multipers 2.3.3b6__cp312-cp312-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-312-x86_64-linux-gnu.so +0 -0
- multipers/function_rips.pyx +105 -0
- multipers/grids.cpython-312-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-312-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-312-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-312-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-312-x86_64-linux-gnu.so +0 -0
- multipers/point_measure.pyx +395 -0
- multipers/simplex_tree_multi.cpython-312-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-312-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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#pragma once
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#include "Simplex_tree_multi_interface.h"
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#include "multi_parameter_rank_invariant/persistence_slices.h"
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#include "tensor/tensor.h"
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#include <algorithm>
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#include <gudhi/One_critical_filtration.h>
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#include <gudhi/truc.h>
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#include <iostream>
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#include <limits>
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#include <oneapi/tbb/enumerable_thread_specific.h>
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#include <oneapi/tbb/parallel_for.h>
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#include <ostream>
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#include <utility> // std::pair
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#include <vector>
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namespace Gudhi {
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namespace multiparameter {
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namespace hilbert_function {
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// TODO : this function is ugly
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template <typename Filtration, typename indices_type>
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inline typename Filtration::value_type horizontal_line_filtration2(const Filtration &x,
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indices_type height,
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indices_type i,
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indices_type j,
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const std::vector<indices_type> &fixed_values) {
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const auto &inf = Filtration::Generator::T_inf;
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for (indices_type k = 0u; k < static_cast<indices_type>(x.size()); k++) {
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if (k == i || k == j) continue; // coordinate in the plane
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if (x[k] > fixed_values[k]) // simplex appears after the plane
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return inf;
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}
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if (x[j] <= height) // simplex apppears in the plane, but is it in the line
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// with height "height"
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return x[i];
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else
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return inf;
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}
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template <typename index_type>
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using hilbert_thread_data = tbb::enumerable_thread_specific<std::pair<Simplex_tree_std, std::vector<index_type>>>;
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template <typename Filtration, typename dtype, typename index_type>
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inline void compute_2d_hilbert_surface(
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python_interface::Simplex_tree_multi_interface<Filtration> &st_multi,
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// Simplex_tree_std &_st,
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hilbert_thread_data<index_type> &thread_simplex_tree,
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const tensor::static_tensor_view<dtype, index_type> &out, // assumes its a zero tensor
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const std::vector<index_type> grid_shape,
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const std::vector<index_type> degrees,
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index_type i,
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index_type j,
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const std::vector<index_type> fixed_values,
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bool mobius_inverion,
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bool zero_pad,
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int expand_collapse_dim = 0) {
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using value_type = typename Filtration::value_type;
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// if (grid_shape.size() < 2 || st_multi.get_number_of_parameters() < 2)
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// throw std::invalid_argument("Grid shape has to have at least 2
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// element."); if (st_multi.get_number_of_parameters() - fixed_values.size()
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// != 2) throw std::invalid_argument("Fix more values for the
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// simplextree, which has a too big number of parameters");
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// assert(fixed_values.size() == st_multi.get_number_of_parameters());
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constexpr const bool verbose = false;
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index_type I = grid_shape[i + 1], J = grid_shape[j + 1];
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if constexpr (verbose) std::cout << "Grid shape : " << I << " " << J << std::endl;
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// grid2d out(I, std::vector<int>(J,0)); // zero of good size
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// std::vector<std::vector<index_type>> free_coordinates(grid_shape.size());
