diff options
Diffstat (limited to 'src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp')
| -rw-r--r-- | src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp | 292 |
1 files changed, 45 insertions, 247 deletions
diff --git a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp index 70c0572d..14f12c0e 100644 --- a/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp +++ b/src/Persistent_cohomology/example/weighted_periodic_alpha_complex_3d_persistence.cpp @@ -27,13 +27,11 @@ #include <gudhi/Points_3D_off_io.h> #include <CGAL/Exact_predicates_inexact_constructions_kernel.h> -#include <CGAL/Periodic_3_Delaunay_triangulation_traits_3.h> -#include <CGAL/Periodic_3_Delaunay_triangulation_3.h> +#include <CGAL/Periodic_3_regular_triangulation_traits_3.h> +#include <CGAL/Periodic_3_regular_triangulation_3.h> #include <CGAL/Alpha_shape_3.h> #include <CGAL/iterator.h> -#include <CGAL/Exact_predicates_inexact_constructions_kernel.h> - #include <fstream> #include <cmath> #include <string> @@ -45,87 +43,33 @@ #include <cstdlib> #include "alpha_complex_3d_helper.h" -/* -// Traits -using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<Kernel>; - -using Vb = CGAL::Alpha_shape_vertex_base_3<PK>; -using Fb = CGAL::Alpha_shape_cell_base_3<PK>; -using Tds = CGAL::Triangulation_data_structure_3<Vb, Fb>; -//using Triangulation_3 = CGAL::Regular_triangulation_3<Gt, Tds>; -using Alpha_shape_3 = CGAL::Alpha_shape_3<Triangulation_3>; - -//vertex type -using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; -using Vb = CGAL::Triangulation_vertex_base_3<PK, DsVb>; -using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>; - -// Cell type -using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; -using Cb = CGAL::Triangulation_cell_base_3<PK, DsCb>; -using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK, Tds>; -using Point_3 = PK::Point_3; - -// From file type definition -using Point_3 = Gt::Bare_point; -using Weighted_point_3 = Gt::Weighted_point; -// 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<Object, Alpha_value_type>, - CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, - std::back_insert_iterator< std::vector<Alpha_value_type> > > >; -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; -using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>; - -// gudhi type definition -using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; -using Filtration_value = ST::Filtration_value; -using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >; -using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< - ST, Gudhi::persistent_cohomology::Field_Zp >; - */ - - - // Traits using Kernel = CGAL::Exact_predicates_inexact_constructions_kernel; -using K = CGAL::Exact_predicates_inexact_constructions_kernel; -using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>; -using Gt = CGAL::Regular_triangulation_euclidean_traits_3<Kernel>; +using PK = CGAL::Periodic_3_regular_triangulation_traits_3<Kernel>; + // Vertex type using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>; -using Vb = CGAL::Triangulation_vertex_base_3<PK, DsVb>; -using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>; +using Vb = CGAL::Regular_triangulation_vertex_base_3<PK,DsVb>; +using AsVb = CGAL::Alpha_shape_vertex_base_3<PK,Vb>; // Cell type using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>; -using Cb = CGAL::Triangulation_cell_base_3<PK, DsCb>; -using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>; -using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>; -using P3DT3 = CGAL::Periodic_3_Delaunay_triangulation_3<PK, Tds>; -using Alpha_shape_3 = CGAL::Alpha_shape_3<P3DT3>; -using Point_3 = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>::Point_3; +using Cb = CGAL::Regular_triangulation_cell_base_3<PK,DsCb>; +using AsCb = CGAL::Alpha_shape_cell_base_3<PK,Cb>; +using Tds = CGAL::Triangulation_data_structure_3<AsVb,AsCb>; +using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK,Tds>; +using Alpha_shape_3 = CGAL::Alpha_shape_3<P3RT3>; -// From file type definition -using Point_3 = Gt::Bare_point; -using Weighted_point_3 = Gt::Weighted_point; +using Point_3 = P3RT3::Bare_point; +using Weighted_point_3 = P3RT3::Weighted_point; // 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<Object, Alpha_value_type>, - CGAL::cpp11::tuple<std::back_insert_iterator< std::vector<Object> >, - std::back_insert_iterator< std::vector<Alpha_value_type> > > >; +using Dispatch = + 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> > > >; using Cell_handle = Alpha_shape_3::Cell_handle; using Facet = Alpha_shape_3::Facet; using Edge_3 = Alpha_shape_3::Edge; @@ -136,24 +80,23 @@ using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>; using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; using Filtration_value = ST::Filtration_value; using Simplex_tree_vertex = ST::Vertex_handle; -using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex >; +using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>; -using Simplex_tree_vector_vertex = std::vector< Simplex_tree_vertex >; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology< - ST, Gudhi::persistent_cohomology::Field_Zp >; - - -void usage(char * const progName) { - std::cerr << "Usage: " << progName << - " path_to_the_OFF_File path_to_weight_file path_to_the_cuboid_file coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; +using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; +using Persistent_cohomology = + Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; + +void usage(char* const