multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.1__cp311-cp311-win_amd64.whl
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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.cp311-win_amd64.pyd +0 -0
- multipers/function_rips.pyx +105 -105
- multipers/grids.cp311-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.cp311-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.cp311-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.cp311-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.cp311-win_amd64.pyd +0 -0
- multipers/point_measure.pyx +322 -320
- multipers/simplex_tree_multi.cp311-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.cp311-win_amd64.pyd +0 -0
- multipers/slicer.pxd +301 -120
- 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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/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
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* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
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* Author(s): Clément Maria
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* Copyright (C) 2014 Inria
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*/
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#ifndef PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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#define PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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#include <boost/intrusive/set.hpp>
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#include <boost/intrusive/list.hpp>
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#include <list>
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namespace Gudhi {
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namespace persistent_cohomology {
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template<typename SimplexKey, typename ArithmeticElement>
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class Persistent_cohomology_column;
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struct cam_h_tag;
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// for horizontal traversal in the CAM
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struct cam_v_tag;
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// for vertical traversal in the CAM
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typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_h_tag>,
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boost::intrusive::link_mode<boost::intrusive::auto_unlink> // allows .unlink()
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> base_hook_cam_h;
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typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_v_tag>,
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boost::intrusive::link_mode<boost::intrusive::normal_link> // faster hook, less safe
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> base_hook_cam_v;
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/** \internal
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* \brief
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*
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*/
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template<typename SimplexKey, typename ArithmeticElement>
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class Persistent_cohomology_cell : public base_hook_cam_h,
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public base_hook_cam_v {
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public:
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template<class T1, class T2> friend class Persistent_cohomology;
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friend class Persistent_cohomology_column<SimplexKey, ArithmeticElement>;
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typedef Persistent_cohomology_column<SimplexKey, ArithmeticElement> Column;
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Persistent_cohomology_cell(SimplexKey key, ArithmeticElement x,
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Column * self_col)
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: key_(key),
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coefficient_(x),
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self_col_(self_col) {
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}
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SimplexKey key_;
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Column * self_col_;
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};
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class Persistent_cohomology_column : public boost::intrusive::set_base_hook<
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boost::intrusive::link_mode<boost::intrusive::normal_link> > {
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typedef Persistent_cohomology_cell<SimplexKey, ArithmeticElement> Cell;
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boost::intrusive::constant_time_size<false>,
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const Persistent_cohomology_column& c2) {
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} // namespace persistent_cohomology
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} // namespace Gudhi
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#endif // PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
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* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
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* Author(s): Clément Maria
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* Copyright (C) 2014 Inria
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*/
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#ifndef PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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#define PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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#include <boost/intrusive/set.hpp>
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#include <boost/intrusive/list.hpp>
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#include <list>
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namespace Gudhi {
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namespace persistent_cohomology {
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template<typename SimplexKey, typename ArithmeticElement>
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class Persistent_cohomology_column;
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struct cam_h_tag;
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// for horizontal traversal in the CAM
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struct cam_v_tag;
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// for vertical traversal in the CAM
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typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_h_tag>,
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boost::intrusive::link_mode<boost::intrusive::auto_unlink> // allows .unlink()
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> base_hook_cam_h;
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typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_v_tag>,
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boost::intrusive::link_mode<boost::intrusive::normal_link> // faster hook, less safe
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> base_hook_cam_v;
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/** \internal
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* \brief
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*
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*/
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template<typename SimplexKey, typename ArithmeticElement>
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class Persistent_cohomology_cell : public base_hook_cam_h,
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public base_hook_cam_v {
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public:
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template<class T1, class T2> friend class Persistent_cohomology;
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friend class Persistent_cohomology_column<SimplexKey, ArithmeticElement>;
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typedef Persistent_cohomology_column<SimplexKey, ArithmeticElement> Column;
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Persistent_cohomology_cell(SimplexKey key, ArithmeticElement x,
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Column * self_col)
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: key_(key),
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coefficient_(x),
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self_col_(self_col) {
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}
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SimplexKey key_;
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ArithmeticElement coefficient_;
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Column * self_col_;
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};
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/*
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* \brief Sparse column for the Compressed Annotation Matrix.
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*
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* The non-zero coefficients of the column are stored in a
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* boost::intrusive::list. Contains a hook to be stored in a
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* boost::intrusive::set.
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*
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* Movable but not Copyable.
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*/
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template<typename SimplexKey, typename ArithmeticElement>
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class Persistent_cohomology_column : public boost::intrusive::set_base_hook<
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boost::intrusive::link_mode<boost::intrusive::normal_link> > {
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template<class T1, class T2> friend class Persistent_cohomology;
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public:
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typedef Persistent_cohomology_cell<SimplexKey, ArithmeticElement> Cell;
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typedef boost::intrusive::list<Cell,
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boost::intrusive::constant_time_size<false>,
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boost::intrusive::base_hook<base_hook_cam_v> > Col_type;
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/** \brief Creates an empty column.*/
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explicit Persistent_cohomology_column(SimplexKey key)
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: col_(),
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class_key_(key) {}
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/** \brief Returns true iff the column is null.*/
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bool is_null() const {
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return col_.empty();
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}
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/** \brief Returns the key of the representative simplex of
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* the set of simplices having this column as annotation vector
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* in the compressed annotation matrix.*/
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SimplexKey class_key() const {
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return class_key_;
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}
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/** \brief Lexicographic comparison of two columns.*/
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friend bool operator<(const Persistent_cohomology_column& c1,
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const Persistent_cohomology_column& c2) {
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typename Col_type::const_iterator it1 = c1.col_.begin();
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typename Col_type::const_iterator it2 = c2.col_.begin();
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while (it1 != c1.col_.end() && it2 != c2.col_.end()) {
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if (it1->key_ == it2->key_) {
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if (it1->coefficient_ == it2->coefficient_) {
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++it1;
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++it2;
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} else {
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return it1->coefficient_ < it2->coefficient_;
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}
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} else {
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return it1->key_ < it2->key_;
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}
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}
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return (it2 != c2.col_.end());
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}
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Col_type col_;
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SimplexKey class_key_;
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};
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} // namespace persistent_cohomology
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} // namespace Gudhi
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#endif // PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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