multipers 2.2.3__cp310-cp310-win_amd64.whl → 2.3.1__cp310-cp310-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.cp310-win_amd64.pyd +0 -0
  18. multipers/function_rips.pyx +105 -105
  19. multipers/grids.cp310-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.cp310-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.cp310-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.cp310-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.cp310-win_amd64.pyd +0 -0
  152. multipers/point_measure.pyx +322 -320
  153. multipers/simplex_tree_multi.cp310-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.cp310-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
@@ -1,277 +1,277 @@
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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) 2020 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 SIMPLEX_TREE_SIMPLEX_TREE_STAR_SIMPLEX_ITERATORS_H_
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- #define SIMPLEX_TREE_SIMPLEX_TREE_STAR_SIMPLEX_ITERATORS_H_
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-
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- #include <gudhi/Debug_utils.h>
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- #include <boost/iterator/iterator_facade.hpp>
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- #include <boost/version.hpp>
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- #include <boost/iterator/filter_iterator.hpp>
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-
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- #include <vector>
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- #include <stdexcept>
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- #include <utility> // for std::move
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- #include <functional> // for std::greater
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- #include <algorithm> // for std::includes
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-
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- namespace Gudhi {
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-
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- /** \private
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- * \brief Iterator over all the roots of subtrees containing cofaces of all
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- * dimension of a given simplex.
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- *
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- * Specifically, consider a simplex \f$\sigma\f$ whose vertices have maximal label
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- * u. A maximal subtree of cofaces for \f$\sigma\f$ is a subtree of the simplex tree
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- * rooted at a Node of label u, for which the root represents itself a coface of
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- * \f$\sigma\f$.
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- *
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- * \details All Nodes of the simplex must store intrusive list hooks (option
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- * link_nodes_by_label == true) in order to connect all nodes with a fixed label u
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- * into a list.
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- *
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- * Forward iterator, value_type is SimplexTree::Simplex_handle.
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- *
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- * The implementation uses a filter iterator on all Nodes of label u, checking
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- * whether they represent a coface of \f$\sigma\f$ or not.
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- */
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- template <class SimplexTree>
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- class Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator
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- : public boost::iterator_facade<Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator<SimplexTree>,
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- typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
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- public:
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- using Simplex_handle = typename SimplexTree::Simplex_handle;
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- using Siblings = typename SimplexTree::Siblings;
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- using Vertex_handle = typename SimplexTree::Vertex_handle;
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- using Node = typename SimplexTree::Node;
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- using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
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-
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- /** \brief Predicate to check whether an input SimplexTree::Node represents a
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- * coface of a simplex simp_, stored as a std::vector of
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- * SimplexTree::Vertex_handle sorted in decreasing Vertex_handle order.
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- *
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- * \details Given a SimplexHandle in a simplex tree cpx_, traverses the tree
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- * upwards
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- * to find the sequence of Vertex_handle of simp_ as a subsequence of labels
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- * encountered.
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- * Does not test sh itself.
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- * Used for filter_iterator in the optimized algorithm for
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- * star_simplex_range.
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- */
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- class is_coface {
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- public:
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- is_coface() : cpx_(nullptr) {}
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- is_coface(SimplexTree* cpx, Static_vertex_vector&& simp) : cpx_(cpx), simp_(simp) {}
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-
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- // Return true iff traversing the Node upwards to the root reads a
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- // coface of simp_
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- bool operator()(typename SimplexTree::Hooks_simplex_base& curr_hooks) {
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- Node& curr_node = static_cast<Node&>(curr_hooks);
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- Simplex_handle sh = cpx_->simplex_handle_from_node(curr_node);
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- // first Node must always have label simp_.begin(); we assume it is true
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- auto&& rng = cpx_->simplex_vertex_range(sh);
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- auto rng_it = rng.begin();
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- GUDHI_CHECK(*rng_it == simp_.front(), std::invalid_argument("first Node must always have label simp_.begin()"));
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- auto simp_it = simp_.begin();
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- // is simp_ a face of the simplex defined by sh ?
