multipers 2.2.3__cp312-cp312-win_amd64.whl → 2.3.1__cp312-cp312-win_amd64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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- multipers/__init__.py +33 -31
- multipers/_signed_measure_meta.py +430 -430
- multipers/_slicer_meta.py +211 -212
- multipers/data/MOL2.py +458 -458
- multipers/data/UCR.py +18 -18
- multipers/data/graphs.py +466 -466
- multipers/data/immuno_regions.py +27 -27
- multipers/data/pytorch2simplextree.py +90 -90
- multipers/data/shape3d.py +101 -101
- multipers/data/synthetic.py +113 -111
- multipers/distances.py +198 -198
- multipers/filtration_conversions.pxd.tp +84 -84
- multipers/filtrations/__init__.py +18 -0
- multipers/{ml/convolutions.py → filtrations/density.py} +563 -520
- multipers/filtrations/filtrations.py +289 -0
- multipers/filtrations.pxd +224 -224
- multipers/function_rips.cp312-win_amd64.pyd +0 -0
- multipers/function_rips.pyx +105 -105
- multipers/grids.cp312-win_amd64.pyd +0 -0
- multipers/grids.pyx +350 -350
- multipers/gudhi/Persistence_slices_interface.h +132 -132
- multipers/gudhi/Simplex_tree_interface.h +239 -245
- multipers/gudhi/Simplex_tree_multi_interface.h +516 -561
- multipers/gudhi/cubical_to_boundary.h +59 -59
- multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -450
- multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -1070
- multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -579
- multipers/gudhi/gudhi/Debug_utils.h +45 -45
- multipers/gudhi/gudhi/Fields/Multi_field.h +484 -484
- multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -455
- multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -450
- multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -531
- multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -507
- multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -531
- multipers/gudhi/gudhi/Fields/Z2_field.h +355 -355
- multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -376
- multipers/gudhi/gudhi/Fields/Zp_field.h +420 -420
- multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -400
- multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -418
- multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -337
- multipers/gudhi/gudhi/Matrix.h +2107 -2107
- multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -1038
- multipers/gudhi/gudhi/Multi_persistence/Box.h +171 -171
- multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -282
- multipers/gudhi/gudhi/Off_reader.h +173 -173
- multipers/gudhi/gudhi/One_critical_filtration.h +1433 -1431
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -769
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -686
- multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -842
- multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -1350
- multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -1105
- multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -859
- multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -910
- multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -139
- multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -230
- multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -211
- multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -60
- multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -60
- multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -136
- multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -190
- multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -616
- multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -150
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -106
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -219
- multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -327
- multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -1140
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -934
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -934
- multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -980
- multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -1092
- multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -192
- multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -921
- multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -1093
- multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -1012
- multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -1244
- multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -186
- multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -164
- multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -156
- multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -376
- multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -540
- multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -118
- multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -173
- multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -128
- multipers/gudhi/gudhi/Persistent_cohomology.h +745 -745
- multipers/gudhi/gudhi/Points_off_io.h +171 -171
- multipers/gudhi/gudhi/Simple_object_pool.h +69 -69
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -463
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -83
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -106
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -277
- multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -62
- multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -27
- multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -62
- multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -157
- multipers/gudhi/gudhi/Simplex_tree.h +2794 -2794
- multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -163
- multipers/gudhi/gudhi/distance_functions.h +62 -62
- multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -104
- multipers/gudhi/gudhi/persistence_interval.h +253 -253
- multipers/gudhi/gudhi/persistence_matrix_options.h +170 -170
- multipers/gudhi/gudhi/reader_utils.h +367 -367
- multipers/gudhi/mma_interface_coh.h +256 -255
- multipers/gudhi/mma_interface_h0.h +223 -231
- multipers/gudhi/mma_interface_matrix.h +291 -282
- multipers/gudhi/naive_merge_tree.h +536 -575
- multipers/gudhi/scc_io.h +310 -289
- multipers/gudhi/truc.h +957 -888
- multipers/io.cp312-win_amd64.pyd +0 -0
- multipers/io.pyx +714 -711
- multipers/ml/accuracies.py +90 -90
- multipers/ml/invariants_with_persistable.py +79 -79
- multipers/ml/kernels.py +176 -176
- multipers/ml/mma.py +713 -714
- multipers/ml/one.py +472 -472
- multipers/ml/point_clouds.py +352 -346
- multipers/ml/signed_measures.py +1589 -1589
- multipers/ml/sliced_wasserstein.py +461 -461
- multipers/ml/tools.py +113 -113
- multipers/mma_structures.cp312-win_amd64.pyd +0 -0
- multipers/mma_structures.pxd +127 -127
- multipers/mma_structures.pyx +4 -8
- multipers/mma_structures.pyx.tp +1083 -1085
- multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -93
- multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -97
- multipers/multi_parameter_rank_invariant/function_rips.h +322 -322
- multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -769
- multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -148
- multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -369
- multipers/multiparameter_edge_collapse.py +41 -41
- multipers/multiparameter_module_approximation/approximation.h +2298 -2295
- multipers/multiparameter_module_approximation/combinatory.h +129 -129
- multipers/multiparameter_module_approximation/debug.h +107 -107
- multipers/multiparameter_module_approximation/format_python-cpp.h +286 -286
- multipers/multiparameter_module_approximation/heap_column.h +238 -238
- multipers/multiparameter_module_approximation/images.h +79 -79
- multipers/multiparameter_module_approximation/list_column.h +174 -174
