multipers 2.3.3b6__cp310-cp310-manylinux_2_39_x86_64.whl
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- multipers/__init__.py +33 -0
- multipers/_signed_measure_meta.py +453 -0
- multipers/_slicer_meta.py +211 -0
- multipers/array_api/__init__.py +45 -0
- multipers/array_api/numpy.py +41 -0
- multipers/array_api/torch.py +58 -0
- multipers/data/MOL2.py +458 -0
- multipers/data/UCR.py +18 -0
- multipers/data/__init__.py +1 -0
- multipers/data/graphs.py +466 -0
- multipers/data/immuno_regions.py +27 -0
- multipers/data/minimal_presentation_to_st_bf.py +0 -0
- multipers/data/pytorch2simplextree.py +91 -0
- multipers/data/shape3d.py +101 -0
- multipers/data/synthetic.py +113 -0
- multipers/distances.py +202 -0
- multipers/filtration_conversions.pxd +229 -0
- multipers/filtration_conversions.pxd.tp +84 -0
- multipers/filtrations/__init__.py +18 -0
- multipers/filtrations/density.py +574 -0
- multipers/filtrations/filtrations.py +361 -0
- multipers/filtrations.pxd +224 -0
- multipers/function_rips.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/function_rips.pyx +105 -0
- multipers/grids.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/grids.pyx +433 -0
- multipers/gudhi/Persistence_slices_interface.h +132 -0
- multipers/gudhi/Simplex_tree_interface.h +239 -0
- multipers/gudhi/Simplex_tree_multi_interface.h +551 -0
- multipers/gudhi/cubical_to_boundary.h +59 -0
- multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -0
- multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -0
- multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -0
- multipers/gudhi/gudhi/Debug_utils.h +45 -0
- multipers/gudhi/gudhi/Fields/Multi_field.h +484 -0
- multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -0
- multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -0
- multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -0
- multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -0
- multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -0
- multipers/gudhi/gudhi/Fields/Z2_field.h +355 -0
- multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -0
- multipers/gudhi/gudhi/Fields/Zp_field.h +420 -0
- multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -0
- multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -0
- multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -0
- multipers/gudhi/gudhi/Matrix.h +2107 -0
- multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -0
- multipers/gudhi/gudhi/Multi_persistence/Box.h +174 -0
- multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -0
- multipers/gudhi/gudhi/Off_reader.h +173 -0
- multipers/gudhi/gudhi/One_critical_filtration.h +1441 -0
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -0
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -0
- multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -0
- multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -0
- multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -0
- multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -0
- multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -0
- multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -0
- multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -0
- multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -0
- multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -0
- multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -0
- multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -0
- multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -0
- multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -0
- multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -0
- multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -0
- multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -0
- multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -0
- multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -0
- multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -0
- multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -0
- multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -0
- multipers/gudhi/gudhi/Persistent_cohomology.h +745 -0
- multipers/gudhi/gudhi/Points_off_io.h +171 -0
- multipers/gudhi/gudhi/Simple_object_pool.h +69 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -0
- multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -0
- multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -0
- multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -0
- multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -0
- multipers/gudhi/gudhi/Simplex_tree.h +2794 -0
- multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -0
- multipers/gudhi/gudhi/distance_functions.h +62 -0
- multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -0
- multipers/gudhi/gudhi/persistence_interval.h +253 -0
- multipers/gudhi/gudhi/persistence_matrix_options.h +170 -0
- multipers/gudhi/gudhi/reader_utils.h +367 -0
- multipers/gudhi/mma_interface_coh.h +256 -0
- multipers/gudhi/mma_interface_h0.h +223 -0
- multipers/gudhi/mma_interface_matrix.h +293 -0
- multipers/gudhi/naive_merge_tree.h +536 -0
- multipers/gudhi/scc_io.h +310 -0
- multipers/gudhi/truc.h +1403 -0
- multipers/io.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/io.pyx +644 -0
- multipers/ml/__init__.py +0 -0
- multipers/ml/accuracies.py +90 -0
- multipers/ml/invariants_with_persistable.py +79 -0
- multipers/ml/kernels.py +176 -0
- multipers/ml/mma.py +713 -0
- multipers/ml/one.py +472 -0
- multipers/ml/point_clouds.py +352 -0
- multipers/ml/signed_measures.py +1589 -0
- multipers/ml/sliced_wasserstein.py +461 -0
- multipers/ml/tools.py +113 -0
- multipers/mma_structures.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/mma_structures.pxd +128 -0
- multipers/mma_structures.pyx +2786 -0
- multipers/mma_structures.pyx.tp +1094 -0
- multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -0
- multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -0
- multipers/multi_parameter_rank_invariant/function_rips.h +322 -0
- multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -0
- multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -0
- multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -0
- multipers/multiparameter_edge_collapse.py +41 -0
- multipers/multiparameter_module_approximation/approximation.h +2330 -0
- multipers/multiparameter_module_approximation/combinatory.h +129 -0
- multipers/multiparameter_module_approximation/debug.h +107 -0
- multipers/multiparameter_module_approximation/euler_curves.h +0 -0
- multipers/multiparameter_module_approximation/format_python-cpp.h +286 -0
- multipers/multiparameter_module_approximation/heap_column.h +238 -0
- multipers/multiparameter_module_approximation/images.h +79 -0
- multipers/multiparameter_module_approximation/list_column.h +174 -0
- multipers/multiparameter_module_approximation/list_column_2.h +232 -0
- multipers/multiparameter_module_approximation/ru_matrix.h +347 -0
- multipers/multiparameter_module_approximation/set_column.h +135 -0
- multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -0
- multipers/multiparameter_module_approximation/unordered_set_column.h +166 -0
- multipers/multiparameter_module_approximation/utilities.h +403 -0
- multipers/multiparameter_module_approximation/vector_column.h +223 -0
- multipers/multiparameter_module_approximation/vector_matrix.h +331 -0
- multipers/multiparameter_module_approximation/vineyards.h +464 -0
- multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -0
- multipers/multiparameter_module_approximation.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/multiparameter_module_approximation.pyx +235 -0
- multipers/pickle.py +90 -0
- multipers/plots.py +456 -0
- multipers/point_measure.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/point_measure.pyx +395 -0
- multipers/simplex_tree_multi.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/simplex_tree_multi.pxd +134 -0
- multipers/simplex_tree_multi.pyx +10840 -0
- multipers/simplex_tree_multi.pyx.tp +2009 -0
