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Diffstat (limited to 'src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp')
| -rw-r--r-- | src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp | 284 |
1 files changed, 284 insertions, 0 deletions
diff --git a/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp b/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp new file mode 100644 index 00000000..dd76dfcf --- /dev/null +++ b/src/Simplex_tree/example/simplex_tree_from_alpha_shapes_3.cpp @@ -0,0 +1,284 @@ + /* 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 <http://www.gnu.org/licenses/>. + */ + +#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> +#include <CGAL/Delaunay_triangulation_3.h> +#include <CGAL/Alpha_shape_3.h> +#include <CGAL/iterator.h> + +#include <fstream> + +#include "gudhi/graph_simplicial_complex.h" +#include "gudhi/Simplex_tree.h" +#include <boost/variant.hpp> + +// Alpha_shape_3 templates type definitions +typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel; +typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb; +typedef CGAL::Alpha_shape_cell_base_3<Kernel> Fb; +typedef CGAL::Triangulation_data_structure_3<Vb,Fb> Tds; +typedef CGAL::Delaunay_triangulation_3<Kernel,Tds> Triangulation_3; +typedef CGAL::Alpha_shape_3<Triangulation_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<Object, Alpha_value_type>, + CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, std::back_insert_iterator< std::vector<Alpha_value_type> > + > > Dispatch; +typedef Alpha_shape_3::Cell_handle Cell_handle; +typedef Alpha_shape_3::Facet Facet; +typedef Alpha_shape_3::Edge Edge; +typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list; + +// gudhi type definition +typedef Gudhi::Simplex_tree<>::Vertex_handle Simplex_tree_vertex; +typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map; +typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair; +typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex; + +//#define DEBUG_TRACES + +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_file_graph \n"; + return 0; // ----- >> + } + + // Read points from file + std::string filegraph = argv[1]; + std::list<Point> lp; + std::ifstream is(filegraph.c_str()); + int n; + is >> n; +#ifdef DEBUG_TRACES + std::cout << "Reading " << n << " points " << std::endl; +#endif // DEBUG_TRACES + Point p; + for( ; n>0 ; n--) { + is >> p; + lp.push_back(p); + } + + // alpha shape construction from points + Alpha_shape_3 as(lp.begin(),lp.end()); +#ifdef DEBUG_TRACES + std::cout << "Alpha shape computed in REGULARIZED mode by default" << 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; + Gudhi::Simplex_tree<> 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); + count_cells++; + } + else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) + { + vertex_list = from(*facet); + count_facets++; + } + else if (const Edge* edge = CGAL::object_cast<Edge>(&object_iterator)) + { + vertex_list = from(*edge); + count_edges++; + } + else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&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 " << vertex << std::endl; +#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(the_simplex_tree, *the_alpha_value_iterator); + 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; +#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 + + std::cout << simplex_tree << std::endl; + +#ifdef DEBUG_TRACES + std::cout << std::endl << std::endl << "Iterator on simplices: " << std::endl; + 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]:" << std::endl; + 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:" << std::endl; + 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; +} |