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
@@ -1,164 +1,164 @@
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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 matrix_row_access.h
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- * @author Hannah Schreiber
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- * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_row_access class and
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- * @ref Gudhi::persistence_matrix::Dummy_matrix_row_access structure.
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- */
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-
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- #ifndef PM_BASE_MATRIX_RA_H
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- #define PM_BASE_MATRIX_RA_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 Matrix_row_access, when the the row access is not enabled.
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- */
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- struct Dummy_matrix_row_access
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- {
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- Dummy_matrix_row_access([[maybe_unused]] unsigned int numberOfRows = 0){};
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-
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- friend void swap([[maybe_unused]] Dummy_matrix_row_access& d1, [[maybe_unused]] Dummy_matrix_row_access& d2) {}
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- };
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-
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- /**
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- * @class Matrix_row_access matrix_row_access.h gudhi/Persistence_matrix/matrix_row_access.h
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- * @ingroup persistence_matrix
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- *
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- * @brief Class managing the row access for the inheriting matrix.
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- *
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- * @tparam Row Either boost::intrusive::list<Matrix_entry,...> if @ref PersistenceMatrixOptions::has_intrusive_rows
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- * is true, or std::set<Matrix_entry, RowEntryComp> otherwise.
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- * @tparam Row_container Either std::map<Index,Row> if @ref PersistenceMatrixOptions::has_removable_rows is
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- * true, or std::vector<Row> otherwise.
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- * @tparam has_removable_rows Value of @ref PersistenceMatrixOptions::has_removable_rows.
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- * @tparam ID_index @ref IDIdx index type.
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- */
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- template <typename Row, typename Row_container, bool has_removable_rows, typename ID_index>
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- class Matrix_row_access
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- {
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- public:
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- /**
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- * @brief Default constructor.
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- */
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- Matrix_row_access() : rows_(new Row_container()){};
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- /**
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- * @brief Constructor reserving space for the given number of rows.
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- *
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- * Has only an effect if @ref PersistenceMatrixOptions::has_removable_rows is false.
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- *
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- * @param numberOfRows Number of rows to reserve space for.
66
- */
67
- Matrix_row_access(unsigned int numberOfRows) : rows_(new Row_container()) {
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- if constexpr (!has_removable_rows) {
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- rows_->resize(numberOfRows);
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- }
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- }
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- /**
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- * @brief Copy constructor.
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- *
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- * @param toCopy Matrix to copy.
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- */
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- Matrix_row_access(const Matrix_row_access& toCopy)
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- : rows_(new Row_container()) // as the matrix is rebuild, the rows should not be copied.
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- {
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- if constexpr (!has_removable_rows) {
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- rows_->resize(toCopy.rows_->size());
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- }
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- }
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- /**
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- * @brief Move constructor.
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- *
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- * @param other Matrix to move.
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- */
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- Matrix_row_access(Matrix_row_access&& other) noexcept : rows_(std::exchange(other.rows_, nullptr)) {}
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- /**
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- * @brief Destructor.
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- */
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- ~Matrix_row_access() { delete rows_; }
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-
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- /**
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- * @brief Returns the row at the given @ref rowindex "row index".
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- * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
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- *
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- * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
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- * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
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- * @return Reference to the row.
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- */
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- Row& get_row(ID_index rowIndex) {
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- if constexpr (has_removable_rows) {
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- return rows_->at(rowIndex);
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- } else {
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- return rows_->operator[](rowIndex);
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- }
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- }
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- /**
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- * @brief Returns the row at the given @ref rowindex "row index".
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- * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
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- *
114
- * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
115
- * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
116
- * @return Const reference to the row.
117
- */
118
- const Row& get_row(ID_index rowIndex) const {
119
- if constexpr (has_removable_rows) {
120
- return rows_->at(rowIndex);
121
- } else {
122
- return rows_->operator[](rowIndex);
123
- }
124
- }
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- /**
126
- * @brief Only available if @ref PersistenceMatrixOptions::has_removable_rows is true. Removes the given row
127
- * from the row container if the row exists and is empty.
128
- *
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- * @param rowIndex @ref rowindex "Row index" of the row to remove.