- multipers/slicer.cpython-310-x86_64-linux-gnu.so +0 -0
- multipers/slicer.pxd +3034 -0
- multipers/slicer.pxd.tp +234 -0
- multipers/slicer.pyx +20481 -0
- multipers/slicer.pyx.tp +1088 -0
- multipers/tensor/tensor.h +672 -0
- multipers/tensor.pxd +13 -0
- multipers/test.pyx +44 -0
- multipers/tests/__init__.py +62 -0
- multipers/torch/__init__.py +1 -0
- multipers/torch/diff_grids.py +240 -0
- multipers/torch/rips_density.py +310 -0
- multipers-2.3.3b6.dist-info/METADATA +128 -0
- multipers-2.3.3b6.dist-info/RECORD +182 -0
- multipers-2.3.3b6.dist-info/WHEEL +5 -0
- multipers-2.3.3b6.dist-info/licenses/LICENSE +21 -0
- multipers-2.3.3b6.dist-info/top_level.txt +1 -0
- multipers.libs/libtbb-ca48af5c.so.12.16 +0 -0
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/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
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* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
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* Author(s): Vincent Rouvreau
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*
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* Copyright (C) 2015 Inria
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*
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* Modification(s):
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* - YYYY/MM Author: Description of the modification
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*/
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#ifndef POINTS_OFF_IO_H_
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#define POINTS_OFF_IO_H_
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#include <gudhi/Off_reader.h>
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#include <string>
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#include <vector>
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#include <fstream>
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#include <map>
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namespace Gudhi {
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/**
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* \brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
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*/
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template<typename Point_d>
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class Points_off_visitor_reader {
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private:
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std::vector<Point_d> point_cloud;
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public:
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/** \brief Off_reader visitor init implementation.
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*
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* The init parameters are set from OFF file header.
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* Dimension value is required in order to construct a vector of points.
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*
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* @param[in] dim space dimension of vertices.
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* @param[in] num_vertices number of vertices in the OFF file (not used).
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* @param[in] num_faces number of faces in the OFF file (not used).
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* @param[in] num_edges number of edges in the OFF file (not used).
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*/
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void init(int dim, int num_vertices, int num_faces, int num_edges) {
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#ifdef DEBUG_TRACES
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std::clog << "Points_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
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num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
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#endif // DEBUG_TRACES
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if (num_faces > 0) {
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std::cerr << "Points_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
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}
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if (num_edges > 0) {
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std::cerr << "Points_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
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}
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}
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/** @brief Off_reader visitor point implementation.
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*
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* The point function is called on each vertex line from OFF file.
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* This function inserts the vertex in the vector of points.
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*
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* @param[in] point vector of vertex coordinates.
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*
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* @details
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* Point_d must have a constructor with the following form:
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*
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* @code template<class InputIterator > Point_d::Point_d(InputIterator first, InputIterator last) @endcode
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*
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*/
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void point(const std::vector<double>& point) {
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#ifdef DEBUG_TRACES
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std::clog << "Points_off_visitor_reader::point ";
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for (auto coordinate : point) {
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std::clog << coordinate << " | ";
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}
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std::clog << std::endl;
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#endif // DEBUG_TRACES
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// Fill the point cloud
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point_cloud.push_back(Point_d(point.begin(), point.end()));
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}
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// Off_reader visitor maximal_face implementation - Only points are read
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void maximal_face(const std::vector<int>& face) { }
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// Off_reader visitor done implementation - Only points are read
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void done() { }
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/** \brief Point cloud getter.
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*
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* @return point_cloud.
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*/
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const std::vector<Point_d>& get_point_cloud() const {
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return point_cloud;
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}
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};
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/**
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* \brief OFF file reader implementation in order to read points from an OFF file.
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*
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* This class is using the Points_off_visitor_reader to visit the OFF file according to Off_reader.
