multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.1__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/{ml/convolutions.py → filtrations/density.py} +563 -520
  15. multipers/filtrations/filtrations.py +289 -0
  16. multipers/filtrations.pxd +224 -224
  17. multipers/function_rips.cp311-win_amd64.pyd +0 -0
  18. multipers/function_rips.pyx +105 -105
  19. multipers/grids.cp311-win_amd64.pyd +0 -0
  20. multipers/grids.pyx +350 -350
  21. multipers/gudhi/Persistence_slices_interface.h +132 -132
  22. multipers/gudhi/Simplex_tree_interface.h +239 -245
  23. multipers/gudhi/Simplex_tree_multi_interface.h +516 -561
  24. multipers/gudhi/cubical_to_boundary.h +59 -59
  25. multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -450
  26. multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -1070
  27. multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -579
  28. multipers/gudhi/gudhi/Debug_utils.h +45 -45
  29. multipers/gudhi/gudhi/Fields/Multi_field.h +484 -484
  30. multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -455
  31. multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -450
  32. multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -531
  33. multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -507
  34. multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -531
  35. multipers/gudhi/gudhi/Fields/Z2_field.h +355 -355
  36. multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -376
  37. multipers/gudhi/gudhi/Fields/Zp_field.h +420 -420
  38. multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -400
  39. multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -418
  40. multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -337
  41. multipers/gudhi/gudhi/Matrix.h +2107 -2107
  42. multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -1038
  43. multipers/gudhi/gudhi/Multi_persistence/Box.h +171 -171
  44. multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -282
  45. multipers/gudhi/gudhi/Off_reader.h +173 -173
  46. multipers/gudhi/gudhi/One_critical_filtration.h +1433 -1431
  47. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -769
  48. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -686
  49. multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -842
  50. multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -1350
  51. multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -1105
  52. multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -859
  53. multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -910
  54. multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -139
  55. multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -230
  56. multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -211
  57. multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -60
  58. multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -60
  59. multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -136
  60. multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -190
  61. multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -616
  62. multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -150
  63. multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -106
  64. multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -219
  65. multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -327
  66. multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -1140
  67. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -934
  68. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -934
  69. multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -980
  70. multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -1092
  71. multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -192
  72. multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -921
  73. multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -1093
  74. multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -1012
  75. multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -1244
  76. multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -186
  77. multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -164
  78. multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -156
  79. multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -376
  80. multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -540
  81. multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -118
  82. multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -173
  83. multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -128
  84. multipers/gudhi/gudhi/Persistent_cohomology.h +745 -745
  85. multipers/gudhi/gudhi/Points_off_io.h +171 -171
  86. multipers/gudhi/gudhi/Simple_object_pool.h +69 -69
  87. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -463
  88. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -83
  89. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -106
  90. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -277
  91. multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -62
  92. multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -27
  93. multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -62
  94. multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -157
  95. multipers/gudhi/gudhi/Simplex_tree.h +2794 -2794
  96. multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -163
  97. multipers/gudhi/gudhi/distance_functions.h +62 -62
  98. multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -104
  99. multipers/gudhi/gudhi/persistence_interval.h +253 -253
  100. multipers/gudhi/gudhi/persistence_matrix_options.h +170 -170
  101. multipers/gudhi/gudhi/reader_utils.h +367 -367
  102. multipers/gudhi/mma_interface_coh.h +256 -255
  103. multipers/gudhi/mma_interface_h0.h +223 -231
  104. multipers/gudhi/mma_interface_matrix.h +291 -282
  105. multipers/gudhi/naive_merge_tree.h +536 -575
  106. multipers/gudhi/scc_io.h +310 -289
