multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.0__cp311-cp311-win_amd64.whl

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  1. multipers/__init__.py +33 -31
  2. multipers/_signed_measure_meta.py +430 -430
  3. multipers/_slicer_meta.py +211 -212
  4. multipers/data/MOL2.py +458 -458
  5. multipers/data/UCR.py +18 -18
  6. multipers/data/graphs.py +466 -466
  7. multipers/data/immuno_regions.py +27 -27
  8. multipers/data/pytorch2simplextree.py +90 -90
  9. multipers/data/shape3d.py +101 -101
  10. multipers/data/synthetic.py +113 -111
  11. multipers/distances.py +198 -198
  12. multipers/filtration_conversions.pxd.tp +84 -84
  13. multipers/filtrations/__init__.py +18 -0
  14. multipers/filtrations/filtrations.py +289 -0
  15. multipers/filtrations.pxd +224 -224
  16. multipers/function_rips.cp311-win_amd64.pyd +0 -0
  17. multipers/function_rips.pyx +105 -105
  18. multipers/grids.cp311-win_amd64.pyd +0 -0
  19. multipers/grids.pyx +350 -350
  20. multipers/gudhi/Persistence_slices_interface.h +132 -132
  21. multipers/gudhi/Simplex_tree_interface.h +239 -245
  22. multipers/gudhi/Simplex_tree_multi_interface.h +516 -561
  23. multipers/gudhi/cubical_to_boundary.h +59 -59
  24. multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -450
  25. multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -1070
  26. multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -579
  27. multipers/gudhi/gudhi/Debug_utils.h +45 -45
  28. multipers/gudhi/gudhi/Fields/Multi_field.h +484 -484
  29. multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -455
  30. multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -450
  31. multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -531
  32. multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -507
  33. multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -531
  34. multipers/gudhi/gudhi/Fields/Z2_field.h +355 -355
  35. multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -376
  36. multipers/gudhi/gudhi/Fields/Zp_field.h +420 -420
  37. multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -400
  38. multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -418
  39. multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -337
  40. multipers/gudhi/gudhi/Matrix.h +2107 -2107
  41. multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -1038
  42. multipers/gudhi/gudhi/Multi_persistence/Box.h +171 -171
  43. multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -282
  44. multipers/gudhi/gudhi/Off_reader.h +173 -173
  45. multipers/gudhi/gudhi/One_critical_filtration.h +1432 -1431
  46. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -769
  47. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -686
  48. multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -842
  49. multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -1350
  50. multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -1105
  51. multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -859
  52. multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -910
  53. multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -139
  54. multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -230
  55. multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -211
  56. multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -60
  57. multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -60
  58. multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -136
  59. multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -190
  60. multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -616
  61. multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -150
  62. multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -106
  63. multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -219
  64. multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -327
  65. multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -1140
  66. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -934
  67. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -934
  68. multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -980
  69. multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -1092
  70. multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -192
  71. multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -921
  72. multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -1093
  73. multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -1012
  74. multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -1244
  75. multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -186
  76. multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -164
  77. multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -156
  78. multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -376
  79. multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -540
  80. multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -118
  81. multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -173
  82. multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -128
  83. multipers/gudhi/gudhi/Persistent_cohomology.h +745 -745
  84. multipers/gudhi/gudhi/Points_off_io.h +171 -171
  85. multipers/gudhi/gudhi/Simple_object_pool.h +69 -69
  86. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -463
  87. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -83
  88. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -106
  89. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -277
  90. multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -62
  91. multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -27
  92. multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -62
  93. multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -157
  94. multipers/gudhi/gudhi/Simplex_tree.h +2794 -2794
  95. multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -163
  96. multipers/gudhi/gudhi/distance_functions.h +62 -62