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// for (auto [r,k] = std::views::zip(free_coordinates,
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// std::ranges::iota(0,free_coordinates.size()))){ if (k==i) r =
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// std::ranges::iota(0,I); else if (k==j) r= std::ranges::iota(0,J);
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// else fixed_values[k];
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// }
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// tensor::static_tensor_view_view<value_type, index_type> dim2_view(out,
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// free_coordinates); auto coordinates_container =
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// Simplex_tree_std _st;
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// flatten<Simplex_tree_float,
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// Gudhi::multi_persistence::Simplex_tree_options_multidimensional_filtration>(_st, st_multi,-1); //
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// copies the st_multi to a standard 1-pers simplextree
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// tbb::enumerable_thread_specific<std::pair<Simplex_tree_std,
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// std::vector<index_type>>> thread_simplex_tree;
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tbb::parallel_for(0, J, [&](index_type height) {
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// SIMPLEXTREE INIT
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auto &[st_std, coordinates_container] = thread_simplex_tree.local();
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// if (st_std.num_simplices() == 0){ st_std = _st;}
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// COORDINATES INIT
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// if (coordinates_container.size() == 0) {
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// //This init is fine as only the j+1th coord is touched
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// coordinates_container.reserve(fixed_values.size()+1);
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// coordinates_container.push_back(0); // degree
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// for (auto c : fixed_values) coordinates_container.push_back(c);
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// }
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// coordinates_container.resize(fixed_values.size()+1); // Not necessary
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// if (coordinates_container.size() != fixed_values.size()+1 ||
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// st_std.num_simplices() == 0){ throw std::runtime_error("Bad tbb thread
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// local storage initialization.");
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// }
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// Coordinate initialization to fixed values
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// coordinates_container[0] = 0; // not necessary
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// for (auto [c, i] : std::views::zip(fixed_values, std::views::iota(0u,
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// fixed_values.size()))) // NIK APPLE CLANG coordinates_container[i+1] = c;
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for (auto i = 0u; i < fixed_values.size(); i++) coordinates_container[i + 1] = fixed_values[i];
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coordinates_container[j + 1] = height;
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Filtration multi_filtration(st_multi.get_number_of_parameters());
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auto sh_standard = st_std.complex_simplex_range().begin();
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auto _end = st_std.complex_simplex_range().end();
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auto sh_multi = st_multi.complex_simplex_range().begin();
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for (; sh_standard != _end; ++sh_multi, ++sh_standard) {
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// for (auto [sh_standard, sh_multi] :
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// std::ranges::views::zip(st_std.complex_simplex_range(),
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// st_multi.complex_simplex_range())){ // too bad apple clang exists
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multi_filtration = st_multi.filtration(*sh_multi);
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typename Simplex_tree_std::Filtration_value horizontal_filtration;
|
|
121
|
+
if constexpr (Filtration::is_multi_critical) {
|
|
122
|
+
horizontal_filtration = std::numeric_limits<typename Simplex_tree_std::Filtration_value>::infinity();
|
|
123
|
+
for (const auto &stuff : multi_filtration)
|
|
124
|
+
horizontal_filtration = std::min(horizontal_filtration,
|
|
125
|
+
static_cast<Simplex_tree_std::Filtration_value>(
|
|
126
|
+
horizontal_line_filtration2(stuff, height, i, j, fixed_values)));
|
|
127
|
+
} else {
|
|
128
|
+
horizontal_filtration = horizontal_line_filtration2(multi_filtration, height, i, j, fixed_values);
|
|
129
|
+
}
|
|
130
|
+
st_std.assign_filtration(*sh_standard, horizontal_filtration);
|
|
131
|
+
|
|
132
|
+
if constexpr (verbose) {
|
|
133
|
+
Gudhi::multi_filtration::One_critical_filtration<int> splx;
|
|
134
|
+
for (auto vertex : st_multi.simplex_vertex_range(*sh_multi)) splx.push_back(vertex);
|
|
135
|
+
std::cout << "Simplex " << splx << "/" << st_std.num_simplices() << " Filtration multi "
|
|
136
|
+
<< st_multi.filtration(*sh_multi) << " Filtration 1d " << st_std.filtration(*sh_standard) << "\n";
|
|
137
|
+
}
|
|
138
|
+
}
|
|
139
|
+
|
|
140
|
+
if constexpr (verbose) {
|
|
141
|
+
std::cout << "Coords : " << height << " [";
|
|
142
|
+
for (auto stuff : fixed_values) std::cout << stuff << " ";
|
|
143
|
+
std::cout << "]" << std::endl;
|
|
144
|
+
}
|
|
145
|
+
const std::vector<Barcode> barcodes = compute_dgms(st_std, degrees, expand_collapse_dim);
|
|
146
|
+
index_type degree_index = 0;
|
|
147
|
+
for (const auto &barcode : barcodes) { // TODO range view cartesian product
|
|
148
|
+
coordinates_container[0] = degree_index;
|
|
149
|
+
for (const auto &bar : barcode) {
|
|
150
|
+
auto birth = bar.first; // float
|
|
151
|
+
auto death = bar.second;
|
|
152
|
+
// if constexpr (verbose) std::cout << "BEFORE " << birth << " " <<
|
|
153
|
+