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- return std::includes(++rng_it, rng.end(), ++simp_it, simp_.end(), std::greater<Vertex_handle>());
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- }
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-
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- private:
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- SimplexTree* cpx_;
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- Static_vertex_vector simp_; // vertices of simplex, in reverse order
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- };
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-
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- typedef boost::filter_iterator<is_coface, typename SimplexTree::List_max_vertex::iterator>
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- Filtered_cofaces_simplex_iterator;
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- // any end() iterator
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- Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator() : predicate_(), st_(nullptr) {}
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-
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- Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator(SimplexTree* cpx,
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- Static_vertex_vector&& simp)
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- : predicate_(cpx, std::move(simp)), st_(cpx) {
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- GUDHI_CHECK(!simp.empty(), std::invalid_argument("cannot call for cofaces of an empty simplex"));
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- auto list_ptr = st_->nodes_by_label(simp.front());
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- GUDHI_CHECK(list_ptr != nullptr, std::runtime_error("invalid call to cofaces forest"));
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-
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- it_ = boost::make_filter_iterator(predicate_, list_ptr->begin(), list_ptr->end());
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- end_ = boost::make_filter_iterator(predicate_, list_ptr->end(), list_ptr->end());
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- Node& curr_node = static_cast<Node&>(*it_);
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- sh_ = st_->simplex_handle_from_node(curr_node);
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- }
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-
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- private:
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- friend class boost::iterator_core_access;
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-
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- // valid when iterating along the SAME list of max vertex.
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- bool equal(Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator const& other) const {
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- if (other.st_ == nullptr) {
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- return (st_ == nullptr);
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- }
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- if (st_ == nullptr) {
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- return false;
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- }
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- return (it_ == other.it_);
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- }
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-
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- Simplex_handle const& dereference() const { return sh_; }
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-
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- void increment() {
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- if (++it_ == end_) {
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- st_ = nullptr;
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- } //== end
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- else { // update sh_
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- Node& curr_node = static_cast<Node&>(*it_);
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- sh_ = st_->simplex_handle_from_node(curr_node);
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- }
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- }
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-
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- // given a Node of label max_v, returns true if the associated simplex is a coface of the simplex {..., max_v}. The
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- // predicate stores the vertices of the simplex whose star we compute.
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- is_coface predicate_;
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- SimplexTree* st_;
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- // filtered iterators over Nodes, filtered with predicate_
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- Filtered_cofaces_simplex_iterator it_;
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- Filtered_cofaces_simplex_iterator end_;
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- // current Simplex_handle corresponding to Node pointed at by it_
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- Simplex_handle sh_;
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- };
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-
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- /** \brief Iterator over the simplices of the star of a simplex.
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- *
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- * \details All Nodes of the simplex must store intrusive list hooks (option
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- * link_nodes_by_label == true) in order to connect all nodes with a fixed label u
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- * into a list.
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- *
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- * Forward iterator, value_type is SimplexTree::Simplex_handle.
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- *
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- * The implementation uses a
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- * Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator to iterate through all
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- * roots of cofaces Nodes, and traverses each such subtree of the simplex tree.
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- */
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- template <class SimplexTree>
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- class Simplex_tree_optimized_star_simplex_iterator
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- : public boost::iterator_facade<Simplex_tree_optimized_star_simplex_iterator<SimplexTree>,
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- typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
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- public:
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- using Simplex_handle = typename SimplexTree::Simplex_handle;
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- using Siblings = typename SimplexTree::Siblings;
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- using Vertex_handle = typename SimplexTree::Vertex_handle;
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- using Node = typename SimplexTree::Node;
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- using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
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-
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- // any end() iterator
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- Simplex_tree_optimized_star_simplex_iterator() : st_(nullptr) {}
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-
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- Simplex_tree_optimized_star_simplex_iterator(SimplexTree* cpx, Static_vertex_vector&& simp)
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- : st_(cpx), it_(cpx, std::move(simp)), end_(), sh_(*it_), sib_(st_->self_siblings(sh_)), children_stack_() {
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- if (it_ == end_) {
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- st_ = nullptr;
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- return;
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- } // no coface subtree => end()
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- is_root_ = true;
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- sh_ = *it_; // sh_ is the root
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- sib_ = st_->self_siblings(sh_); // Siblings containing sh_
182
- if (st_->has_children(sh_)) {
183
- children_stack_.push_back(st_->children(sh_));
184
- }
185
- return; // first root of coface subtree
186
- }
187
-
188
- private:
189
- friend class boost::iterator_core_access;
190
-
191
- // valid when iterating along the SAME list of max vertex.