  97. multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -104
  98. multipers/gudhi/gudhi/persistence_interval.h +253 -253
  99. multipers/gudhi/gudhi/persistence_matrix_options.h +170 -170
  100. multipers/gudhi/gudhi/reader_utils.h +367 -367
  101. multipers/gudhi/mma_interface_coh.h +256 -255
  102. multipers/gudhi/mma_interface_h0.h +223 -231
  103. multipers/gudhi/mma_interface_matrix.h +284 -282
  104. multipers/gudhi/naive_merge_tree.h +536 -575
  105. multipers/gudhi/scc_io.h +310 -289
  106. multipers/gudhi/truc.h +890 -888
  107. multipers/io.cp311-win_amd64.pyd +0 -0
  108. multipers/io.pyx +711 -711
  109. multipers/ml/accuracies.py +90 -90
  110. multipers/ml/convolutions.py +520 -520
  111. multipers/ml/invariants_with_persistable.py +79 -79
  112. multipers/ml/kernels.py +176 -176
  113. multipers/ml/mma.py +713 -714
  114. multipers/ml/one.py +472 -472
  115. multipers/ml/point_clouds.py +352 -346
  116. multipers/ml/signed_measures.py +1589 -1589
  117. multipers/ml/sliced_wasserstein.py +461 -461
  118. multipers/ml/tools.py +113 -113
  119. multipers/mma_structures.cp311-win_amd64.pyd +0 -0
  120. multipers/mma_structures.pxd +127 -127
  121. multipers/mma_structures.pyx +4 -4
  122. multipers/mma_structures.pyx.tp +1085 -1085
  123. multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -93
  124. multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -97
  125. multipers/multi_parameter_rank_invariant/function_rips.h +322 -322
  126. multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -769
  127. multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -148
  128. multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -369
  129. multipers/multiparameter_edge_collapse.py +41 -41
  130. multipers/multiparameter_module_approximation/approximation.h +2296 -2295
  131. multipers/multiparameter_module_approximation/combinatory.h +129 -129
  132. multipers/multiparameter_module_approximation/debug.h +107 -107
  133. multipers/multiparameter_module_approximation/format_python-cpp.h +286 -286
  134. multipers/multiparameter_module_approximation/heap_column.h +238 -238
  135. multipers/multiparameter_module_approximation/images.h +79 -79
  136. multipers/multiparameter_module_approximation/list_column.h +174 -174
  137. multipers/multiparameter_module_approximation/list_column_2.h +232 -232
  138. multipers/multiparameter_module_approximation/ru_matrix.h +347 -347
  139. multipers/multiparameter_module_approximation/set_column.h +135 -135
  140. multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -36
  141. multipers/multiparameter_module_approximation/unordered_set_column.h +166 -166
  142. multipers/multiparameter_module_approximation/utilities.h +403 -419
  143. multipers/multiparameter_module_approximation/vector_column.h +223 -223
  144. multipers/multiparameter_module_approximation/vector_matrix.h +331 -331
  145. multipers/multiparameter_module_approximation/vineyards.h +464 -464
  146. multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -649
  147. multipers/multiparameter_module_approximation.cp311-win_amd64.pyd +0 -0
  148. multipers/multiparameter_module_approximation.pyx +216 -217
  149. multipers/pickle.py +90 -53
  150. multipers/plots.py +342 -334
  151. multipers/point_measure.cp311-win_amd64.pyd +0 -0
  152. multipers/point_measure.pyx +322 -320
  153. multipers/simplex_tree_multi.cp311-win_amd64.pyd +0 -0
  154. multipers/simplex_tree_multi.pxd +133 -133
  155. multipers/simplex_tree_multi.pyx +18 -15
  156. multipers/simplex_tree_multi.pyx.tp +1939 -1935
  157. multipers/slicer.cp311-win_amd64.pyd +0 -0
  158. multipers/slicer.pxd +81 -20
  159. multipers/slicer.pxd.tp +215 -214
  160. multipers/slicer.pyx +1091 -308
  161. multipers/slicer.pyx.tp +924 -914
  162. multipers/tensor/tensor.h +672 -672
  163. multipers/tensor.pxd +13 -13
  164. multipers/test.pyx +44 -44
  165. multipers/tests/__init__.py +57 -57
  166. multipers/torch/diff_grids.py +217 -217
  167. multipers/torch/rips_density.py +310 -304
  168. {multipers-2.2.3.dist-info → multipers-2.3.0.dist-info}/LICENSE +21 -21
  169. {multipers-2.2.3.dist-info → multipers-2.3.0.dist-info}/METADATA +21 -11
  170. multipers-2.3.0.dist-info/RECORD +182 -0
  171. multipers/tests/test_diff_helper.py +0 -73
  172. multipers/tests/test_hilbert_function.py +0 -82
  173. multipers/tests/test_mma.py +0 -83
  174. multipers/tests/test_point_clouds.py +0 -49
  175. multipers/tests/test_python-cpp_conversion.py +0 -82
  176. multipers/tests/test_signed_betti.py +0 -181
  177. multipers/tests/test_signed_measure.py +0 -89
  178. multipers/tests/test_simplextreemulti.py +0 -221
  179. multipers/tests/test_slicer.py +0 -221
  180. multipers-2.2.3.dist-info/RECORD +0 -189
  181. {multipers-2.2.3.dist-info → multipers-2.3.0.dist-info}/WHEEL +0 -0
  182. {multipers-2.2.3.dist-info → multipers-2.3.0.dist-info}/top_level.txt +0 -0
@@ -1,136 +1,136 @@
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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): Hannah Schreiber
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- *
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- * Copyright (C) 2022-24 Inria
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- *
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- * Modification(s):
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- * - YYYY/MM Author: Description of the modification
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- */
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-
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- /**
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- * @file chain_pairing.h
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- * @author Hannah Schreiber
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- * @brief Contains the @ref Gudhi::persistence_matrix::Chain_pairing class and
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- * @ref Gudhi::persistence_matrix::Dummy_chain_pairing structure.