// death << " " << I << " \n"; death = death > I ? I : death; // TODO
|
|
154
|
+
// FIXME if constexpr (verbose) std::cout <<"AFTER" << birth << " " <<
|
|
155
|
+
// death << " " << I << " \n";
|
|
156
|
+
if (birth > I) // some birth can be infinite
|
|
157
|
+
continue;
|
|
158
|
+
|
|
159
|
+
if (!mobius_inverion) {
|
|
160
|
+
// throw std::logic_error("Not implemented");
|
|
161
|
+
// death = death > I ? I : death;
|
|
162
|
+
// for (int index = static_cast<int>(birth); index <
|
|
163
|
+
// static_cast<int>(death); index ++){
|
|
164
|
+
// out[degree_index][index][height]++;
|
|
165
|
+
// }
|
|
166
|
+
|
|
167
|
+
// Seems to bug on linux ????
|
|
168
|
+
|
|
169
|
+
coordinates_container[i + 1] = static_cast<index_type>(birth);
|
|
170
|
+
index_type shift_value = out.get_cum_resolution()[i + 1];
|
|
171
|
+
index_type border = I;
|
|
172
|
+
// index_type border = out.get_resolution()[i+1];
|
|
173
|
+
dtype *ptr = &out[coordinates_container];
|
|
174
|
+
auto stop_value = death > static_cast<value_type>(border) ? border : static_cast<index_type>(death);
|
|
175
|
+
// Warning : for some reason linux static casts float inf to -min_int
|
|
176
|
+
// so min doesnt work.
|
|
177
|
+
if constexpr (verbose) {
|
|
178
|
+
std::cout << "Adding : (";
|
|
179
|
+
for (auto stuff : coordinates_container) std::cout << stuff << ", ";
|
|
180
|
+
std::cout << ") With death " << death << " casted at " << static_cast<index_type>(death)
|
|
181
|
+
<< "with threshold at" << stop_value << " with " << border << std::endl;
|
|
182
|
+
}
|
|
183
|
+
for (index_type b = birth; b < stop_value; b++) {
|
|
184
|
+
(*ptr)++; // adds one to the vector
|
|
185
|
+
ptr += shift_value; // shift the pointer to the next element in the
|
|
186
|
+
// segment [birth, death]
|
|
187
|
+
}
|
|
188
|
+
} else {
|
|
189
|
+
// out[degree_index][static_cast<int>(birth)][height]++; // No need to
|
|
190
|
+
// do mobius inversion on this axis, it can be done here if (death <
|
|
191
|
+
// I) out[degree_index][static_cast<int>(death)][height]--;
|
|
192
|
+
// else if (zero_pad)
|
|
193
|
+
// {
|
|
194
|
+
// out[degree_index].back()[height]--;
|
|
195
|
+
// }
|
|
196
|
+
// coordinates_container[0] = degree_index;
|
|
197
|
+
coordinates_container[i + 1] = static_cast<index_type>(birth);
|
|
198
|
+
out[coordinates_container]++;
|
|
199
|
+
|
|
200
|
+
if constexpr (verbose) {
|
|
201
|
+
std::cout << "Coordinate : ";
|
|
202
|
+
for (auto c : coordinates_container) std::cout << c << ", ";
|
|
203
|
+
std::cout << std::endl;
|
|
204
|
+
std::cout << "axis, death, resolution : " << i + 1 << ", " << std::to_string(death) << ", "
|
|
205
|
+
<< out.get_resolution()[i + 1];
|
|
206
|
+
std::cout << std::endl;
|
|
207
|
+
}
|
|
208
|
+
|
|
209
|
+
if (death < I) {
|
|
210
|
+
coordinates_container[i + 1] = static_cast<index_type>(death);
|
|
211
|
+
out[coordinates_container]--;
|
|
212
|
+
} else if (zero_pad) {
|
|
213
|
+
coordinates_container[i + 1] = I - 1;
|
|
214
|
+
out[coordinates_container]--;
|
|
215
|
+
}
|
|
216
|
+
}
|
|
217
|
+
// else
|
|
218
|
+
// out[I-1][height]--;
|
|
219
|
+
}
|
|
220
|
+
degree_index++;
|
|
221
|
+
}
|
|
222
|
+
});
|
|
223
|
+
return;
|
|
224
|
+
}
|
|
225
|
+
|
|
226
|
+
template <typename Filtration, typename dtype, typename index_type>
|
|
227
|
+
void _rec_get_hilbert_surface(python_interface::Simplex_tree_multi_interface<Filtration> &st_multi,
|
|
228
|
+
// Simplex_tree_std &_st,
|
|
229
|
+
hilbert_thread_data<index_type> &thread_simplex_tree,
|
|
230
|
+
const tensor::static_tensor_view<dtype, index_type> &out, // assumes its a zero tensor
|
|
231
|
+
const std::vector<index_type> grid_shape,
|
|
232
|
+
const std::vector<index_type> degrees,
|
|
233
|
+
std::vector<index_type> coordinates_to_compute,
|
|
234
|
+
const std::vector<index_type> fixed_values,
|
|
235
|
+
bool mobius_inverion = true,
|
|
236
|
+
bool zero_pad = false,
|
|
237
|
+
int expand_collapse_dim = 0) {
|
|
238
|
+
constexpr const bool verbose = false;
|
|
239
|
+
|
|
240
|
+
if constexpr (verbose) {
|
|
241
|
+
std::cout << "Computing coordinates (";
|
|
242
|
+
for (auto c : coordinates_to_compute) std::cout << c << ", ";
|
|
243
|
+
std::cout << "). with fixed values (";
|
|
244
|
+
for (auto c : fixed_values) {
|
|
245
|
+
std::cout << c << ", ";
|
|
246
|
+
}
|
|
247
|
+
std::cout << ")." << std::endl;
|
|
248
|
+
}
|
|
249
|
+
if (coordinates_to_compute.size() == 2) {
|
|
250
|
+
compute_2d_hilbert_surface(st_multi,
|
|
251
|
+
// _st,
|
|
252
|
+
thread_simplex_tree,
|
|
253
|
+
out, // assumes its a zero tensor
|
|
254
|
+
grid_shape,
|
|
255
|
+
degrees,
|
|
256
|
+
coordinates_to_compute[0],
|
|
257
|
+
coordinates_to_compute[1],
|
|
258
|
+
fixed_values,
|
|
259
|
+
mobius_inverion,
|
|
260
|
+
zero_pad,
|
|
261
|
+
expand_collapse_dim);
|
|
262
|
+
return;
|
|
263
|
+
}
|
|
264
|
+
|
|
265
|
+
// coordinate to iterate.size --
|
|
266
|
+
auto coordinate_to_iterate = coordinates_to_compute.back();
|
|
267
|
+
coordinates_to_compute.pop_back();
|
|
268
|
+
tbb::parallel_for(0, grid_shape[coordinate_to_iterate + 1], [&](index_type z) {
|
|
269
|
+
// Updates fixes values that defines the slice
|
|
270
|
+
std::vector<index_type> _fixed_values = fixed_values; // TODO : do not copy this //thread local
|
|
271
|
+
_fixed_values[coordinate_to_iterate] = z;
|
|
272
|
+
_rec_get_hilbert_surface(st_multi,
|
|
273
|
+
thread_simplex_tree,
|
|
274
|
+
out,
|
|
275
|
+
grid_shape,
|
|
276
|
+
degrees,
|
|
277
|
+
coordinates_to_compute,
|
|
278
|
+
_fixed_values,
|
|
279
|
+
mobius_inverion,
|
|
280
|
+
zero_pad,
|
|
281
|
+
expand_collapse_dim);
|
|
282
|
+
});
|
|
283
|
+
// rmq : with mobius_inversion + rec, the coordinates to compute size is 2 =>
|
|
284
|
+
// first coord is always the initial 1st coord.
|
|
285
|
+
// => inversion is only needed for coords > 2
|
|
286
|
+
}
|
|
287
|
+
|
|
288
|
+
template <typename Filtration, typename dtype, typename index_type>
|
|
289
|
+
void get_hilbert_surface(python_interface::Simplex_tree_multi_interface<Filtration> &st_multi,
|
|
290
|
+
const tensor::static_tensor_view<dtype, index_type> &out, // assumes its a zero tensor
|
|
291
|
+
const std::vector<index_type> &grid_shape,
|
|
292
|
+
const std::vector<index_type> °rees,
|
|
293
|
+
std::vector<index_type> coordinates_to_compute,
|
|
294
|
+
const std::vector<index_type> &fixed_values,
|
|
295
|
+
bool mobius_inverion = true,
|
|
296
|
+
bool zero_pad = false,
|
|
297
|
+
bool expand_collapse = false) {
|
|
298
|
+
if (degrees.size() == 0) return;
|
|
299
|
+
// wrapper arount the rec version, that initialize the thread variables.
