multipers 2.3.3b6__cp310-cp310-macosx_11_0_arm64.whl

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  1. multipers/.dylibs/libc++.1.0.dylib +0 -0
  2. multipers/.dylibs/libtbb.12.16.dylib +0 -0
  3. multipers/__init__.py +33 -0
  4. multipers/_signed_measure_meta.py +453 -0
  5. multipers/_slicer_meta.py +211 -0
  6. multipers/array_api/__init__.py +45 -0
  7. multipers/array_api/numpy.py +41 -0
  8. multipers/array_api/torch.py +58 -0
  9. multipers/data/MOL2.py +458 -0
  10. multipers/data/UCR.py +18 -0
  11. multipers/data/__init__.py +1 -0
  12. multipers/data/graphs.py +466 -0
  13. multipers/data/immuno_regions.py +27 -0
  14. multipers/data/minimal_presentation_to_st_bf.py +0 -0
  15. multipers/data/pytorch2simplextree.py +91 -0
  16. multipers/data/shape3d.py +101 -0
  17. multipers/data/synthetic.py +113 -0
  18. multipers/distances.py +202 -0
  19. multipers/filtration_conversions.pxd +229 -0
  20. multipers/filtration_conversions.pxd.tp +84 -0
  21. multipers/filtrations/__init__.py +18 -0
  22. multipers/filtrations/density.py +574 -0
  23. multipers/filtrations/filtrations.py +361 -0
  24. multipers/filtrations.pxd +224 -0
  25. multipers/function_rips.cpython-310-darwin.so +0 -0
  26. multipers/function_rips.pyx +105 -0
  27. multipers/grids.cpython-310-darwin.so +0 -0
  28. multipers/grids.pyx +433 -0
  29. multipers/gudhi/Persistence_slices_interface.h +132 -0
  30. multipers/gudhi/Simplex_tree_interface.h +239 -0
  31. multipers/gudhi/Simplex_tree_multi_interface.h +551 -0
  32. multipers/gudhi/cubical_to_boundary.h +59 -0
  33. multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -0
  34. multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -0
  35. multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -0
  36. multipers/gudhi/gudhi/Debug_utils.h +45 -0
  37. multipers/gudhi/gudhi/Fields/Multi_field.h +484 -0
  38. multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -0
  39. multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -0
  40. multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -0
  41. multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -0
  42. multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -0
  43. multipers/gudhi/gudhi/Fields/Z2_field.h +355 -0
  44. multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -0
  45. multipers/gudhi/gudhi/Fields/Zp_field.h +420 -0
  46. multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -0
  47. multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -0
  48. multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -0
  49. multipers/gudhi/gudhi/Matrix.h +2107 -0
  50. multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -0
  51. multipers/gudhi/gudhi/Multi_persistence/Box.h +174 -0
  52. multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -0
  53. multipers/gudhi/gudhi/Off_reader.h +173 -0
  54. multipers/gudhi/gudhi/One_critical_filtration.h +1441 -0
  55. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -0
  56. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -0
  57. multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -0
  58. multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -0
  59. multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -0
  60. multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -0
  61. multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -0
  62. multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -0
  63. multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -0
  64. multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -0
  65. multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -0
  66. multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -0
  67. multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -0
  68. multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -0
  69. multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -0
  70. multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -0
  71. multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -0
  72. multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -0
  73. multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -0
  74. multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -0
  75. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -0
  76. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -0
  77. multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -0
  78. multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -0
  79. multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -0
  80. multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -0
  81. multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -0
  82. multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -0
  83. multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -0
  84. multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -0
  85. multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -0
  86. multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -0
  87. multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -0
  88. multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -0
  89. multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -0
  90. multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -0
  91. multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -0
  92. multipers/gudhi/gudhi/Persistent_cohomology.h +745 -0
  93. multipers/gudhi/gudhi/Points_off_io.h +171 -0
  94. multipers/gudhi/gudhi/Simple_object_pool.h +69 -0
  95. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -0
  96. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -0
  97. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -0
  98. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -0
  99. multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -0
  100. multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -0
  101. multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -0
  102. multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -0
  103. multipers/gudhi/gudhi/Simplex_tree.h +2794 -0
  104. multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -0
  105. multipers/gudhi/gudhi/distance_functions.h +62 -0