- multipers/multiparameter_module_approximation/list_column_2.h +232 -232
- multipers/multiparameter_module_approximation/ru_matrix.h +347 -347
- multipers/multiparameter_module_approximation/set_column.h +135 -135
- multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -36
- multipers/multiparameter_module_approximation/unordered_set_column.h +166 -166
- multipers/multiparameter_module_approximation/utilities.h +403 -419
- multipers/multiparameter_module_approximation/vector_column.h +223 -223
- multipers/multiparameter_module_approximation/vector_matrix.h +331 -331
- multipers/multiparameter_module_approximation/vineyards.h +464 -464
- multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -649
- multipers/multiparameter_module_approximation.cp312-win_amd64.pyd +0 -0
- multipers/multiparameter_module_approximation.pyx +218 -217
- multipers/pickle.py +90 -53
- multipers/plots.py +342 -334
- multipers/point_measure.cp312-win_amd64.pyd +0 -0
- multipers/point_measure.pyx +322 -320
- multipers/simplex_tree_multi.cp312-win_amd64.pyd +0 -0
- multipers/simplex_tree_multi.pxd +133 -133
- multipers/simplex_tree_multi.pyx +115 -48
- multipers/simplex_tree_multi.pyx.tp +1947 -1935
- multipers/slicer.cp312-win_amd64.pyd +0 -0
- multipers/slicer.pxd +281 -100
- multipers/slicer.pxd.tp +218 -214
- multipers/slicer.pyx +1570 -507
- multipers/slicer.pyx.tp +931 -914
- multipers/tensor/tensor.h +672 -672
- multipers/tensor.pxd +13 -13
- multipers/test.pyx +44 -44
- multipers/tests/__init__.py +57 -57
- multipers/torch/diff_grids.py +217 -217
- multipers/torch/rips_density.py +310 -304
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/LICENSE +21 -21
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/METADATA +21 -11
- multipers-2.3.1.dist-info/RECORD +182 -0
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/WHEEL +1 -1
- multipers/tests/test_diff_helper.py +0 -73
- multipers/tests/test_hilbert_function.py +0 -82
- multipers/tests/test_mma.py +0 -83
- multipers/tests/test_point_clouds.py +0 -49
- multipers/tests/test_python-cpp_conversion.py +0 -82
- multipers/tests/test_signed_betti.py +0 -181
- multipers/tests/test_signed_measure.py +0 -89
- multipers/tests/test_simplextreemulti.py +0 -221
- multipers/tests/test_slicer.py +0 -221
- multipers-2.2.3.dist-info/RECORD +0 -189
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/top_level.txt +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 <gudhi/One_critical_filtration.h>
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#include <gudhi/Simplex_tree_multi.h>
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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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namespace Gudhi {
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namespace multiparameter {
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namespace function_rips {
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using value_type = typename python_interface::interface_std::Filtration_value;
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using _multifiltration = typename Gudhi::multi_filtration::One_critical_filtration<value_type>;
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using _multist = python_interface::Simplex_tree_multi_interface<_multifiltration>;
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using interface_multi = _multist;
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std::pair<std::map<value_type, unsigned int>, std::vector<value_type>>
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inline radius_to_coordinate(Simplex_tree_std &st) {
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unsigned int count = 0;
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std::map<value_type, unsigned int> out;
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std::vector<value_type> filtration_values;
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filtration_values.reserve(st.num_simplices());
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for (auto sh : st.filtration_simplex_range()) { // ordered by filtration, so
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// should be sorted
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auto filtration = st.filtration(sh);
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if (!out.contains(filtration)) {
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out[filtration] = count;
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filtration_values.push_back(filtration);
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count++;
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}
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}
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return {out, filtration_values};
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}
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// Takes a standard simplextree and turn it into a simplextreemulti, whose first
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// axis is the rips, and the others are the filtrations of the node at each
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// degree in degrees Assumes that the degrees are sorted, and unique
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std::tuple<_multist,
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std::vector<value_type>, int>
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inline get_degree_filtrations( // also return max_degree,filtration_values
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python_interface::interface_std &st, const std::vector<int> °rees) {
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constexpr const bool verbose = false;
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using filtration_lists = std::vector<std::vector<value_type>>;
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assert(st.dimension() ==
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1); // the st slices will be expanded + collapsed after being filled.
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_multist st_multi;
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std::vector<value_type> rips_filtration_values = {
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0}; // vector that will hold the used filtration values
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rips_filtration_values.reserve(st.num_simplices());
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int max_st_degree = 0;
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int num_degrees = degrees.size();
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Gudhi::multi_persistence::multify(st, st_multi, 0); // puts the st filtration in axis 0 + fitrations for
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// each degrees afterward
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// preprocess
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filtration_lists edge_filtration_of_nodes(st.num_vertices());
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for (auto sh : st.complex_simplex_range()) {
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if (st.dimension() == 0)
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continue;
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value_type filtration = st.filtration(sh);
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for (auto node : st.simplex_vertex_range(sh)) {
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edge_filtration_of_nodes[node].push_back(filtration);
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}
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}
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for (auto &filtrations : edge_filtration_of_nodes) { // todo : parallel ?