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- */
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-
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- #ifndef PM_CHAIN_PAIRING_H
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- #define PM_CHAIN_PAIRING_H
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-
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- #include <utility> //std::move
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-
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- namespace Gudhi {
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- namespace persistence_matrix {
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-
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- /**
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- * @ingroup persistence_matrix
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- *
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- * @brief Empty structure.
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- * Inherited instead of @ref Chain_pairing, when the computation of the barcode was not enabled or if the pairing
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- * is already managed by the vine update classes.
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- */
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- struct Dummy_chain_pairing
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- {
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- friend void swap([[maybe_unused]] Dummy_chain_pairing& d1, [[maybe_unused]] Dummy_chain_pairing& d2) {}
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- };
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-
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- /**
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- * @class Chain_pairing chain_pairing.h gudhi/Persistence_matrix/chain_pairing.h
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- * @ingroup persistence_matrix
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- *
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- * @brief Class managing the barcode for @ref Chain_matrix if the option was enabled.
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- *
44
- * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
45
- */
46
- template <class Master_matrix>
47
- class Chain_pairing
48
- {
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- public:
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- using Barcode = typename Master_matrix::Barcode; /**< Barcode type. */
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- using Dimension = typename Master_matrix::Dimension; /**< Dimension value type. */
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-
53
- /**
54
- * @brief Default constructor.
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- */
56
- Chain_pairing();
57
- /**
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- * @brief Copy constructor.
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- *
60
- * @param matrixToCopy Matrix to copy.
61
- */
62
- Chain_pairing(const Chain_pairing& matrixToCopy);
63
- /**
64
- * @brief Move constructor.
65
- *
66
- * @param other Matrix to move.
67
- */
68
- Chain_pairing(Chain_pairing&& other) noexcept;
69
-
70
- /**
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- * @brief Returns the current barcode which is maintained at any insertion, removal or vine swap.
72
- *
73
- * @return Const reference to the barcode.
74
- */
75
- const Barcode& get_current_barcode() const;
76
-
77
- /**
78
- * @brief Assign operator.
79
- */
80
- Chain_pairing& operator=(Chain_pairing other);
81
- /**
82
- * @brief Swap operator.
83
- */
84
- friend void swap(Chain_pairing& pairing1, Chain_pairing& pairing2) {
85
- pairing1.barcode_.swap(pairing2.barcode_);
86
- pairing1.indexToBar_.swap(pairing2.indexToBar_);
87
- std::swap(pairing1.nextPosition_, pairing2.nextPosition_);
88
- }
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-
90
- protected:
91
- using Dictionary = typename Master_matrix::Bar_dictionary;
92
- using Pos_index = typename Master_matrix::Pos_index;
93
-
94
- Barcode barcode_; /**< Bar container. */
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- Dictionary indexToBar_; /**< Map from @ref MatIdx index to bar index. */
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- Pos_index nextPosition_; /**< Next relative position in the filtration. */
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- };
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-
99
- template <class Master_matrix>
100
- inline Chain_pairing<Master_matrix>::Chain_pairing() : nextPosition_(0)
101
- {}
102
-
103
- template <class Master_matrix>
104
- inline Chain_pairing<Master_matrix>::Chain_pairing(const Chain_pairing& matrixToCopy)
105
- : barcode_(matrixToCopy.barcode_),
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- indexToBar_(matrixToCopy.indexToBar_),
107
- nextPosition_(matrixToCopy.nextPosition_)
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- {}
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-
110
- template <class Master_matrix>
111
- inline Chain_pairing<Master_matrix>::Chain_pairing(Chain_pairing<Master_matrix>&& other) noexcept
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- : barcode_(std::move(other.barcode_)),
113
- indexToBar_(std::move(other.indexToBar_)),
114
- nextPosition_(std::exchange(other.nextPosition_, 0))
115
- {}
116
-
117
- template <class Master_matrix>
118
- inline const typename Chain_pairing<Master_matrix>::Barcode& Chain_pairing<Master_matrix>::get_current_barcode()
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- const
120
- {
121
- return barcode_;
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- }
123
-
124
- template <class Master_matrix>
125
- inline Chain_pairing<Master_matrix>& Chain_pairing<Master_matrix>::operator=(Chain_pairing<Master_matrix> other)
126
- {
127
- barcode_.swap(other.barcode_);
128
- indexToBar_.swap(other.indexToBar_);
129
- std::swap(nextPosition_, other.nextPosition_);
130
- return *this;
131
- }
132
-
133
- } // namespace persistence_matrix
134
- } // namespace Gudhi
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-
136
- #endif // PM_CHAIN_PAIRING_H
1
+ /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
+ * Author(s): Hannah Schreiber
4
+ *
5
+ * Copyright (C) 2022-24 Inria
6
+ *
7
+ * Modification(s):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
10
+
11
+ /**
12
+ * @file chain_pairing.h
13
+ * @author Hannah Schreiber
14
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_pairing class and
15
+ * @ref Gudhi::persistence_matrix::Dummy_chain_pairing structure.