  106. multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -0
  107. multipers/gudhi/gudhi/persistence_interval.h +253 -0
  108. multipers/gudhi/gudhi/persistence_matrix_options.h +170 -0
  109. multipers/gudhi/gudhi/reader_utils.h +367 -0
  110. multipers/gudhi/mma_interface_coh.h +256 -0
  111. multipers/gudhi/mma_interface_h0.h +223 -0
  112. multipers/gudhi/mma_interface_matrix.h +293 -0
  113. multipers/gudhi/naive_merge_tree.h +536 -0
  114. multipers/gudhi/scc_io.h +310 -0
  115. multipers/gudhi/truc.h +1403 -0
  116. multipers/io.cpython-310-darwin.so +0 -0
  117. multipers/io.pyx +644 -0
  118. multipers/ml/__init__.py +0 -0
  119. multipers/ml/accuracies.py +90 -0
  120. multipers/ml/invariants_with_persistable.py +79 -0
  121. multipers/ml/kernels.py +176 -0
  122. multipers/ml/mma.py +713 -0
  123. multipers/ml/one.py +472 -0
  124. multipers/ml/point_clouds.py +352 -0
  125. multipers/ml/signed_measures.py +1589 -0
  126. multipers/ml/sliced_wasserstein.py +461 -0
  127. multipers/ml/tools.py +113 -0
  128. multipers/mma_structures.cpython-310-darwin.so +0 -0
  129. multipers/mma_structures.pxd +128 -0
  130. multipers/mma_structures.pyx +2786 -0
  131. multipers/mma_structures.pyx.tp +1094 -0
  132. multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -0
  133. multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -0
  134. multipers/multi_parameter_rank_invariant/function_rips.h +322 -0
  135. multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -0
  136. multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -0
  137. multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -0
  138. multipers/multiparameter_edge_collapse.py +41 -0
  139. multipers/multiparameter_module_approximation/approximation.h +2330 -0
  140. multipers/multiparameter_module_approximation/combinatory.h +129 -0
  141. multipers/multiparameter_module_approximation/debug.h +107 -0
  142. multipers/multiparameter_module_approximation/euler_curves.h +0 -0
  143. multipers/multiparameter_module_approximation/format_python-cpp.h +286 -0
  144. multipers/multiparameter_module_approximation/heap_column.h +238 -0
  145. multipers/multiparameter_module_approximation/images.h +79 -0
  146. multipers/multiparameter_module_approximation/list_column.h +174 -0
  147. multipers/multiparameter_module_approximation/list_column_2.h +232 -0
  148. multipers/multiparameter_module_approximation/ru_matrix.h +347 -0
  149. multipers/multiparameter_module_approximation/set_column.h +135 -0
  150. multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -0
  151. multipers/multiparameter_module_approximation/unordered_set_column.h +166 -0
  152. multipers/multiparameter_module_approximation/utilities.h +403 -0
  153. multipers/multiparameter_module_approximation/vector_column.h +223 -0
  154. multipers/multiparameter_module_approximation/vector_matrix.h +331 -0
  155. multipers/multiparameter_module_approximation/vineyards.h +464 -0
  156. multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -0
  157. multipers/multiparameter_module_approximation.cpython-310-darwin.so +0 -0
  158. multipers/multiparameter_module_approximation.pyx +235 -0
  159. multipers/pickle.py +90 -0
  160. multipers/plots.py +456 -0
  161. multipers/point_measure.cpython-310-darwin.so +0 -0
  162. multipers/point_measure.pyx +395 -0
  163. multipers/simplex_tree_multi.cpython-310-darwin.so +0 -0
  164. multipers/simplex_tree_multi.pxd +134 -0
  165. multipers/simplex_tree_multi.pyx +10840 -0
  166. multipers/simplex_tree_multi.pyx.tp +2009 -0
  167. multipers/slicer.cpython-310-darwin.so +0 -0
  168. multipers/slicer.pxd +3034 -0
  169. multipers/slicer.pxd.tp +234 -0
  170. multipers/slicer.pyx +20481 -0
  171. multipers/slicer.pyx.tp +1088 -0
  172. multipers/tensor/tensor.h +672 -0
  173. multipers/tensor.pxd +13 -0
  174. multipers/test.pyx +44 -0
  175. multipers/tests/__init__.py +62 -0
  176. multipers/torch/__init__.py +1 -0
  177. multipers/torch/diff_grids.py +240 -0
  178. multipers/torch/rips_density.py +310 -0
  179. multipers-2.3.3b6.dist-info/METADATA +128 -0
  180. multipers-2.3.3b6.dist-info/RECORD +183 -0
  181. multipers-2.3.3b6.dist-info/WHEEL +6 -0
  182. multipers-2.3.3b6.dist-info/licenses/LICENSE +21 -0
  183. multipers-2.3.3b6.dist-info/top_level.txt +1 -0
@@ -0,0 +1,171 @@
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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): Vincent Rouvreau
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+ *
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+ * Copyright (C) 2015 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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+ #ifndef POINTS_OFF_IO_H_
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+ #define POINTS_OFF_IO_H_
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+
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+ #include <gudhi/Off_reader.h>
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+
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+ #include <string>
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+ #include <vector>
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+ #include <fstream>
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+ #include <map>
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+
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+ namespace Gudhi {
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+
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+ /**
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+ * \brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
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+ */
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+ template<typename Point_d>
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+ class Points_off_visitor_reader {
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+ private:
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+ std::vector<Point_d> point_cloud;
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+
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+ public:
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+ /** \brief Off_reader visitor init implementation.