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std::sort(filtrations.begin(), filtrations.end());
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max_st_degree = std::max(node_degree, max_st_degree);
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filtrations.resize(std::max(num_degrees, node_degree));
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if constexpr (verbose)
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std::cout << "Filtration of node ";
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for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
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if (degrees[degree_index] < node_degree)
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filtrations[degree_index] = filtrations[degrees[degree_index]];
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else
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filtrations[degree_index] = std::numeric_limits<value_type>::infinity();
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if constexpr (verbose)
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std::cout << filtrations[degree_index] << " ";
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}
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filtrations.resize(num_degrees);
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std::reverse(filtrations.begin(),
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filtrations.end()); // degree is in opposite direction
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for (value_type filtration_value : filtrations)
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rips_filtration_values.push_back(
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filtration_value); // we only do that here to have a smaller grid.
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if constexpr (verbose)
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std::cout << "\n";
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}
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// sort + unique the filtration values
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st.complex_simplex_range()
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.begin(); // waiting for c++23 & zip to remove this garbage
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auto _end = st.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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if (st.dimension(*sh_standard) == 0) // only fill using the node
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continue; // will be filled afterward
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// dimension is 1 by assumption. fill using the node + rips value
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value_type edge_filtration = st.filtration(*sh_standard);
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_multifiltration &edge_degree_rips_filtration =
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st_multi.filtration_mutable(*sh_multi); // the filtration vector to fill
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edge_degree_rips_filtration.resize(num_degrees);
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for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
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value_type edge_filtration_of_degree =
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edge_filtration; // copy as we do the max with edges of degree index
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for (int node : st.simplex_vertex_range(*sh_standard)) {
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edge_filtration_of_degree =
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std::max(edge_filtration_of_degree,
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edge_filtration_of_nodes[node][degree_index]);
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}
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edge_degree_rips_filtration[degree_index] =
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edge_filtration_of_degree; // fills the correct value in the edge
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// filtration
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}
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}
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// fills the dimension 0 simplices
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{ // scope for count;
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for (auto vertex :
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st_multi.complex_vertex_range()) { // should be in increasing order
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auto &vertex_filtration =
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st_multi.filtration_mutable(st_multi.find({vertex}));
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if constexpr (verbose) {
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std::cout << "Setting filtration of node " << vertex << " to ";
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for (auto degree_index = 0u; degree_index < num_degrees;
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degree_index++) {
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std::cout << edge_filtration_of_nodes[vertex][degree_index] << " ";
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}
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std::cout << "\n";
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}
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vertex_filtration.swap(edge_filtration_of_nodes[vertex]);
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}
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}
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148
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return {st_multi, rips_filtration_values, max_st_degree};
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}
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150
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151
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// assumes that the degree is 1
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152
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inline void fill_st_slice(Simplex_tree_std &st_container,
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153
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_multist °ree_rips_st, int degree) {
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154
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auto sh_std = st_container.complex_simplex_range().begin();
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155
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auto sh_multi = degree_rips_st.complex_simplex_range().begin();
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156
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auto sh_end = st_container.complex_simplex_range().end();
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157
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for (; sh_std != sh_end; ++sh_std, ++sh_multi) {
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158
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value_type splx_filtration =
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159
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degree_rips_st.filtration_mutable(*sh_multi)[degree];
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160
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st_container.assign_filtration(*sh_std, splx_filtration);
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}
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return;
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163
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}
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template <typename dtype, typename index_type>
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inline void
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167
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compute_2d_function_rips(_multist &st_multi, // Function rips
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168
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// Simplex_tree_std &_st,
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169
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const tensor::static_tensor_view<dtype, index_type>
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&out, // assumes its a zero tensor
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const std::vector<index_type> degrees, index_type I,
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index_type J, // grid_shape
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bool mobius_inverion, bool zero_pad) {
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constexpr bool verbose = false;
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if constexpr (verbose)
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std::cout << "Grid shape : " << I << " " << J << std::endl;
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178
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// inits default simplextrees
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179
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Simplex_tree_std _st;
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180
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Gudhi::multi_persistence::flatten(_st, st_multi,
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181
|
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-1); // copies the st_multi to a standard 1-pers simplextree
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182
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tbb::enumerable_thread_specific<Simplex_tree_std> thread_simplex_tree(_st);
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183
|
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int max_simplex_dimension =
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184
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*std::max_element(degrees.begin(), degrees.end()) + 1;
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185
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tbb::parallel_for(0, J, [&](index_type function_value) {
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186
|
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auto &st_std = thread_simplex_tree.local();
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187
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fill_st_slice(st_std, st_multi, function_value);
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188
|
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constexpr int num_collapses = 10;
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189
|
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const std::vector<Barcode> barcodes =
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190
|
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compute_dgms(st_std, degrees, num_collapses, max_simplex_dimension);
|
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191
|
-
|
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192
|
-
index_type degree_index = 0;
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193
|
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for (const auto &barcode : barcodes) { // TODO range view cartesian product
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194
|
-
// coordinates_container[0] = degree_index;
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195
|
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for (const auto &bar : barcode) {
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196
|
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auto birth = bar.first; // float
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197
|
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auto death = bar.second;
|
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198
|
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if (birth > I) // some birth can be infinite
|
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199
|
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continue;
|
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200
|
-
|
|
201
|
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if (!mobius_inverion) {
|
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202
|
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index_type shift_value =
|
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203
|
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out.get_cum_resolution()[1]; // degree, x coord, y coord
|
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204
|
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index_type border = I;
|
|
205
|
-
// index_type border = out.get_resolution()[i+1];
|
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206
|
-
// dtype* ptr = &out[coordinates_container];
|
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207
|
-
dtype *ptr = &out[{degree_index, static_cast<index_type>(birth),
|
|
208
|
-
function_value}];
|
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209
|
-
auto stop_value = death > static_cast<value_type>(border)
|
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210
|
-
? border
|
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211
|
-
: static_cast<index_type>(death);
|
|
212
|
-
// Warning : for some reason linux static casts float inf to -min_int
|
|
213
|
-
// so min doesnt work.