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*
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* Point_d must have a constructor with the following form:
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*
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* \code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) \endcode
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*
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* where d is the point dimension.
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*
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* \section pointoffioexample Example
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*
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* This example loads points from an OFF file and builds a vector of points (vector of double).
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* Then, it is asked to display the points.
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*
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* \include example_vector_double_points_off_reader.cpp
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*
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* When launching:
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*
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* \code $> ./vector_double_off_reader ../../data/points/alphacomplexdoc.off
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* \endcode
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*
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* the program outputs a file ../../data/points/alphacomplexdoc.off.txt:
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*
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* \include vectordoubleoffreader_result.txt
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*/
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template<typename Point_d>
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class Points_off_reader {
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public:
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/** \brief Reads the OFF file and constructs a vector of points from the points
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* that are in the OFF file.
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*
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* @param[in] name_file OFF file to read.
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*
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* \post Check with is_valid() function to see if read operation was successful.
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*/
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Points_off_reader(const std::string& name_file)
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: valid_(false) {
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std::ifstream stream(name_file);
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if (stream.is_open()) {
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Off_reader off_reader(stream);
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Points_off_visitor_reader<Point_d> off_visitor;
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valid_ = off_reader.read(off_visitor);
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if (valid_) {
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point_cloud = off_visitor.get_point_cloud();
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}
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} else {
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std::cerr << "Points_off_reader::Points_off_reader could not open file " << name_file << "\n";
|
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|
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}
|
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}
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+
|
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/** \brief Returns if the OFF file read operation was successful or not.
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*
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* @return OFF file read status.
|
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*/
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bool is_valid() const {
|
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return valid_;
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}
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+
|
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/** \brief Point cloud getter.
|
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*
|
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* @return point_cloud.
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*/
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const std::vector<Point_d>& get_point_cloud() const {
|
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return point_cloud;
|
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+
}
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|
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|
+
|
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|
+
private:
|
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/** \brief point_cloud.*/
|
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std::vector<Point_d> point_cloud;
|
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/** \brief OFF file read status.*/
|
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+
bool valid_;
|
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+
};
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+
|
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} // namespace Gudhi
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+
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#endif // POINTS_OFF_IO_H_
|
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@@ -0,0 +1,69 @@
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1
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/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
|
|
2
|
+
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
|
|
3
|
+
* Author(s): Marc Glisse
|
|
4
|
+
*
|
|
5
|
+
* Copyright (C) 2015 Inria
|
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+
*
|
|
7
|
+
* Modification(s):
|
|
8
|
+
* - YYYY/MM Author: Description of the modification
|
|
9
|
+
*/
|
|
10
|
+
|
|