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+ *
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+ * The init parameters are set from OFF file header.
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+ * Dimension value is required in order to construct a vector of points.
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+ *
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+ * @param[in] dim space dimension of vertices.
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+ * @param[in] num_vertices number of vertices in the OFF file (not used).
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+ * @param[in] num_faces number of faces in the OFF file (not used).
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+ * @param[in] num_edges number of edges in the OFF file (not used).
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+ */
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+ void init(int dim, int num_vertices, int num_faces, int num_edges) {
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+ #ifdef DEBUG_TRACES
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+ std::clog << "Points_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
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+ num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
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+ #endif // DEBUG_TRACES
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+ if (num_faces > 0) {
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+ std::cerr << "Points_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
48
+ }
49
+ if (num_edges > 0) {
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+ std::cerr << "Points_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
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+ }
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+ }
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+
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+ /** @brief Off_reader visitor point implementation.
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+ *
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+ * The point function is called on each vertex line from OFF file.
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+ * This function inserts the vertex in the vector of points.
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+ *
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+ * @param[in] point vector of vertex coordinates.
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+ *
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+ * @details
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+ * Point_d must have a constructor with the following form:
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+ *
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+ * @code template<class InputIterator > Point_d::Point_d(InputIterator first, InputIterator last) @endcode
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+ *
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+ */
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+ void point(const std::vector<double>& point) {
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+ #ifdef DEBUG_TRACES
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+ std::clog << "Points_off_visitor_reader::point ";
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+ for (auto coordinate : point) {
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+ std::clog << coordinate << " | ";
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+ }
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+ std::clog << std::endl;
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+ #endif // DEBUG_TRACES
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+ // Fill the point cloud
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+ point_cloud.push_back(Point_d(point.begin(), point.end()));
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+ }
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+
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+ // Off_reader visitor maximal_face implementation - Only points are read
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+ void maximal_face(const std::vector<int>& face) { }
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+
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+ // Off_reader visitor done implementation - Only points are read
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+ void done() { }
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+
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+ /** \brief Point cloud getter.
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+ *
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+ * @return point_cloud.
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+ */
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+ const std::vector<Point_d>& get_point_cloud() const {
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+ return point_cloud;
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+ }
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+ };
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+
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+ /**
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+ * \brief OFF file reader implementation in order to read points from an OFF file.
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+ *
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+ * This class is using the Points_off_visitor_reader to visit the OFF file according to Off_reader.
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+ *
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+ * Point_d must have a constructor with the following form:
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+ *
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+ * \code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) \endcode
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+ *
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+ * where d is the point dimension.
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+ *
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+ * \section pointoffioexample Example
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+ *
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+ * This example loads points from an OFF file and builds a vector of points (vector of double).
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+ * Then, it is asked to display the points.
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+ *
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+ * \include example_vector_double_points_off_reader.cpp
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+ *
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+ * When launching:
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+ *
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+ * \code $> ./vector_double_off_reader ../../data/points/alphacomplexdoc.off
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+ * \endcode
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+ *
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+ * the program outputs a file ../../data/points/alphacomplexdoc.off.txt:
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+ *
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+ * \include vectordoubleoffreader_result.txt
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+ */
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+ template<typename Point_d>
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+ class Points_off_reader {
123
+ public:
124
+ /** \brief Reads the OFF file and constructs a vector of points from the points
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+ * that are in the OFF file.
126
+ *
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+ * @param[in] name_file OFF file to read.
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+ *
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+ * \post Check with is_valid() function to see if read operation was successful.
