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
@@ -1,322 +1,322 @@
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- #pragma once
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-
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- #include "Simplex_tree_multi_interface.h"
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- #include "multi_parameter_rank_invariant/persistence_slices.h"
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- #include "tensor/tensor.h"
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- #include <gudhi/One_critical_filtration.h>
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- #include <gudhi/Simplex_tree_multi.h>
8
- #include <oneapi/tbb/enumerable_thread_specific.h>
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- #include <oneapi/tbb/parallel_for.h>
10
-
11
- namespace Gudhi {
12
- namespace multiparameter {
13
- namespace function_rips {
14
-
15
- using value_type = typename python_interface::interface_std::Filtration_value;
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- using _multifiltration = typename Gudhi::multi_filtration::One_critical_filtration<value_type>;
17
- using _multist = python_interface::Simplex_tree_multi_interface<_multifiltration>;
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- using interface_multi = _multist;
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-
20
-
21
- std::pair<std::map<value_type, unsigned int>, std::vector<value_type>>
22
- inline radius_to_coordinate(Simplex_tree_std &st) {
23
- unsigned int count = 0;
24
- std::map<value_type, unsigned int> out;
25
- std::vector<value_type> filtration_values;
26
- filtration_values.reserve(st.num_simplices());
27
- for (auto sh : st.filtration_simplex_range()) { // ordered by filtration, so
28
- // should be sorted
29
- auto filtration = st.filtration(sh);
30
- if (!out.contains(filtration)) {
31
- out[filtration] = count;
32
- filtration_values.push_back(filtration);
33
- count++;
34
- }
35
- }
36
- return {out, filtration_values};
37
- }
38
-
39
- // Takes a standard simplextree and turn it into a simplextreemulti, whose first
40
- // axis is the rips, and the others are the filtrations of the node at each
41
- // degree in degrees Assumes that the degrees are sorted, and unique
42
-
43
- std::tuple<_multist,
44
- std::vector<value_type>, int>
45
- inline get_degree_filtrations( // also return max_degree,filtration_values
46
- python_interface::interface_std &st, const std::vector<int> &degrees) {
47
- constexpr const bool verbose = false;
48
- using filtration_lists = std::vector<std::vector<value_type>>;
49
-
50
- assert(st.dimension() ==
51
- 1); // the st slices will be expanded + collapsed after being filled.
52
- _multist st_multi;
53
- std::vector<value_type> rips_filtration_values = {
54
- 0}; // vector that will hold the used filtration values
55
- rips_filtration_values.reserve(st.num_simplices());
56
- int max_st_degree = 0;
57
-
58
- int num_degrees = degrees.size();
59
- Gudhi::multi_persistence::multify(st, st_multi, 0); // puts the st filtration in axis 0 + fitrations for
60
- // each degrees afterward
61
- // preprocess
62
- filtration_lists edge_filtration_of_nodes(st.num_vertices());
63
- for (auto sh : st.complex_simplex_range()) {
64
- if (st.dimension() == 0)
65
- continue;
66
- value_type filtration = st.filtration(sh);
67
- for (auto node : st.simplex_vertex_range(sh)) {
68
- edge_filtration_of_nodes[node].push_back(filtration);
69
- }
70
- }
71
-
72
- for (auto &filtrations : edge_filtration_of_nodes) { // todo : parallel ?
73
- std::sort(filtrations.begin(), filtrations.end());
74
- int node_degree = filtrations.size();
75
- max_st_degree = std::max(node_degree, max_st_degree);
76
- filtrations.resize(std::max(num_degrees, node_degree));
77
- if constexpr (verbose)
78
- std::cout << "Filtration of node ";
79
- for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
80
- if (degrees[degree_index] < node_degree)
81
- filtrations[degree_index] = filtrations[degrees[degree_index]];
82
- else
83
- filtrations[degree_index] = std::numeric_limits<value_type>::infinity();
84
- if constexpr (verbose)
85
- std::cout << filtrations[degree_index] << " ";
86
- }
87
- filtrations.resize(num_degrees);
88
- std::reverse(filtrations.begin(),
89
- filtrations.end()); // degree is in opposite direction
90
- for (value_type filtration_value : filtrations)
91
- rips_filtration_values.push_back(
92
- filtration_value); // we only do that here to have a smaller grid.