|
|
300
|
+
if (coordinates_to_compute.size() < 2)
|
|
301
|
+
throw std::logic_error("Not implemented for " + std::to_string(coordinates_to_compute.size()) + "<2 parameters.");
|
|
302
|
+
|
|
303
|
+
Simplex_tree_std _st;
|
|
304
|
+
Gudhi::multi_persistence::flatten(_st, st_multi,
|
|
305
|
+
-1); // copies the st_multi to a standard 1-pers simplextree
|
|
306
|
+
std::vector<index_type> coordinates_container(st_multi.get_number_of_parameters() + 1); // +1 for degree
|
|
307
|
+
// coordinates_container.reserve(fixed_values.size()+1);
|
|
308
|
+
// coordinates_container.push_back(0); // degree
|
|
309
|
+
// for (auto c : fixed_values) coordinates_container.push_back(c);
|
|
310
|
+
std::pair<Simplex_tree_std, std::vector<index_type>> thread_data_initialization = {_st, coordinates_container};
|
|
311
|
+
const int max_dim = expand_collapse ? *std::max_element(degrees.begin(), degrees.end()) + 1 : 0;
|
|
312
|
+
tbb::enumerable_thread_specific<std::pair<Simplex_tree_std, std::vector<index_type>>> thread_simplex_tree(
|
|
313
|
+
thread_data_initialization); // this has a fixed size, so init should
|
|
314
|
+
// be benefic
|
|
315
|
+
_rec_get_hilbert_surface(st_multi,
|
|
316
|
+
thread_simplex_tree,
|
|
317
|
+
out,
|
|
318
|
+
grid_shape,
|
|
319
|
+
degrees,
|
|
320
|
+
coordinates_to_compute,
|
|
321
|
+
fixed_values,
|
|
322
|
+
mobius_inverion,
|
|
323
|
+
zero_pad,
|
|
324
|
+
max_dim);
|
|
325
|
+
}
|
|
326
|
+
|
|
327
|
+
template <typename Filtration, typename dtype = int, typename indices_type>
|
|
328
|
+
std::pair<std::vector<std::vector<indices_type>>, std::vector<dtype>> get_hilbert_signed_measure(
|
|
329
|
+
python_interface::Simplex_tree_multi_interface<Filtration> &st_multi,
|
|
330
|
+
dtype *data_ptr,
|
|
331
|
+
std::vector<indices_type> grid_shape,
|
|
332
|
+
const std::vector<indices_type> degrees,
|
|
333
|
+
bool zero_pad = false,
|
|
334
|
+
indices_type n_jobs = 0,
|
|
335
|
+
const bool verbose = false,
|
|
336
|
+
const bool expand_collapse = false) {
|
|
337
|
+
if (degrees.size() == 0) return {{}, {}};
|
|
338
|
+
// const bool verbose = false;
|
|
339
|
+
// auto &st_multi =
|
|
340
|
+
// get_simplextree_from_pointer<python_interface::interface_multi<Filtration>>(simplextree_ptr);
|
|
341
|
+
tensor::static_tensor_view<dtype, indices_type> container(data_ptr, grid_shape); // assumes its a zero tensor
|
|
342
|
+
std::vector<indices_type> coordinates_to_compute(st_multi.get_number_of_parameters());
|
|
343
|
+
for (auto i = 0u; i < coordinates_to_compute.size(); i++) coordinates_to_compute[i] = i;
|
|
344
|
+
// for (auto [c,i] : std::views::zip(coordinates_to_compute,
|
|
345
|
+
// std::views::iota(0,st_multi.get_number_of_parameters()))) c=i; // NIK apple
|
|
346
|
+
// clang
|
|
347
|
+
std::vector<indices_type> fixed_values(st_multi.get_number_of_parameters());
|
|
348
|
+
|
|
349
|
+
if (verbose) {
|
|
350
|
+
std::cout << "Container shape : ";
|
|
351
|
+
for (auto r : container.get_resolution()) std::cout << r << ", ";
|
|
352
|
+
std::cout << "\nContainer size : " << container.size();
|
|
353
|
+
std::cout << "\nComputing hilbert invariant ..." << std::flush;
|
|
354
|
+
}
|
|
355
|
+
if (zero_pad) {
|
|
356
|
+
// +1 is bc degree is on first axis.
|
|
357
|
+
for (auto i = 1; i < st_multi.get_number_of_parameters() + 1; i++)
|
|
358
|
+
grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
359
|
+
// for (auto i : std::views::iota(1,st_multi.get_number_of_parameters()+1))
|
|
360
|
+
// grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
361
|
+
}
|
|
362
|
+
|
|
363
|
+
oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
|
|
364
|
+
arena.execute([&] {
|
|
365
|
+
get_hilbert_surface(st_multi,
|
|
366
|
+
container,
|
|
367
|
+
grid_shape,
|
|
368
|
+
degrees,
|
|
369
|
+
coordinates_to_compute,
|
|
370
|
+
fixed_values,
|
|
371
|
+
true,
|
|
372
|
+
zero_pad,
|
|
373
|
+
expand_collapse);
|
|
374
|
+
});
|
|
375
|
+
|
|
376
|
+
if (verbose) {
|
|
377
|
+
std::cout << "Done.\n";
|
|
378
|
+
std::cout << "Computing mobius inversion ..." << std::flush;
|
|
379
|
+
}
|
|
380
|
+
|
|
381
|
+
// for (indices_type axis :
|
|
382
|
+
// std::views::iota(2,st_multi.get_number_of_parameters()+1)) // +1 for the
|
|
383
|
+
// degree in axis 0
|
|
384
|
+
for (indices_type axis = 2u; axis < st_multi.get_number_of_parameters() + 1; axis++) container.differentiate(axis);
|
|
385
|
+
if (verbose) {
|
|
386
|
+
std::cout << "Done.\n";
|
|
387
|
+
std::cout << "Sparsifying the measure ..." << std::flush;
|
|
388
|
+
}
|
|
389
|
+
auto raw_signed_measure = container.sparsify();
|
|
390
|
+
if (verbose) {
|
|
391
|
+
std::cout << "Done.\n";
|
|
392
|
+
}
|
|
393
|
+
return raw_signed_measure;
|
|
394
|
+
}
|
|
395
|
+
|
|
396
|
+
template <typename Filtration, typename dtype, typename indices_type, typename... Args>
|
|
397
|
+
void get_hilbert_surface_python(python_interface::Simplex_tree_multi_interface<Filtration> &st_multi,
|
|
398
|
+
dtype *data_ptr,
|
|
399
|
+
std::vector<indices_type> grid_shape,
|
|
400
|
+
const std::vector<indices_type> degrees,
|
|
401
|
+
const bool mobius_inversion,
|
|
402
|
+
const bool zero_pad,
|
|
403
|
+
indices_type n_jobs,
|
|
404
|
+
bool expand_collapse) {
|
|
405
|
+
constexpr const bool verbose = false;
|
|
406
|
+
if (degrees.size() == 0) return;
|
|
407
|
+
// const bool verbose = false;
|
|
408
|
+
// auto &st_multi =
|
|
409
|
+
// get_simplextree_from_pointer<python_interface::interface_multi<Filtration>>(simplextree_ptr);
|
|
410
|
+
tensor::static_tensor_view<dtype, indices_type> container(data_ptr, grid_shape); // assumes its a zero tensor
|
|
411
|
+
std::vector<indices_type> coordinates_to_compute(st_multi.get_number_of_parameters());
|
|
412
|
+
for (auto i = 0u; i < coordinates_to_compute.size(); i++) coordinates_to_compute[i] = i;
|
|
413
|
+
// for (auto [c,i] : std::views::zip(coordinates_to_compute,
|
|
414
|
+
// std::views::iota(0,st_multi.get_number_of_parameters()))) c=i; // NIK apple
|
|
415
|
+
// clang
|
|
416
|
+
std::vector<indices_type> fixed_values(st_multi.get_number_of_parameters());
|
|
417
|
+
|
|
418
|
+
if (verbose) {
|
|
419
|
+
std::cout << "Container shape : ";
|
|
420
|
+
for (auto r : container.get_resolution()) std::cout << r << ", ";
|
|
421
|
+
std::cout << "\nContainer size : " << container.size();
|
|
422
|
+
std::cout << "\nComputing hilbert invariant ...";
|
|
423
|
+
}
|
|
424
|
+
if (zero_pad) {
|
|
425
|
+
// +1 is bc degree is on first axis.