11
|
+
#ifndef SIMPLE_OBJECT_POOL_H_
|
|
12
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+
#define SIMPLE_OBJECT_POOL_H_
|
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+
|
|
14
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+
#include <boost/pool/pool.hpp>
|
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+
#include <utility>
|
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+
|
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+
namespace Gudhi {
|
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+
|
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+
/** \private
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+
* This is a simpler version of boost::object_pool, that requires
|
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+
* that users explicitly destroy all objects. This lets the
|
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+
* performance scale much better, see
|
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+
* https://svn.boost.org/trac/boost/ticket/3789 .
|
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|
+
*/
|
|
25
|
+
template <class T>
|
|
26
|
+
class Simple_object_pool : protected boost::pool<boost::default_user_allocator_malloc_free> {
|
|
27
|
+
protected:
|
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typedef boost::pool<boost::default_user_allocator_malloc_free> Base;
|
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+
typedef T* pointer;
|
|
30
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+
|
|
31
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Base& base() {
|
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+
return *this;
|
|
33
|
+
}
|
|
34
|
+
|
|
35
|
+
Base const& base()const {
|
|
36
|
+
return *this;
|
|
37
|
+
}
|
|
38
|
+
|
|
39
|
+
public:
|
|
40
|
+
typedef T element_type;
|
|
41
|
+
typedef boost::default_user_allocator_malloc_free user_allocator;
|
|
42
|
+
typedef typename Base::size_type size_type;
|
|
43
|
+
typedef typename Base::difference_type difference_type;
|
|
44
|
+
|
|
45
|
+
template<class...U>
|
|
46
|
+
Simple_object_pool(U&&...u) : Base(sizeof (T), std::forward<U>(u)...) { }
|
|
47
|
+
|
|
48
|
+
template<class...U>
|
|
49
|
+
pointer construct(U&&...u) {
|
|
50
|
+
void* p = base().malloc BOOST_PREVENT_MACRO_SUBSTITUTION();
|
|
51
|
+
assert(p);
|
|
52
|
+
try {
|
|
53
|
+
new(p) T(std::forward<U>(u)...);
|
|
54
|
+
} catch (...) {
|
|
55
|
+
base().free BOOST_PREVENT_MACRO_SUBSTITUTION(p);
|
|
56
|
+
throw;
|
|
57
|
+
}
|
|
58
|
+
return static_cast<pointer> (p);
|
|
59
|
+
}
|
|
60
|
+
|
|
61
|
+
void destroy(pointer p) {
|
|
62
|
+
p->~T();
|
|
63
|
+
base().free BOOST_PREVENT_MACRO_SUBSTITUTION(p);
|
|
64
|
+
}
|
|
65
|
+
};
|
|
66
|
+
|
|
67
|
+
} // namespace Gudhi
|
|
68
|
+
|
|
69
|
+
#endif // SIMPLE_OBJECT_POOL_H_
|
|
@@ -0,0 +1,463 @@
|
|
|
1
|
+
/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
|
|
2
|
+
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
|
|
3
|
+
* Author(s): Clément Maria
|
|
4
|
+
*
|
|
5
|
+
* Copyright (C) 2014 Inria
|
|
6
|
+
*
|
|
7
|
+
* Modification(s):
|
|
8
|
+
* - 2022/04 Vincent Rouvreau: Add Simplex_tree_boundary_opposite_vertex_simplex_iterator for alpha and cech purpose
|
|
9
|
+
* - YYYY/MM Author: Description of the modification
|
|
10
|
+
*/
|
|
11
|
+
|
|
12
|
+
#ifndef SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
|
|
13
|
+
#define SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
|
|
14
|
+
|
|
15
|
+
#include <gudhi/Debug_utils.h>
|
|
16
|
+
|
|
17
|
+
#include <boost/iterator/iterator_facade.hpp>
|
|
18
|
+
|
|
19
|
+
#include <vector>
|
|
20
|
+
#include <utility> // for std::pair
|
|
21
|
+
|
|
22
|
+
namespace Gudhi {
|
|
23
|
+
|
|
24
|
+
/** \addtogroup simplex_tree
|
|
25
|
+
* Iterators and range types for the Simplex_tree.
|
|
26
|
+
* @{
|
|
27
|
+
*/
|
|
28
|
+
|
|
29
|
+
/** \brief Iterator over the vertices of a simplex
|
|
30
|
+
* in a SimplexTree.
|
|
31
|
+
*
|
|
32
|
+
* Forward iterator, 'value_type' is SimplexTree::Vertex_handle.*/
|
|
33
|
+
template<class SimplexTree>
|
|
34
|
+
class Simplex_tree_simplex_vertex_iterator : public boost::iterator_facade<
|
|
35
|
+
Simplex_tree_simplex_vertex_iterator<SimplexTree>,
|
|
36
|
+
typename SimplexTree::Vertex_handle const, boost::forward_traversal_tag,
|
|
37
|
+
typename SimplexTree::Vertex_handle const> {
|
|
38
|
+
public:
|
|
39
|
+
typedef typename SimplexTree::Simplex_handle Simplex_handle;
|
|
40
|
+
typedef typename SimplexTree::Siblings Siblings;
|
|
41
|
+
typedef typename SimplexTree::Vertex_handle Vertex_handle;
|
|
42
|
+
|
|
43
|
+
explicit Simplex_tree_simplex_vertex_iterator(SimplexTree const* st)
|
|
44
|
+
: // any end() iterator
|
|
45
|
+
sib_(nullptr),
|
|
46
|
+
v_(st->null_vertex()) {
|
|
47
|
+
}
|
|
48
|
+
|
|
49
|
+
Simplex_tree_simplex_vertex_iterator(SimplexTree const* st, Simplex_handle sh)
|
|
50
|
+
: sib_(st->self_siblings(sh)),
|
|
51
|
+
v_(sh->first) {
|
|
52
|
+
}
|
|
53
|
+
|
|
54
|
+
private:
|
|
55
|
+
friend class boost::iterator_core_access;
|
|
56
|
+
|
|
57
|
+
bool equal(Simplex_tree_simplex_vertex_iterator const &other) const {
|
|
58
|
+
return sib_ == other.sib_ && v_ == other.v_;
|
|
59
|
+
}
|
|
60
|
+
|
|
61
|
+
Vertex_handle const& dereference() const {
|
|
62
|
+
return v_;
|
|
63
|
+
}
|
|
64
|
+
|
|
65
|
+
void increment() {
|
|
66
|
+
v_ = sib_->parent();
|
|
67
|
+
sib_ = sib_->oncles();
|
|
68
|
+
}
|
|
69
|
+
|
|
70
|
+
Siblings * sib_;
|
|
71
|
+
Vertex_handle v_;
|
|
72
|
+
};
|
|
73
|
+
|
|
74
|
+
/*---------------------------------------------------------------------------*/
|
|
75
|
+
/** \brief Iterator over the simplices of the boundary of a
|
|
76
|
+
* simplex.
|
|
77
|
+
*
|
|
78
|
+
* Forward iterator, value_type is SimplexTree::Simplex_handle.*/
|
|
79
|
+
template<class SimplexTree>
|
|
80
|
+
class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
|
|
81
|
+
Simplex_tree_boundary_simplex_iterator<SimplexTree>,
|
|
82
|
+
typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
|
|
83
|
+
public:
|
|
84
|
+
using Simplex_handle = typename SimplexTree::Simplex_handle;
|
|
85
|
+
using Vertex_handle = typename SimplexTree::Vertex_handle;
|
|
86
|
+
using Siblings = typename SimplexTree::Siblings;
|
|
87
|
+
using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
|
|
88
|
+
|
|
89
|
+
// For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is overwritten.