16
+ */
17
+
18
+ #ifndef PM_CHAIN_PAIRING_H
19
+ #define PM_CHAIN_PAIRING_H
20
+
21
+ #include <utility> //std::move
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+
23
+ namespace Gudhi {
24
+ namespace persistence_matrix {
25
+
26
+ /**
27
+ * @ingroup persistence_matrix
28
+ *
29
+ * @brief Empty structure.
30
+ * Inherited instead of @ref Chain_pairing, when the computation of the barcode was not enabled or if the pairing
31
+ * is already managed by the vine update classes.
32
+ */
33
+ struct Dummy_chain_pairing
34
+ {
35
+ friend void swap([[maybe_unused]] Dummy_chain_pairing& d1, [[maybe_unused]] Dummy_chain_pairing& d2) {}
36
+ };
37
+
38
+ /**
39
+ * @class Chain_pairing chain_pairing.h gudhi/Persistence_matrix/chain_pairing.h
40
+ * @ingroup persistence_matrix
41
+ *
42
+ * @brief Class managing the barcode for @ref Chain_matrix if the option was enabled.
43
+ *
44
+ * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
45
+ */
46
+ template <class Master_matrix>
47
+ class Chain_pairing
48
+ {
49
+ public:
50
+ using Barcode = typename Master_matrix::Barcode; /**< Barcode type. */
51
+ using Dimension = typename Master_matrix::Dimension; /**< Dimension value type. */
52
+
53
+ /**
54
+ * @brief Default constructor.
55
+ */
56
+ Chain_pairing();
57
+ /**
58
+ * @brief Copy constructor.
59
+ *
60
+ * @param matrixToCopy Matrix to copy.
61
+ */
62
+ Chain_pairing(const Chain_pairing& matrixToCopy);
63
+ /**
64
+ * @brief Move constructor.
65
+ *
66
+ * @param other Matrix to move.
67
+ */
68
+ Chain_pairing(Chain_pairing&& other) noexcept;
69
+
70
+ /**
71
+ * @brief Returns the current barcode which is maintained at any insertion, removal or vine swap.
72
+ *
73
+ * @return Const reference to the barcode.
74
+ */
75
+ const Barcode& get_current_barcode() const;
76
+
77
+ /**
78
+ * @brief Assign operator.
79
+ */
80
+ Chain_pairing& operator=(Chain_pairing other);
81
+ /**
82
+ * @brief Swap operator.