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+ */
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+ Points_off_reader(const std::string& name_file)
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+ : valid_(false) {
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+ std::ifstream stream(name_file);
134
+ if (stream.is_open()) {
135
+ Off_reader off_reader(stream);
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+ Points_off_visitor_reader<Point_d> off_visitor;
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+ valid_ = off_reader.read(off_visitor);
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+ if (valid_) {
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+ point_cloud = off_visitor.get_point_cloud();
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+ }
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+ } else {
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+ std::cerr << "Points_off_reader::Points_off_reader could not open file " << name_file << "\n";
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+ }
144
+ }
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+
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+ /** \brief Returns if the OFF file read operation was successful or not.
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+ *
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+ * @return OFF file read status.
149
+ */
150
+ bool is_valid() const {
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+ return valid_;
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+ }
153
+
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+ /** \brief Point cloud getter.
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+ *
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+ * @return point_cloud.
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+ */
158
+ const std::vector<Point_d>& get_point_cloud() const {
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+ return point_cloud;
160
+ }
161
+
162
+ private:
163
+ /** \brief point_cloud.*/
164
+ std::vector<Point_d> point_cloud;
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+ /** \brief OFF file read status.*/
166
+ bool valid_;
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+ };
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+
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+ } // namespace Gudhi
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+
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+ #endif // POINTS_OFF_IO_H_
@@ -0,0 +1,69 @@
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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): Marc Glisse
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+ *
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+ * Copyright (C) 2015 Inria
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+ *
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+ * Modification(s):
8
+ * - YYYY/MM Author: Description of the modification
9
+ */
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+
11
+ #ifndef SIMPLE_OBJECT_POOL_H_
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+ #define SIMPLE_OBJECT_POOL_H_
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+
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+ #include <boost/pool/pool.hpp>
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+ #include <utility>
16
+
17
+ namespace Gudhi {
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+
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+ /** \private
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+ * This is a simpler version of boost::object_pool, that requires
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+ * that users explicitly destroy all objects. This lets the
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+ * performance scale much better, see
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+ * https://svn.boost.org/trac/boost/ticket/3789 .
24
+ */
25
+ template <class T>
26
+ class Simple_object_pool : protected boost::pool<boost::default_user_allocator_malloc_free> {
27
+ protected:
28
+ typedef boost::pool<boost::default_user_allocator_malloc_free> Base;
29
+ typedef T* pointer;
30
+
31
+ Base& base() {
32
+ return *this;
33
+ }
34
+
35
+ Base const& base()const {
36
+ return *this;
37
+ }
38
+
39
+ public:
40
+ typedef T element_type;
41
+ typedef boost::default_user_allocator_malloc_free user_allocator;
42
+ typedef typename Base::size_type size_type;
43
+ typedef typename Base::difference_type difference_type;
44
+
45
+ template<class...U>
46
+ Simple_object_pool(U&&...u) : Base(sizeof (T), std::forward<U>(u)...) { }
47
+
48
+ template<class...U>
49
+ pointer construct(U&&...u) {
50
+ void* p = base().malloc BOOST_PREVENT_MACRO_SUBSTITUTION();
51
+ assert(p);
52
+ try {
53
+ new(p) T(std::forward<U>(u)...);
54
+ } catch (...) {
55
+ base().free BOOST_PREVENT_MACRO_SUBSTITUTION(p);
56
+ throw;
57
+ }
58
+ return static_cast<pointer> (p);
59
+ }
60
+
61
+ void destroy(pointer p) {
62
+ p->~T();
63
+ base().free BOOST_PREVENT_MACRO_SUBSTITUTION(p);
64
+ }
65
+ };
66
+
67
+ } // namespace Gudhi
68
+
69
+ #endif // SIMPLE_OBJECT_POOL_H_
@@ -0,0 +1,463 @@
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
+ * - 2022/04 Vincent Rouvreau: Add Simplex_tree_boundary_opposite_vertex_simplex_iterator for alpha and cech purpose
9
+ * - YYYY/MM Author: Description of the modification
10
+ */
11
+
12
+ #ifndef SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
13
+ #define SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_
14
+
15
+ #include <gudhi/Debug_utils.h>
16
+
17
+ #include <boost/iterator/iterator_facade.hpp>
18
+
19
+ #include <vector>
20
+ #include <utility> // for std::pair
21
+
22
+ namespace Gudhi {
23
+
24
+ /** \addtogroup simplex_tree
25
+ * Iterators and range types for the Simplex_tree.
26
+ * @{
27
+ */
28
+
29
+ /** \brief Iterator over the vertices of a simplex
30
+ * in a SimplexTree.