|
|
90
|
+
Simplex_tree_boundary_simplex_iterator()
|
|
91
|
+
: sib_(nullptr),
|
|
92
|
+
st_(nullptr) {
|
|
93
|
+
}
|
|
94
|
+
|
|
95
|
+
// any end() iterator
|
|
96
|
+
explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st)
|
|
97
|
+
: last_(st->null_vertex()),
|
|
98
|
+
next_(st->null_vertex()),
|
|
99
|
+
sib_(nullptr),
|
|
100
|
+
sh_(st->null_simplex()),
|
|
101
|
+
st_(st) {
|
|
102
|
+
}
|
|
103
|
+
|
|
104
|
+
template<class SimplexHandle>
|
|
105
|
+
Simplex_tree_boundary_simplex_iterator(SimplexTree * st, SimplexHandle sh)
|
|
106
|
+
: last_(sh->first),
|
|
107
|
+
next_(st->null_vertex()),
|
|
108
|
+
sib_(nullptr),
|
|
109
|
+
sh_(st->null_simplex()),
|
|
110
|
+
st_(st) {
|
|
111
|
+
// Only check once at the beginning instead of for every increment, as this is expensive.
|
|
112
|
+
if constexpr (SimplexTree::Options::contiguous_vertices)
|
|
113
|
+
GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes");
|
|
114
|
+
Siblings * sib = st->self_siblings(sh);
|
|
115
|
+
next_ = sib->parent();
|
|
116
|
+
sib_ = sib->oncles();
|
|
117
|
+
if (sib_ != nullptr) {
|
|
118
|
+
if constexpr (SimplexTree::Options::contiguous_vertices &&
|
|
119
|
+
!SimplexTree::Options::stable_simplex_handles)
|
|
120
|
+
{
|
|
121
|
+
if (sib_->oncles() == nullptr) // Only relevant for edges
|
|
122
|
+
sh_ = sib_->members_.begin() + next_;
|
|
123
|
+
else
|
|
124
|
+
sh_ = sib_->find(next_);
|
|
125
|
+
} else {
|
|
126
|
+
sh_ = sib_->find(next_);
|
|
127
|
+
}
|
|
128
|
+
}
|
|
129
|
+
}
|
|
130
|
+
|
|
131
|
+
private:
|
|
132
|
+
friend class boost::iterator_core_access;
|
|
133
|
+
// valid when iterating along the SAME boundary.
|
|
134
|
+
bool equal(Simplex_tree_boundary_simplex_iterator const& other) const {
|
|
135
|
+
return sh_ == other.sh_;
|
|
136
|
+
}
|
|
137
|
+
|
|
138
|
+
Simplex_handle const& dereference() const {
|
|
139
|
+
assert(sh_ != st_->null_simplex());
|
|
140
|
+
return sh_;
|
|
141
|
+
}
|
|
142
|
+
|
|
143
|
+
void increment() {
|
|
144
|
+
if (sib_ == nullptr) {
|
|
145
|
+
sh_ = st_->null_simplex();
|
|
146
|
+
return;
|
|
147
|
+
}
|
|
148
|
+
|
|
149
|
+
Siblings * for_sib = sib_;
|
|
150
|
+
Siblings * new_sib = sib_->oncles();
|
|
151
|
+
auto rit = suffix_.rbegin();
|
|
152
|
+
if constexpr (SimplexTree::Options::contiguous_vertices && !SimplexTree::Options::stable_simplex_handles) {
|
|
153
|
+
if (new_sib == nullptr) {
|
|
154
|
+
// We reached the root, use a short-cut to find a vertex.
|
|
155
|
+
if (rit == suffix_.rend()) {
|
|
156
|
+
// Segment, this vertex is the last boundary simplex
|
|
157
|
+
sh_ = for_sib->members_.begin() + last_;
|
|
158
|
+
sib_ = nullptr;
|
|
159
|
+
return;
|
|
160
|
+
} else {
|
|
161
|
+
// Dim >= 2, initial step of the descent
|
|
162
|
+
sh_ = for_sib->members_.begin() + *rit;
|
|
163
|
+
for_sib = sh_->second.children();
|
|
164
|
+
++rit;
|
|
165
|
+
}
|
|
166
|
+
}
|
|
167
|
+
}
|
|
168
|
+
|
|
169
|
+
for (; rit != suffix_.rend(); ++rit) {
|
|
170
|
+
sh_ = for_sib->find(*rit);
|
|
171
|
+
for_sib = sh_->second.children();
|
|
172
|
+
}
|
|
173
|
+
sh_ = for_sib->find(last_); // sh_ points to the right simplex now
|
|
174
|
+
suffix_.push_back(next_);
|
|
175
|
+
next_ = sib_->parent();
|
|
176
|
+
sib_ = new_sib;
|
|
177
|
+
}
|
|
178
|
+
|
|
179
|
+
// Most of the storage should be moved to the range, iterators should be light.