  107. multipers/gudhi/truc.h +957 -888
  108. multipers/io.cp311-win_amd64.pyd +0 -0
  109. multipers/io.pyx +714 -711
  110. multipers/ml/accuracies.py +90 -90
  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 -8
  122. multipers/mma_structures.pyx.tp +1083 -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 +2298 -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 +218 -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 +115 -48
  156. multipers/simplex_tree_multi.pyx.tp +1947 -1935
  157. multipers/slicer.cp311-win_amd64.pyd +0 -0
  158. multipers/slicer.pxd +301 -120
  159. multipers/slicer.pxd.tp +218 -214
  160. multipers/slicer.pyx +1570 -507
  161. multipers/slicer.pyx.tp +931 -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-2.3.1.dist-info}/LICENSE +21 -21
  169. {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/METADATA +21 -11
  170. multipers-2.3.1.dist-info/RECORD +182 -0
  171. {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/WHEEL +1 -1
  172. multipers/tests/test_diff_helper.py +0 -73
  173. multipers/tests/test_hilbert_function.py +0 -82
  174. multipers/tests/test_mma.py +0 -83
  175. multipers/tests/test_point_clouds.py +0 -49
  176. multipers/tests/test_python-cpp_conversion.py +0 -82
  177. multipers/tests/test_signed_betti.py +0 -181
  178. multipers/tests/test_signed_measure.py +0 -89
  179. multipers/tests/test_simplextreemulti.py +0 -221
  180. multipers/tests/test_slicer.py +0 -221
  181. multipers-2.2.3.dist-info/RECORD +0 -189
  182. {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/top_level.txt +0 -0
@@ -1,128 +1,128 @@
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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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- *
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- * Copyright (C) 2014 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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- #ifndef PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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- #define PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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-
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- #include <boost/intrusive/set.hpp>
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- #include <boost/intrusive/list.hpp>
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-
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- #include <list>
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-
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- namespace Gudhi {
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-
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- namespace persistent_cohomology {
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-
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- template<typename SimplexKey, typename ArithmeticElement>
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- class Persistent_cohomology_column;
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-
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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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-
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- typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_h_tag>,
32
- boost::intrusive::link_mode<boost::intrusive::auto_unlink> // allows .unlink()
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- > base_hook_cam_h;
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-
35
- typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_v_tag>,
36
- boost::intrusive::link_mode<boost::intrusive::normal_link> // faster hook, less safe
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- > base_hook_cam_v;
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-
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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>
44
- class Persistent_cohomology_cell : public base_hook_cam_h,
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- public base_hook_cam_v {
46
- public:
47
- template<class T1, class T2> friend class Persistent_cohomology;
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- friend class Persistent_cohomology_column<SimplexKey, ArithmeticElement>;
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-
50
- typedef Persistent_cohomology_column<SimplexKey, ArithmeticElement> Column;
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-
52
- Persistent_cohomology_cell(SimplexKey key, ArithmeticElement x,
53
- Column * self_col)
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- : key_(key),
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- coefficient_(x),
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- self_col_(self_col) {
57
- }
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-
59
- SimplexKey key_;
60
- ArithmeticElement coefficient_;
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- Column * self_col_;
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- };
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-
64
- /*
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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>
74
- class Persistent_cohomology_column : public boost::intrusive::set_base_hook<
75
- boost::intrusive::link_mode<boost::intrusive::normal_link> > {
76
- template<class T1, class T2> friend class Persistent_cohomology;
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-
78
- public:
79
- typedef Persistent_cohomology_cell<SimplexKey, ArithmeticElement> Cell;
80
- typedef boost::intrusive::list<Cell,
81
- boost::intrusive::constant_time_size<false>,
82
- boost::intrusive::base_hook<base_hook_cam_v> > Col_type;
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-
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- /** \brief Creates an empty column.*/