|
|
214
|
-
if constexpr (verbose) {
|
|
215
|
-
std::cout << "Adding : (";
|
|
216
|
-
// for (auto stuff : coordinates_container) std::cout << stuff << ",
|
|
217
|
-
// ";
|
|
218
|
-
std::cout << ") With death " << death << " casted at "
|
|
219
|
-
<< static_cast<index_type>(death) << "with threshold at"
|
|
220
|
-
<< stop_value << " with " << border << std::endl;
|
|
221
|
-
}
|
|
222
|
-
for (index_type b = birth; b < stop_value; b++) {
|
|
223
|
-
(*ptr)++; // adds one to the vector
|
|
224
|
-
ptr += shift_value; // shift the pointer to the next element in the
|
|
225
|
-
// segment [birth, death]
|
|
226
|
-
}
|
|
227
|
-
} else {
|
|
228
|
-
// adds birth
|
|
229
|
-
out[{degree_index, static_cast<index_type>(birth), function_value}]++;
|
|
230
|
-
if constexpr (verbose) {
|
|
231
|
-
std::cout << "Coordinate : ";
|
|
232
|
-
// for (auto c : coordinates_container) std::cout << c << ", ";
|
|
233
|
-
std::cout << std::endl;
|
|
234
|
-
std::cout << "axis, death, resolution : " << 1 << ", "
|
|
235
|
-
<< std::to_string(death) << ", "
|
|
236
|
-
<< out.get_resolution()[1];
|
|
237
|
-
std::cout << std::endl;
|
|
238
|
-
}
|
|
239
|
-
// removes death
|
|
240
|
-
if (death < I) {
|
|
241
|
-
out[{degree_index, static_cast<index_type>(death),
|
|
242
|
-
function_value}]--;
|
|
243
|
-
} else if (zero_pad) {
|
|
244
|
-
out[{degree_index, I - 1, function_value}]--;
|
|
245
|
-
}
|
|
246
|
-
}
|
|
247
|
-
}
|
|
248
|
-
degree_index++;
|
|
249
|
-
}
|
|
250
|
-
});
|
|
251
|
-
}
|
|
252
|
-
|
|
253
|
-
// python interface
|
|
254
|
-
|
|
255
|
-
std::pair<std::vector<value_type>, int>
|
|
256
|
-
inline get_degree_rips_st_python(const intptr_t simplextree_ptr,
|
|
257
|
-
const intptr_t st_multi_ptr,
|
|
258
|
-
const std::vector<int> °rees) {
|
|
259
|
-
auto &st_std = python_interface::get_simplextree_from_pointer<python_interface::interface_std>(simplextree_ptr);
|
|
260
|
-
auto &st_multi_python_container =
|
|
261
|
-
python_interface::get_simplextree_from_pointer<_multist>(st_multi_ptr);
|
|
262
|
-
auto [st_multi, rips_filtration_values, max_node_degree] =
|
|
263
|
-
get_degree_filtrations(st_std, degrees);
|
|
264
|
-
st_multi_python_container = std::move(st_multi);
|
|
265
|
-
return {rips_filtration_values, max_node_degree};
|
|
266
|
-
}
|
|
267
|
-
|
|
268
|
-
template <typename dtype, typename indices_type>
|
|
269
|
-
void compute_function_rips_surface_python(
|
|
270
|
-
const intptr_t st_multi_ptr, dtype *data_ptr,
|
|
271
|
-
const std::vector<indices_type> degrees, indices_type I, indices_type J,
|
|
272
|
-
const bool mobius_inversion = false, const bool zero_pad = false,
|
|
273
|
-
indices_type n_jobs = 0) {
|
|
274
|
-
if (degrees.size() == 0)
|
|
275
|
-
return;
|
|
276
|
-
// const bool verbose = false;
|
|
277
|
-
auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
|
|
278
|
-
tensor::static_tensor_view<dtype, indices_type> container(
|
|
279
|
-
data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
|
|
280
|
-
if (zero_pad) {
|
|
281
|
-
I--;
|
|
282
|
-
J--;
|
|
283
|
-
}
|
|
284
|
-
|
|
285
|
-
oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
|
|
286
|
-
arena.execute([&] {
|
|
287
|
-
compute_2d_function_rips(st_multi, container, degrees, I, J,
|
|
288
|
-
mobius_inversion, zero_pad);
|
|
289
|
-
});
|
|
290
|
-
if (mobius_inversion)
|
|
291
|
-
container.differentiate(2); // degree,x axis (already inversed), y axis
|
|
292
|
-
}
|
|
293
|
-
|
|
294
|
-
template <typename dtype, typename indices_type>
|
|
295
|
-
std::pair<std::vector<std::vector<indices_type>>, std::vector<dtype>>
|
|
