From f5afe3f0d4ca486ea530850e9bb724643dc18877 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 23 Sep 2016 16:01:25 +0000 Subject: Examples shall use only off files git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/off_files_only@1555 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 73833d163f3b76604a5111dc4374b635d60afade --- ...e_alpha_shapes_3_simplex_tree_from_off_file.cpp | 274 +++++++++++++++++++++ 1 file changed, 274 insertions(+) create mode 100644 src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp (limited to 'src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp') diff --git a/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp new file mode 100644 index 00000000..ff2eebcb --- /dev/null +++ b/src/Simplex_tree/example/example_alpha_shapes_3_simplex_tree_from_off_file.cpp @@ -0,0 +1,274 @@ +/* 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 Saclay (France) + * + * 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 + +#include +#include +#include +#include + +#include +#include +#include +#include // for tuple<> +#include +#include // for pair<> +#include +#include + +// Alpha_shape_3 templates type definitions +typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; +typedef CGAL::Alpha_shape_vertex_base_3 Vb; +typedef CGAL::Alpha_shape_cell_base_3 Fb; +typedef CGAL::Triangulation_data_structure_3 Tds; +typedef CGAL::Delaunay_triangulation_3 Triangulation_3; +typedef CGAL::Alpha_shape_3 Alpha_shape_3; + +// From file type definition +typedef Kernel::Point_3 Point; + +// filtration with alpha values needed type definition +typedef Alpha_shape_3::FT Alpha_value_type; +typedef CGAL::Object Object; +typedef CGAL::Dispatch_output_iterator< +CGAL::cpp11::tuple, +CGAL::cpp11::tuple >, + std::back_insert_iterator< std::vector > > > Dispatch; +typedef Alpha_shape_3::Cell_handle Cell_handle; +typedef Alpha_shape_3::Facet Facet; +typedef Alpha_shape_3::Edge Edge; +typedef std::list Vertex_list; + +// gudhi type definition +typedef Gudhi::Simplex_tree<> Simplex_tree; +typedef Simplex_tree::Vertex_handle Simplex_tree_vertex; +typedef std::map Alpha_shape_simplex_tree_map; +typedef std::pair Alpha_shape_simplex_tree_pair; +typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; + +Vertex_list from(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; +} + +Vertex_list from(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; +} + +Vertex_list from(const Edge& edg) { + Vertex_list the_list; + for (auto i = 0; i < 4; i++) { + if ((edg.second == i) || (edg.third == i)) { +#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; +} + +Vertex_list from(const Alpha_shape_3::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; +} + +int main(int argc, char * const argv[]) { + // program args management + if (argc != 2) { + std::cerr << "Usage: " << argv[0] + << " path_to_off_file \n"; + return 0; + } + + // Read points from file + std::string offInputFile(argv[1]); + // Read the OFF file (input file name given as parameter) and triangulate points + Gudhi::Points_3D_off_reader off_reader(offInputFile); + // Check the read operation was correct + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << argv[1] << std::endl; + return 0; + } + // Retrieve the triangulation + 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; + Simplex_tree 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); + count_cells++; + } else if (const Facet * facet = CGAL::object_cast(&object_iterator)) { + vertex_list = from(*facet); + count_facets++; + } else if (const Edge * edge = CGAL::object_cast(&object_iterator)) { + vertex_list = from(*edge); + count_edges++; + } else if (const Alpha_shape_3::Vertex_handle * vertex = + CGAL::object_cast(&object_iterator)) { + count_vertices++; + vertex_list = from(*vertex); + } + // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex + Simplex_tree_vector_vertex the_simplex_tree; + 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_simplex " << vertex << "\n"; +#endif // DEBUG_TRACES + the_simplex_tree.push_back(vertex); + map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(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_tree.push_back(vertex); + } + } + // Construction of the simplex_tree +#ifdef DEBUG_TRACES + std::cout << "filtration = " << *the_alpha_value_iterator << std::endl; +#endif // DEBUG_TRACES + simplex_tree.insert_simplex(the_simplex_tree, std::sqrt(*the_alpha_value_iterator)); + if (the_alpha_value_iterator != the_alpha_values.end()) + ++the_alpha_value_iterator; + else + std::cerr << "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:\n"; + std::cout << " Number of vertices = " << simplex_tree.num_vertices() << " "; + std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; +#endif // DEBUG_TRACES + +#ifdef DEBUG_TRACES + std::cout << "Iterator on vertices: \n"; + for (auto vertex : simplex_tree.complex_vertex_range()) { + std::cout << vertex << " "; + } +#endif // DEBUG_TRACES + + std::cout << simplex_tree << std::endl; + +#ifdef DEBUG_TRACES + std::cout << std::endl << std::endl << "Iterator on simplices:\n"; + for (auto simplex : simplex_tree.complex_simplex_range()) { + std::cout << " "; + for (auto vertex : simplex_tree.simplex_vertex_range(simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } +#endif // DEBUG_TRACES +#ifdef DEBUG_TRACES + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, with [filtration value]:\n"; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } +#endif // DEBUG_TRACES +#ifdef DEBUG_TRACES + std::cout << std::endl << std::endl << "Iterator on Simplices in the filtration, and their boundary simplices:\n"; + for (auto f_simplex : simplex_tree.filtration_simplex_range()) { + std::cout << " " << "[" << simplex_tree.filtration(f_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(f_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + + for (auto b_simplex : simplex_tree.boundary_simplex_range(f_simplex)) { + std::cout << " " << "[" << simplex_tree.filtration(b_simplex) << "] "; + for (auto vertex : simplex_tree.simplex_vertex_range(b_simplex)) { + std::cout << vertex << " "; + } + std::cout << std::endl; + } + } +#endif // DEBUG_TRACES + + return 0; +} -- cgit v1.2.3