progName) { + std::cerr << "Usage: " << progName << " path_to_the_OFF_File path_to_weight_file path_to_the_cuboid_file " + "coeff_field_characteristic[integer > 0] min_persistence[float >= -1.0]\n"; exit(-1); -} - -int main(int argc, char * const argv[]) { +} + +int main(int argc, char* const argv[]) { // program args management if (argc != 6) { std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - //file with points, file with weights, cuboid file, field characteristics, minimum persistence. + // file with points, file with weights, cuboid file, field characteristics, minimum persistence. usage(argv[0]); } @@ -169,10 +112,10 @@ int main(int argc, char * const argv[]) { std::cerr << "Unable to read file " << offInputFile << std::endl; usage(argv[0]); } - + // Retrieve the triangulation std::vector<Point_3> lp = off_reader.get_point_cloud(); - + // Read weights information from file std::ifstream weights_ifstr(argv[2]); std::vector<Weighted_point_3> wp; @@ -182,7 +125,7 @@ int main(int argc, char * const argv[]) { wp.reserve(lp.size()); // Attempt read the weight in a double format, return false if it fails while ((weights_ifstr >> weight) && (index < lp.size())) { - wp.push_back(Weighted_point_3(lp[index], weight)); + wp.push_back(Weighted_point_3(lp[index], weight)); index++; } if (index != lp.size()) { @@ -193,7 +136,7 @@ int main(int argc, char * const argv[]) { std::cerr << "Unable to read file " << argv[2] << std::endl; usage(argv[0]); } - + // Read iso_cuboid_3 information from file std::ifstream iso_cuboid_str(argv[3]); double x_min, y_min, z_min, x_max, y_max, z_max; @@ -203,164 +146,21 @@ int main(int argc, char * const argv[]) { std::cerr << "Unable to read file " << argv[3] << std::endl; usage(argv[0]); } - + std::cout << "wp.size() : " << wp.size() << std::endl; // Define the periodic cube - P3DT3 pdt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); + P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max)); // Heuristic for inserting large point sets (if pts is reasonably large) - pdt.insert(wp.begin(), wp.end(), true); - // As pdt won't be modified anymore switch to 1-sheeted cover if possible - if (pdt.is_triangulation_in_1_sheet()) pdt.convert_to_1_sheeted_covering(); + prt.insert(wp.begin(), wp.end(), true); + // As prt won't be modified anymore switch to 1-sheeted cover if possible + if (prt.is_triangulation_in_1_sheet()) prt.convert_to_1_sheeted_covering(); std::cout << "Periodic Delaunay computed." << std::endl; // alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode // Maybe need to set it to GENERAL mode - Alpha_shape_3 as(pdt, 0, Alpha_shape_3::GENERAL); - - - - - - - - - - - // 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; - ST 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) { - // Retrieve Alpha shape vertex list from object - if (const Cell_handle * cell = CGAL::object_cast<Cell_handle>(&object_iterator)) { - vertex_list = from_cell<Vertex_list, Cell_handle>(*cell); - count_cells++; - if (dim_max < 3) { - // Cell is of dim 3 - dim_max = 3; - } - } else if (const Facet * facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from_facet<Vertex_list, Facet>(*facet); - count_facets++; - if (dim_max < 2) { - // Facet is of dim 2 - dim_max = 2; - } - } else if (const Edge_3 * edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from_edge<Vertex_list, Edge_3>(*edge); - count_edges++; - if (dim_max < 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)) { - count_vertices++; - vertex_list = from_vertex<Vertex_list, Vertex_handle>(*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 - Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator); -#ifdef DEBUG_TRACES - std::cout << "filtration = " << filtr << std::endl; -#endif // DEBUG_TRACES - if (filtr > filtration_max) { - filtration_max = filtr; - } - simplex_tree.insert_simplex(the_simplex_tree, filtr); - if (the_alpha_value_iterator != the_alpha_values.end()) - ++the_alpha_value_iterator; - else - std::cout << "This shall not happen" << std::endl; - } - simplex_tree.set_filtration(filtration_max); - simplex_tree.set_dimension(dim_max); + Alpha_shape_3 as(prt, 0, Alpha_shape_3::GENERAL); -#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() << " "; - std::cout << " filtration = " << simplex_tree.filtration() << 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 - - // 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); - - pcoh.output_diagram(); - - - - - - - - - - -/* // filtration with alpha values from alpha shape std::vector<Object> the_objects; std::vector<Alpha_value_type> the_alpha_values; @@ -387,29 +187,29 @@ int main(int argc, char * const argv[]) { 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<Vertex_list, Cell_handle>(*cell); count_cells++; if (dim_max < 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<Vertex_list, Facet>(*facet); count_facets++; if (dim_max < 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<Vertex_list, Edge_3>(*edge); count_edges++; if (dim_max < 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<Vertex_list, Vertex_handle>(*vertex); } @@ -435,7 +235,7 @@ int main(int argc, char * const argv[]) { } } // Construction of the simplex_tree - Filtration_value filtr = (*the_alpha_value_iterator); + Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES @@ -457,7 +257,6 @@ int main(int argc, char * const argv[]) { 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; @@ -484,7 +283,6 @@ int main(int argc, char * const argv[]) { pcoh.compute_persistent_cohomology(min_persistence); pcoh.output_diagram(); - */ return 0; } |