31
+ *
32
+ * Forward iterator, 'value_type' is SimplexTree::Vertex_handle.*/
33
+ template<class SimplexTree>
34
+ class Simplex_tree_simplex_vertex_iterator : public boost::iterator_facade<
35
+ Simplex_tree_simplex_vertex_iterator<SimplexTree>,
36
+ typename SimplexTree::Vertex_handle const, boost::forward_traversal_tag,
37
+ typename SimplexTree::Vertex_handle const> {
38
+ public:
39
+ typedef typename SimplexTree::Simplex_handle Simplex_handle;
40
+ typedef typename SimplexTree::Siblings Siblings;
41
+ typedef typename SimplexTree::Vertex_handle Vertex_handle;
42
+
43
+ explicit Simplex_tree_simplex_vertex_iterator(SimplexTree const* st)
44
+ : // any end() iterator
45
+ sib_(nullptr),
46
+ v_(st->null_vertex()) {
47
+ }
48
+
49
+ Simplex_tree_simplex_vertex_iterator(SimplexTree const* st, Simplex_handle sh)
50
+ : sib_(st->self_siblings(sh)),
51
+ v_(sh->first) {
52
+ }
53
+
54
+ private:
55
+ friend class boost::iterator_core_access;
56
+
57
+ bool equal(Simplex_tree_simplex_vertex_iterator const &other) const {
58
+ return sib_ == other.sib_ && v_ == other.v_;
59
+ }
60
+
61
+ Vertex_handle const& dereference() const {
62
+ return v_;
63
+ }
64
+
65
+ void increment() {
66
+ v_ = sib_->parent();
67
+ sib_ = sib_->oncles();
68
+ }
69
+
70
+ Siblings * sib_;
71
+ Vertex_handle v_;
72
+ };
73
+
74
+ /*---------------------------------------------------------------------------*/
75
+ /** \brief Iterator over the simplices of the boundary of a
76
+ * simplex.
77
+ *
78
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
79
+ template<class SimplexTree>
80
+ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
81
+ Simplex_tree_boundary_simplex_iterator<SimplexTree>,
82
+ typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
83
+ public:
84
+ using Simplex_handle = typename SimplexTree::Simplex_handle;
85
+ using Vertex_handle = typename SimplexTree::Vertex_handle;
86
+ using Siblings = typename SimplexTree::Siblings;
87
+ using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
88
+
89
+ // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is overwritten.
90
+ Simplex_tree_boundary_simplex_iterator()
91
+ : sib_(nullptr),
92
+ st_(nullptr) {
93
+ }
94
+
95
+ // any end() iterator
96
+ explicit Simplex_tree_boundary_simplex_iterator(SimplexTree * st)
97
+ : last_(st->null_vertex()),
98
+ next_(st->null_vertex()),
99
+ sib_(nullptr),
100
+ sh_(st->null_simplex()),
101
+ st_(st) {
102
+ }
103
+
104
+ template<class SimplexHandle>
105
+ Simplex_tree_boundary_simplex_iterator(SimplexTree * st, SimplexHandle sh)
106
+ : last_(sh->first),
107
+ next_(st->null_vertex()),
108
+ sib_(nullptr),
109
+ sh_(st->null_simplex()),
110
+ st_(st) {
111
+ // Only check once at the beginning instead of for every increment, as this is expensive.
112
+ if constexpr (SimplexTree::Options::contiguous_vertices)
113
+ GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes");
114
+ Siblings * sib = st->self_siblings(sh);
115
+ next_ = sib->parent();
116
+ sib_ = sib->oncles();
117
+ if (sib_ != nullptr) {
118
+ if constexpr (SimplexTree::Options::contiguous_vertices &&
119
+ !SimplexTree::Options::stable_simplex_handles)
120
+ {
121
+ if (sib_->oncles() == nullptr) // Only relevant for edges
122
+ sh_ = sib_->members_.begin() + next_;
123
+ else
124
+ sh_ = sib_->find(next_);
125
+ } else {
126
+ sh_ = sib_->find(next_);
127
+ }
128
+ }
129
+ }
130
+
131
+ private:
132
+ friend class boost::iterator_core_access;
133
+ // valid when iterating along the SAME boundary.