|
|
426
|
+
for (auto i = 1; i < st_multi.get_number_of_parameters() + 1; i++)
|
|
427
|
+
grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
428
|
+
// for (auto i : std::views::iota(1,st_multi.get_number_of_parameters()+1))
|
|
429
|
+
// grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
430
|
+
}
|
|
431
|
+
|
|
432
|
+
oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
|
|
433
|
+
arena.execute([&] {
|
|
434
|
+
get_hilbert_surface(st_multi,
|
|
435
|
+
container,
|
|
436
|
+
grid_shape,
|
|
437
|
+
degrees,
|
|
438
|
+
coordinates_to_compute,
|
|
439
|
+
fixed_values,
|
|
440
|
+
mobius_inversion,
|
|
441
|
+
zero_pad,
|
|
442
|
+
expand_collapse);
|
|
443
|
+
});
|
|
444
|
+
|
|
445
|
+
if (mobius_inversion)
|
|
446
|
+
for (indices_type axis = 2u; axis < st_multi.get_number_of_parameters() + 1; axis++) container.differentiate(axis);
|
|
447
|
+
return;
|
|
448
|
+
}
|
|
449
|
+
|
|
450
|
+
/// FROM SLICER
|
|
451
|
+
///
|
|
452
|
+
///
|
|
453
|
+
|
|
454
|
+
template <typename PersBackend, typename Structure, typename Filtration, typename dtype, typename index_type>
|
|
455
|
+
inline void compute_2d_hilbert_surface(
|
|
456
|
+
tbb::enumerable_thread_specific<std::pair<typename truc_interface::Truc<PersBackend, Structure, Filtration>::ThreadSafe,
|
|
457
|
+
std::vector<index_type>>> &thread_stuff,
|
|
458
|
+
const tensor::static_tensor_view<dtype, index_type> &out, // assumes its a zero tensor
|
|
459
|
+
const std::vector<index_type> grid_shape,
|
|
460
|
+
const std::vector<index_type> degrees,
|
|
461
|
+
index_type i,
|
|
462
|
+
index_type j,
|
|
463
|
+
const std::vector<index_type> fixed_values,
|
|
464
|
+
const bool mobius_inverion,
|
|
465
|
+
const bool zero_pad,
|
|
466
|
+
const bool ignore_inf = true ) {
|
|
467
|
+
using value_type = typename Filtration::value_type;
|
|
468
|
+
|
|
469
|
+
constexpr const bool verbose = false;
|
|
470
|
+
index_type I = grid_shape[i + 1], J = grid_shape[j + 1];
|
|
471
|
+
if constexpr (verbose) std::cout << "Grid shape : " << I << " " << J << std::endl;
|
|
472
|
+
tbb::parallel_for(0, J, [&](index_type height) {
|
|
473
|
+
// SIMPLEXTREE INIT
|
|
474
|
+
auto &[slicer, coordinates_container] = thread_stuff.local();
|
|
475
|
+
for (auto i = 0u; i < fixed_values.size(); i++) coordinates_container[i + 1] = fixed_values[i];
|
|
476
|
+
|
|
477
|
+
coordinates_container[j + 1] = height;
|
|
478
|
+
|
|
479
|
+
auto &slice_filtration = slicer.get_one_filtration();
|
|
480
|
+
const auto &multi_filtration = slicer.get_filtrations();
|
|
481
|
+
|
|
482
|
+
for (std::size_t k = 0; k < multi_filtration.size(); k++) {
|
|
483
|
+
value_type horizontal_filtration;
|
|
484
|
+
if constexpr (Filtration::is_multi_critical) {
|
|
485
|
+
horizontal_filtration = Filtration::Generator::T_inf;
|
|
486
|
+
for (const auto &stuff : multi_filtration[k])
|
|
487
|
+
horizontal_filtration =
|
|
488
|
+
std::min(horizontal_filtration,
|
|
489
|
+
static_cast<value_type>(horizontal_line_filtration2(stuff, height, i, j, fixed_values)));
|
|
490
|
+
} else {
|
|
491
|
+
horizontal_filtration = horizontal_line_filtration2(multi_filtration[k], height, i, j, fixed_values);
|
|
492
|
+
}
|
|
493
|
+
slice_filtration[k] = horizontal_filtration;
|
|
494
|
+
}
|
|
495
|
+
|
|
496
|
+
if constexpr (verbose) {
|
|
497
|
+
std::cout << "Coords : " << height << " [";
|
|
498
|
+
for (auto stuff : fixed_values) std::cout << stuff << " ";
|
|
499
|
+
std::cout << "]" << std::endl;
|
|
500
|
+
}
|
|
501
|
+
using bc_type = typename truc_interface::Truc<PersBackend, Structure, Filtration>::split_barcode;
|
|
502
|
+
if constexpr (PersBackend::is_vine) {
|
|
503
|
+
if (!slicer.has_persistence()) [[unlikely]] {
|
|
504
|
+
slicer.compute_persistence();
|
|
505
|
+
} else {
|
|
506
|
+
slicer.vineyard_update();
|
|
507
|
+
}
|
|
508
|
+
} else {
|
|
509
|
+
slicer.compute_persistence(ignore_inf);
|
|
510
|
+
}
|
|
511
|
+
bc_type barcodes = slicer.get_barcode();
|
|
512
|
+
index_type degree_index = 0;
|
|
513
|
+
for (auto degree : degrees) { // TODO range view cartesian product
|
|
514
|
+
const auto &barcode = barcodes[degree];
|
|
515
|
+
coordinates_container[0] = degree_index;
|
|
516
|
+
for (const auto &bar : barcode) {
|
|
517
|
+
auto birth = bar.first; // float
|
|
518
|
+
auto death = bar.second;
|
|
519
|
+
if (birth > I) // some birth can be infinite
|
|
520
|
+
continue;
|
|
521
|
+
|
|
522
|
+
if (!mobius_inverion) {
|
|
523
|
+
coordinates_container[i + 1] = static_cast<index_type>(birth);
|
|
524
|
+