130
- */
131
- void erase_empty_row(ID_index rowIndex) {
132
- static_assert(has_removable_rows, "'erase_empty_row' is not implemented for the chosen options.");
133
-
134
- auto it = rows_->find(rowIndex);
135
- if (it != rows_->end() && it->second.empty()) rows_->erase(it);
136
- }
137
-
138
- /**
139
- * @brief Assign operator.
140
- */
141
- Matrix_row_access& operator=(const Matrix_row_access& other) {
142
- if constexpr (has_removable_rows)
143
- rows_->reserve(other.rows_->size());
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- else
145
- rows_->resize(other.rows_->size());
146
- return *this;
147
- }
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- /**
149
- * @brief Swap operator.
150
- */
151
- friend void swap(Matrix_row_access& matrix1, Matrix_row_access& matrix2) { std::swap(matrix1.rows_, matrix2.rows_); }
152
-
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- protected:
154
- /**
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- * @brief Row container. A pointer to facilitate column swaps when two matrices are swapped.
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- * Has to be destroyed after matrix_, therefore has to be inherited.
157
- */
158
- Row_container* rows_;
159
- };
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-
161
- } // namespace persistence_matrix
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- } // namespace Gudhi
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-
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- #endif // PM_BASE_MATRIX_RA_H
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+ /* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
2
+ * See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
3
+ * Author(s): 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):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
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+
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+ /**
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+ * @file matrix_row_access.h
13
+ * @author Hannah Schreiber
14
+ * @brief Contains the @ref Gudhi::persistence_matrix::Matrix_row_access class and
15
+ * @ref Gudhi::persistence_matrix::Dummy_matrix_row_access structure.
16
+ */
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+
18
+ #ifndef PM_BASE_MATRIX_RA_H
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+ #define PM_BASE_MATRIX_RA_H
20
+
21
+ #include <utility> //std::move
22
+
23
+ namespace Gudhi {
24
+ namespace persistence_matrix {
25
+
26
+ /**
27
+ * @ingroup persistence_matrix
28
+ *
29
+ * @brief Empty structure.
30
+ * Inherited instead of @ref Matrix_row_access, when the the row access is not enabled.
31
+ */
32
+ struct Dummy_matrix_row_access
33
+ {
34
+ Dummy_matrix_row_access([[maybe_unused]] unsigned int numberOfRows = 0){};
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+
36
+ friend void swap([[maybe_unused]] Dummy_matrix_row_access& d1, [[maybe_unused]] Dummy_matrix_row_access& d2) {}
37
+ };
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+
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+ /**
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+ * @class Matrix_row_access matrix_row_access.h gudhi/Persistence_matrix/matrix_row_access.h
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+ * @ingroup persistence_matrix
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+ *
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+ * @brief Class managing the row access for the inheriting matrix.
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+ *
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+ * @tparam Row Either boost::intrusive::list<Matrix_entry,...> if @ref PersistenceMatrixOptions::has_intrusive_rows
46
+ * is true, or std::set<Matrix_entry, RowEntryComp> otherwise.
47
+ * @tparam Row_container Either std::map<Index,Row> if @ref PersistenceMatrixOptions::has_removable_rows is
48
+ * true, or std::vector<Row> otherwise.
49
+ * @tparam has_removable_rows Value of @ref PersistenceMatrixOptions::has_removable_rows.
50
+ * @tparam ID_index @ref IDIdx index type.
51
+ */
52
+ template <typename Row, typename Row_container, bool has_removable_rows, typename ID_index>
53
+ class Matrix_row_access
54
+ {
55
+ public:
56
+ /**
57
+ * @brief Default constructor.
58
+ */
59
+ Matrix_row_access() : rows_(new Row_container()){};
60
+ /**
61
+ * @brief Constructor reserving space for the given number of rows.
62
+ *
63
+ * Has only an effect if @ref PersistenceMatrixOptions::has_removable_rows is false.
64
+ *
65
+ * @param numberOfRows Number of rows to reserve space for.