192
- bool equal(Simplex_tree_optimized_star_simplex_iterator const& other) const {
193
- if (other.st_ == nullptr) {
194
- return (st_ == nullptr);
195
- }
196
- if (st_ == nullptr) {
197
- return false;
198
- }
199
- return (&(sh_->second) == &(other.sh_->second));
200
- }
201
-
202
- Simplex_handle const& dereference() const { return sh_; }
203
-
204
- /* Go to the next valid Simplex_handle for a coface, using a breadth first
205
- * search approach.
206
- *
207
- * Invariant:
208
- *
209
- * sh_ is a coface,
210
- * sib_ the Siblings containing sh_,
211
- * it_ the root of a coface subtree, such that dim_root_ <= exact_dim_cofaces_.
212
- * bfs_queue contains Siblings inside the coface subtree.
213
- *
214
- * Additionally,
215
- *
216
- * - computing all cofaces: sh_ points to a coface of any dimension. bfs_queue
217
- * contains a collection of Siblings* that must be considered (as well as there
218
- * children). These are all sets of children of simplices in
219
- * [ sib_->members().begin(), sh_ ]
220
- */
221
- void increment_all_cofaces() {
222
- ++sh_; // next sibling
223
- // if no more sibling or root of coface tree, go down or to next subtree
224
- if (is_root_ || sh_ == sib_->members().end()) {
225
- is_root_ = false;
226
- if (!children_stack_.empty()) {
227
- sib_ = children_stack_.back();
228
- children_stack_.pop_back();
229
- sh_ = sib_->members().begin(); // don't track dimensions
230
- if (st_->has_children(sh_)) {
231
- children_stack_.push_back(st_->children(sh_));
232
- }
233
- } else { // bfs_queue == empty, go to root of next coface subtree
234
- if (++it_ == end_) {
235
- st_ = nullptr;
236
- return;
237
- } // no more subtree => end()
238
- is_root_ = true;
239
- sh_ = *it_; // sh_ is the root
240
- sib_ = st_->self_siblings(sh_); // Siblings containing sh_
241
- if (st_->has_children(sh_)) {
242
- children_stack_.push_back(st_->children(sh_));
243
- }
244
- return; // next root of coface
245
- }
246
- } else { // sh_ is valid, simply add its children to the queue
247
- if (st_->has_children(sh_)) {
248
- children_stack_.push_back(st_->children(sh_));
249
- }
250
- }
251
- }
252
-
253
- // For cofaces, enumerating all the star and testing which simplices have the right dimension is suboptimal.
254
- // This could be optimized later.
255
- void increment() { increment_all_cofaces(); }
256
-
257
- // Let s be the simplex in a complex C whose star is
258
- // iterated through. Let max_v denote the maximal label of vertices in s.
259
- SimplexTree* st_; // Simplex tree for complex C
260
- // The cofaces of s form a subforest of the simplex tree. The roots of trees in this
261
- // forest have label max_v.
262
- //[it_,end_) == range of Simplex_handles of the roots of the cofaces trees (any dim)
263
- Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator<SimplexTree> it_;
264
- Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator<SimplexTree> end_;
265
- // curr Simplex_handle, returned by operator*, pointing to a coface of s
266
- Simplex_handle sh_;
267
- // set of siblings containing sh_ in the Simplex_tree
268
- Siblings* sib_; //
269
- // Save children in a list to avoid calling sib_->members().find(.)
