multipers 2.3.3b6__cp311-cp311-macosx_11_0_arm64.whl
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- multipers/.dylibs/libc++.1.0.dylib +0 -0
- multipers/.dylibs/libtbb.12.16.dylib +0 -0
- 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-311-darwin.so +0 -0
- multipers/function_rips.pyx +105 -0
- multipers/grids.cpython-311-darwin.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-311-darwin.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-311-darwin.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-311-darwin.so +0 -0
- multipers/multiparameter_module_approximation.pyx +235 -0
- multipers/pickle.py +90 -0
- multipers/plots.py +456 -0
- multipers/point_measure.cpython-311-darwin.so +0 -0
- multipers/point_measure.pyx +395 -0
- multipers/simplex_tree_multi.cpython-311-darwin.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-311-darwin.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 +183 -0
- multipers-2.3.3b6.dist-info/WHEEL +6 -0
- multipers-2.3.3b6.dist-info/licenses/LICENSE +21 -0
- multipers-2.3.3b6.dist-info/top_level.txt +1 -0
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/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which
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* is released under MIT. See file LICENSE or go to
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* https://gudhi.inria.fr/licensing/ for full license details. Author(s): David
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* Loiseaux, Hannah Schreiber
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*
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* Copyright (C) 2023 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 SIMPLEX_TREE_MULTI_H_
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#define SIMPLEX_TREE_MULTI_H_
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#include <algorithm>
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#include <cstdint>
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#include <vector>
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#include <gudhi/Simplex_tree.h>
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namespace Gudhi {
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namespace multi_persistence {
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/** Model of SimplexTreeOptions, with a multiparameter filtration.
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* \ingroup multi_persistence
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* */
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template <typename Filtration>
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struct Simplex_tree_options_multidimensional_filtration {
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public:
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typedef linear_indexing_tag Indexing_tag;
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typedef int Vertex_handle;
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using Filtration_value = Filtration;
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typedef typename Filtration::value_type value_type;
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typedef std::uint32_t Simplex_key;
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static const bool store_key = true;
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static const bool store_filtration = true;
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static const bool contiguous_vertices = false;
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static const bool link_nodes_by_label = false;
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static const bool stable_simplex_handles = false;
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static const bool is_multi_parameter = true;
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};
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/**
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* \brief Turns a 1-parameter simplextree into a multiparameter simplextree,
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* and keeps the 1-filtration in the 1st axis.
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* Default values can be specified.
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* \ingroup multi_persistence
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* \tparam simplextree_std A non-multi simplextree
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* \tparam simplextree_multi A multi simplextree
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* \param st Simplextree to copy
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* \param st_multi Multiparameter simplextree container to fill.
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* \param default_values If given, this vector is assume to be of size `num_parameters-1` and contains the default
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* values of axes `1` to `num_parameters`.
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* */
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template <class simplextree_std, class simplextree_multi>
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void multify(simplextree_std &st,
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simplextree_multi &st_multi,
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const int num_parameters,
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const typename simplextree_multi::Options::Filtration_value &default_values = {}) {
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typename simplextree_multi::Options::Filtration_value f(num_parameters);
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static_assert(!simplextree_std::Options::is_multi_parameter && simplextree_multi::Options::is_multi_parameter,
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"Can only convert non-multiparameter to multiparameter simplextree.");
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unsigned int num_default_values = 0;
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if constexpr (simplextree_multi::Options::Filtration_value::is_multi_critical) {
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num_default_values = default_values[0].size();
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} else {
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num_default_values = default_values.size();
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}
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for (auto i = 0u;
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i < std::min(num_default_values, num_parameters < 1 ? 0u : static_cast<unsigned int>(num_parameters - 1));
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i++) {
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if constexpr (simplextree_multi::Options::Filtration_value::is_multi_critical) {
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f[0][i + 1] = default_values[0][i];
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} else {
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f[i + 1] = default_values[i];
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}
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}
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std::vector<int> simplex;
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simplex.reserve(st.dimension() + 1);
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for (auto &simplex_handle : st.complex_simplex_range()) {
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simplex.clear();
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for (auto vertex : st.simplex_vertex_range(simplex_handle)) simplex.push_back(vertex);
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if (num_parameters > 0) {
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if constexpr (simplextree_multi::Options::Filtration_value::is_multi_critical) {
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f[0][0] = st.filtration(simplex_handle);
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} else {
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f[0] = st.filtration(simplex_handle);
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}
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}
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st_multi.insert_simplex(simplex, f);
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}
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st_multi.set_number_of_parameters(num_parameters);
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}
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/**
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* \brief Turns a multiparameter-parameter simplextree into a 1-parameter
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* simplextree.