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- explicit Persistent_cohomology_column(SimplexKey key)
86
- : col_(),
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- class_key_(key) {}
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-
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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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-
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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) {
103
- typename Col_type::const_iterator it1 = c1.col_.begin();
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- typename Col_type::const_iterator it2 = c2.col_.begin();
105
- while (it1 != c1.col_.end() && it2 != c2.col_.end()) {
106
- if (it1->key_ == it2->key_) {
107
- if (it1->coefficient_ == it2->coefficient_) {
108
- ++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_;
115
- }
116
- }
117
- return (it2 != c2.col_.end());
118
- }
119
-
120
- Col_type col_;
121
- SimplexKey class_key_;
122
- };
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-
124
- } // namespace persistent_cohomology
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-
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- } // namespace Gudhi
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-
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- #endif // PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_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): Clément Maria
4
+ *
5
+ * Copyright (C) 2014 Inria
6
+ *
7
+ * Modification(s):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
10
+
11
+ #ifndef PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
12
+ #define PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_
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+
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+ #include <boost/intrusive/set.hpp>
15
+ #include <boost/intrusive/list.hpp>
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+
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+ #include <list>
18
+
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+ namespace Gudhi {
20
+
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+ namespace persistent_cohomology {
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+
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+ template<typename SimplexKey, typename ArithmeticElement>
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+ class Persistent_cohomology_column;
25
+
26
+ struct cam_h_tag;
27
+ // for horizontal traversal in the CAM
28
+ struct cam_v_tag;
29
+ // for vertical traversal in the CAM
30
+
31
+ typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_h_tag>,
32
+ boost::intrusive::link_mode<boost::intrusive::auto_unlink> // allows .unlink()
33
+ > base_hook_cam_h;
34
+
35
+ typedef boost::intrusive::list_base_hook<boost::intrusive::tag<cam_v_tag>,
36
+ boost::intrusive::link_mode<boost::intrusive::normal_link> // faster hook, less safe
37
+ > base_hook_cam_v;
38
+
39
+ /** \internal
40
+ * \brief
41
+ *
42
+ */
43
+ template<typename SimplexKey, typename ArithmeticElement>
44
+ class Persistent_cohomology_cell : public base_hook_cam_h,
45
+ public base_hook_cam_v {
46
+ public:
47
+ template<class T1, class T2> friend class Persistent_cohomology;
48
+ friend class Persistent_cohomology_column<SimplexKey, ArithmeticElement>;
49
+
50
+ typedef Persistent_cohomology_column<SimplexKey, ArithmeticElement> Column;
51
+
52
+ Persistent_cohomology_cell(SimplexKey key, ArithmeticElement x,
53
+ Column * self_col)
54
+ : key_(key),
55
+ coefficient_(x),
56
+ self_col_(self_col) {
57
+ }
58
+
59
+ SimplexKey key_;
60
+ ArithmeticElement coefficient_;
61
+ Column * self_col_;
62
+ };
63
+
64
+ /*
65
+ * \brief Sparse column for the Compressed Annotation Matrix.
66
+ *
67
+ * The non-zero coefficients of the column are stored in a
68
+ * boost::intrusive::list. Contains a hook to be stored in a
69
+ * boost::intrusive::set.
70
+ *
71
+ * Movable but not Copyable.
72
+ */
73
+ template<typename SimplexKey, typename ArithmeticElement>
74
+ class Persistent_cohomology_column : public boost::intrusive::set_base_hook<
75
+ boost::intrusive::link_mode<boost::intrusive::normal_link> > {
76
+ template<class T1, class T2> friend class Persistent_cohomology;
77
+
78
+ public:
79
+ typedef Persistent_cohomology_cell<SimplexKey, ArithmeticElement> Cell;
80
+ typedef boost::intrusive::list<Cell,
81
+ boost::intrusive::constant_time_size<false>,
82
+ boost::intrusive::base_hook<base_hook_cam_v> > Col_type;
83
+
84
+ /** \brief Creates an empty column.*/
85
+ explicit Persistent_cohomology_column(SimplexKey key)
86
+ : col_(),
87
+ class_key_(key) {}
88
+
89
+ /** \brief Returns true iff the column is null.*/
90
+ bool is_null() const {
91
+ return col_.empty();
92
+ }
93
+ /** \brief Returns the key of the representative simplex of
94
+ * the set of simplices having this column as annotation vector
95
+ * in the compressed annotation matrix.*/
96
+ SimplexKey class_key() const {
97
+ return class_key_;
98
+ }
99
+
100
+ /** \brief Lexicographic comparison of two columns.*/
101
+ friend bool operator<(const Persistent_cohomology_column& c1,
102
+ const Persistent_cohomology_column& c2) {
103
+ typename Col_type::const_iterator it1 = c1.col_.begin();
104
+ typename Col_type::const_iterator it2 = c2.col_.begin();
105
+ while (it1 != c1.col_.end() && it2 != c2.col_.end()) {
106
+ if (it1->key_ == it2->key_) {
107
+ if (it1->coefficient_ == it2->coefficient_) {
108
+ ++it1;
109
+ ++it2;
110
+ } else {
111
+ return it1->coefficient_ < it2->coefficient_;
112
+ }
113
+ } else {
114
+ return it1->key_ < it2->key_;
115
+ }
116
+ }
117
+ return (it2 != c2.col_.end());
118
+ }
119
+
120
+ Col_type col_;
121
+ SimplexKey class_key_;
122
+ };
123
+
124
+ } // namespace persistent_cohomology
125
+
126
+ } // namespace Gudhi
127
+
128
+ #endif // PERSISTENT_COHOMOLOGY_PERSISTENT_COHOMOLOGY_COLUMN_H_