diff options
Diffstat (limited to 'src/python/include')
| -rw-r--r-- | src/python/include/Alpha_complex_factory.h | 9 | ||||
| -rw-r--r-- | src/python/include/Simplex_tree_interface.h | 16 | ||||
| -rw-r--r-- | src/python/include/Subsampling_interface.h | 10 |
3 files changed, 27 insertions, 8 deletions
diff --git a/src/python/include/Alpha_complex_factory.h b/src/python/include/Alpha_complex_factory.h index d699ad9b..3405fdd6 100644 --- a/src/python/include/Alpha_complex_factory.h +++ b/src/python/include/Alpha_complex_factory.h @@ -48,11 +48,14 @@ static CgalPointType pt_cython_to_cgal(std::vector<double> const& vec) { class Abstract_alpha_complex { public: virtual std::vector<double> get_point(int vh) = 0; + virtual bool create_simplex_tree(Simplex_tree_interface<>* simplex_tree, double max_alpha_square, bool default_filtration_value) = 0; + + virtual ~Abstract_alpha_complex() = default; }; -class Exact_Alphacomplex_dD : public Abstract_alpha_complex { +class Exact_Alphacomplex_dD final : public Abstract_alpha_complex { private: using Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>; using Point = typename Kernel::Point_d; @@ -78,7 +81,7 @@ class Exact_Alphacomplex_dD : public Abstract_alpha_complex { Alpha_complex<Kernel> alpha_complex_; }; -class Inexact_Alphacomplex_dD : public Abstract_alpha_complex { +class Inexact_Alphacomplex_dD final : public Abstract_alpha_complex { private: using Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; using Point = typename Kernel::Point_d; @@ -104,7 +107,7 @@ class Inexact_Alphacomplex_dD : public Abstract_alpha_complex { }; template <complexity Complexity> -class Alphacomplex_3D : public Abstract_alpha_complex { +class Alphacomplex_3D final : public Abstract_alpha_complex { private: using Point = typename Alpha_complex_3d<Complexity, false, false>::Bare_point_3; diff --git a/src/python/include/Simplex_tree_interface.h b/src/python/include/Simplex_tree_interface.h index e288a8cf..629f6083 100644 --- a/src/python/include/Simplex_tree_interface.h +++ b/src/python/include/Simplex_tree_interface.h @@ -15,7 +15,9 @@ #include <gudhi/distance_functions.h> #include <gudhi/Simplex_tree.h> #include <gudhi/Points_off_io.h> +#ifdef GUDHI_USE_EIGEN3 #include <gudhi/Flag_complex_edge_collapser.h> +#endif #include <iostream> #include <vector> @@ -39,6 +41,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { using Skeleton_simplex_iterator = typename Base::Skeleton_simplex_iterator; using Complex_simplex_iterator = typename Base::Complex_simplex_iterator; using Extended_filtration_data = typename Base::Extended_filtration_data; + using Boundary_simplex_iterator = typename Base::Boundary_simplex_iterator; public: @@ -161,6 +164,7 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { } Simplex_tree_interface* collapse_edges(int nb_collapse_iteration) { +#ifdef GUDHI_USE_EIGEN3 using Filtered_edge = std::tuple<Vertex_handle, Vertex_handle, Filtration_value>; std::vector<Filtered_edge> edges; for (Simplex_handle sh : Base::skeleton_simplex_range(1)) { @@ -186,6 +190,9 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { collapsed_stree_ptr->insert({std::get<0>(remaining_edge), std::get<1>(remaining_edge)}, std::get<2>(remaining_edge)); } return collapsed_stree_ptr; +#else + throw std::runtime_error("Unable to collapse edges as it requires Eigen3 >= 3.1.0."); +#endif } // Iterator over the simplex tree @@ -219,6 +226,15 @@ class Simplex_tree_interface : public Simplex_tree<SimplexTreeOptions> { // this specific case works because the range is just a pair of iterators - won't work if range was a vector return Base::skeleton_simplex_range(dimension).end(); } + + std::pair<Boundary_simplex_iterator, Boundary_simplex_iterator> get_boundary_iterators(const Simplex& simplex) { + auto bd_sh = Base::find(simplex); + if (bd_sh == Base::null_simplex()) + throw std::runtime_error("simplex not found - cannot find boundaries"); + // this specific case works because the range is just a pair of iterators - won't work if range was a vector + auto boundary_srange = Base::boundary_simplex_range(bd_sh); + return std::make_pair(boundary_srange.begin(), boundary_srange.end()); + } }; } // namespace Gudhi diff --git a/src/python/include/Subsampling_interface.h b/src/python/include/Subsampling_interface.h index cdda851f..6aee7231 100644 --- a/src/python/include/Subsampling_interface.h +++ b/src/python/include/Subsampling_interface.h @@ -11,6 +11,7 @@ #ifndef INCLUDE_SUBSAMPLING_INTERFACE_H_ #define INCLUDE_SUBSAMPLING_INTERFACE_H_ +#include <gudhi/distance_functions.h> #include <gudhi/choose_n_farthest_points.h> #include <gudhi/pick_n_random_points.h> #include <gudhi/sparsify_point_set.h> @@ -27,14 +28,13 @@ namespace subsampling { using Subsampling_dynamic_kernel = CGAL::Epick_d< CGAL::Dynamic_dimension_tag >; using Subsampling_point_d = Subsampling_dynamic_kernel::Point_d; -using Subsampling_ft = Subsampling_dynamic_kernel::FT; // ------ choose_n_farthest_points ------ std::vector<std::vector<double>> subsampling_n_farthest_points(const std::vector<std::vector<double>>& points, unsigned nb_points) { std::vector<std::vector<double>> landmarks; - Subsampling_dynamic_kernel k; - choose_n_farthest_points(k, points, nb_points, random_starting_point, std::back_inserter(landmarks)); + choose_n_farthest_points(Euclidean_distance(), points, nb_points, + random_starting_point, std::back_inserter(landmarks)); return landmarks; } @@ -42,8 +42,8 @@ std::vector<std::vector<double>> subsampling_n_farthest_points(const std::vector std::vector<std::vector<double>> subsampling_n_farthest_points(const std::vector<std::vector<double>>& points, unsigned nb_points, unsigned starting_point) { std::vector<std::vector<double>> landmarks; - Subsampling_dynamic_kernel k; - choose_n_farthest_points(k, points, nb_points, starting_point, std::back_inserter(landmarks)); + choose_n_farthest_points(Euclidean_distance(), points, nb_points, + starting_point, std::back_inserter(landmarks)); return landmarks; } |