|
|
180
|
+
Vertex_handle last_; // last vertex of the simplex
|
|
181
|
+
Vertex_handle next_; // next vertex to push in suffix_
|
|
182
|
+
Static_vertex_vector suffix_;
|
|
183
|
+
Siblings * sib_; // where the next search will start from
|
|
184
|
+
Simplex_handle sh_; // current Simplex_handle in the boundary
|
|
185
|
+
SimplexTree * st_; // simplex containing the simplicial complex
|
|
186
|
+
};
|
|
187
|
+
|
|
188
|
+
/** \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices.
|
|
189
|
+
*
|
|
190
|
+
* Forward iterator, value_type is std::pair<SimplexTree::Simplex_handle, SimplexTree::Vertex_handle>.*/
|
|
191
|
+
template<class SimplexTree>
|
|
192
|
+
class Simplex_tree_boundary_opposite_vertex_simplex_iterator : public boost::iterator_facade<
|
|
193
|
+
Simplex_tree_boundary_opposite_vertex_simplex_iterator<SimplexTree>,
|
|
194
|
+
std::pair<typename SimplexTree::Simplex_handle, typename SimplexTree::Vertex_handle> const, boost::forward_traversal_tag> {
|
|
195
|
+
public:
|
|
196
|
+
using Simplex_handle = typename SimplexTree::Simplex_handle;
|
|
197
|
+
using Vertex_handle = typename SimplexTree::Vertex_handle;
|
|
198
|
+
using Siblings = typename SimplexTree::Siblings;
|
|
199
|
+
using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
|
|
200
|
+
|
|
201
|
+
// For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is
|
|
202
|
+
// overwritten.
|
|
203
|
+
Simplex_tree_boundary_opposite_vertex_simplex_iterator()
|
|
204
|
+
: sib_(nullptr),
|
|
205
|
+
st_(nullptr) {
|
|
206
|
+
}
|
|
207
|
+
|
|
208
|
+
// any end() iterator
|
|
209
|
+
explicit Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st)
|
|
210
|
+
: last_(st->null_vertex()),
|
|
211
|
+
next_(st->null_vertex()),
|
|
212
|
+
sib_(nullptr),
|
|
213
|
+
baov_(st->null_simplex(), st->null_vertex()),
|
|
214
|
+
st_(st) {
|
|
215
|
+
}
|
|
216
|
+
|
|
217
|
+
template<class SimplexHandle>
|
|
218
|
+
Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st, SimplexHandle sh)
|
|
219
|
+
: last_(sh->first),
|
|
220
|
+
next_(st->null_vertex()),
|
|
221
|
+
sib_(nullptr),
|
|
222
|
+
baov_(st->null_simplex(), sh->first),
|
|
223
|
+
st_(st) {
|
|
224
|
+
// Only check once at the beginning instead of for every increment, as this is expensive.
|
|
225
|
+
if constexpr (SimplexTree::Options::contiguous_vertices)
|
|
226
|
+
GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes");
|
|
227
|
+
Siblings * sib = st->self_siblings(sh);
|
|
228
|
+
next_ = sib->parent();
|
|
229
|
+
sib_ = sib->oncles();
|
|
230
|
+
if (sib_ != nullptr) {
|
|
231
|
+
if constexpr (SimplexTree::Options::contiguous_vertices &&
|
|
232
|
+
!SimplexTree::Options::stable_simplex_handles) {
|
|
233
|
+
if (sib_->oncles() == nullptr)
|
|
234
|
+
// Only relevant for edges
|
|
235
|
+
baov_.first = sib_->members_.begin() + next_;
|
|
236
|
+
else
|
|
237
|
+
baov_.first = sib_->find(next_);
|
|
238
|
+
} else {
|
|
239
|
+
baov_.first = sib_->find(next_);
|
|
240
|
+
}
|
|
241
|
+
}
|
|
242
|
+
}
|
|
243
|
+
|
|
244
|
+
private:
|
|
245
|
+
friend class boost::iterator_core_access;
|
|
246
|
+
|
|
247
|
+
// valid when iterating along the SAME boundary.
|
|
248
|
+
bool equal(Simplex_tree_boundary_opposite_vertex_simplex_iterator const& other) const {
|
|
249
|
+
return (baov_.first == other.baov_.first);
|
|
250
|
+
}
|
|
251
|
+
|
|
252
|
+
std::pair<Simplex_handle, Vertex_handle> const& dereference() const {
|
|
253
|
+
return baov_;
|
|
254
|
+
}
|
|
255
|
+
|
|
256
|
+
void increment() {
|
|
257
|
+
if (sib_ == nullptr) {
|
|
258
|
+
baov_.first = st_->null_simplex();
|
|
259
|
+
return; // ------>>
|
|
260
|
+
}
|
|
261
|
+
Siblings * for_sib = sib_;
|
|
262
|
+
Siblings * new_sib = sib_->oncles();
|
|
263
|
+
auto rit = suffix_.rbegin();
|
|
264
|
+
if constexpr (SimplexTree::Options::contiguous_vertices && !SimplexTree::Options::stable_simplex_handles) {
|
|
265
|
+
if (new_sib == nullptr) {
|
|
266
|
+
// We reached the root, use a short-cut to find a vertex.