66
+ */
67
+ Matrix_row_access(unsigned int numberOfRows) : rows_(new Row_container()) {
68
+ if constexpr (!has_removable_rows) {
69
+ rows_->resize(numberOfRows);
70
+ }
71
+ }
72
+ /**
73
+ * @brief Copy constructor.
74
+ *
75
+ * @param toCopy Matrix to copy.
76
+ */
77
+ Matrix_row_access(const Matrix_row_access& toCopy)
78
+ : rows_(new Row_container()) // as the matrix is rebuild, the rows should not be copied.
79
+ {
80
+ if constexpr (!has_removable_rows) {
81
+ rows_->resize(toCopy.rows_->size());
82
+ }
83
+ }
84
+ /**
85
+ * @brief Move constructor.
86
+ *
87
+ * @param other Matrix to move.
88
+ */
89
+ Matrix_row_access(Matrix_row_access&& other) noexcept : rows_(std::exchange(other.rows_, nullptr)) {}
90
+ /**
91
+ * @brief Destructor.
92
+ */
93
+ ~Matrix_row_access() { delete rows_; }
94
+
95
+ /**
96
+ * @brief Returns the row at the given @ref rowindex "row index".
97
+ * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
98
+ *
99
+ * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
100
+ * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
101
+ * @return Reference to the row.
102
+ */
103
+ Row& get_row(ID_index rowIndex) {
104
+ if constexpr (has_removable_rows) {
105
+ return rows_->at(rowIndex);
106
+ } else {
107
+ return rows_->operator[](rowIndex);
108
+ }
109
+ }
110
+ /**
111
+ * @brief Returns the row at the given @ref rowindex "row index".
112
+ * The type of the row depends on the choosen options, see @ref PersistenceMatrixOptions::has_intrusive_rows.
113
+ *
114
+ * @param rowIndex @ref rowindex "Row index" of the row to return: @ref IDIdx for @ref chainmatrix "chain matrices"
115
+ * or updated @ref IDIdx for @ref boundarymatrix "boundary matrices" if swaps occurred.
116
+ * @return Const reference to the row.
117
+ */
118
+ const Row& get_row(ID_index rowIndex) const {
119
+ if constexpr (has_removable_rows) {
120
+ return rows_->at(rowIndex);
121
+ } else {
122
+ return rows_->operator[](rowIndex);
123
+ }
124
+ }
125
+ /**
126
+ * @brief Only available if @ref PersistenceMatrixOptions::has_removable_rows is true. Removes the given row
127
+ * from the row container if the row exists and is empty.
128
+ *
129
+ * @param rowIndex @ref rowindex "Row index" of the row to remove.
130
+ */
131
+ void erase_empty_row(ID_index rowIndex) {
132
+ static_assert(has_removable_rows, "'erase_empty_row' is not implemented for the chosen options.");
133
+
134
+ auto it = rows_->find(rowIndex);
135
+ if (it != rows_->end() && it->second.empty()) rows_->erase(it);
136
+ }
137
+
138
+ /**
139
+ * @brief Assign operator.
140
+ */
141
+ Matrix_row_access& operator=(const Matrix_row_access& other) {
142
+ if constexpr (has_removable_rows)
143
+ rows_->reserve(other.rows_->size());
144
+ else
145
+ rows_->resize(other.rows_->size());
146
+ return *this;
147
+ }
148
+ /**
149
+ * @brief Swap operator.
150
+ */
151
+ friend void swap(Matrix_row_access& matrix1, Matrix_row_access& matrix2) { std::swap(matrix1.rows_, matrix2.rows_); }
152
+
153
+ protected:
154
+ /**
155
+ * @brief Row container. A pointer to facilitate column swaps when two matrices are swapped.
156
+ * Has to be destroyed after matrix_, therefore has to be inherited.
157
+ */
158
+ Row_container* rows_;
159
+ };
160
+
161
+ } // namespace persistence_matrix
162
+ } // namespace Gudhi
163
+
164
+ #endif // PM_BASE_MATRIX_RA_H
@@ -1,156 +1,156 @@
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 ru_pairing.h
13
- * @author Hannah Schreiber
14
- * @brief Contains the @ref Gudhi::persistence_matrix::RU_pairing class and
15
- * @ref Gudhi::persistence_matrix::Dummy_ru_pairing structure.