296
|
-
compute_function_rips_signed_measure_python(
|
|
297
|
-
const intptr_t st_multi_ptr, dtype *data_ptr,
|
|
298
|
-
const std::vector<indices_type> degrees, indices_type I, indices_type J,
|
|
299
|
-
const bool mobius_inversion = false, const bool zero_pad = false,
|
|
300
|
-
indices_type n_jobs = 0) {
|
|
301
|
-
if (degrees.size() == 0)
|
|
302
|
-
return {{}, {}};
|
|
303
|
-
// const bool verbose = false;
|
|
304
|
-
auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
|
|
305
|
-
tensor::static_tensor_view<dtype, indices_type> container(
|
|
306
|
-
data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
|
|
307
|
-
if (zero_pad) {
|
|
308
|
-
I--;
|
|
309
|
-
J--;
|
|
310
|
-
}
|
|
311
|
-
|
|
312
|
-
oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
|
|
313
|
-
arena.execute([&] {
|
|
314
|
-
compute_2d_function_rips(st_multi, container, degrees, I, J,
|
|
315
|
-
mobius_inversion, zero_pad);
|
|
316
|
-
});
|
|
317
|
-
if (mobius_inversion)
|
|
318
|
-
container.differentiate(2); // degree,x axis (already inversed), y axis
|
|
319
|
-
return container.sparsify();
|
|
320
|
-
}
|
|
321
|
-
|
|
322
|
-
}}} // namespace Gudhi::multiparameter::function_rips
|
|
1
|
+
#pragma once
|
|
2
|
+
|
|
3
|
+
#include "Simplex_tree_multi_interface.h"
|
|
4
|
+
#include "multi_parameter_rank_invariant/persistence_slices.h"
|
|
5
|
+
#include "tensor/tensor.h"
|
|
6
|
+
#include <gudhi/One_critical_filtration.h>
|
|
7
|
+
#include <gudhi/Simplex_tree_multi.h>
|
|
8
|
+
#include <oneapi/tbb/enumerable_thread_specific.h>
|
|
9
|
+
#include <oneapi/tbb/parallel_for.h>
|
|
10
|
+
|
|
11
|
+
namespace Gudhi {
|
|
12
|
+
namespace multiparameter {
|
|
13
|
+
namespace function_rips {
|
|
14
|
+
|
|
15
|
+
using value_type = typename python_interface::interface_std::Filtration_value;
|
|
16
|
+
using _multifiltration = typename Gudhi::multi_filtration::One_critical_filtration<value_type>;
|
|
17
|
+
using _multist = python_interface::Simplex_tree_multi_interface<_multifiltration>;
|
|
18
|
+
using interface_multi = _multist;
|
|
19
|
+
|
|
20
|
+
|
|
21
|
+
std::pair<std::map<value_type, unsigned int>, std::vector<value_type>>
|
|
22
|
+
inline radius_to_coordinate(Simplex_tree_std &st) {
|
|
23
|
+
unsigned int count = 0;
|
|
24
|
+
std::map<value_type, unsigned int> out;
|
|
25
|
+
std::vector<value_type> filtration_values;
|
|
26
|
+
filtration_values.reserve(st.num_simplices());
|
|
27
|
+
for (auto sh : st.filtration_simplex_range()) { // ordered by filtration, so
|
|
28
|
+
// should be sorted
|
|
29
|
+
auto filtration = st.filtration(sh);
|
|
30
|
+
if (!out.contains(filtration)) {
|
|
31
|
+
out[filtration] = count;
|
|
32
|
+
filtration_values.push_back(filtration);
|
|
33
|
+
count++;
|
|
34
|
+
}
|
|
35
|
+
}
|
|
36
|
+
return {out, filtration_values};
|
|
37
|
+
}
|
|
38
|
+
|
|
39
|
+
// Takes a standard simplextree and turn it into a simplextreemulti, whose first
|
|
40
|
+
// axis is the rips, and the others are the filtrations of the node at each
|
|
41
|
+
// degree in degrees Assumes that the degrees are sorted, and unique
|
|
42
|
+
|
|
43
|
+
std::tuple<_multist,
|
|
44
|
+
std::vector<value_type>, int>
|
|
45
|
+
inline get_degree_filtrations( // also return max_degree,filtration_values
|
|
46
|
+
python_interface::interface_std &st, const std::vector<int> °rees) {
|
|
47
|
+
constexpr const bool verbose = false;
|
|
48
|
+
using filtration_lists = std::vector<std::vector<value_type>>;
|
|
49
|
+
|
|
50
|
+
assert(st.dimension() ==
|
|
51
|
+
1); // the st slices will be expanded + collapsed after being filled.
