), lp.end(), true); + // As pdt won't be modified anymore switch to 1-sheeted cover if possible + if (pdt.is_triangulation_in_1_sheet()) { + pdt.convert_to_1_sheeted_covering(); + } else { + std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; + exit(-1); + } + std::cout << "Periodic Delaunay computed." << std::endl; + + // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode + // Maybe need to set it to GENERAL mode + Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); + + // 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); + } + } + // 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); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cout << "This shall not happen" << std::endl; + } + +#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; + + 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 + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: " << std::endl; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + // Sort the simplices in the order of the filtration + simplex_tree.initialize_filtration(); + + std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl; + // Compute the persistence diagram of the complex + Persistent_cohomology pcoh(simplex_tree, true); + // 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 &cuboid_file, + std::string &output_file_diag, 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 ")( + "cuboid-file", po::value<std::string>(&cuboid_file), + "Name of file describing the periodic domain. Format is: min_hx min_hy min_hz\nmax_hx max_hy max_hz"); + + 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")( + "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); + pos.add("cuboid-file", 2); + + 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") || !vm.count("cuboid-file")) { + std::cout << std::endl; + std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; + std::cout << "of a periodic 3D 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 cuboid-file" << std::endl << std::endl; + std::cout << visible << std::endl; + std::abort(); + } +} |