diff options
-rw-r--r-- | src/Alpha_complex/include/gudhi/Alpha_complex_3d.h | 26 | ||||
-rw-r--r-- | src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp | 166 |
2 files changed, 28 insertions, 164 deletions
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h index ff6eb3e6..58364802 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex_3d.h @@ -225,16 +225,17 @@ public: (z_max - z_min == y_max - y_min), std::invalid_argument("The size of the cuboid in every directions is not the same.")); -#ifdef GUDHI_DEBUG - // Defined in GUDHI_DEBUG to avoid unused variable warning - double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); -#endif - using Weighted_point_3 = typename AlphaComplex3dOptions::Weighted_point_3; std::vector<Weighted_point_3> weighted_points_3; std::size_t index = 0; weighted_points_3.reserve(points.size()); + +#ifdef GUDHI_DEBUG + // Defined in GUDHI_DEBUG to avoid unused variable warning for GUDHI_CHECK + double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min); +#endif + while ((index < weights.size()) && (index < points.size())) { GUDHI_CHECK((weights[index] < maximal_possible_weight) || (weights[index] >= 0), std::invalid_argument("Invalid weight at line" + std::to_string(index + 1) + @@ -325,7 +326,9 @@ public: #endif // DEBUG_TRACES vertex_list.push_back((*cell)->vertex(i)); } +#ifdef DEBUG_TRACES count_cells++; +#endif // DEBUG_TRACES } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) { for (auto i = 0; i < 4; i++) { if ((*facet).second != i) { @@ -335,7 +338,9 @@ public: vertex_list.push_back((*facet).first->vertex(i)); } } +#ifdef DEBUG_TRACES count_facets++; +#endif // DEBUG_TRACES } else if (const Edge *edge = CGAL::object_cast<Edge>(&object_iterator)) { for (auto i : {(*edge).second, (*edge).third}) { #ifdef DEBUG_TRACES @@ -343,13 +348,15 @@ public: #endif // DEBUG_TRACES vertex_list.push_back((*edge).first->vertex(i)); } +#ifdef DEBUG_TRACES count_edges++; +#endif // DEBUG_TRACES } else if (const Alpha_vertex_handle *vertex = CGAL::object_cast<Alpha_vertex_handle>(&object_iterator)) { - count_vertices++; #ifdef DEBUG_TRACES - std::cout << "from vertex=" << (*vertex)->point() << std::endl; + count_vertices++; + std::cout << "from vertex=" << (*vertex)->point() << std::endl; #endif // DEBUG_TRACES - vertex_list.push_back((*vertex)); + vertex_list.push_back((*vertex)); } // Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex Simplex_tree_vector_vertex the_simplex; @@ -378,11 +385,10 @@ public: AlphaComplex3dOptions::template value_from_iterator<Filtration_value, typename std::vector<Alpha_value_type>::iterator> (the_alpha_value_iterator); - //Filtration_value filtr = CGAL::to_double(the_alpha_value_iterator->exact()); #ifdef DEBUG_TRACES std::cout << "filtration = " << filtr << std::endl; #endif // DEBUG_TRACES - //complex.insert_simplex(the_simplex, static_cast<Filtration_value>(filtr)); + complex.insert_simplex(the_simplex, static_cast<Filtration_value>(filtr)); GUDHI_CHECK(the_alpha_value_iterator != alpha_values_.end(), "CGAL provided more simplices than values"); ++the_alpha_value_iterator; } diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp index 42f3ddcb..6a3728fb 100644 --- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp +++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp @@ -24,18 +24,12 @@ #include <boost/program_options.hpp> #include <boost/variant.hpp> +#include <gudhi/Alpha_complex_3d.h> +#include <gudhi/Alpha_complex_3d_options.h> #include <gudhi/Simplex_tree.h> #include <gudhi/Persistent_cohomology.h> #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/Alpha_shape_3.h> -#include <CGAL/Alpha_shape_cell_base_3.h> -#include <CGAL/Alpha_shape_vertex_base_3.h> -#include <CGAL/iterator.h> - #include <fstream> #include <cmath> #include <string> @@ -45,45 +39,12 @@ #include <vector> #include <cstdlib> -#include "alpha_complex_3d_helper.h" - -// Traits -using K = CGAL::Exact_predicates_inexact_constructions_kernel; -using PK = CGAL::Periodic_3_Delaunay_triangulation_traits_3<K>; -// 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 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 = PK::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<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::vector<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 Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>; +using Alpha_complex_3d = Gudhi::alpha_complex::Alpha_complex_3d<Gudhi::alpha_complex::Periodic_alpha_shapes_3d>; +using Simplex_tree = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>; +using Filtration_value = Simplex_tree::Filtration_value; using Persistent_cohomology = - Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>; + Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp>; void program_options(int argc, char *argv[], std::string &off_file_points, std::string &cuboid_file, std::string &output_file_diag, int &coeff_field_characteristic, Filtration_value &min_persistence); @@ -99,10 +60,10 @@ int main(int argc, char **argv) { min_persistence); // Read the OFF file (input file name given as parameter) and triangulate points - Gudhi::Points_3D_off_reader<Point_3> off_reader(off_file_points); + Gudhi::Points_3D_off_reader<Alpha_complex_3d::Point_3> off_reader(off_file_points); // Check the read operation was correct - if (off_reader.is_valid()) { - std::cerr << "Unable to read OFF file " << off_file_points << std::endl; + if (!off_reader.is_valid()) { + std::cerr << "Unable to read file " << off_file_points << std::endl; exit(-1); } @@ -121,114 +82,11 @@ int main(int argc, char **argv) { exit(-1); } - // Retrieve the points - std::vector<Point_3> lp = off_reader.get_point_cloud(); - - // Define the periodic cube - P3DT3 pdt(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(lp.begin(), lp.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(); - } else { - std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl; - exit(-1); - } - 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); + Alpha_complex_3d alpha_complex(off_reader.get_point_cloud(), x_min, y_min, z_min, x_max, y_max, z_max); - // filtration with alpha values from alpha shape - std::vector<Object> the_objects; - std::vector<Alpha_value_type> the_alpha_values; + Simplex_tree simplex_tree; - 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(); - 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++; - } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) { - vertex_list = from_facet<Vertex_list, Facet>(*facet); - count_facets++; - } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) { - vertex_list = from_edge<Vertex_list, Edge_3>(*edge); - count_edges++; - } else if (const Vertex_handle *vertex = CGAL::object_cast<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; - 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); - 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; - 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 + alpha_complex.create_complex(simplex_tree); // Sort the simplices in the order of the filtration simplex_tree.initialize_filtration(); |