|
|
52
|
+
_multist st_multi;
|
|
53
|
+
std::vector<value_type> rips_filtration_values = {
|
|
54
|
+
0}; // vector that will hold the used filtration values
|
|
55
|
+
rips_filtration_values.reserve(st.num_simplices());
|
|
56
|
+
int max_st_degree = 0;
|
|
57
|
+
|
|
58
|
+
int num_degrees = degrees.size();
|
|
59
|
+
Gudhi::multi_persistence::multify(st, st_multi, 0); // puts the st filtration in axis 0 + fitrations for
|
|
60
|
+
// each degrees afterward
|
|
61
|
+
// preprocess
|
|
62
|
+
filtration_lists edge_filtration_of_nodes(st.num_vertices());
|
|
63
|
+
for (auto sh : st.complex_simplex_range()) {
|
|
64
|
+
if (st.dimension() == 0)
|
|
65
|
+
continue;
|
|
66
|
+
value_type filtration = st.filtration(sh);
|
|
67
|
+
for (auto node : st.simplex_vertex_range(sh)) {
|
|
68
|
+
edge_filtration_of_nodes[node].push_back(filtration);
|
|
69
|
+
}
|
|
70
|
+
}
|
|
71
|
+
|
|
72
|
+
for (auto &filtrations : edge_filtration_of_nodes) { // todo : parallel ?
|
|
73
|
+
std::sort(filtrations.begin(), filtrations.end());
|
|
74
|
+
int node_degree = filtrations.size();
|
|
75
|
+
max_st_degree = std::max(node_degree, max_st_degree);
|
|
76
|
+
filtrations.resize(std::max(num_degrees, node_degree));
|
|
77
|
+
if constexpr (verbose)
|
|
78
|
+
std::cout << "Filtration of node ";
|
|
79
|
+
for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
|
|
80
|
+
if (degrees[degree_index] < node_degree)
|
|
81
|
+
filtrations[degree_index] = filtrations[degrees[degree_index]];
|
|
82
|
+
else
|
|
83
|
+
filtrations[degree_index] = std::numeric_limits<value_type>::infinity();
|
|
84
|
+
if constexpr (verbose)
|
|
85
|
+
std::cout << filtrations[degree_index] << " ";
|
|
86
|
+
}
|
|
87
|
+
filtrations.resize(num_degrees);
|
|
88
|
+
std::reverse(filtrations.begin(),
|
|
89
|
+
filtrations.end()); // degree is in opposite direction
|
|
90
|
+
for (value_type filtration_value : filtrations)
|
|
91
|
+
rips_filtration_values.push_back(
|
|
92
|
+
filtration_value); // we only do that here to have a smaller grid.
|
|
93
|
+
if constexpr (verbose)
|
|
94
|
+
std::cout << "\n";
|
|
95
|
+
}
|
|
96
|
+
// sort + unique the filtration values
|
|
97
|
+
std::sort(rips_filtration_values.begin(), rips_filtration_values.end());
|
|
98
|
+
rips_filtration_values.erase(
|
|
99
|
+
std::unique(rips_filtration_values.begin(), rips_filtration_values.end()),
|
|
100
|
+
rips_filtration_values.end());
|
|
101
|
+
|
|
102
|
+
// fills the degree_rips simplextree with lower star
|
|
103
|
+
auto sh_standard =
|
|
104
|
+
st.complex_simplex_range()
|
|
105
|
+
.begin(); // waiting for c++23 & zip to remove this garbage
|
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106
|
+
auto _end = st.complex_simplex_range().end();
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107
|
+
auto sh_multi = st_multi.complex_simplex_range().begin();
|
|
108
|
+
for (; sh_standard != _end; ++sh_multi, ++sh_standard) {
|
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109
|
+
if (st.dimension(*sh_standard) == 0) // only fill using the node
|
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110
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+
continue; // will be filled afterward
|
|
111
|
+
// dimension is 1 by assumption. fill using the node + rips value
|
|
112
|
+
value_type edge_filtration = st.filtration(*sh_standard);
|
|
113
|
+
_multifiltration &edge_degree_rips_filtration =
|
|
114
|
+
st_multi.filtration_mutable(*sh_multi); // the filtration vector to fill
|
|
115
|
+
edge_degree_rips_filtration.resize(num_degrees);
|
|
116
|
+
for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
|
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117
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+
value_type edge_filtration_of_degree =
|
|
118
|
+
edge_filtration; // copy as we do the max with edges of degree index
|
|
119
|
+
for (int node : st.simplex_vertex_range(*sh_standard)) {
|
|
120
|
+
edge_filtration_of_degree =
|
|
121
|
+
std::max(edge_filtration_of_degree,
|
|
122
|
+
edge_filtration_of_nodes[node][degree_index]);
|
|
123
|
+
}
|
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124
|
+
edge_degree_rips_filtration[degree_index] =