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* \ingroup multi_persistence
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* \tparam simplextree_std A non-multi simplextree
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* \tparam simplextree_multi A multi simplextree
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* \param st Simplextree to fill.
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* \param st_multi Multiparameter simplextree to convert into a 1 parameter simplex tree.
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* \param dimension The filtration parameter to put into the 1 parameter simplextree.
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* */
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template <class simplextree_std, class simplextree_multi>
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void flatten(simplextree_std &st, simplextree_multi &st_multi, const int dimension = 0) {
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static_assert(!simplextree_std::Options::is_multi_parameter && simplextree_multi::Options::is_multi_parameter,
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"Can only convert multiparameter to non-multiparameter simplextree.");
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for (const auto &simplex_handle : st_multi.complex_simplex_range()) {
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std::vector<int> simplex;
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typename simplextree_multi::Options::value_type f;
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for (auto vertex : st_multi.simplex_vertex_range(simplex_handle)) simplex.push_back(vertex);
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if constexpr (simplextree_multi::Filtration_value::is_multi_critical) {
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f = dimension >= 0 ? st_multi.filtration(simplex_handle)[0][dimension] : 0;
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} else {
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f = dimension >= 0 ? st_multi.filtration(simplex_handle)[dimension] : 0;
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}
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st.insert_simplex(simplex, f);
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}
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}
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// TODO: following not in the planned version in Gudhi. So either remove from here, or add there.
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/**
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* \brief Applies a linear form (given by a scalar product, via Riesz
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* representation) to the filtration values of the multiparameter simplextree to
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* get a 1 parameter simplextree. \ingroup multiparameter \tparam
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* simplextree_std A non-multi simplextree \tparam simplextree_multi A multi
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* simplextree \param st Simplextree, with the same simplicial complex as
|
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* st_multi, whose filtration has to be filled. \param st_multi Multiparameter
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+
* simplextree to convert into a 1 parameter simplex tree. \param linear_form
|
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+
* the linear form to apply.
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* */
|
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+
template <class simplextree_std, class simplextree_multi>
|
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+
void linear_projection(simplextree_std &st, simplextree_multi &st_multi, const std::vector<double> &linear_form) {
|
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|
+
static_assert(!simplextree_std::Options::is_multi_parameter && simplextree_multi::Options::is_multi_parameter,
|
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|
+
"Can only convert multiparameter to non-multiparameter simplextree.");
|
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|
+
auto sh = st.complex_simplex_range().begin();
|
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+
auto sh_multi = st_multi.complex_simplex_range().begin();
|
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+
auto end = st.complex_simplex_range().end();
|
|
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|
+
typename simplextree_multi::Options::Filtration_value multi_filtration;
|
|
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|
+
for (; sh != end; ++sh, ++sh_multi) {
|
|
143
|
+
multi_filtration = st_multi.filtration(*sh_multi);
|
|
144
|
+
auto projected_filtration = compute_linear_projection(multi_filtration, linear_form);
|
|
145
|