93
- if constexpr (verbose)
94
- std::cout << "\n";
95
- }
96
- // sort + unique the filtration values
97
- std::sort(rips_filtration_values.begin(), rips_filtration_values.end());
98
- rips_filtration_values.erase(
99
- std::unique(rips_filtration_values.begin(), rips_filtration_values.end()),
100
- rips_filtration_values.end());
101
-
102
- // fills the degree_rips simplextree with lower star
103
- auto sh_standard =
104
- st.complex_simplex_range()
105
- .begin(); // waiting for c++23 & zip to remove this garbage
106
- auto _end = st.complex_simplex_range().end();
107
- auto sh_multi = st_multi.complex_simplex_range().begin();
108
- for (; sh_standard != _end; ++sh_multi, ++sh_standard) {
109
- if (st.dimension(*sh_standard) == 0) // only fill using the node
110
- continue; // will be filled afterward
111
- // dimension is 1 by assumption. fill using the node + rips value
112
- value_type edge_filtration = st.filtration(*sh_standard);
113
- _multifiltration &edge_degree_rips_filtration =
114
- st_multi.filtration_mutable(*sh_multi); // the filtration vector to fill
115
- edge_degree_rips_filtration.resize(num_degrees);
116
- for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
117
- value_type edge_filtration_of_degree =
118
- edge_filtration; // copy as we do the max with edges of degree index
119
- for (int node : st.simplex_vertex_range(*sh_standard)) {
120
- edge_filtration_of_degree =
121
- std::max(edge_filtration_of_degree,
122
- edge_filtration_of_nodes[node][degree_index]);
123
- }
124
- edge_degree_rips_filtration[degree_index] =
125
- edge_filtration_of_degree; // fills the correct value in the edge
126
- // filtration
127
- }
128
- }
129
-
130
- // fills the dimension 0 simplices
131
- { // scope for count;
132
- for (auto vertex :
133
- st_multi.complex_vertex_range()) { // should be in increasing order
134
- auto &vertex_filtration =
135
- st_multi.filtration_mutable(st_multi.find({vertex}));
136
- if constexpr (verbose) {
137
- std::cout << "Setting filtration of node " << vertex << " to ";
138
- for (auto degree_index = 0u; degree_index < num_degrees;
139
- degree_index++) {
140
- std::cout << edge_filtration_of_nodes[vertex][degree_index] << " ";
141
- }
142
- std::cout << "\n";
143
- }
144
- vertex_filtration.swap(edge_filtration_of_nodes[vertex]);
145
- }
146
- }
147
-
148
- return {st_multi, rips_filtration_values, max_st_degree};
149
- }
150
-
151
- // assumes that the degree is 1
152
- inline void fill_st_slice(Simplex_tree_std &st_container,
153
- _multist &degree_rips_st, int degree) {
154
- auto sh_std = st_container.complex_simplex_range().begin();
155
- auto sh_multi = degree_rips_st.complex_simplex_range().begin();
156
- auto sh_end = st_container.complex_simplex_range().end();
157
- for (; sh_std != sh_end; ++sh_std, ++sh_multi) {
158
- value_type splx_filtration =
159
- degree_rips_st.filtration_mutable(*sh_multi)[degree];
160
- st_container.assign_filtration(*sh_std, splx_filtration);
161
- }
162
- return;
163
- }
164
-
165
- template <typename dtype, typename index_type>
166
- inline void
167
- compute_2d_function_rips(_multist &st_multi, // Function rips
168
- // Simplex_tree_std &_st,
169
- const tensor::static_tensor_view<dtype, index_type>
170
- &out, // assumes its a zero tensor
171
- const std::vector<index_type> degrees, index_type I,
172
- index_type J, // grid_shape
173
- bool mobius_inverion, bool zero_pad) {
174
- constexpr bool verbose = false;
175
- if constexpr (verbose)
176
- std::cout << "Grid shape : " << I << " " << J << std::endl;
177
-
178
- // inits default simplextrees
179
- Simplex_tree_std _st;
180
- Gudhi::multi_persistence::flatten(_st, st_multi,
181
- -1); // copies the st_multi to a standard 1-pers simplextree
182
- tbb::enumerable_thread_specific<Simplex_tree_std> thread_simplex_tree(_st);
183
- int max_simplex_dimension =
184
- *std::max_element(degrees.begin(), degrees.end()) + 1;
185
- tbb::parallel_for(0, J, [&](index_type function_value) {
186
- auto &st_std = thread_simplex_tree.local();
187
- fill_st_slice(st_std, st_multi, function_value);
188
- constexpr int num_collapses = 10;
189
- const std::vector<Barcode> barcodes =
190
- compute_dgms(st_std, degrees, num_collapses, max_simplex_dimension);
191
-
192
- index_type degree_index = 0;
193
- for (const auto &barcode : barcodes) { // TODO range view cartesian product
194
- // coordinates_container[0] = degree_index;
195
- for (const auto &bar : barcode) {
196
- auto birth = bar.first; // float
197
- auto death = bar.second;
198
- if (birth > I) // some birth can be infinite
199
- continue;
200
-
201
- if (!mobius_inverion) {
202
- index_type shift_value =
203
- out.get_cum_resolution()[1]; // degree, x coord, y coord
204
- index_type border = I;
205
- // index_type border = out.get_resolution()[i+1];
206
- // dtype* ptr = &out[coordinates_container];
207
- dtype *ptr = &out[{degree_index, static_cast<index_type>(birth),
208
- function_value}];
209
- auto stop_value = death > static_cast<value_type>(border)
210
- ? border
211
- : static_cast<index_type>(death);
212
- // Warning : for some reason linux static casts float inf to -min_int
213
- // so min doesnt work.