270
- std::vector<Siblings*> children_stack_;
271
- // true iff sh_ points to the root of a coface subtree
272
- bool is_root_;
273
- };
274
-
275
- } // namespace Gudhi
276
-
277
- #endif // SIMPLEX_TREE_SIMPLEX_TREE_STAR_SIMPLEX_ITERATORS_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) 2020 Inria
6
+ *
7
+ * Modification(s):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
10
+
11
+ #ifndef SIMPLEX_TREE_SIMPLEX_TREE_STAR_SIMPLEX_ITERATORS_H_
12
+ #define SIMPLEX_TREE_SIMPLEX_TREE_STAR_SIMPLEX_ITERATORS_H_
13
+
14
+ #include <gudhi/Debug_utils.h>
15
+ #include <boost/iterator/iterator_facade.hpp>
16
+ #include <boost/version.hpp>
17
+ #include <boost/iterator/filter_iterator.hpp>
18
+
19
+ #include <vector>
20
+ #include <stdexcept>
21
+ #include <utility> // for std::move
22
+ #include <functional> // for std::greater
23
+ #include <algorithm> // for std::includes
24
+
25
+ namespace Gudhi {
26
+
27
+ /** \private
28
+ * \brief Iterator over all the roots of subtrees containing cofaces of all
29
+ * dimension of a given simplex.
30
+ *
31
+ * Specifically, consider a simplex \f$\sigma\f$ whose vertices have maximal label
32
+ * u. A maximal subtree of cofaces for \f$\sigma\f$ is a subtree of the simplex tree
33
+ * rooted at a Node of label u, for which the root represents itself a coface of
34
+ * \f$\sigma\f$.
35
+ *
36
+ * \details All Nodes of the simplex must store intrusive list hooks (option
37
+ * link_nodes_by_label == true) in order to connect all nodes with a fixed label u
38
+ * into a list.
39
+ *
40
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.
41
+ *
42
+ * The implementation uses a filter iterator on all Nodes of label u, checking
43
+ * whether they represent a coface of \f$\sigma\f$ or not.
44
+ */
45
+ template <class SimplexTree>
46
+ class Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator
47
+ : public boost::iterator_facade<Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator<SimplexTree>,
48
+ typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
49
+ public:
50
+ using Simplex_handle = typename SimplexTree::Simplex_handle;
51
+ using Siblings = typename SimplexTree::Siblings;
52
+ using Vertex_handle = typename SimplexTree::Vertex_handle;
53
+ using Node = typename SimplexTree::Node;
54
+ using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
55
+
56
+ /** \brief Predicate to check whether an input SimplexTree::Node represents a
57
+ * coface of a simplex simp_, stored as a std::vector of
58
+ * SimplexTree::Vertex_handle sorted in decreasing Vertex_handle order.
59
+ *
60
+ * \details Given a SimplexHandle in a simplex tree cpx_, traverses the tree
61
+ * upwards
62
+ * to find the sequence of Vertex_handle of simp_ as a subsequence of labels
63
+ * encountered.
64
+ * Does not test sh itself.
65
+ * Used for filter_iterator in the optimized algorithm for
66
+ * star_simplex_range.
67
+ */
68
+ class is_coface {
69
+ public:
70
+ is_coface() : cpx_(nullptr) {}
71
+ is_coface(SimplexTree* cpx, Static_vertex_vector&& simp) : cpx_(cpx), simp_(simp) {}
72
+
73
+ // Return true iff traversing the Node upwards to the root reads a
74
+ // coface of simp_
75
+ bool operator()(typename SimplexTree::Hooks_simplex_base& curr_hooks) {
76
+ Node& curr_node = static_cast<Node&>(curr_hooks);
77
+ Simplex_handle sh = cpx_->simplex_handle_from_node(curr_node);
78
+ // first Node must always have label simp_.begin(); we assume it is true
79
+ auto&& rng = cpx_->simplex_vertex_range(sh);
80
+ auto rng_it = rng.begin();
81
+ GUDHI_CHECK(*rng_it == simp_.front(), std::invalid_argument("first Node must always have label simp_.begin()"));
82
+ auto simp_it = simp_.begin();
83
+ // is simp_ a face of the simplex defined by sh ?