134
+ bool equal(Simplex_tree_boundary_simplex_iterator const& other) const {
135
+ return sh_ == other.sh_;
136
+ }
137
+
138
+ Simplex_handle const& dereference() const {
139
+ assert(sh_ != st_->null_simplex());
140
+ return sh_;
141
+ }
142
+
143
+ void increment() {
144
+ if (sib_ == nullptr) {
145
+ sh_ = st_->null_simplex();
146
+ return;
147
+ }
148
+
149
+ Siblings * for_sib = sib_;
150
+ Siblings * new_sib = sib_->oncles();
151
+ auto rit = suffix_.rbegin();
152
+ if constexpr (SimplexTree::Options::contiguous_vertices && !SimplexTree::Options::stable_simplex_handles) {
153
+ if (new_sib == nullptr) {
154
+ // We reached the root, use a short-cut to find a vertex.
155
+ if (rit == suffix_.rend()) {
156
+ // Segment, this vertex is the last boundary simplex
157
+ sh_ = for_sib->members_.begin() + last_;
158
+ sib_ = nullptr;
159
+ return;
160
+ } else {
161
+ // Dim >= 2, initial step of the descent
162
+ sh_ = for_sib->members_.begin() + *rit;
163
+ for_sib = sh_->second.children();
164
+ ++rit;
165
+ }
166
+ }
167
+ }
168
+
169
+ for (; rit != suffix_.rend(); ++rit) {
170
+ sh_ = for_sib->find(*rit);
171
+ for_sib = sh_->second.children();
172
+ }
173
+ sh_ = for_sib->find(last_); // sh_ points to the right simplex now
174
+ suffix_.push_back(next_);
175
+ next_ = sib_->parent();
176
+ sib_ = new_sib;
177
+ }
178
+
179
+ // Most of the storage should be moved to the range, iterators should be light.
180
+ Vertex_handle last_; // last vertex of the simplex
181
+ Vertex_handle next_; // next vertex to push in suffix_
182
+ Static_vertex_vector suffix_;
183
+ Siblings * sib_; // where the next search will start from
184
+ Simplex_handle sh_; // current Simplex_handle in the boundary
185
+ SimplexTree * st_; // simplex containing the simplicial complex
186
+ };
187
+
188
+ /** \brief Iterator over the simplices of the boundary of a simplex and their opposite vertices.
189
+ *
190
+ * Forward iterator, value_type is std::pair<SimplexTree::Simplex_handle, SimplexTree::Vertex_handle>.*/
191
+ template<class SimplexTree>
192
+ class Simplex_tree_boundary_opposite_vertex_simplex_iterator : public boost::iterator_facade<
193
+ Simplex_tree_boundary_opposite_vertex_simplex_iterator<SimplexTree>,
194
+ std::pair<typename SimplexTree::Simplex_handle, typename SimplexTree::Vertex_handle> const, boost::forward_traversal_tag> {
195
+ public:
196
+ using Simplex_handle = typename SimplexTree::Simplex_handle;
197
+ using Vertex_handle = typename SimplexTree::Vertex_handle;
198
+ using Siblings = typename SimplexTree::Siblings;
199
+ using Static_vertex_vector = typename SimplexTree::Static_vertex_vector;
200
+
201
+ // For cython purpose only. The object it initializes should be overwritten ASAP and never used before it is
202
+ // overwritten.
203
+ Simplex_tree_boundary_opposite_vertex_simplex_iterator()
204
+ : sib_(nullptr),
205
+ st_(nullptr) {
206
+ }
207
+
208
+ // any end() iterator
209
+ explicit Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st)
210
+ : last_(st->null_vertex()),
211
+ next_(st->null_vertex()),
212
+ sib_(nullptr),
213
+ baov_(st->null_simplex(), st->null_vertex()),
214
+ st_(st) {
215
+ }
216
+
217
+ template<class SimplexHandle>
218
+ Simplex_tree_boundary_opposite_vertex_simplex_iterator(SimplexTree * st, SimplexHandle sh)
219
+ : last_(sh->first),
220
+ next_(st->null_vertex()),
221
+ sib_(nullptr),
222
+ baov_(st->null_simplex(), sh->first),
223
+ st_(st) {
224
+ // Only check once at the beginning instead of for every increment, as this is expensive.
225
+ if constexpr (SimplexTree::Options::contiguous_vertices)
226
+ GUDHI_CHECK(st_->contiguous_vertices(), "The set of vertices is not { 0, ..., n } without holes");
227
+ Siblings * sib = st->self_siblings(sh);
228
+ next_ = sib->parent();
229
+ sib_ = sib->oncles();
230
+ if (sib_ != nullptr) {
231
+ if constexpr (SimplexTree::Options::contiguous_vertices &&
232
+ !SimplexTree::Options::stable_simplex_handles) {
233
+ if (sib_->oncles() == nullptr)
234
+ // Only relevant for edges
235
+ baov_.first = sib_->members_.begin() + next_;
236
+ else
237
+ baov_.first = sib_->find(next_);
238
+ } else {
239
+ baov_.first = sib_->find(next_);
240
+ }
241
+ }
242
+ }
243
+
244
+ private:
245
+ friend class boost::iterator_core_access;
246
+
247
+ // valid when iterating along the SAME boundary.