83
+ */
84
+ friend void swap(Chain_pairing& pairing1, Chain_pairing& pairing2) {
85
+ pairing1.barcode_.swap(pairing2.barcode_);
86
+ pairing1.indexToBar_.swap(pairing2.indexToBar_);
87
+ std::swap(pairing1.nextPosition_, pairing2.nextPosition_);
88
+ }
89
+
90
+ protected:
91
+ using Dictionary = typename Master_matrix::Bar_dictionary;
92
+ using Pos_index = typename Master_matrix::Pos_index;
93
+
94
+ Barcode barcode_; /**< Bar container. */
95
+ Dictionary indexToBar_; /**< Map from @ref MatIdx index to bar index. */
96
+ Pos_index nextPosition_; /**< Next relative position in the filtration. */
97
+ };
98
+
99
+ template <class Master_matrix>
100
+ inline Chain_pairing<Master_matrix>::Chain_pairing() : nextPosition_(0)
101
+ {}
102
+
103
+ template <class Master_matrix>
104
+ inline Chain_pairing<Master_matrix>::Chain_pairing(const Chain_pairing& matrixToCopy)
105
+ : barcode_(matrixToCopy.barcode_),
106
+ indexToBar_(matrixToCopy.indexToBar_),
107
+ nextPosition_(matrixToCopy.nextPosition_)
108
+ {}
109
+
110
+ template <class Master_matrix>
111
+ inline Chain_pairing<Master_matrix>::Chain_pairing(Chain_pairing<Master_matrix>&& other) noexcept
112
+ : barcode_(std::move(other.barcode_)),
113
+ indexToBar_(std::move(other.indexToBar_)),
114
+ nextPosition_(std::exchange(other.nextPosition_, 0))
115
+ {}
116
+
117
+ template <class Master_matrix>
118
+ inline const typename Chain_pairing<Master_matrix>::Barcode& Chain_pairing<Master_matrix>::get_current_barcode()
119
+ const
120
+ {
121
+ return barcode_;
122
+ }
123
+
124
+ template <class Master_matrix>
125
+ inline Chain_pairing<Master_matrix>& Chain_pairing<Master_matrix>::operator=(Chain_pairing<Master_matrix> other)
126
+ {
127
+ barcode_.swap(other.barcode_);
128
+ indexToBar_.swap(other.indexToBar_);
129
+ std::swap(nextPosition_, other.nextPosition_);
130
+ return *this;
131
+ }
132
+
133
+ } // namespace persistence_matrix
134
+ } // namespace Gudhi
135
+
136
+ #endif // PM_CHAIN_PAIRING_H
@@ -1,190 +1,190 @@
1
- /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
- * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
- * Author(s): Hannah Schreiber
4
- *
5
- * Copyright (C) 2022-24 Inria
6
- *
7
- * Modification(s):
8
- * - YYYY/MM Author: Description of the modification
9
- */
10
-
11
- /**
12
- * @file chain_rep_cycles.h
13
- * @author Hannah Schreiber
14
- * @brief Contains the @ref Gudhi::persistence_matrix::Chain_representative_cycles class and
15
- * @ref Gudhi::persistence_matrix::Dummy_chain_representative_cycles structure.
16
- */
17
-
18
- #ifndef PM_CHAIN_REP_CYCLES_H
19
- #define PM_CHAIN_REP_CYCLES_H
20
-
21
- #include <utility> //std::move
22
- #include <algorithm> //std::sort
23
- #include <vector>
24
-
25
- namespace Gudhi {
26
- namespace persistence_matrix {
27
-
28
- /**
29
- * @ingroup persistence_matrix
30
- *
31
- * @brief Empty structure.
32
- * Inherited instead of @ref Chain_representative_cycles, when the computation of the representative cycles
33
- * were not enabled.
34
- */
35
- struct Dummy_chain_representative_cycles
36
- {
37
- friend void swap([[maybe_unused]] Dummy_chain_representative_cycles& d1,
38
- [[maybe_unused]] Dummy_chain_representative_cycles& d2) {}
39
- };
40
-
41
- // TODO: add coefficients ? Only Z2 token into account for now.
42
- /**
43
- * @class Chain_representative_cycles chain_rep_cycles.h gudhi/Persistence_matrix/chain_rep_cycles.h
44
- * @ingroup persistence_matrix
45
- *
46
- * @brief Class managing the representative cycles for @ref Chain_matrix if the option was enabled.
47
- *
48
- * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
49
- */
50
- template <class Master_matrix>
51
- class Chain_representative_cycles
52
- {
53
- public:
54
- using Bar = typename Master_matrix::Bar; /**< Bar type. */
55
- using Cycle = typename Master_matrix::Cycle; /**< Cycle type. */
56
- using Column_container = typename Master_matrix::Column_container; /**< Column container type. */
57
-
58
- /**
59
- * @brief Default constructor.
60
- */
61
- Chain_representative_cycles();
62
- /**
63
- * @brief Copy constructor.
64
- *
65
- * @param matrixToCopy Matrix to copy.
66
- */
67
- Chain_representative_cycles(const Chain_representative_cycles& matrixToCopy);
68
- /**
69
- * @brief Move constructor.
70
- *
71
- * @param other Matrix to move.
72
- */
73
- Chain_representative_cycles(Chain_representative_cycles&& other) noexcept;
74
-
75
- /**
76
- * @brief Computes the current representative cycles of the matrix.
77
- */
78
- void update_representative_cycles();
79
-
80
- /**
81
- * @brief Returns the current representative cycles. If the matrix is modified later after the first call,
82
- * @ref update_representative_cycles has to be called to update the returned cycles.
83
- *
84
- * @return A const reference to a vector of @ref Matrix::Cycle containing all representative cycles.