index_type shift_value = out.get_cum_resolution()[i + 1];
|
|
525
|
+
index_type border = I;
|
|
526
|
+
// index_type border = out.get_resolution()[i+1];
|
|
527
|
+
dtype *ptr = &out[coordinates_container];
|
|
528
|
+
auto stop_value = death > static_cast<value_type>(border) ? border : static_cast<index_type>(death);
|
|
529
|
+
// Warning : for some reason linux static casts float inf to -min_int
|
|
530
|
+
// so min doesnt work.
|
|
531
|
+
if constexpr (verbose) {
|
|
532
|
+
std::cout << "Adding : (";
|
|
533
|
+
for (auto stuff : coordinates_container) std::cout << stuff << ", ";
|
|
534
|
+
std::cout << ") With death " << death << " casted at " << static_cast<index_type>(death)
|
|
535
|
+
<< "with threshold at" << stop_value << " with " << border << std::endl;
|
|
536
|
+
}
|
|
537
|
+
for (index_type b = birth; b < stop_value; b++) {
|
|
538
|
+
(*ptr)++; // adds one to the vector
|
|
539
|
+
ptr += shift_value; // shift the pointer to the next element in the
|
|
540
|
+
// segment [birth, death]
|
|
541
|
+
}
|
|
542
|
+
} else {
|
|
543
|
+
coordinates_container[i + 1] = static_cast<index_type>(birth);
|
|
544
|
+
out[coordinates_container]++;
|
|
545
|
+
|
|
546
|
+
if constexpr (verbose) {
|
|
547
|
+
std::cout << "Coordinate : ";
|
|
548
|
+
for (auto c : coordinates_container) std::cout << c << ", ";
|
|
549
|
+
std::cout << std::endl;
|
|
550
|
+
std::cout << "axis, death, resolution : " << i + 1 << ", " << std::to_string(death) << ", "
|
|
551
|
+
<< out.get_resolution()[i + 1];
|
|
552
|
+
std::cout << std::endl;
|
|
553
|
+
}
|
|
554
|
+
|
|
555
|
+
if (death < I) {
|
|
556
|
+
coordinates_container[i + 1] = static_cast<index_type>(death);
|
|
557
|
+
out[coordinates_container]--;
|
|
558
|
+
} else if (zero_pad) {
|
|
559
|
+
coordinates_container[i + 1] = I - 1;
|
|
560
|
+
out[coordinates_container]--;
|
|
561
|
+
}
|
|
562
|
+
}
|
|
563
|
+
}
|
|
564
|
+
degree_index++;
|
|
565
|
+
}
|
|
566
|
+
});
|
|
567
|
+
return;
|
|
568
|
+
}
|
|
569
|
+
|
|
570
|
+
template <typename PersBackend, typename Structure, typename Filtration, typename dtype, typename index_type>
|
|
571
|
+
void _rec_get_hilbert_surface(
|
|
572
|
+
tbb::enumerable_thread_specific<std::pair<typename truc_interface::Truc<PersBackend, Structure, Filtration>::ThreadSafe,
|
|
573
|
+
std::vector<index_type>>> &thread_stuff,
|
|
574
|
+
const tensor::static_tensor_view<dtype, index_type> &out, // assumes its a zero tensor
|
|
575
|
+
const std::vector<index_type> grid_shape,
|
|
576
|
+
const std::vector<index_type> degrees,
|
|
577
|
+
std::vector<index_type> coordinates_to_compute,
|
|
578
|
+
const std::vector<index_type> fixed_values,
|
|
579
|
+
const bool mobius_inverion = true,
|
|
580
|
+
const bool zero_pad = false,
|
|
581
|
+
const bool ignore_inf = true) {
|
|
582
|
+
constexpr const bool verbose = false;
|
|
583
|
+
|
|
584
|
+
if constexpr (verbose) {
|
|
585
|
+
std::cout << "Computing coordinates (";
|
|
586
|
+
for (auto c : coordinates_to_compute) std::cout << c << ", ";
|
|
587
|
+
std::cout << "). with fixed values (";
|
|
588
|
+
for (auto c : fixed_values) {
|
|
589
|
+
std::cout << c << ", ";
|
|
590
|
+
}
|
|
591
|
+
std::cout << ")." << std::endl;
|
|
592
|
+
}
|
|
593
|
+
if (coordinates_to_compute.size() == 2) {
|
|
594
|
+
compute_2d_hilbert_surface<PersBackend, Structure, Filtration, dtype, index_type>(thread_stuff,
|
|
595
|
+
out, // assumes its a zero tensor
|
|
596
|
+
grid_shape,
|
|
597
|
+
degrees,
|
|
598
|
+
coordinates_to_compute[0],
|
|
599
|
+
coordinates_to_compute[1],
|
|
600
|
+
fixed_values,
|
|
601
|
+
mobius_inverion,
|
|
602
|
+
zero_pad, ignore_inf);
|
|
603
|
+
return;
|
|
604
|
+
}
|
|
605
|
+
|
|
606
|
+
// coordinate to iterate.size --
|
|
607
|
+
auto coordinate_to_iterate = coordinates_to_compute.back();
|
|
608
|
+
coordinates_to_compute.pop_back();
|
|
609
|
+
tbb::parallel_for(0, grid_shape[coordinate_to_iterate + 1], [&](index_type z) {
|
|
610
|
+
// Updates fixes values that defines the slice
|
|
611
|
+
std::vector<index_type> _fixed_values = fixed_values; // TODO : do not copy this //thread local
|
|
612
|
+
_fixed_values[coordinate_to_iterate] = z;
|
|
613
|
+
_rec_get_hilbert_surface<PersBackend, Structure, Filtration, dtype, index_type>(
|
|
614
|
+
thread_stuff, out, grid_shape, degrees, coordinates_to_compute, _fixed_values, mobius_inverion, zero_pad, ignore_inf);
|
|
615
|
+
});
|
|
616
|
+
// rmq : with mobius_inversion + rec, the coordinates to compute size is 2 =>
|
|
617
|
+
// first coord is always the initial 1st coord.
