diff options
Diffstat (limited to 'src/Persistent_cohomology/example/alpha_shapes_persistence.cpp')
| -rw-r--r-- | src/Persistent_cohomology/example/alpha_shapes_persistence.cpp | 230 |
1 files changed, 111 insertions, 119 deletions
diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp index 1e907040..6d5eebcf 100644 --- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp +++ b/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp @@ -1,24 +1,29 @@ - /* 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/>. - */ +/* 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 <gudhi/graph_simplicial_complex.h> +#include <gudhi/Simplex_tree.h> +#include <gudhi/Persistent_cohomology.h> +#include <boost/variant.hpp> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> #include <CGAL/Delaunay_triangulation_3.h> @@ -27,36 +32,37 @@ #include <fstream> #include <cmath> - -#include "gudhi/graph_simplicial_complex.h" -#include "gudhi/Simplex_tree.h" -#include "gudhi/Persistent_cohomology.h" -#include <boost/variant.hpp> +#include <string> +#include <tuple> +#include <map> +#include <utility> +#include <list> +#include <vector> using namespace Gudhi; using namespace Gudhi::persistent_cohomology; // 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; +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_3; +typedef Kernel::Point_3 Point_3; // filtration with alpha values needed type definition typedef Alpha_shape_3::FT Alpha_value_type; -typedef CGAL::Object Object; +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_3; +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_3; typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list; // gudhi type definition @@ -65,70 +71,60 @@ typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape 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 from(const Cell_handle& ch) { Vertex_list the_list; - for (auto i = 0; i < 4; i++) - { + for (auto i = 0; i < 4; i++) { #ifdef DEBUG_TRACES std::cout << "from cell[" << i << "]=" << ch->vertex(i)->point() << std::endl; -#endif // DEBUG_TRACES +#endif // DEBUG_TRACES the_list.push_back(ch->vertex(i)); } return the_list; } -Vertex_list from (const Facet& fct) -{ + +Vertex_list from(const Facet& fct) { Vertex_list the_list; - for (auto i = 0; i < 4; i++) - { - if (fct.second != i) - { + 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 +#endif // DEBUG_TRACES the_list.push_back(fct.first->vertex(i)); } } return the_list; } -Vertex_list from (const Edge_3& edg) -{ + +Vertex_list from(const Edge_3& edg) { Vertex_list the_list; - for (auto i = 0; i < 4; i++) - { - if ((edg.second == i) ||(edg.third == i)) - { + 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 +#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 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 +#endif // DEBUG_TRACES the_list.push_back(vh); return the_list; } -void usage(char * const progName) -{ - std::cerr << "Usage: " << progName << " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; - exit(-1); // ----- >> +void usage(char * const progName) { + std::cerr << "Usage: " << progName << + " path_to_file_graph coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; + exit(-1); } -int main (int argc, char * const argv[]) -{ - - int coeff_field_characteristic=0; +int main(int argc, char * const argv[]) { + int coeff_field_characteristic = 0; int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic); if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) { std::cerr << "Error: " << argv[2] << " is not correct\n"; @@ -149,102 +145,96 @@ int main (int argc, char * const argv[]) } // Read points from file - std::string filegraph = argv[1]; + std::string filegraph = argv[1]; std::list<Point_3> lp; std::ifstream is(filegraph.c_str()); int n; is >> n; #ifdef DEBUG_TRACES std::cout << "Reading " << n << " points " << std::endl; -#endif // DEBUG_TRACES +#endif // DEBUG_TRACES Point_3 p; - for( ; n>0 ; n--) { + for (; n > 0; n--) { is >> p; lp.push_back(p); } // 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); + 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 +#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)); + 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 +#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; + 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<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin(); - int dim_max=0; - Filtration_value filtration_max=0.0; - for(auto object_iterator: the_objects) - { + int dim_max = 0; + Filtration_value filtration_max = 0.0; + 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)) - { + if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { vertex_list = from(*cell); count_cells++; if (dim_max < 3) { - dim_max=3; // Cell is of dim 3 + // Cell is of dim 3 + dim_max = 3; } - } - else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) - { + } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { vertex_list = from(*facet); count_facets++; if (dim_max < 2) { - dim_max=2; // Facet is of dim 2 + // Facet is of dim 2 + dim_max = 2; } - } - else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) - { + } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { vertex_list = from(*edge); count_edges++; if (dim_max < 1) { - dim_max=1; // Edge_3 is of dim 1 + // Edge_3 is of dim 1 + dim_max = 1; } - } - else if (const Alpha_shape_3::Vertex_handle* vertex = CGAL::object_cast<Alpha_shape_3::Vertex_handle>(&object_iterator)) - { + } 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) - { + 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()) - { + 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 +#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 - { + 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 +#endif // DEBUG_TRACES the_simplex_tree.push_back(vertex); } } @@ -252,7 +242,7 @@ int main (int argc, char * const argv[]) Filtration_value filtr = std::sqrt(*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES +#endif // DEBUG_TRACES if (filtr > filtration_max) { filtration_max = filtr; } @@ -267,9 +257,9 @@ int main (int argc, char * const argv[]) #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 << "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; @@ -277,23 +267,25 @@ int main (int argc, char * const argv[]) std::cout << " Number of simplices = " << simplex_tree.num_simplices() << std::endl << std::endl; std::cout << " Dimension = " << simplex_tree.dimension() << " "; std::cout << " filtration = " << simplex_tree.filtration() << std::endl << std::endl; -#endif // DEBUG_TRACES +#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 + 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< Simplex_tree<>, Field_Zp > pcoh( simplex_tree ); - pcoh.init_coefficients( coeff_field_characteristic ); //initializes the coefficient field for homology + Persistent_cohomology< Simplex_tree<>, Field_Zp > pcoh(simplex_tree); + // initializes the coefficient field for homology + pcoh.init_coefficients(coeff_field_characteristic); - pcoh.compute_persistent_cohomology( min_persistence ); + pcoh.compute_persistent_cohomology(min_persistence); pcoh.output_diagram(); |