|
|
267
|
+
if (rit == suffix_.rend()) {
|
|
268
|
+
baov_.second = baov_.first->first;
|
|
269
|
+
// Segment, this vertex is the last boundary simplex
|
|
270
|
+
baov_.first = for_sib->members_.begin() + last_;
|
|
271
|
+
sib_ = nullptr;
|
|
272
|
+
return;
|
|
273
|
+
} else {
|
|
274
|
+
// Dim >= 2, initial step of the descent
|
|
275
|
+
baov_.first = for_sib->members_.begin() + *rit;
|
|
276
|
+
for_sib = baov_.first->second.children();
|
|
277
|
+
++rit;
|
|
278
|
+
}
|
|
279
|
+
}
|
|
280
|
+
}
|
|
281
|
+
|
|
282
|
+
for (; rit != suffix_.rend(); ++rit) {
|
|
283
|
+
baov_.first = for_sib->find(*rit);
|
|
284
|
+
for_sib = baov_.first->second.children();
|
|
285
|
+
}
|
|
286
|
+
baov_.first = for_sib->find(last_); // baov_.first points to the right simplex now
|
|
287
|
+
suffix_.push_back(next_);
|
|
288
|
+
next_ = sib_->parent();
|
|
289
|
+
sib_ = new_sib;
|
|
290
|
+
baov_.second = suffix_.back();
|
|
291
|
+
}
|
|
292
|
+
|
|
293
|
+
// Most of the storage should be moved to the range, iterators should be light.
|
|
294
|
+
Vertex_handle last_; // last vertex of the simplex
|
|
295
|
+
Vertex_handle next_; // next vertex to push in suffix_
|
|
296
|
+
Static_vertex_vector suffix_;
|
|
297
|
+
Siblings * sib_; // where the next search will start from
|
|
298
|
+
std::pair<Simplex_handle, Vertex_handle> baov_; // a pair containing the current Simplex_handle in the boundary and its opposite vertex
|
|
299
|
+
SimplexTree * st_; // simplex containing the simplicial complex
|
|
300
|
+
};
|
|
301
|
+
|
|
302
|
+
/*---------------------------------------------------------------------------*/
|
|
303
|
+
/** \brief Iterator over the simplices of a simplicial complex.
|
|
304
|
+
*
|
|
305
|
+
* Forward iterator, value_type is SimplexTree::Simplex_handle.*/
|
|
306
|
+
template<class SimplexTree>
|
|
307
|
+
class Simplex_tree_complex_simplex_iterator : public boost::iterator_facade<
|
|
308
|
+
Simplex_tree_complex_simplex_iterator<SimplexTree>,
|
|
309
|
+
typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
|
|
310
|
+
public:
|
|
311
|
+
typedef typename SimplexTree::Simplex_handle Simplex_handle;
|
|
312
|
+
typedef typename SimplexTree::Siblings Siblings;
|
|
313
|
+
typedef typename SimplexTree::Vertex_handle Vertex_handle;
|
|
314
|
+
|
|
315
|
+
// any end() iterator
|
|
316
|
+
Simplex_tree_complex_simplex_iterator()
|
|
317
|
+
: sib_(nullptr),
|
|
318
|
+
st_(nullptr) {
|
|
319
|
+
}
|
|
320
|
+
|
|
321
|
+
explicit Simplex_tree_complex_simplex_iterator(SimplexTree * st)
|
|
322
|
+
: sib_(nullptr),
|
|
323
|
+
st_(st) {
|
|
324
|
+
if (st == nullptr || st->root() == nullptr || st->root()->members().empty()) {
|
|
325
|
+
st_ = nullptr;
|
|
326
|
+
} else {
|
|
327
|
+
sh_ = st->root()->members().begin();
|
|
328
|
+
sib_ = st->root();
|
|
329
|
+
while (st->has_children(sh_)) {
|
|
330
|
+
sib_ = sh_->second.children();
|
|
331
|
+
sh_ = sib_->members().begin();
|
|
332
|
+
}
|
|
333
|
+
}
|
|
334
|
+
}
|
|
335
|
+
private:
|
|
336
|
+
friend class boost::iterator_core_access;
|
|
337
|
+
|
|
338
|
+
// valid when iterating along the SAME boundary.
|
|
339
|
+
bool equal(Simplex_tree_complex_simplex_iterator const& other) const {
|
|
340
|
+
if (other.st_ == nullptr) {
|
|
341
|
+
return (st_ == nullptr);
|
|
342
|
+
}
|
|
343
|
+
if (st_ == nullptr) {
|
|
344
|
+
return false;
|
|
345
|
+
}
|
|
346
|
+
return (&(sh_->second) == &(other.sh_->second));
|
|
347
|
+
}
|
|
348
|
+
|
|
349
|
+
Simplex_handle const& dereference() const {
|
|
350
|
+
return sh_;
|
|
351
|
+
}
|
|
352
|
+
|
|
353
|
+
// Depth first traversal.