|
|
618
|
+
// => inversion is only needed for coords > 2
|
|
619
|
+
}
|
|
620
|
+
|
|
621
|
+
template <typename PersBackend, typename Structure, typename Filtration, typename dtype, typename index_type>
|
|
622
|
+
void get_hilbert_surface(truc_interface::Truc<PersBackend, Structure, Filtration> &slicer,
|
|
623
|
+
const tensor::static_tensor_view<dtype, index_type> &out, // assumes its a zero tensor
|
|
624
|
+
const std::vector<index_type> &grid_shape,
|
|
625
|
+
const std::vector<index_type> °rees,
|
|
626
|
+
std::vector<index_type> coordinates_to_compute,
|
|
627
|
+
const std::vector<index_type> &fixed_values,
|
|
628
|
+
const bool mobius_inverion = true,
|
|
629
|
+
const bool zero_pad = false,
|
|
630
|
+
const bool ignore_inf = true) {
|
|
631
|
+
|
|
632
|
+
if (degrees.size() == 0) return;
|
|
633
|
+
// wrapper arount the rec version, that initialize the thread variables.
|
|
634
|
+
if (coordinates_to_compute.size() < 2)
|
|
635
|
+
throw std::logic_error("Not implemented for " + std::to_string(coordinates_to_compute.size()) + "<2 parameters.");
|
|
636
|
+
using ThreadSafe = typename truc_interface::Truc<PersBackend, Structure, Filtration>::ThreadSafe;
|
|
637
|
+
ThreadSafe slicer_thread(slicer);
|
|
638
|
+
std::vector<index_type> coordinates_container(slicer_thread.num_parameters() + 1); // +1 for degree
|
|
639
|
+
// coordinates_container.reserve(fixed_values.size()+1);
|
|
640
|
+
// coordinates_container.push_back(0); // degree
|
|
641
|
+
// for (auto c : fixed_values) coordinates_container.push_back(c);
|
|
642
|
+
std::pair<ThreadSafe, std::vector<index_type>> thread_data_initialization = {slicer_thread, coordinates_container};
|
|
643
|
+
tbb::enumerable_thread_specific<std::pair<ThreadSafe, std::vector<index_type>>> thread_stuff(
|
|
644
|
+
thread_data_initialization); // this has a fixed size, so
|
|
645
|
+
// init should be benefic
|
|
646
|
+
_rec_get_hilbert_surface<PersBackend, Structure, Filtration, dtype, index_type>(
|
|
647
|
+
thread_stuff, out, grid_shape, degrees, coordinates_to_compute, fixed_values, mobius_inverion, zero_pad, ignore_inf);
|
|
648
|
+
}
|
|
649
|
+
|
|
650
|
+
template <typename PersBackend,
|
|
651
|
+
typename Structure,
|
|
652
|
+
typename Filtration,
|
|
653
|
+
typename dtype,
|
|
654
|
+
typename indices_type,
|
|
655
|
+
typename... Args>
|
|
656
|
+
void get_hilbert_surface_python(truc_interface::Truc<PersBackend, Structure, Filtration> &slicer,
|
|
657
|
+
dtype *data_ptr,
|
|
658
|
+
std::vector<indices_type> grid_shape,
|
|
659
|
+
const std::vector<indices_type> degrees,
|
|
660
|
+
const bool mobius_inversion,
|
|
661
|
+
const bool zero_pad,
|
|
662
|
+
const bool ignore_inf,
|
|
663
|
+
indices_type n_jobs) {
|
|
664
|
+
const bool verbose = false;
|
|
665
|
+
if (degrees.size() == 0) return;
|
|
666
|
+
// const bool verbose = false;
|
|
667
|
+
// auto &st_multi =
|
|
668
|
+
// get_simplextree_from_pointer<python_interface::interface_multi<Filtration>>(simplextree_ptr);
|
|
669
|
+
tensor::static_tensor_view<dtype, indices_type> container(data_ptr, grid_shape); // assumes its a zero tensor
|
|
670
|
+
int num_parameters = slicer.num_parameters();
|
|
671
|
+
std::vector<indices_type> coordinates_to_compute(num_parameters);
|
|
672
|
+
for (auto i = 0u; i < coordinates_to_compute.size(); i++) coordinates_to_compute[i] = i;
|
|
673
|
+
// for (auto [c,i] : std::views::zip(coordinates_to_compute,
|
|
674
|
+
// std::views::iota(0,st_multi.get_number_of_parameters()))) c=i; // NIK apple
|
|
675
|
+
// clang
|
|
676
|
+
std::vector<indices_type> fixed_values(num_parameters);
|
|
677
|
+
|
|
678
|
+
if (verbose) {
|
|
679
|
+
std::cout << "Container shape : ";
|
|
680
|
+
for (auto r : container.get_resolution()) std::cout << r << ", ";
|
|
681
|
+
std::cout << "\nContainer size : " << container.size();
|
|
682
|
+
std::cout << "\nComputing hilbert invariant ...";
|
|
683
|
+
}
|
|
684
|
+
if (zero_pad) {
|
|
685
|
+
// +1 is bc degree is on first axis.