84
+ return std::includes(++rng_it, rng.end(), ++simp_it, simp_.end(), std::greater<Vertex_handle>());
85
+ }
86
+
87
+ private:
88
+ SimplexTree* cpx_;
89
+ Static_vertex_vector simp_; // vertices of simplex, in reverse order
90
+ };
91
+
92
+ typedef boost::filter_iterator<is_coface, typename SimplexTree::List_max_vertex::iterator>
93
+ Filtered_cofaces_simplex_iterator;
94
+ // any end() iterator
95
+ Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator() : predicate_(), st_(nullptr) {}
96
+
97
+ Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator(SimplexTree* cpx,
98
+ Static_vertex_vector&& simp)
99
+ : predicate_(cpx, std::move(simp)), st_(cpx) {
100
+ GUDHI_CHECK(!simp.empty(), std::invalid_argument("cannot call for cofaces of an empty simplex"));
101
+ auto list_ptr = st_->nodes_by_label(simp.front());
102
+ GUDHI_CHECK(list_ptr != nullptr, std::runtime_error("invalid call to cofaces forest"));
103
+
104
+ it_ = boost::make_filter_iterator(predicate_, list_ptr->begin(), list_ptr->end());
105
+ end_ = boost::make_filter_iterator(predicate_, list_ptr->end(), list_ptr->end());
106
+ Node& curr_node = static_cast<Node&>(*it_);
107
+ sh_ = st_->simplex_handle_from_node(curr_node);
108
+ }
109
+
110
+ private:
111
+ friend class boost::iterator_core_access;
112
+
113
+ // valid when iterating along the SAME list of max vertex.
114
+ bool equal(Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator const& other) const {
115
+ if (other.st_ == nullptr) {
116
+ return (st_ == nullptr);
117
+ }
118
+ if (st_ == nullptr) {
119
+ return false;
120
+ }
121
+ return (it_ == other.it_);
122
+ }
123
+
124
+ Simplex_handle const& dereference() const { return sh_; }
125
+
126
+ void increment() {
127
+ if (++it_ == end_) {
128
+ st_ = nullptr;
129
+ } //== end
130
+ else { // update sh_
131
+ Node& curr_node = static_cast<Node&>(*it_);
132
+ sh_ = st_->simplex_handle_from_node(curr_node);
133
+ }
134
+ }
135
+
136
+ // given a Node of label max_v, returns true if the associated simplex is a coface of the simplex {..., max_v}. The
137
+ // predicate stores the vertices of the simplex whose star we compute.
138
+ is_coface predicate_;
139
+ SimplexTree* st_;
140
+ // filtered iterators over Nodes, filtered with predicate_
141
+ Filtered_cofaces_simplex_iterator it_;
142
+ Filtered_cofaces_simplex_iterator end_;
143
+ // current Simplex_handle corresponding to Node pointed at by it_
144
+ Simplex_handle sh_;
145
+ };
146
+
147
+ /** \brief Iterator over the simplices of the star of a simplex.
148
+ *
149
+ * \details All Nodes of the simplex must store intrusive list hooks (option
150
+ * link_nodes_by_label == true) in order to connect all nodes with a fixed label u
151
+ * into a list.
152
+ *
153
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.
154
+ *
155
+ * The implementation uses a
156
+ * Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator to iterate through all
157
+ * roots of cofaces Nodes, and traverses each such subtree of the simplex tree.
158
+ */
159
+ template <class SimplexTree>
160
+ class Simplex_tree_optimized_star_simplex_iterator
161
+ : public boost::iterator_facade<Simplex_tree_optimized_star_simplex_iterator<SimplexTree>,
162
+ typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
163
+ public:
164
+ using Simplex_handle = typename SimplexTree::Simplex_handle;
165
+ using Siblings = typename SimplexTree::Siblings;
166
+ using Vertex_handle = typename SimplexTree::Vertex_handle;
167
+ using Node = typename SimplexTree::Node;
168
+ using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
169
+
170
+ // any end() iterator
171
+ Simplex_tree_optimized_star_simplex_iterator() : st_(nullptr) {}
172
+
173
+ Simplex_tree_optimized_star_simplex_iterator(SimplexTree* cpx, Static_vertex_vector&& simp)
174
+ : st_(cpx), it_(cpx, std::move(simp)), end_(), sh_(*it_), sib_(st_->self_siblings(sh_)), children_stack_() {
175
+ if (it_ == end_) {
176
+ st_ = nullptr;
177
+ return;
178
+ } // no coface subtree => end()
179
+ is_root_ = true;
180
+ sh_ = *it_; // sh_ is the root
181
+ sib_ = st_->self_siblings(sh_); // Siblings containing sh_
182
+ if (st_->has_children(sh_)) {
183
+ children_stack_.push_back(st_->children(sh_));
184
+ }
185
+ return; // first root of coface subtree
186
+ }
187
+
188
+ private:
189
+ friend class boost::iterator_core_access;
190
+
191
+ // valid when iterating along the SAME list of max vertex.