|
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125
|
+
edge_filtration_of_degree; // fills the correct value in the edge
|
|
126
|
+
// filtration
|
|
127
|
+
}
|
|
128
|
+
}
|
|
129
|
+
|
|
130
|
+
// fills the dimension 0 simplices
|
|
131
|
+
{ // scope for count;
|
|
132
|
+
for (auto vertex :
|
|
133
|
+
st_multi.complex_vertex_range()) { // should be in increasing order
|
|
134
|
+
auto &vertex_filtration =
|
|
135
|
+
st_multi.filtration_mutable(st_multi.find({vertex}));
|
|
136
|
+
if constexpr (verbose) {
|
|
137
|
+
std::cout << "Setting filtration of node " << vertex << " to ";
|
|
138
|
+
for (auto degree_index = 0u; degree_index < num_degrees;
|
|
139
|
+
degree_index++) {
|
|
140
|
+
std::cout << edge_filtration_of_nodes[vertex][degree_index] << " ";
|
|
141
|
+
}
|
|
142
|
+
std::cout << "\n";
|
|
143
|
+
}
|
|
144
|
+
vertex_filtration.swap(edge_filtration_of_nodes[vertex]);
|
|
145
|
+
}
|
|
146
|
+
}
|
|
147
|
+
|
|
148
|
+
return {st_multi, rips_filtration_values, max_st_degree};
|
|
149
|
+
}
|
|
150
|
+
|
|
151
|
+
// assumes that the degree is 1
|
|
152
|
+
inline void fill_st_slice(Simplex_tree_std &st_container,
|
|
153
|
+
_multist °ree_rips_st, int degree) {
|
|
154
|
+
auto sh_std = st_container.complex_simplex_range().begin();
|
|
155
|
+
auto sh_multi = degree_rips_st.complex_simplex_range().begin();
|
|
156
|
+
auto sh_end = st_container.complex_simplex_range().end();
|
|
157
|
+
for (; sh_std != sh_end; ++sh_std, ++sh_multi) {
|
|
158
|
+
value_type splx_filtration =
|
|
159
|
+
degree_rips_st.filtration_mutable(*sh_multi)[degree];
|
|
160
|
+
st_container.assign_filtration(*sh_std, splx_filtration);
|
|
161
|
+
}
|
|
162
|
+
return;
|
|
163
|
+
}
|
|
164
|
+
|
|
165
|
+
template <typename dtype, typename index_type>
|
|
166
|
+
inline void
|
|
167
|
+
compute_2d_function_rips(_multist &st_multi, // Function rips
|
|
168
|
+
// Simplex_tree_std &_st,
|
|
169
|
+
const tensor::static_tensor_view<dtype, index_type>
|
|
170
|
+
&out, // assumes its a zero tensor
|
|
171
|
+
const std::vector<index_type> degrees, index_type I,
|
|
172
|
+
index_type J, // grid_shape
|
|
173
|
+
bool mobius_inverion, bool zero_pad) {
|
|
174
|
+
constexpr bool verbose = false;
|
|
175
|
+
if constexpr (verbose)
|
|
176
|
+
std::cout << "Grid shape : " << I << " " << J << std::endl;
|
|
177
|
+
|
|
178
|
+
// inits default simplextrees
|
|
179
|
+
Simplex_tree_std _st;
|
|
180
|
+
Gudhi::multi_persistence::flatten(_st, st_multi,
|
|
181
|
+
-1); // copies the st_multi to a standard 1-pers simplextree
|
|
182
|
+
tbb::enumerable_thread_specific<Simplex_tree_std> thread_simplex_tree(_st);
|
|
183
|
+
int max_simplex_dimension =
|
|
184
|
+
*std::max_element(degrees.begin(), degrees.end()) + 1;
|
|
185
|
+
tbb::parallel_for(0, J, [&](index_type function_value) {
|
|
186
|
+
auto &st_std = thread_simplex_tree.local();
|
|
187
|
+
fill_st_slice(st_std, st_multi, function_value);
|
|
188
|
+
constexpr int num_collapses = 10;
|
|
189
|
+
const std::vector<Barcode> barcodes =
|
|
190
|
+
compute_dgms(st_std, degrees, num_collapses, max_simplex_dimension);
|
|
191
|
+
|
|
192
|
+
index_type degree_index = 0;
|
|
193
|
+
for (const auto &barcode : barcodes) { // TODO range view cartesian product
|
|
194
|
+
// coordinates_container[0] = degree_index;
|
|
195
|
+
for (const auto &bar : barcode) {
|
|
196
|
+
auto birth = bar.first; // float
|
|
197
|
+
auto death = bar.second;
|
|
198
|
+
if (birth > I) // some birth can be infinite
|
|
199
|
+
continue;
|
|
200
|
+
|
|
201
|
+
if (!mobius_inverion) {
|
|
202
|
+
index_type shift_value =
|
|
203
|
+
out.get_cum_resolution()[1]; // degree, x coord, y coord
|
|
204
|
+
index_type border = I;
|
|
205
|
+
// index_type border = out.get_resolution()[i+1];
|
|
206
|
+
// dtype* ptr = &out[coordinates_container];
|
|
207
|
+
dtype *ptr = &out[{degree_index, static_cast<index_type>(birth),
|
|
208
|
+
function_value}];
|
|
209
|
+
auto stop_value = death > static_cast<value_type>(border)
|
|
210
|
+
? border
|
|
211
|
+
: static_cast<index_type>(death);
|
|
212
|
+
// Warning : for some reason linux static casts float inf to -min_int
|
|
213
|
+
// so min doesnt work.