248
+ bool equal(Simplex_tree_boundary_opposite_vertex_simplex_iterator const& other) const {
249
+ return (baov_.first == other.baov_.first);
250
+ }
251
+
252
+ std::pair<Simplex_handle, Vertex_handle> const& dereference() const {
253
+ return baov_;
254
+ }
255
+
256
+ void increment() {
257
+ if (sib_ == nullptr) {
258
+ baov_.first = st_->null_simplex();
259
+ return; // ------>>
260
+ }
261
+ Siblings * for_sib = sib_;
262
+ Siblings * new_sib = sib_->oncles();
263
+ auto rit = suffix_.rbegin();
264
+ if constexpr (SimplexTree::Options::contiguous_vertices && !SimplexTree::Options::stable_simplex_handles) {
265
+ if (new_sib == nullptr) {
266
+ // We reached the root, use a short-cut to find a vertex.
267
+ if (rit == suffix_.rend()) {
268
+ baov_.second = baov_.first->first;
269
+ // Segment, this vertex is the last boundary simplex
270
+ baov_.first = for_sib->members_.begin() + last_;
271
+ sib_ = nullptr;
272
+ return;
273
+ } else {
274
+ // Dim >= 2, initial step of the descent
275
+ baov_.first = for_sib->members_.begin() + *rit;
276
+ for_sib = baov_.first->second.children();
277
+ ++rit;
278
+ }
279
+ }
280
+ }
281
+
282
+ for (; rit != suffix_.rend(); ++rit) {
283
+ baov_.first = for_sib->find(*rit);
284
+ for_sib = baov_.first->second.children();
285
+ }
286
+ baov_.first = for_sib->find(last_); // baov_.first points to the right simplex now
287
+ suffix_.push_back(next_);
288
+ next_ = sib_->parent();
289
+ sib_ = new_sib;
290
+ baov_.second = suffix_.back();
291
+ }
292
+
293
+ // Most of the storage should be moved to the range, iterators should be light.
294
+ Vertex_handle last_; // last vertex of the simplex
295
+ Vertex_handle next_; // next vertex to push in suffix_
296
+ Static_vertex_vector suffix_;
297
+ Siblings * sib_; // where the next search will start from
298
+ std::pair<Simplex_handle, Vertex_handle> baov_; // a pair containing the current Simplex_handle in the boundary and its opposite vertex
299
+ SimplexTree * st_; // simplex containing the simplicial complex
300
+ };
301
+
302
+ /*---------------------------------------------------------------------------*/
303
+ /** \brief Iterator over the simplices of a simplicial complex.
304
+ *
305
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
306
+ template<class SimplexTree>
307
+ class Simplex_tree_complex_simplex_iterator : public boost::iterator_facade<
308
+ Simplex_tree_complex_simplex_iterator<SimplexTree>,
309
+ typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
310
+ public:
311
+ typedef typename SimplexTree::Simplex_handle Simplex_handle;
312
+ typedef typename SimplexTree::Siblings Siblings;
313
+ typedef typename SimplexTree::Vertex_handle Vertex_handle;
314
+
315
+ // any end() iterator
316
+ Simplex_tree_complex_simplex_iterator()
317
+ : sib_(nullptr),
318
+ st_(nullptr) {
319
+ }
320
+
321
+ explicit Simplex_tree_complex_simplex_iterator(SimplexTree * st)
322
+ : sib_(nullptr),
323
+ st_(st) {
324
+ if (st == nullptr || st->root() == nullptr || st->root()->members().empty()) {
325
+ st_ = nullptr;
326
+ } else {
327
+ sh_ = st->root()->members().begin();
328
+ sib_ = st->root();
329
+ while (st->has_children(sh_)) {
330
+ sib_ = sh_->second.children();
331
+ sh_ = sib_->members().begin();
332
+ }
333
+ }
334
+ }
335
+ private:
336
+ friend class boost::iterator_core_access;
337
+
338
+ // valid when iterating along the SAME boundary.