16
- */
17
-
18
- #ifndef PM_RU_PAIRING_H
19
- #define PM_RU_PAIRING_H
20
-
21
- #include <unordered_map>
22
-
23
- #include "boundary_cell_position_to_id_mapper.h"
24
-
25
- namespace Gudhi {
26
- namespace persistence_matrix {
27
-
28
- /**
29
- * @ingroup persistence_matrix
30
- *
31
- * @brief Empty structure.
32
- * Inherited instead of @ref RU_pairing, when the computation of the barcode was not enabled or if the pairing
33
- * is already managed by the vine update classes.
34
- */
35
- struct Dummy_ru_pairing
36
- {
37
- friend void swap([[maybe_unused]] Dummy_ru_pairing& d1, [[maybe_unused]] Dummy_ru_pairing& d2) {}
38
- };
39
-
40
- /**
41
- * @class RU_pairing ru_pairing.h gudhi/Persistence_matrix/ru_pairing.h
42
- * @ingroup persistence_matrix
43
- *
44
- * @brief Class managing the barcode for @ref RU_matrix if the option was enabled.
45
- *
46
- * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
47
- */
48
- template <class Master_matrix>
49
- class RU_pairing : public std::conditional<
50
- Master_matrix::Option_list::has_removable_columns,
51
- Cell_position_to_ID_mapper<typename Master_matrix::ID_index, typename Master_matrix::Pos_index>,
52
- Dummy_pos_mapper
53
- >::type
54
- {
55
- protected:
56
- using Pos_index = typename Master_matrix::Pos_index;
57
- using ID_index = typename Master_matrix::ID_index;
58
- //PIDM = Position to ID Map
59
- using PIDM = typename std::conditional<Master_matrix::Option_list::has_removable_columns,
60
- Cell_position_to_ID_mapper<ID_index, Pos_index>,
61
- Dummy_pos_mapper
62
- >::type;
63
-
64
- public:
65
- using Barcode = typename Master_matrix::Barcode; /**< Barcode type. */
66
-
67
- /**
68
- * @brief Default constructor.
69
- */
70
- RU_pairing() : PIDM() {}
71
-
72
- /**
73
- * @brief Returns the current barcode which is maintained at any insertion, removal or vine swap.
74
- *
75
- * @return Const reference to the barcode.
76
- */
77
- const Barcode& get_current_barcode() const { return barcode_; }
78
-
79
- /**
80
- * @brief Swap operator.
81
- */
82
- friend void swap(RU_pairing& pairing1, RU_pairing& pairing2) {
83
- swap(static_cast<PIDM&>(pairing1), static_cast<PIDM&>(pairing2));
84
- pairing1.barcode_.swap(pairing2.barcode_);
85
- pairing1.indexToBar_.swap(pairing2.indexToBar_);
86
- pairing1.idToPosition_.swap(pairing2.idToPosition_);
87
- }
88
-
89
- protected:
90
- using Dimension = typename Master_matrix::Dimension;
91
- using Dictionary = typename Master_matrix::Bar_dictionary;
92
-
93
- Barcode barcode_; /**< Bar container. */
94
- Dictionary indexToBar_; /**< Map from @ref MatIdx index to bar index. */
95
- /**
96
- * @brief Map from cell ID to cell position. Only stores a pair if ID != position.