|
|
686
|
+
for (auto i = 1; i < num_parameters + 1; i++)
|
|
687
|
+
grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
688
|
+
// for (auto i : std::views::iota(1,st_multi.get_number_of_parameters()+1))
|
|
689
|
+
// grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
690
|
+
}
|
|
691
|
+
|
|
692
|
+
oneapi::tbb::task_arena arena(PersBackend::is_vine ? 1 : n_jobs); // limits the number of threads
|
|
693
|
+
arena.execute([&] {
|
|
694
|
+
get_hilbert_surface(
|
|
695
|
+
slicer, container, grid_shape, degrees, coordinates_to_compute, fixed_values, mobius_inversion, zero_pad, ignore_inf);
|
|
696
|
+
});
|
|
697
|
+
|
|
698
|
+
if (mobius_inversion)
|
|
699
|
+
for (indices_type axis = 2u; axis < num_parameters + 1; axis++) container.differentiate(axis);
|
|
700
|
+
return;
|
|
701
|
+
}
|
|
702
|
+
|
|
703
|
+
template <typename PersBackend,
|
|
704
|
+
typename Structure,
|
|
705
|
+
typename Filtration,
|
|
706
|
+
typename dtype,
|
|
707
|
+
typename indices_type,
|
|
708
|
+
typename... Args>
|
|
709
|
+
std::pair<std::vector<std::vector<indices_type>>, std::vector<dtype>> get_hilbert_signed_measure(
|
|
710
|
+
truc_interface::Truc<PersBackend, Structure, Filtration> &slicer,
|
|
711
|
+
dtype *data_ptr,
|
|
712
|
+
std::vector<indices_type> grid_shape,
|
|
713
|
+
const std::vector<indices_type> degrees,
|
|
714
|
+
bool zero_pad = false,
|
|
715
|
+
indices_type n_jobs = 0,
|
|
716
|
+
const bool verbose = false,
|
|
717
|
+
const bool ignore_inf = true){
|
|
718
|
+
if (degrees.size() == 0) return {{}, {}};
|
|
719
|
+
// const bool verbose = false;
|
|
720
|
+
// auto &st_multi =
|
|
721
|
+
// get_simplextree_from_pointer<python_interface::interface_multi<Filtration>>(simplextree_ptr);
|
|
722
|
+
tensor::static_tensor_view<dtype, indices_type> container(data_ptr, grid_shape); // assumes its a zero tensor
|
|
723
|
+
std::vector<indices_type> coordinates_to_compute(slicer.num_parameters());
|
|
724
|
+
for (auto i = 0u; i < coordinates_to_compute.size(); i++) coordinates_to_compute[i] = i;
|
|
725
|
+
// for (auto [c,i] : std::views::zip(coordinates_to_compute,
|
|
726
|
+
// std::views::iota(0,st_multi.get_number_of_parameters()))) c=i; // NIK apple
|
|
727
|
+
// clang
|
|
728
|
+
std::vector<indices_type> fixed_values(slicer.num_parameters());
|
|
729
|
+
|
|
730
|
+
if (verbose) {
|
|
731
|
+
std::cout << "Container shape : ";
|
|
732
|
+
for (auto r : container.get_resolution()) std::cout << r << ", ";
|
|
733
|
+
std::cout << "\nContainer size : " << container.size();
|
|
734
|
+
std::cout << "\nComputing hilbert invariant ..." << std::flush;
|
|
735
|
+
}
|
|
736
|
+
if (zero_pad) {
|
|
737
|
+
// +1 is bc degree is on first axis.
|
|
738
|
+
for (auto i = 1u; i < slicer.num_parameters() + 1; i++)
|
|
739
|
+
grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
740
|
+
// for (auto i : std::views::iota(1,st_multi.get_number_of_parameters()+1))
|
|
741
|
+
// grid_shape[i]--; // get hilbert surface computes according to grid_shape.
|
|
742
|
+
}
|
|
743
|
+
|
|
744
|
+
oneapi::tbb::task_arena arena(PersBackend::is_vine ? 1 : n_jobs); // limits the number of threads
|
|
745
|
+
arena.execute([&] {
|
|
746
|
+
get_hilbert_surface(slicer, container, grid_shape, degrees, coordinates_to_compute, fixed_values, true, zero_pad, ignore_inf);
|
|
747
|
+
});
|
|
748
|
+
|
|
749
|
+
if (verbose) {
|
|
750
|
+
std::cout << "Done.\n";
|
|
751
|
+
std::cout << "Computing mobius inversion ..." << std::flush;
|
|
752
|
+
}
|
|
753
|
+
|
|
754
|
+
// for (indices_type axis :
|
|
755
|
+
// std::views::iota(2,st_multi.get_number_of_parameters()+1)) // +1 for the
|
|
756
|
+
// degree in axis 0
|
|
757
|
+
for (indices_type axis = 2; axis < static_cast<indices_type>(slicer.num_parameters() + 1); axis++)
|
|
758
|
+
container.differentiate(axis);
|
|
759
|
+
if (verbose) {
|
|
760
|
+
std::cout << "Done.\n";
|
|
761
|
+
std::cout << "Sparsifying the measure ..." << std::flush;
|
|
762
|
+
}
|
|
763
|
+
auto raw_signed_measure = container.sparsify();
|
|
764
|
+
if (verbose) {
|
|
765
|
+
std::cout << "Done." << std::endl;
|
|
766
|
+
}
|
|
767
|
+
return raw_signed_measure;
|
|
768
|
+
}
|
|
769
|
+
}}} // namespace Gudhi::multiparameter::hilbert_function
|