+
st.assign_filtration(*sh, projected_filtration);
|
|
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|
+
}
|
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|
+
}
|
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|
+
|
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+
} // namespace multi_persistence
|
|
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|
+
} // namespace Gudhi
|
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|
+
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+
#endif // SIMPLEX_TREE_MULTI_H_
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@@ -0,0 +1,62 @@
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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): Clément Maria
|
|
4
|
+
*
|
|
5
|
+
* Copyright (C) 2014 Inria
|
|
6
|
+
*
|
|
7
|
+
* Modification(s):
|
|
8
|
+
* - YYYY/MM Author: Description of the modification
|
|
9
|
+
*/
|
|
10
|
+
|
|
11
|
+
#ifndef DISTANCE_FUNCTIONS_H_
|
|
12
|
+
#define DISTANCE_FUNCTIONS_H_
|
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13
|
+
|
|
14
|
+
#include <gudhi/Debug_utils.h>
|
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15
|
+
|
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16
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+
#include <boost/range/metafunctions.hpp>
|
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|
+
#include <boost/range/size.hpp>
|
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18
|
+
|
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19
|
+
#include <cmath> // for std::sqrt
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+
#include <type_traits> // for std::decay
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+
#include <iterator> // for std::begin, std::end
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+
#include <utility>
|
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+
|
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|
+
namespace Gudhi {
|
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+
|
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+
/** @file
|
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|
+
* @brief Global distance functions
|
|
28
|
+
*/
|
|
29
|
+
|
|
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+
/** @brief Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to
|
|
31
|
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* have the same dimension. */
|
|
32
|
+
class Euclidean_distance {
|
|
33
|
+
public:
|
|
34
|
+
// boost::range_value is not SFINAE-friendly so we cannot use it in the return type
|
|
35
|
+
template< typename Point >
|
|
36
|
+
typename std::iterator_traits<typename boost::range_iterator<Point>::type>::value_type
|
|
37
|
+
operator()(const Point& p1, const Point& p2) const {
|
|
38
|
+
auto it1 = std::begin(p1);
|
|
39
|
+
auto it2 = std::begin(p2);
|
|
40
|
+
typedef typename boost::range_value<Point>::type NT;
|
|
41
|
+
NT dist = 0;
|
|
42
|
+
for (; it1 != std::end(p1); ++it1, ++it2) {
|
|
43
|
+
GUDHI_CHECK(it2 != std::end(p2), "inconsistent point dimensions");
|
|
44
|
+
NT tmp = *it1 - *it2;
|
|
45
|
+
dist += tmp*tmp;
|
|
46
|
+
}
|
|
47
|
+
GUDHI_CHECK(it2 == std::end(p2), "inconsistent point dimensions");
|
|
48
|
+
using std::sqrt;
|
|
49
|
+
return sqrt(dist);
|
|
50
|
+
}
|
|
51
|
+
template< typename T >
|
|
52
|
+
T operator() (const std::pair< T, T >& f, const std::pair< T, T >& s) const {
|
|
53
|
+
T dx = f.first - s.first;
|
|
54
|
+
T dy = f.second - s.second;
|
|
55
|
+
using std::sqrt;
|
|
56
|
+
return sqrt(dx*dx + dy*dy);
|
|
57
|
+
}
|
|
58
|
+
};
|
|
59
|
+
|
|
60
|
+
} // namespace Gudhi
|
|
61
|
+
|
|
62
|
+
#endif // DISTANCE_FUNCTIONS_H_
|
|
@@ -0,0 +1,104 @@
|
|
|
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
|
+
* - YYYY/MM Author: Description of the modification
|
|
9
|
+
*/
|
|
10
|
+
|
|
11
|
+
#ifndef GRAPH_SIMPLICIAL_COMPLEX_H_
|
|
12
|
+
#define GRAPH_SIMPLICIAL_COMPLEX_H_
|
|
13
|
+
|
|
14
|
+
#include <boost/graph/adjacency_list.hpp>
|
|
15
|
+
|
|
16
|
+
#include <utility> // for pair<>
|
|
17
|
+
#include <vector>
|
|
18
|
+
#include <map>
|
|
19
|
+
#include <tuple> // for std::tie
|
|
20
|
+
|
|
21
|
+
namespace Gudhi {
|
|
22
|
+
/** @file
|
|
23
|
+
* @brief Graph simplicial complex methods
|
|
24
|
+
*/
|
|
25
|
+
|
|
26
|
+
/* Edge tag for Boost PropertyGraph. */
|
|
27
|
+
struct edge_filtration_t {
|
|
28
|
+
typedef boost::edge_property_tag kind;
|
|
29
|
+
};
|
|
30
|
+
|
|
31
|
+
/* Vertex tag for Boost PropertyGraph. */
|
|
32
|
+
struct vertex_filtration_t {
|
|
33
|
+
typedef boost::vertex_property_tag kind;
|
|
34
|
+
};
|
|
35
|
+
|
|
36
|
+
/** \brief Proximity_graph contains the vertices and edges with their filtration values in order to store the result
|
|
37
|
+
* of `Gudhi::compute_proximity_graph` function.
|
|
38
|
+
*
|
|
39
|
+
* \tparam SimplicialComplexForProximityGraph furnishes `Filtration_value` type definition.
