From 599d68cd916f533bdb66dd9e684dd5703233b6bb Mon Sep 17 00:00:00 2001 From: Gard Spreemann Date: Wed, 25 Sep 2019 14:29:41 +0200 Subject: Delete all files in order to incorporate upstream's move to git. --- .../Alpha_complex/alpha_complex_3d_persistence.cpp | 271 --------------------- 1 file changed, 271 deletions(-) delete mode 100644 utilities/Alpha_complex/alpha_complex_3d_persistence.cpp (limited to 'utilities/Alpha_complex/alpha_complex_3d_persistence.cpp') diff --git a/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp b/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp deleted file mode 100644 index 6e603155..00000000 --- a/utilities/Alpha_complex/alpha_complex_3d_persistence.cpp +++ /dev/null @@ -1,271 +0,0 @@ -/* 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 - * - * 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 . - */ - -#include -#include -#include - -#if BOOST_VERSION >= 105400 -#include -#endif - -#include -#include -#include - -#include -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include - -#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; -using Fb = CGAL::Alpha_shape_cell_base_3; -using Tds = CGAL::Triangulation_data_structure_3; -using Triangulation_3 = CGAL::Delaunay_triangulation_3; -using Alpha_shape_3 = CGAL::Alpha_shape_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 >, - std::back_insert_iterator > > >; -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; -#else -using Vertex_list = std::vector; -#endif - -// gudhi type definition -using ST = Gudhi::Simplex_tree; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map; -using Simplex_tree_vector_vertex = std::vector; -using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology; - -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; - - program_options(argc, argv, off_file_points, 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 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; - exit(-1); - } - - // Retrieve the points - std::vector 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 the_objects; - std::vector the_alpha_values; - - Dispatch disp = CGAL::dispatch_output(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::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(&object_iterator)) { - vertex_list = from_cell(*cell); - count_cells++; - } else if (const Facet *facet = CGAL::object_cast(&object_iterator)) { - vertex_list = from_facet(*facet); - count_facets++; - } else if (const Edge_3 *edge = CGAL::object_cast(&object_iterator)) { - vertex_list = from_edge(*edge); - count_edges++; - } else if (const Vertex_handle *vertex = CGAL::object_cast(&object_iterator)) { - count_vertices++; - vertex_list = from_vertex(*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); - GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values"); - ++the_alpha_value_iterator; - } - -#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 &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(&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")( - "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 a 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" << std::endl << std::endl; - std::cout << visible << std::endl; - exit(-1); - } -} -- cgit v1.2.3