85
- */
86
- const std::vector<Cycle>& get_representative_cycles();
87
- /**
88
- * @brief Returns the representative cycle corresponding to the given bar.
89
- * If the matrix is modified later after the first call,
90
- * @ref update_representative_cycles has to be called to update the returned cycles.
91
- *
92
- * @param bar Bar corresponding to the wanted representative cycle.
93
- * @return A const reference to the representative cycle.
94
- */
95
- const Cycle& get_representative_cycle(const Bar& bar);
96
-
97
- /**
98
- * @brief Assign operator.
99
- */
100
- Chain_representative_cycles& operator=(Chain_representative_cycles other);
101
- /**
102
- * @brief Swap operator.
103
- */
104
- friend void swap(Chain_representative_cycles& base1, Chain_representative_cycles& base2) {
105
- base1.representativeCycles_.swap(base2.representativeCycles_);
106
- base1.birthToCycle_.swap(base2.birthToCycle_);
107
- }
108
-
109
- private:
110
- using Master_chain_matrix = typename Master_matrix::Master_chain_matrix;
111
-
112
- std::vector<Cycle> representativeCycles_; /**< Cycle container. */
113
- std::vector<typename Master_matrix::Index> birthToCycle_; /**< Map from birth index to cycle index. */
114
-
115
- //access to inheriting Chain_matrix class
116
- constexpr Master_chain_matrix* _matrix() { return static_cast<Master_chain_matrix*>(this); }
117
- constexpr const Master_chain_matrix* _matrix() const { return static_cast<const Master_chain_matrix*>(this); }
118
- };
119
-
120
- template <class Master_matrix>
121
- inline Chain_representative_cycles<Master_matrix>::Chain_representative_cycles()
122
- {}
123
-
124
- template <class Master_matrix>
125
- inline Chain_representative_cycles<Master_matrix>::Chain_representative_cycles(
126
- const Chain_representative_cycles<Master_matrix>& matrixToCopy)
127
- : representativeCycles_(matrixToCopy.representativeCycles_), birthToCycle_(matrixToCopy.birthToCycle_)
128
- {}
129
-
130
- template <class Master_matrix>
131
- inline Chain_representative_cycles<Master_matrix>::Chain_representative_cycles(
132
- Chain_representative_cycles<Master_matrix>&& other) noexcept
133
- : representativeCycles_(std::move(other.representativeCycles_)), birthToCycle_(std::move(other.birthToCycle_))
134
- {}
135
-
136
- template <class Master_matrix>
137
- inline void Chain_representative_cycles<Master_matrix>::update_representative_cycles()
138
- {
139
- birthToCycle_.clear();
140
- birthToCycle_.resize(_matrix()->get_number_of_columns(), -1);
141
- representativeCycles_.clear();
142
-
143
- // for birthToCycle_, assumes that @ref PosIdx == @ref IDIdx, ie pivot == birth index... which is not true with
144
- // vineyards
145
- // TODO: with vineyard, there is a @ref IDIdx --> @ref PosIdx map stored. somehow get access to it here
146
- for (typename Master_matrix::ID_index i = 0; i < _matrix()->get_number_of_columns(); i++) {
147
- auto& col = _matrix()->get_column(_matrix()->get_column_with_pivot(i));
148
- if (!col.is_paired() || i < col.get_paired_chain_index()) {
149
- Cycle cycle;
150
- for (auto& c : col) {
151
- cycle.push_back(c.get_row_index());
152
- }
153
- if constexpr (std::is_same_v<typename Master_matrix::Column, typename Master_matrix::Matrix_heap_column> ||
154
- std::is_same_v<typename Master_matrix::Column, typename Master_matrix::Matrix_unordered_set_column>)
155
- std::sort(cycle.begin(), cycle.end());
156
- representativeCycles_.push_back(cycle);
157
- birthToCycle_[i] = representativeCycles_.size() - 1;
158
- }
159
- }
160
- }
161
-
162
- template <class Master_matrix>
163
- inline const std::vector<typename Chain_representative_cycles<Master_matrix>::Cycle>&
164
- Chain_representative_cycles<Master_matrix>::get_representative_cycles()
165
- {
166
- if (representativeCycles_.empty()) update_representative_cycles();
167
- return representativeCycles_;
168
- }
169
-
170
- template <class Master_matrix>
171
- inline const typename Chain_representative_cycles<Master_matrix>::Cycle&
172
- Chain_representative_cycles<Master_matrix>::get_representative_cycle(const Bar& bar)
173
- {
174
- if (representativeCycles_.empty()) update_representative_cycles();
175
- return representativeCycles_[birthToCycle_[bar.birth]];
176
- }
177
-
178
- template <class Master_matrix>
179
- inline Chain_representative_cycles<Master_matrix>& Chain_representative_cycles<Master_matrix>::operator=(
180
- Chain_representative_cycles<Master_matrix> other)
181
- {
182
- representativeCycles_.swap(other.representativeCycles_);
183
- birthToCycle_.swap(other.birthToCycle_);
184
- return *this;
185
- }
186
-
187
- } // namespace persistence_matrix
188
- } // namespace Gudhi
189
-
190
- #endif // PM_CHAIN_REP_CYCLES_H
1
+ /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
+ * Author(s): Hannah Schreiber
4
+ *
5
+ * Copyright (C) 2022-24 Inria
6
+ *
7
+ * Modification(s):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
10
+
11
+ /**
12
+ * @file chain_rep_cycles.h
13
+ * @author Hannah Schreiber
14
+ * @brief Contains the @ref Gudhi::persistence_matrix::Chain_representative_cycles class and
15
+ * @ref Gudhi::persistence_matrix::Dummy_chain_representative_cycles structure.