|
|
354
|
+
void increment() {
|
|
355
|
+
++sh_;
|
|
356
|
+
if (sh_ == sib_->members().end()) {
|
|
357
|
+
if (sib_->oncles() == nullptr) {
|
|
358
|
+
st_ = nullptr;
|
|
359
|
+
return;
|
|
360
|
+
} // reach the end
|
|
361
|
+
sh_ = sib_->oncles()->members().find(sib_->parent());
|
|
362
|
+
sib_ = sib_->oncles();
|
|
363
|
+
return;
|
|
364
|
+
}
|
|
365
|
+
while (st_->has_children(sh_)) {
|
|
366
|
+
sib_ = sh_->second.children();
|
|
367
|
+
sh_ = sib_->members().begin();
|
|
368
|
+
}
|
|
369
|
+
}
|
|
370
|
+
|
|
371
|
+
Simplex_handle sh_;
|
|
372
|
+
Siblings * sib_;
|
|
373
|
+
SimplexTree * st_;
|
|
374
|
+
};
|
|
375
|
+
|
|
376
|
+
/** \brief Iterator over the simplices of the skeleton of a given
|
|
377
|
+
* dimension of the simplicial complex.
|
|
378
|
+
*
|
|
379
|
+
* Forward iterator, value_type is SimplexTree::Simplex_handle.*/
|
|
380
|
+
template<class SimplexTree>
|
|
381
|
+
class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade<
|
|
382
|
+
Simplex_tree_skeleton_simplex_iterator<SimplexTree>,
|
|
383
|
+
typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
|
|
384
|
+
public:
|
|
385
|
+
typedef typename SimplexTree::Simplex_handle Simplex_handle;
|
|
386
|
+
typedef typename SimplexTree::Siblings Siblings;
|
|
387
|
+
typedef typename SimplexTree::Vertex_handle Vertex_handle;
|
|
388
|
+
|
|
389
|
+
// any end() iterator
|
|
390
|
+
Simplex_tree_skeleton_simplex_iterator()
|
|
391
|
+
: sib_(nullptr),
|
|
392
|
+
st_(nullptr),
|
|
393
|
+
dim_skel_(0),
|
|
394
|
+
curr_dim_(0) {
|
|
395
|
+
}
|
|
396
|
+
|
|
397
|
+
Simplex_tree_skeleton_simplex_iterator(SimplexTree * st, int dim_skel)
|
|
398
|
+
: sib_(nullptr),
|
|
399
|
+
st_(st),
|
|
400
|
+
dim_skel_(dim_skel),
|
|
401
|
+
curr_dim_(0) {
|
|
402
|
+
if (st == nullptr || st->root() == nullptr || st->root()->members().empty()) {
|
|
403
|
+
st_ = nullptr;
|
|
404
|
+
} else {
|
|
405
|
+
sh_ = st->root()->members().begin();
|
|
406
|
+
sib_ = st->root();
|
|
407
|
+
while (st->has_children(sh_) && curr_dim_ < dim_skel_) {
|
|
408
|
+
sib_ = sh_->second.children();
|
|
409
|
+
sh_ = sib_->members().begin();
|
|
410
|
+
++curr_dim_;
|
|
411
|
+
}
|
|
412
|
+
}
|
|
413
|
+
}
|
|
414
|
+
private:
|
|
415
|
+
friend class boost::iterator_core_access;
|
|
416
|
+
|
|
417
|
+
// valid when iterating along the SAME boundary.
|
|
418
|
+
bool equal(Simplex_tree_skeleton_simplex_iterator const& other) const {
|
|
419
|
+
if (other.st_ == nullptr) {
|
|
420
|
+
return (st_ == nullptr);
|
|
421
|
+
}
|
|
422
|
+
if (st_ == nullptr) {
|
|
423
|
+
return false;
|
|
424
|
+
}
|
|
425
|
+
return (&(sh_->second) == &(other.sh_->second));
|
|
426
|
+
}
|
|
427
|
+
|
|
428
|
+
Simplex_handle const& dereference() const {
|
|
429
|
+
return sh_;
|
|
430
|
+
}
|
|
431
|
+
|
|
432
|
+
// Depth first traversal of the skeleton.
|
|
433
|
+
void increment() {
|
|
434
|
+
++sh_;
|
|
435
|
+
if (sh_ == sib_->members().end()) {
|
|
436
|
+
if (sib_->oncles() == nullptr) {
|
|
437
|
+
st_ = nullptr;
|
|
438
|
+
return;
|
|
439
|
+
} // reach the end
|
|
440
|
+
sh_ = sib_->oncles()->members().find(sib_->parent());
|
|
441
|
+
sib_ = sib_->oncles();
|
|
442
|
+
--curr_dim_;
|
|
443
|
+
return;
|
|
444
|
+
}
|
|
445
|
+
while (st_->has_children(sh_) && curr_dim_ < dim_skel_) {
|
|
446
|
+
sib_ = sh_->second.children();
|
|
447
|
+
sh_ = sib_->members().begin();
|
|
448
|
+
++curr_dim_;
|
|
449
|
+
}
|
|
450
|
+
}
|
|
451
|
+
|
|
452
|
+
Simplex_handle sh_;
|
|
453
|
+
Siblings * sib_;
|
|
454
|
+
SimplexTree * st_;
|
|
455
|
+
int dim_skel_;
|
|
456
|
+
int curr_dim_;
|
|
457
|
+
};
|
|
458
|
+
|
|
459
|
+
/** @}*/ // end addtogroup simplex_tree
|
|
460
|
+
|
|
461
|
+
} // namespace Gudhi
|
|
462
|
+
|
|
463
|
+
#endif // SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
|