|
|
40
|
+
*
|
|
41
|
+
*/
|
|
42
|
+
template <typename SimplicialComplexForProximityGraph>
|
|
43
|
+
using Proximity_graph = typename boost::adjacency_list < boost::vecS, boost::vecS, boost::directedS
|
|
44
|
+
, boost::property < vertex_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >
|
|
45
|
+
, boost::property < edge_filtration_t, typename SimplicialComplexForProximityGraph::Filtration_value >>;
|
|
46
|
+
|
|
47
|
+
/** \brief Computes the proximity graph of the points.
|
|
48
|
+
*
|
|
49
|
+
* If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the
|
|
50
|
+
* distance function between points u and v is smaller than threshold.
|
|
51
|
+
*
|
|
52
|
+
* \tparam SimplicialComplexForProximityGraph furnishes `Filtration_value` and `Vertex_handle` type definitions.
|
|
53
|
+
*
|
|
54
|
+
* \tparam ForwardPointRange furnishes `.begin()` and `.end()` methods.
|
|
55
|
+
*
|
|
56
|
+
* \tparam Distance furnishes `operator()(const Point& p1, const Point& p2)`, where
|
|
57
|
+
* `Point` is a point from the `ForwardPointRange`, and that returns a `Filtration_value`.
|
|
58
|
+
*/
|
|
59
|
+
template< typename SimplicialComplexForProximityGraph
|
|
60
|
+
, typename ForwardPointRange
|
|
61
|
+
, typename Distance >
|
|
62
|
+
Proximity_graph<SimplicialComplexForProximityGraph> compute_proximity_graph(
|
|
63
|
+
const ForwardPointRange& points,
|
|
64
|
+
typename SimplicialComplexForProximityGraph::Filtration_value threshold,
|
|
65
|
+
Distance distance) {
|
|
66
|
+
using Vertex_handle = typename SimplicialComplexForProximityGraph::Vertex_handle;
|
|
67
|
+
using Filtration_value = typename SimplicialComplexForProximityGraph::Filtration_value;
|
|
68
|
+
|
|
69
|
+
std::vector<std::pair< Vertex_handle, Vertex_handle >> edges;
|
|
70
|
+
std::vector< Filtration_value > edges_fil;
|
|
71
|
+
std::map< Vertex_handle, Filtration_value > vertices;
|
|
72
|
+
|
|
73
|
+
Vertex_handle idx_u, idx_v;
|
|
74
|
+
Filtration_value fil;
|
|
75
|
+
idx_u = 0;
|
|
76
|
+
for (auto it_u = points.begin(); it_u != points.end(); ++it_u) {
|
|
77
|
+
idx_v = idx_u + 1;
|
|
78
|
+
for (auto it_v = it_u + 1; it_v != points.end(); ++it_v, ++idx_v) {
|
|
79
|
+
fil = distance(*it_u, *it_v);
|
|
80
|
+
if (fil <= threshold) {
|
|
81
|
+
edges.emplace_back(idx_u, idx_v);
|
|
82
|
+
edges_fil.push_back(fil);
|
|
83
|
+
}
|
|
84
|
+
}
|
|
85
|
+
++idx_u;
|
|
86
|
+
}
|
|
87
|
+
|
|
88
|
+
// Points are labeled from 0 to idx_u-1
|
|
89
|
+
Proximity_graph<SimplicialComplexForProximityGraph> skel_graph(edges.begin(), edges.end(), edges_fil.begin(), idx_u);
|
|
90
|
+
|
|
91
|
+
auto vertex_prop = boost::get(vertex_filtration_t(), skel_graph);
|
|
92
|
+
|
|
93
|
+
typename boost::graph_traits<Proximity_graph<SimplicialComplexForProximityGraph>>::vertex_iterator vi, vi_end;
|
|
94
|
+
for (std::tie(vi, vi_end) = boost::vertices(skel_graph);
|
|
95
|
+
vi != vi_end; ++vi) {
|
|
96
|
+
boost::put(vertex_prop, *vi, 0.);
|
|
97
|
+
}
|
|
98
|
+
|
|
99
|
+
return skel_graph;
|
|
100
|
+
}
|
|
101
|
+
|
|
102
|
+
} // namespace Gudhi
|
|
103
|
+
|
|
104
|
+
#endif // GRAPH_SIMPLICIAL_COMPLEX_H_
|
|
@@ -0,0 +1,253 @@
|
|
|
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): Hannah Schreiber
|
|
4
|
+
*
|
|
5
|
+
* Copyright (C) 2024 Inria
|
|
6
|
+
*
|
|
7
|
+
* Modification(s):
|
|
8
|
+
* - YYYY/MM Author: Description of the modification
|
|
9
|
+
*/
|
|
10
|
+
|
|
11
|
+
/**
|
|
12
|
+
* @file persistence_interval.h
|
|
13
|
+
* @author Hannah Schreiber
|
|
14
|
+
* @brief Contains @ref Gudhi::persistence_matrix::Persistence_interval class.