192
+ bool equal(Simplex_tree_optimized_star_simplex_iterator const& other) const {
193
+ if (other.st_ == nullptr) {
194
+ return (st_ == nullptr);
195
+ }
196
+ if (st_ == nullptr) {
197
+ return false;
198
+ }
199
+ return (&(sh_->second) == &(other.sh_->second));
200
+ }
201
+
202
+ Simplex_handle const& dereference() const { return sh_; }
203
+
204
+ /* Go to the next valid Simplex_handle for a coface, using a breadth first
205
+ * search approach.
206
+ *
207
+ * Invariant:
208
+ *
209
+ * sh_ is a coface,
210
+ * sib_ the Siblings containing sh_,
211
+ * it_ the root of a coface subtree, such that dim_root_ <= exact_dim_cofaces_.
212
+ * bfs_queue contains Siblings inside the coface subtree.
213
+ *
214
+ * Additionally,
215
+ *
216
+ * - computing all cofaces: sh_ points to a coface of any dimension. bfs_queue
217
+ * contains a collection of Siblings* that must be considered (as well as there
218
+ * children). These are all sets of children of simplices in
219
+ * [ sib_->members().begin(), sh_ ]
220
+ */
221
+ void increment_all_cofaces() {
222
+ ++sh_; // next sibling
223
+ // if no more sibling or root of coface tree, go down or to next subtree
224
+ if (is_root_ || sh_ == sib_->members().end()) {
225
+ is_root_ = false;
226
+ if (!children_stack_.empty()) {
227
+ sib_ = children_stack_.back();
228
+ children_stack_.pop_back();
229
+ sh_ = sib_->members().begin(); // don't track dimensions
230
+ if (st_->has_children(sh_)) {
231
+ children_stack_.push_back(st_->children(sh_));
232
+ }
233
+ } else { // bfs_queue == empty, go to root of next coface subtree
234
+ if (++it_ == end_) {
235
+ st_ = nullptr;
236
+ return;
237
+ } // no more subtree => end()
238
+ is_root_ = true;
239
+ sh_ = *it_; // sh_ is the root
240
+ sib_ = st_->self_siblings(sh_); // Siblings containing sh_
241
+ if (st_->has_children(sh_)) {
242
+ children_stack_.push_back(st_->children(sh_));
243
+ }
244
+ return; // next root of coface
245
+ }
246
+ } else { // sh_ is valid, simply add its children to the queue
247
+ if (st_->has_children(sh_)) {
248
+ children_stack_.push_back(st_->children(sh_));
249
+ }
250
+ }
251
+ }
252
+
253
+ // For cofaces, enumerating all the star and testing which simplices have the right dimension is suboptimal.
254
+ // This could be optimized later.
255
+ void increment() { increment_all_cofaces(); }
256
+
257
+ // Let s be the simplex in a complex C whose star is
258
+ // iterated through. Let max_v denote the maximal label of vertices in s.
259
+ SimplexTree* st_; // Simplex tree for complex C
260
+ // The cofaces of s form a subforest of the simplex tree. The roots of trees in this
261
+ // forest have label max_v.
262
+ //[it_,end_) == range of Simplex_handles of the roots of the cofaces trees (any dim)
263
+ Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator<SimplexTree> it_;
264
+ Simplex_tree_optimized_cofaces_rooted_subtrees_simplex_iterator<SimplexTree> end_;
265
+ // curr Simplex_handle, returned by operator*, pointing to a coface of s
266
+ Simplex_handle sh_;
267
+ // set of siblings containing sh_ in the Simplex_tree
268
+ Siblings* sib_; //
269
+ // Save children in a list to avoid calling sib_->members().find(.)
270
+ std::vector<Siblings*> children_stack_;
271
+ // true iff sh_ points to the root of a coface subtree
272
+ bool is_root_;
273
+ };
274
+
275
+ } // namespace Gudhi
276
+
277
+ #endif // SIMPLEX_TREE_SIMPLEX_TREE_STAR_SIMPLEX_ITERATORS_H_