|
|
214
|
+
if constexpr (verbose) {
|
|
215
|
+
std::cout << "Adding : (";
|
|
216
|
+
// for (auto stuff : coordinates_container) std::cout << stuff << ",
|
|
217
|
+
// ";
|
|
218
|
+
std::cout << ") With death " << death << " casted at "
|
|
219
|
+
<< static_cast<index_type>(death) << "with threshold at"
|
|
220
|
+
<< stop_value << " with " << border << std::endl;
|
|
221
|
+
}
|
|
222
|
+
for (index_type b = birth; b < stop_value; b++) {
|
|
223
|
+
(*ptr)++; // adds one to the vector
|
|
224
|
+
ptr += shift_value; // shift the pointer to the next element in the
|
|
225
|
+
// segment [birth, death]
|
|
226
|
+
}
|
|
227
|
+
} else {
|
|
228
|
+
// adds birth
|
|
229
|
+
out[{degree_index, static_cast<index_type>(birth), function_value}]++;
|
|
230
|
+
if constexpr (verbose) {
|
|
231
|
+
std::cout << "Coordinate : ";
|
|
232
|
+
// for (auto c : coordinates_container) std::cout << c << ", ";
|
|
233
|
+
std::cout << std::endl;
|
|
234
|
+
std::cout << "axis, death, resolution : " << 1 << ", "
|
|
235
|
+
<< std::to_string(death) << ", "
|
|
236
|
+
<< out.get_resolution()[1];
|
|
237
|
+
std::cout << std::endl;
|
|
238
|
+
}
|
|
239
|
+
// removes death
|
|
240
|
+
if (death < I) {
|
|
241
|
+
out[{degree_index, static_cast<index_type>(death),
|
|
242
|
+
function_value}]--;
|
|
243
|
+
} else if (zero_pad) {
|
|
244
|
+
out[{degree_index, I - 1, function_value}]--;
|
|
245
|
+
}
|
|
246
|
+
}
|
|
247
|
+
}
|
|
248
|
+
degree_index++;
|
|
249
|
+
}
|
|
250
|
+
});
|
|
251
|
+
}
|
|
252
|
+
|
|
253
|
+
// python interface
|
|
254
|
+
|
|
255
|
+
std::pair<std::vector<value_type>, int>
|
|
256
|
+
inline get_degree_rips_st_python(const intptr_t simplextree_ptr,
|
|
257
|
+
const intptr_t st_multi_ptr,
|
|
258
|
+
const std::vector<int> °rees) {
|
|
259
|
+
auto &st_std = python_interface::get_simplextree_from_pointer<python_interface::interface_std>(simplextree_ptr);
|
|
260
|
+
auto &st_multi_python_container =
|
|
261
|
+
python_interface::get_simplextree_from_pointer<_multist>(st_multi_ptr);
|
|
262
|
+
auto [st_multi, rips_filtration_values, max_node_degree] =
|
|
263
|
+
get_degree_filtrations(st_std, degrees);
|
|
264
|
+
st_multi_python_container = std::move(st_multi);
|
|
265
|
+
return {rips_filtration_values, max_node_degree};
|
|
266
|
+
}
|
|
267
|
+
|
|
268
|
+
template <typename dtype, typename indices_type>
|
|
269
|
+
void compute_function_rips_surface_python(
|
|
270
|
+
const intptr_t st_multi_ptr, dtype *data_ptr,
|
|
271
|
+
const std::vector<indices_type> degrees, indices_type I, indices_type J,
|
|
272
|
+
const bool mobius_inversion = false, const bool zero_pad = false,
|
|
273
|
+
indices_type n_jobs = 0) {
|
|
274
|
+
if (degrees.size() == 0)
|
|
275
|
+
return;
|
|
276
|
+
// const bool verbose = false;
|
|
277
|
+
auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
|
|
278
|
+
tensor::static_tensor_view<dtype, indices_type> container(
|
|
279
|
+
data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
|
|
280
|
+
if (zero_pad) {
|
|
281
|
+
I--;
|
|
282
|
+
J--;
|
|
283
|
+
}
|
|
284
|
+
|
|
285
|
+
oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
|
|
286
|
+
arena.execute([&] {
|
|
287
|
+
compute_2d_function_rips(st_multi, container, degrees, I, J,
|
|
288
|
+
mobius_inversion, zero_pad);
|
|
289
|
+
});
|
|
290
|
+
if (mobius_inversion)
|
|
291
|
+
container.differentiate(2); // degree,x axis (already inversed), y axis
|
|
292
|
+
}
|
|
293
|
+
|
|
294
|
+
template <typename dtype, typename indices_type>
|
|
295
|
+
std::pair<std::vector<std::vector<indices_type>>, std::vector<dtype>>
|
|
296
|
+
compute_function_rips_signed_measure_python(
|
|
297
|
+
const intptr_t st_multi_ptr, dtype *data_ptr,
|
|
298
|
+
const std::vector<indices_type> degrees, indices_type I, indices_type J,
|
|
299
|
+
const bool mobius_inversion = false, const bool zero_pad = false,
|
|
300
|
+
indices_type n_jobs = 0) {
|
|
301
|
+
if (degrees.size() == 0)
|
|
302
|
+
return {{}, {}};
|
|
303
|
+
// const bool verbose = false;
|
|
304
|
+
auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
|
|
305
|
+
tensor::static_tensor_view<dtype, indices_type> container(
|
|
306
|
+
data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
|
|
307
|
+
if (zero_pad) {
|
|
308
|
+
I--;
|
|
309
|
+
J--;
|
|
310
|
+
}
|
|
311
|
+
|
|
312
|
+
oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
|
|
313
|
+
arena.execute([&] {
|
|
314
|
+
compute_2d_function_rips(st_multi, container, degrees, I, J,
|
|
315
|
+
mobius_inversion, zero_pad);
|
|
316
|
+
});
|
|
317
|
+
if (mobius_inversion)
|
|
318
|
+
container.differentiate(2); // degree,x axis (already inversed), y axis
|
|
319
|
+
return container.sparsify();
|
|
320
|
+
}
|
|
321
|
+
|
|
322
|
+
}}} // namespace Gudhi::multiparameter::function_rips
|