|
|
15
|
+
*/
|
|
16
|
+
|
|
17
|
+
#ifndef PM_INTERVAL_INCLUDED
|
|
18
|
+
#define PM_INTERVAL_INCLUDED
|
|
19
|
+
|
|
20
|
+
#include <ostream> //std::ostream
|
|
21
|
+
#include <limits> //std::numeric_limits
|
|
22
|
+
#include <tuple>
|
|
23
|
+
#include <utility> //std::move
|
|
24
|
+
|
|
25
|
+
namespace Gudhi {
|
|
26
|
+
namespace persistence_matrix {
|
|
27
|
+
|
|
28
|
+
/**
|
|
29
|
+
* @class Persistence_interval persistence_interval.h gudhi/persistence_interval.h
|
|
30
|
+
* @ingroup persistence_matrix
|
|
31
|
+
*
|
|
32
|
+
* @brief Type for an interval in a persistent diagram or barcode. Stores the birth, death and dimension of the
|
|
33
|
+
* interval. It can be used as a tuple with `get`/`std::get` (birth, death and dimension in this order),
|
|
34
|
+
* `std::tuple_element` and `std::tuple_size`, as well as structured binding.
|
|
35
|
+
*
|
|
36
|
+
* @tparam Dimension Type of the dimension value.
|
|
37
|
+
* @tparam Event_value Type of the birth and death value.
|
|
38
|
+
*/
|
|
39
|
+
template <typename Dimension, typename Event_value>
|
|
40
|
+
struct Persistence_interval {
|
|
41
|
+
/**
|
|
42
|
+
* @brief Stores the infinity value for birth and death events. Its value depends on the template parameter
|
|
43
|
+
* `Event_value`:
|
|
44
|
+
* - if `Event_value` has a native infinity value, it takes this value,
|
|
45
|
+
* - otherwise, if `Event_value` is a signed type, it takes value -1,
|
|
46
|
+
* - otherwise, if `Event_value` is a unsigned type, it takes the maximal possible value.
|
|
47
|
+
*
|
|
48
|
+
* Is also used as default value for birth and death attributes when not initialized.
|
|
49
|
+
*/
|
|
50
|
+
static constexpr Event_value inf = std::numeric_limits<Event_value>::has_infinity
|
|
51
|
+
? std::numeric_limits<Event_value>::infinity()
|
|
52
|
+
: static_cast<Event_value>(-1);
|
|
53
|
+
|
|
54
|
+
/**
|
|
55
|
+
* @brief Constructor.
|
|
56
|
+
*
|
|
57
|
+
* @param birth Birth value of the cycle. Default value: @ref inf.
|
|
58
|
+
* @param death Death value of the cycle. Default value: @ref inf.
|
|
59
|
+
* @param dim Dimension of the cycle. Default value: -1.
