From a114ccb40558615139eeb23dfc05e3ceeb909d7f Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Tue, 31 Jul 2018 15:47:22 +0000 Subject: Fix documentation for CGAL version required by 3d version Remove duplicated example (cf. the one in the Simplex tree) Add the example for documentation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@3713 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 204f77982c61bc30a6ad3218c82b98f8bb49d711 --- .../example/alpha_complex_3d_step_by_step.cpp | 309 --------------------- src/common/doc/examples.h | 1 + src/common/doc/installation.h | 10 +- 3 files changed, 9 insertions(+), 311 deletions(-) delete mode 100644 src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp (limited to 'src') diff --git a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp b/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp deleted file mode 100644 index d76402e5..00000000 --- a/src/Alpha_complex/example/alpha_complex_3d_step_by_step.cpp +++ /dev/null @@ -1,309 +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 - -template -Vertex_list from_cell(const Cell_handle& ch) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { -#ifdef DEBUG_TRACES - std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(ch->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_facet(const Facet& fct) { - Vertex_list the_list; - for (auto i = 0; i < 4; i++) { - if (fct.second != i) { -#ifdef DEBUG_TRACES - std::cout << "from facet=[" << i << "]" << fct.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(fct.first->vertex(i)); - } - } - return the_list; -} - -template -Vertex_list from_edge(const Edge_3& edg) { - Vertex_list the_list; - for (auto i : {edg.second, edg.third}) { -#ifdef DEBUG_TRACES - std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(edg.first->vertex(i)); - } - return the_list; -} - -template -Vertex_list from_vertex(const Vertex_handle& vh) { - Vertex_list the_list; -#ifdef DEBUG_TRACES - std::cout << "from vertex=" << vh->point() << std::endl; -#endif // DEBUG_TRACES - the_list.push_back(vh); - return the_list; -} - -// 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; - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag); - -int main(int argc, char **argv) { - std::string off_file_points; - std::string output_file_diag; - - program_options(argc, argv, off_file_points, output_file_diag); - - // 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::streambuf* streambufffer; - std::ofstream ouput_file_stream; - if (output_file_diag != std::string()) { - ouput_file_stream.open(output_file_diag); - streambufffer = ouput_file_stream.rdbuf(); - } else { - streambufffer = std::cout.rdbuf(); - } - - std::ostream output_stream(streambufffer); - - // ---------------------------------------------------------------------------- - // Display information about the alpha complex - // ---------------------------------------------------------------------------- - output_stream << "Alpha complex is of dimension " << simplex_tree.dimension() << - " - " << simplex_tree.num_simplices() << " simplices - " << - simplex_tree.num_vertices() << " vertices." << std::endl; - - output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << - std::endl; - for (auto f_simplex : simplex_tree.filtration_simplex_range()) { - output_stream << " ( "; - for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { - output_stream << vertex << " "; - } - output_stream << ") -> " << "[" << simplex_tree.filtration(f_simplex) << "] "; - output_stream << std::endl; - } - - return 0; -} - -void program_options(int argc, char *argv[], std::string &off_file_points, std::string &output_file_diag) { - 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"); - - 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 and displays the 3D Alpha complex defined on a set of input points.\n \n"; - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - exit(-1); - } -} diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h index 7c2a8f69..c19b3444 100644 --- a/src/common/doc/examples.h +++ b/src/common/doc/examples.h @@ -53,6 +53,7 @@ * @example Spatial_searching/example_spatial_searching.cpp * @example Alpha_complex/alpha_complex_3d_persistence.cpp * @example Alpha_complex/alpha_complex_persistence.cpp + * @example Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * @example Bottleneck_distance/bottleneck_distance.cpp * @example Witness_complex/weak_witness_persistence.cpp * @example Witness_complex/strong_witness_persistence.cpp diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h index 8f91e9c1..d36a216f 100644 --- a/src/common/doc/installation.h +++ b/src/common/doc/installation.h @@ -56,8 +56,6 @@ make doxygen * * The following examples/utilities require the Computational Geometry Algorithms * Library (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed: - * \li - * Alpha_complex/alpha_complex_3d_persistence.cpp * \li * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp * @@ -113,6 +111,12 @@ make doxygen * \li * Tangential_complex/example_with_perturb.cpp * + * The following example requires CGAL version ≥ 4.11.0: + * \li + * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp + * \li + * Alpha_complex/alpha_complex_3d_persistence.cpp + * * \subsection eigen3 Eigen3 * The \ref alpha_complex data structure and few examples requires * Eigen3 is a C++ template library for linear algebra: @@ -128,6 +132,8 @@ make doxygen * Alpha_complex/alpha_complex_persistence.cpp * \li * Alpha_complex/alpha_complex_3d_persistence.cpp + * \li + * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp * \li * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp * \li -- cgit v1.2.3