16
+ */
17
+
18
+ #ifndef PM_CHAIN_REP_CYCLES_H
19
+ #define PM_CHAIN_REP_CYCLES_H
20
+
21
+ #include <utility> //std::move
22
+ #include <algorithm> //std::sort
23
+ #include <vector>
24
+
25
+ namespace Gudhi {
26
+ namespace persistence_matrix {
27
+
28
+ /**
29
+ * @ingroup persistence_matrix
30
+ *
31
+ * @brief Empty structure.
32
+ * Inherited instead of @ref Chain_representative_cycles, when the computation of the representative cycles
33
+ * were not enabled.
34
+ */
35
+ struct Dummy_chain_representative_cycles
36
+ {
37
+ friend void swap([[maybe_unused]] Dummy_chain_representative_cycles& d1,
38
+ [[maybe_unused]] Dummy_chain_representative_cycles& d2) {}
39
+ };
40
+
41
+ // TODO: add coefficients ? Only Z2 token into account for now.
42
+ /**
43
+ * @class Chain_representative_cycles chain_rep_cycles.h gudhi/Persistence_matrix/chain_rep_cycles.h
44
+ * @ingroup persistence_matrix
45
+ *
46
+ * @brief Class managing the representative cycles for @ref Chain_matrix if the option was enabled.
47
+ *
48
+ * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
49
+ */
50
+ template <class Master_matrix>
51
+ class Chain_representative_cycles
52
+ {
53
+ public:
54
+ using Bar = typename Master_matrix::Bar; /**< Bar type. */
55
+ using Cycle = typename Master_matrix::Cycle; /**< Cycle type. */
56
+ using Column_container = typename Master_matrix::Column_container; /**< Column container type. */
57
+
58
+ /**
59
+ * @brief Default constructor.
60
+ */
61
+ Chain_representative_cycles();
62
+ /**
63
+ * @brief Copy constructor.
64
+ *
65
+ * @param matrixToCopy Matrix to copy.
66
+ */
67
+ Chain_representative_cycles(const Chain_representative_cycles& matrixToCopy);
68
+ /**
69
+ * @brief Move constructor.
70
+ *
71
+ * @param other Matrix to move.
72
+ */
73
+ Chain_representative_cycles(Chain_representative_cycles&& other) noexcept;
74
+
75
+ /**
76
+ * @brief Computes the current representative cycles of the matrix.
77
+ */
78
+ void update_representative_cycles();
79
+
80
+ /**
81
+ * @brief Returns the current representative cycles. If the matrix is modified later after the first call,
82
+ * @ref update_representative_cycles has to be called to update the returned cycles.
83
+ *
84
+ * @return A const reference to a vector of @ref Matrix::Cycle containing all representative cycles.
85
+ */
86
+ const std::vector<Cycle>& get_representative_cycles();
87
+ /**
88
+ * @brief Returns the representative cycle corresponding to the given bar.
89
+ * If the matrix is modified later after the first call,
90
+ * @ref update_representative_cycles has to be called to update the returned cycles.
91
+ *
92
+ * @param bar Bar corresponding to the wanted representative cycle.
93
+ * @return A const reference to the representative cycle.
94
+ */
95
+ const Cycle& get_representative_cycle(const Bar& bar);
96
+
97
+ /**
98
+ * @brief Assign operator.
99
+ */
100
+ Chain_representative_cycles& operator=(Chain_representative_cycles other);
101
+ /**
102
+ * @brief Swap operator.