|
|
60
|
+
*/
|
|
61
|
+
Persistence_interval(Event_value birth = inf, Event_value death = inf, Dimension dim = -1)
|
|
62
|
+
: dim(dim), birth(birth), death(death) {}
|
|
63
|
+
|
|
64
|
+
Dimension dim; /**< Dimension of the cycle.*/
|
|
65
|
+
Event_value birth; /**< Birth value of the cycle. */
|
|
66
|
+
Event_value death; /**< Death value of the cycle. */
|
|
67
|
+
|
|
68
|
+
/**
|
|
69
|
+
* @brief operator<<
|
|
70
|
+
*
|
|
71
|
+
* @param stream outstream
|
|
72
|
+
* @param interval interval to stream
|
|
73
|
+
*/
|
|
74
|
+
inline friend std::ostream& operator<<(std::ostream& stream, const Persistence_interval& interval) {
|
|
75
|
+
stream << "[" << interval.dim << "] ";
|
|
76
|
+
if constexpr (std::numeric_limits<Event_value>::has_infinity) {
|
|
77
|
+
stream << interval.birth << " - " << interval.death;
|
|
78
|
+
} else {
|
|
79
|
+
if (interval.birth == inf)
|
|
80
|
+
stream << "inf";
|
|
81
|
+
else
|
|
82
|
+
stream << interval.birth;
|
|
83
|
+
stream << " - ";
|
|
84
|
+
if (interval.death == inf)
|
|
85
|
+
stream << "inf";
|
|
86
|
+
else
|
|
87
|
+
stream << interval.death;
|
|
88
|
+
}
|
|
89
|
+
return stream;
|
|
90
|
+
}
|
|
91
|
+
|
|
92
|
+
/**
|
|
93
|
+
* @brief Specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
94
|
+
*
|
|
95
|
+
* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
|
|
96
|
+
* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
|
|
97
|
+
*/
|
|
98
|
+
template <std::size_t I>
|
|
99
|
+
constexpr auto& get() & noexcept {
|
|
100
|
+
static_assert(I < 3, "Value mismatch at argument 1 in template parameter list. Maximal possible value is 2.");
|
|
101
|
+
|
|
102
|
+
if constexpr (I == 0) return birth;
|
|
103
|
+
if constexpr (I == 1) return death;
|
|
104
|
+
if constexpr (I == 2) return dim;
|
|
105
|
+
}
|
|
106
|
+
|
|
107
|
+
/**
|
|
108
|
+
* @brief Specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
109
|
+
*
|
|
110
|
+
* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
|
|
111
|
+
* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
|
|
112
|
+
*/
|
|
113
|
+
template <std::size_t I>
|
|
114
|
+
constexpr const auto& get() const& noexcept {
|
|
115
|
+
static_assert(I < 3, "Value mismatch at argument 1 in template parameter list. Maximal possible value is 2.");
|
|
116
|
+
|
|
117
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if constexpr (I == 0) return birth;
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118
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if constexpr (I == 1) return death;
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119
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if constexpr (I == 2) return dim;
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}
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121
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+
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122
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+
/**
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123
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* @brief Specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
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*
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* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
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* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
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*/
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template <std::size_t I>
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constexpr auto&& get() && noexcept {
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static_assert(I < 3, "Value mismatch at argument 1 in template parameter list. Maximal possible value is 2.");
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131
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+
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132
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if constexpr (I == 0) return std::move(birth);
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if constexpr (I == 1) return std::move(death);
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if constexpr (I == 2) return std::move(dim);
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+
}
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136
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+
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137
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+
/**
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138
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+
* @brief Specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
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139
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+
*
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140
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+
* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
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* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
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142
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+
*/
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143
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+
template <std::size_t I>
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144
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+
constexpr const auto&& get() const&& noexcept {
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145
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+
static_assert(I < 3, "Value mismatch at argument 1 in template parameter list. Maximal possible value is 2.");
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146
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+
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147
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+
if constexpr (I == 0) return std::move(birth);
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148
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+
if constexpr (I == 1) return std::move(death);
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149
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+
if constexpr (I == 2) return std::move(dim);
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150
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+
}
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151
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+
};
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152
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+
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153
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+
} // namespace persistence_matrix
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154
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+
} // namespace Gudhi
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155
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+
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156
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+
namespace std {
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157
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+
|
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158
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+
/**
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159
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+
* @ingroup persistence_matrix
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160
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+
*
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161
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+
* @brief Partial specialization of `std::tuple_size` for @ref Gudhi::persistence_matrix::Persistence_interval.
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162
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+
*
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163
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+
* @tparam Dimension First template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
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164
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+
* @tparam Event_value Second template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
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165
|
+
*/
|
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166
|
+
template <typename Dimension, typename Event_value>
|
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167
|
+
struct tuple_size<Gudhi::persistence_matrix::Persistence_interval<Dimension, Event_value> >
|
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168
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+
: integral_constant<size_t, 3> {};
|
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169
|
+
|
|
170
|
+
/**
|
|
171
|
+
* @ingroup persistence_matrix
|
|
172
|
+
*
|
|
173
|
+
* @brief Partial specialization of `std::tuple_element` for @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
174
|
+
*
|
|
175
|
+
* @tparam I Index of the type to store: 0 for the birth value type, 1 for the death value type and 2 for the
|
|
176
|
+
* dimension value type.