97
- */
98
- std::unordered_map<ID_index, Pos_index> idToPosition_; //TODO: test other map types
99
-
100
- void _update_barcode(ID_index birthPivot, Pos_index death) {
101
- auto it = idToPosition_.find(birthPivot);
102
- Pos_index pivotBirth = it == idToPosition_.end() ? birthPivot : it->second;
103
- if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
104
- barcode_[indexToBar_[pivotBirth]].death = death;
105
- indexToBar_.push_back(indexToBar_[pivotBirth]);
106
- } else {
107
- auto& barIt = indexToBar_.at(pivotBirth);
108
- barIt->death = death;
109
- indexToBar_.try_emplace(death, barIt); // list so iterators are stable
110
- }
111
- }
112
-
113
- void _add_bar(Dimension dim, Pos_index birth) {
114
- barcode_.emplace_back(birth, -1, dim);
115
- if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
116
- indexToBar_.push_back(barcode_.size() - 1);
117
- } else {
118
- indexToBar_.try_emplace(birth, --barcode_.end());
119
- }
120
- }
121
-
122
- void _remove_last(Pos_index eventIndex) {
123
- static_assert(Master_matrix::Option_list::has_removable_columns, "_remove_last not available.");
124
-
125
- if constexpr (Master_matrix::hasFixedBarcode) {
126
- auto& bar = barcode_[indexToBar_[eventIndex]];
127
- if (bar.death == static_cast<Pos_index>(-1)) { // birth
128
- barcode_.pop_back(); // sorted by birth and eventIndex has to be the highest one
129
- } else { // death
130
- bar.death = -1;
131
- };
132
- indexToBar_.pop_back();
133
- } else { // birth order eventually shuffled by vine updates. No sort possible to keep the matchings.
134
- auto it = indexToBar_.find(eventIndex);
135
- typename Barcode::iterator bar = it->second;
136
-
137
- if (bar->death == static_cast<Pos_index>(-1))
138
- barcode_.erase(bar);
139
- else
140
- bar->death = -1;
141
-
142
- indexToBar_.erase(it);
143
- }
144
-
145
- auto it = PIDM::map_.find(eventIndex);
146
- if (it != PIDM::map_.end()){
147
- idToPosition_.erase(it->second);
148
- PIDM::map_.erase(it);
149
- }
150
- }
151
- };
152
-
153
- } // namespace persistence_matrix
154
- } // namespace Gudhi
155
-
156
- #endif // PM_RU_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 ru_pairing.h
13
+ * @author Hannah Schreiber
14
+ * @brief Contains the @ref Gudhi::persistence_matrix::RU_pairing class and
15
+ * @ref Gudhi::persistence_matrix::Dummy_ru_pairing structure.
16
+ */
17
+
18
+ #ifndef PM_RU_PAIRING_H
19
+ #define PM_RU_PAIRING_H
20
+
21
+ #include <unordered_map>
22
+
23
+ #include "boundary_cell_position_to_id_mapper.h"
24
+
25
+ namespace Gudhi {
26
+ namespace persistence_matrix {
27
+
28
+ /**
29
+ * @ingroup persistence_matrix
30
+ *
31
+ * @brief Empty structure.
32
+ * Inherited instead of @ref RU_pairing, when the computation of the barcode was not enabled or if the pairing
33
+ * is already managed by the vine update classes.
34
+ */
35
+ struct Dummy_ru_pairing
36
+ {
37
+ friend void swap([[maybe_unused]] Dummy_ru_pairing& d1, [[maybe_unused]] Dummy_ru_pairing& d2) {}
38
+ };
39
+
40
+ /**
41
+ * @class RU_pairing ru_pairing.h gudhi/Persistence_matrix/ru_pairing.h
42
+ * @ingroup persistence_matrix
43
+ *
44
+ * @brief Class managing the barcode for @ref RU_matrix if the option was enabled.
45
+ *
46
+ * @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
47
+ */
48
+ template <class Master_matrix>
49
+ class RU_pairing : public std::conditional<
50
+ Master_matrix::Option_list::has_removable_columns,
51
+ Cell_position_to_ID_mapper<typename Master_matrix::ID_index, typename Master_matrix::Pos_index>,
52
+ Dummy_pos_mapper
53
+ >::type
54
+ {
55
+ protected:
56
+ using Pos_index = typename Master_matrix::Pos_index;
57
+ using ID_index = typename Master_matrix::ID_index;
58
+ //PIDM = Position to ID Map
59
+ using PIDM = typename std::conditional<Master_matrix::Option_list::has_removable_columns,
60
+ Cell_position_to_ID_mapper<ID_index, Pos_index>,
61
+ Dummy_pos_mapper
62
+ >::type;
63
+
64
+ public:
65
+ using Barcode = typename Master_matrix::Barcode; /**< Barcode type. */
66
+
67
+ /**
68
+ * @brief Default constructor.