339
+ bool equal(Simplex_tree_complex_simplex_iterator const& other) const {
340
+ if (other.st_ == nullptr) {
341
+ return (st_ == nullptr);
342
+ }
343
+ if (st_ == nullptr) {
344
+ return false;
345
+ }
346
+ return (&(sh_->second) == &(other.sh_->second));
347
+ }
348
+
349
+ Simplex_handle const& dereference() const {
350
+ return sh_;
351
+ }
352
+
353
+ // Depth first traversal.
354
+ void increment() {
355
+ ++sh_;
356
+ if (sh_ == sib_->members().end()) {
357
+ if (sib_->oncles() == nullptr) {
358
+ st_ = nullptr;
359
+ return;
360
+ } // reach the end
361
+ sh_ = sib_->oncles()->members().find(sib_->parent());
362
+ sib_ = sib_->oncles();
363
+ return;
364
+ }
365
+ while (st_->has_children(sh_)) {
366
+ sib_ = sh_->second.children();
367
+ sh_ = sib_->members().begin();
368
+ }
369
+ }
370
+
371
+ Simplex_handle sh_;
372
+ Siblings * sib_;
373
+ SimplexTree * st_;
374
+ };
375
+
376
+ /** \brief Iterator over the simplices of the skeleton of a given
377
+ * dimension of the simplicial complex.
378
+ *
379
+ * Forward iterator, value_type is SimplexTree::Simplex_handle.*/
380
+ template<class SimplexTree>
381
+ class Simplex_tree_skeleton_simplex_iterator : public boost::iterator_facade<
382
+ Simplex_tree_skeleton_simplex_iterator<SimplexTree>,
383
+ typename SimplexTree::Simplex_handle const, boost::forward_traversal_tag> {
384
+ public:
385
+ typedef typename SimplexTree::Simplex_handle Simplex_handle;
386
+ typedef typename SimplexTree::Siblings Siblings;
387
+ typedef typename SimplexTree::Vertex_handle Vertex_handle;
388
+
389
+ // any end() iterator
390
+ Simplex_tree_skeleton_simplex_iterator()
391
+ : sib_(nullptr),
392
+ st_(nullptr),
393
+ dim_skel_(0),
394
+ curr_dim_(0) {
395
+ }
396
+
397
+ Simplex_tree_skeleton_simplex_iterator(SimplexTree * st, int dim_skel)
398
+ : sib_(nullptr),
399
+ st_(st),
400
+ dim_skel_(dim_skel),
401
+ curr_dim_(0) {
402
+ if (st == nullptr || st->root() == nullptr || st->root()->members().empty()) {
403
+ st_ = nullptr;
404
+ } else {
405
+ sh_ = st->root()->members().begin();
406
+ sib_ = st->root();
407
+ while (st->has_children(sh_) && curr_dim_ < dim_skel_) {
408
+ sib_ = sh_->second.children();
409
+ sh_ = sib_->members().begin();
410
+ ++curr_dim_;
411
+ }
412
+ }
413
+ }
414
+ private:
415
+ friend class boost::iterator_core_access;
416
+
417
+ // valid when iterating along the SAME boundary.
418
+ bool equal(Simplex_tree_skeleton_simplex_iterator const& other) const {
419
+ if (other.st_ == nullptr) {
420
+ return (st_ == nullptr);
421
+ }
422
+ if (st_ == nullptr) {
423
+ return false;
424
+ }
425
+ return (&(sh_->second) == &(other.sh_->second));
426
+ }
427
+
428
+ Simplex_handle const& dereference() const {
429
+ return sh_;
430
+ }
431
+
432
+ // Depth first traversal of the skeleton.
433
+ void increment() {
434
+ ++sh_;
435
+ if (sh_ == sib_->members().end()) {
436
+ if (sib_->oncles() == nullptr) {
437
+ st_ = nullptr;
438
+ return;
439
+ } // reach the end
440
+ sh_ = sib_->oncles()->members().find(sib_->parent());
441
+ sib_ = sib_->oncles();
442
+ --curr_dim_;
443
+ return;
444
+ }
445
+ while (st_->has_children(sh_) && curr_dim_ < dim_skel_) {
446
+ sib_ = sh_->second.children();
447
+ sh_ = sib_->members().begin();
448
+ ++curr_dim_;
449
+ }
450
+ }
451
+
452
+ Simplex_handle sh_;
453
+ Siblings * sib_;
454
+ SimplexTree * st_;
455
+ int dim_skel_;
456
+ int curr_dim_;
457
+ };
458
+
459
+ /** @}*/ // end addtogroup simplex_tree
460
+
461
+ } // namespace Gudhi
462
+
463
+ #endif // SIMPLEX_TREE_SIMPLEX_TREE_ITERATORS_H_