103
+ */
104
+ friend void swap(Chain_representative_cycles& base1, Chain_representative_cycles& base2) {
105
+ base1.representativeCycles_.swap(base2.representativeCycles_);
106
+ base1.birthToCycle_.swap(base2.birthToCycle_);
107
+ }
108
+
109
+ private:
110
+ using Master_chain_matrix = typename Master_matrix::Master_chain_matrix;
111
+
112
+ std::vector<Cycle> representativeCycles_; /**< Cycle container. */
113
+ std::vector<typename Master_matrix::Index> birthToCycle_; /**< Map from birth index to cycle index. */
114
+
115
+ //access to inheriting Chain_matrix class
116
+ constexpr Master_chain_matrix* _matrix() { return static_cast<Master_chain_matrix*>(this); }
117
+ constexpr const Master_chain_matrix* _matrix() const { return static_cast<const Master_chain_matrix*>(this); }
118
+ };
119
+
120
+ template <class Master_matrix>
121
+ inline Chain_representative_cycles<Master_matrix>::Chain_representative_cycles()
122
+ {}
123
+
124
+ template <class Master_matrix>
125
+ inline Chain_representative_cycles<Master_matrix>::Chain_representative_cycles(
126
+ const Chain_representative_cycles<Master_matrix>& matrixToCopy)
127
+ : representativeCycles_(matrixToCopy.representativeCycles_), birthToCycle_(matrixToCopy.birthToCycle_)
128
+ {}
129
+
130
+ template <class Master_matrix>
131
+ inline Chain_representative_cycles<Master_matrix>::Chain_representative_cycles(
132
+ Chain_representative_cycles<Master_matrix>&& other) noexcept
133
+ : representativeCycles_(std::move(other.representativeCycles_)), birthToCycle_(std::move(other.birthToCycle_))
134
+ {}
135
+
136
+ template <class Master_matrix>
137
+ inline void Chain_representative_cycles<Master_matrix>::update_representative_cycles()
138
+ {
139
+ birthToCycle_.clear();
140
+ birthToCycle_.resize(_matrix()->get_number_of_columns(), -1);
141
+ representativeCycles_.clear();
142
+
143
+ // for birthToCycle_, assumes that @ref PosIdx == @ref IDIdx, ie pivot == birth index... which is not true with
144
+ // vineyards
145
+ // TODO: with vineyard, there is a @ref IDIdx --> @ref PosIdx map stored. somehow get access to it here
146
+ for (typename Master_matrix::ID_index i = 0; i < _matrix()->get_number_of_columns(); i++) {
147
+ auto& col = _matrix()->get_column(_matrix()->get_column_with_pivot(i));
148
+ if (!col.is_paired() || i < col.get_paired_chain_index()) {
149
+ Cycle cycle;
150
+ for (auto& c : col) {
151
+ cycle.push_back(c.get_row_index());
152
+ }
153
+ if constexpr (std::is_same_v<typename Master_matrix::Column, typename Master_matrix::Matrix_heap_column> ||
154
+ std::is_same_v<typename Master_matrix::Column, typename Master_matrix::Matrix_unordered_set_column>)
155
+ std::sort(cycle.begin(), cycle.end());
156
+ representativeCycles_.push_back(cycle);
157
+ birthToCycle_[i] = representativeCycles_.size() - 1;
158
+ }
159
+ }
160
+ }
161
+
162
+ template <class Master_matrix>
163
+ inline const std::vector<typename Chain_representative_cycles<Master_matrix>::Cycle>&
164
+ Chain_representative_cycles<Master_matrix>::get_representative_cycles()
165
+ {
166
+ if (representativeCycles_.empty()) update_representative_cycles();
167
+ return representativeCycles_;
168
+ }
169
+
170
+ template <class Master_matrix>
171
+ inline const typename Chain_representative_cycles<Master_matrix>::Cycle&
172
+ Chain_representative_cycles<Master_matrix>::get_representative_cycle(const Bar& bar)
173
+ {
174
+ if (representativeCycles_.empty()) update_representative_cycles();
175
+ return representativeCycles_[birthToCycle_[bar.birth]];
176
+ }
177
+
178
+ template <class Master_matrix>
179
+ inline Chain_representative_cycles<Master_matrix>& Chain_representative_cycles<Master_matrix>::operator=(
180
+ Chain_representative_cycles<Master_matrix> other)
181
+ {
182
+ representativeCycles_.swap(other.representativeCycles_);
183
+ birthToCycle_.swap(other.birthToCycle_);
184
+ return *this;
185
+ }
186
+
187
+ } // namespace persistence_matrix
188
+ } // namespace Gudhi
189
+
190
+ #endif // PM_CHAIN_REP_CYCLES_H