69
+ */
70
+ RU_pairing() : PIDM() {}
71
+
72
+ /**
73
+ * @brief Returns the current barcode which is maintained at any insertion, removal or vine swap.
74
+ *
75
+ * @return Const reference to the barcode.
76
+ */
77
+ const Barcode& get_current_barcode() const { return barcode_; }
78
+
79
+ /**
80
+ * @brief Swap operator.
81
+ */
82
+ friend void swap(RU_pairing& pairing1, RU_pairing& pairing2) {
83
+ swap(static_cast<PIDM&>(pairing1), static_cast<PIDM&>(pairing2));
84
+ pairing1.barcode_.swap(pairing2.barcode_);
85
+ pairing1.indexToBar_.swap(pairing2.indexToBar_);
86
+ pairing1.idToPosition_.swap(pairing2.idToPosition_);
87
+ }
88
+
89
+ protected:
90
+ using Dimension = typename Master_matrix::Dimension;
91
+ using Dictionary = typename Master_matrix::Bar_dictionary;
92
+
93
+ Barcode barcode_; /**< Bar container. */
94
+ Dictionary indexToBar_; /**< Map from @ref MatIdx index to bar index. */
95
+ /**
96
+ * @brief Map from cell ID to cell position. Only stores a pair if ID != position.
97
+ */
98
+ std::unordered_map<ID_index, Pos_index> idToPosition_; //TODO: test other map types
99
+
100
+ void _update_barcode(ID_index birthPivot, Pos_index death) {
101
+ auto it = idToPosition_.find(birthPivot);
102
+ Pos_index pivotBirth = it == idToPosition_.end() ? birthPivot : it->second;
103
+ if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
104
+ barcode_[indexToBar_[pivotBirth]].death = death;
105
+ indexToBar_.push_back(indexToBar_[pivotBirth]);
106
+ } else {
107
+ auto& barIt = indexToBar_.at(pivotBirth);
108
+ barIt->death = death;
109
+ indexToBar_.try_emplace(death, barIt); // list so iterators are stable
110
+ }
111
+ }
112
+
113
+ void _add_bar(Dimension dim, Pos_index birth) {
114
+ barcode_.emplace_back(birth, -1, dim);
115
+ if constexpr (Master_matrix::hasFixedBarcode || !Master_matrix::Option_list::has_removable_columns) {
116
+ indexToBar_.push_back(barcode_.size() - 1);
117
+ } else {
118
+ indexToBar_.try_emplace(birth, --barcode_.end());
119
+ }
120
+ }
121
+
122
+ void _remove_last(Pos_index eventIndex) {
123
+ static_assert(Master_matrix::Option_list::has_removable_columns, "_remove_last not available.");
124
+
125
+ if constexpr (Master_matrix::hasFixedBarcode) {
126
+ auto& bar = barcode_[indexToBar_[eventIndex]];
127
+ if (bar.death == static_cast<Pos_index>(-1)) { // birth
128
+ barcode_.pop_back(); // sorted by birth and eventIndex has to be the highest one
129
+ } else { // death
130
+ bar.death = -1;
131
+ };
132
+ indexToBar_.pop_back();
133
+ } else { // birth order eventually shuffled by vine updates. No sort possible to keep the matchings.
134
+ auto it = indexToBar_.find(eventIndex);
135
+ typename Barcode::iterator bar = it->second;
136
+
137
+ if (bar->death == static_cast<Pos_index>(-1))
138
+ barcode_.erase(bar);
139
+ else
140
+ bar->death = -1;
141
+
142
+ indexToBar_.erase(it);
143
+ }
144
+
145
+ auto it = PIDM::map_.find(eventIndex);
146
+ if (it != PIDM::map_.end()){
147
+ idToPosition_.erase(it->second);
148
+ PIDM::map_.erase(it);
149
+ }
150
+ }
151
+ };
152
+
153
+ } // namespace persistence_matrix
154
+ } // namespace Gudhi
155
+
156
+ #endif // PM_RU_PAIRING_H