|
|
177
|
+
* @tparam Dimension First template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
178
|
+
* @tparam Event_value Second template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
179
|
+
*/
|
|
180
|
+
template <size_t I, typename Dimension, typename Event_value>
|
|
181
|
+
struct tuple_element<I, Gudhi::persistence_matrix::Persistence_interval<Dimension, Event_value> > {
|
|
182
|
+
static_assert(I < 3, "Value mismatch at argument 1 in template parameter list. Maximal possible value is 2.");
|
|
183
|
+
|
|
184
|
+
using type = typename conditional <I < 2, Event_value, Dimension>::type;
|
|
185
|
+
};
|
|
186
|
+
|
|
187
|
+
/**
|
|
188
|
+
* @ingroup persistence_matrix
|
|
189
|
+
*
|
|
190
|
+
* @brief Partial specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
191
|
+
*
|
|
192
|
+
* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
|
|
193
|
+
* @tparam Dimension First template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
194
|
+
* @tparam Event_value Second template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
195
|
+
* @param i Interval from which the value should be returned.
|
|
196
|
+
* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
|
|
197
|
+
*/
|
|
198
|
+
template <size_t I, typename Dimension, typename Event_value>
|
|
199
|
+
constexpr auto& get(Gudhi::persistence_matrix::Persistence_interval<Dimension, Event_value>& i) noexcept {
|
|
200
|
+
return i.template get<I>();
|
|
201
|
+
}
|
|
202
|
+
|
|
203
|
+
/**
|
|
204
|
+
* @ingroup persistence_matrix
|
|
205
|
+
*
|
|
206
|
+
* @brief Partial specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
207
|
+
*
|
|
208
|
+
* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
|
|
209
|
+
* @tparam Dimension First template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
210
|
+
* @tparam Event_value Second template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
211
|
+
* @param i Interval from which the value should be returned.
|
|
212
|
+
* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
|
|
213
|
+
*/
|
|
214
|
+
template <size_t I, typename Dimension, typename Event_value>
|
|
215
|
+
constexpr const auto& get(const Gudhi::persistence_matrix::Persistence_interval<Dimension, Event_value>& i) noexcept {
|
|
216
|
+
return i.template get<I>();
|
|
217
|
+
}
|
|
218
|
+
|
|
219
|
+
/**
|
|
220
|
+
* @ingroup persistence_matrix
|
|
221
|
+
*
|
|
222
|
+
* @brief Partial specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
223
|
+
*
|
|
224
|
+
* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
|
|
225
|
+
* @tparam Dimension First template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
226
|
+
* @tparam Event_value Second template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
227
|
+
* @param i Interval from which the value should be returned.
|
|
228
|
+
* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
|
|
229
|
+
*/
|
|
230
|
+
template <size_t I, typename Dimension, typename Event_value>
|
|
231
|
+
constexpr auto&& get(Gudhi::persistence_matrix::Persistence_interval<Dimension, Event_value>&& i) noexcept {
|
|
232
|
+
return std::move(i).template get<I>();
|
|
233
|
+
}
|
|
234
|
+
|
|
235
|
+
/**
|
|
236
|
+
* @ingroup persistence_matrix
|
|
237
|
+
*
|
|
238
|
+
* @brief Partial specialization of `get` for @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
239
|
+
*
|
|
240
|
+
* @tparam I Index of the value to return: 0 for the birth value, 1 for the death value and 2 for the dimension.
|
|
241
|
+
* @tparam Dimension First template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
242
|
+
* @tparam Event_value Second template parameter of @ref Gudhi::persistence_matrix::Persistence_interval.
|
|
243
|
+
* @param i Interval from which the value should be returned.
|
|
244
|
+
* @return Either the birth value if @p I == 0, the death value if @p I == 1 or the dimension if @p I == 2.
|
|
245
|
+
*/
|
|
246
|
+
template <size_t I, typename Dimension, typename Event_value>
|
|
247
|
+
constexpr const auto&& get(const Gudhi::persistence_matrix::Persistence_interval<Dimension, Event_value>&& i) noexcept {
|
|
248
|
+
return std::move(i).template get<I>();
|
|
249
|
+
}
|
|
250
|
+
|
|
251
|
+
} // namespace std
|
|
252
|
+
|
|
253
|
+
#endif // PM_INTERVAL_INCLUDED
|