214
- if constexpr (verbose) {
215
- std::cout << "Adding : (";
216
- // for (auto stuff : coordinates_container) std::cout << stuff << ",
217
- // ";
218
- std::cout << ") With death " << death << " casted at "
219
- << static_cast<index_type>(death) << "with threshold at"
220
- << stop_value << " with " << border << std::endl;
221
- }
222
- for (index_type b = birth; b < stop_value; b++) {
223
- (*ptr)++; // adds one to the vector
224
- ptr += shift_value; // shift the pointer to the next element in the
225
- // segment [birth, death]
226
- }
227
- } else {
228
- // adds birth
229
- out[{degree_index, static_cast<index_type>(birth), function_value}]++;
230
- if constexpr (verbose) {
231
- std::cout << "Coordinate : ";
232
- // for (auto c : coordinates_container) std::cout << c << ", ";
233
- std::cout << std::endl;
234
- std::cout << "axis, death, resolution : " << 1 << ", "
235
- << std::to_string(death) << ", "
236
- << out.get_resolution()[1];
237
- std::cout << std::endl;
238
- }
239
- // removes death
240
- if (death < I) {
241
- out[{degree_index, static_cast<index_type>(death),
242
- function_value}]--;
243
- } else if (zero_pad) {
244
- out[{degree_index, I - 1, function_value}]--;
245
- }
246
- }
247
- }
248
- degree_index++;
249
- }
250
- });
251
- }
252
-
253
- // python interface
254
-
255
- std::pair<std::vector<value_type>, int>
256
- inline get_degree_rips_st_python(const intptr_t simplextree_ptr,
257
- const intptr_t st_multi_ptr,
258
- const std::vector<int> &degrees) {
259
- auto &st_std = python_interface::get_simplextree_from_pointer<python_interface::interface_std>(simplextree_ptr);
260
- auto &st_multi_python_container =
261
- python_interface::get_simplextree_from_pointer<_multist>(st_multi_ptr);
262
- auto [st_multi, rips_filtration_values, max_node_degree] =
263
- get_degree_filtrations(st_std, degrees);
264
- st_multi_python_container = std::move(st_multi);
265
- return {rips_filtration_values, max_node_degree};
266
- }
267
-
268
- template <typename dtype, typename indices_type>
269
- void compute_function_rips_surface_python(
270
- const intptr_t st_multi_ptr, dtype *data_ptr,
271
- const std::vector<indices_type> degrees, indices_type I, indices_type J,
272
- const bool mobius_inversion = false, const bool zero_pad = false,
273
- indices_type n_jobs = 0) {
274
- if (degrees.size() == 0)
275
- return;
276
- // const bool verbose = false;
277
- auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
278
- tensor::static_tensor_view<dtype, indices_type> container(
279
- data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
280
- if (zero_pad) {
281
- I--;
282
- J--;
283
- }
284
-
285
- oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
286
- arena.execute([&] {
287
- compute_2d_function_rips(st_multi, container, degrees, I, J,
288
- mobius_inversion, zero_pad);
289
- });
290
- if (mobius_inversion)
291
- container.differentiate(2); // degree,x axis (already inversed), y axis
292
- }
293
-
294
- template <typename dtype, typename indices_type>
295
- std::pair<std::vector<std::vector<indices_type>>, std::vector<dtype>>
296
- compute_function_rips_signed_measure_python(
297
- const intptr_t st_multi_ptr, dtype *data_ptr,
298
- const std::vector<indices_type> degrees, indices_type I, indices_type J,
299
- const bool mobius_inversion = false, const bool zero_pad = false,
300
- indices_type n_jobs = 0) {
301
- if (degrees.size() == 0)
302
- return {{}, {}};
303
- // const bool verbose = false;
304
- auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
305
- tensor::static_tensor_view<dtype, indices_type> container(
306
- data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
307
- if (zero_pad) {
308
- I--;
309
- J--;
310
- }
311
-
312
- oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
313
- arena.execute([&] {
314
- compute_2d_function_rips(st_multi, container, degrees, I, J,
315
- mobius_inversion, zero_pad);
316
- });
317
- if (mobius_inversion)
318
- container.differentiate(2); // degree,x axis (already inversed), y axis
319
- return container.sparsify();
320
- }
321
-
322
- }}} // namespace Gudhi::multiparameter::function_rips
1
+ #pragma once
2
+
3
+ #include "Simplex_tree_multi_interface.h"
4
+ #include "multi_parameter_rank_invariant/persistence_slices.h"
5
+ #include "tensor/tensor.h"
6
+ #include <gudhi/One_critical_filtration.h>
7
+ #include <gudhi/Simplex_tree_multi.h>
8
+ #include <oneapi/tbb/enumerable_thread_specific.h>
9
+ #include <oneapi/tbb/parallel_for.h>
10
+
11
+ namespace Gudhi {
12
+ namespace multiparameter {
13
+ namespace function_rips {
14
+
15
+ using value_type = typename python_interface::interface_std::Filtration_value;
16
+ using _multifiltration = typename Gudhi::multi_filtration::One_critical_filtration<value_type>;
17
+ using _multist = python_interface::Simplex_tree_multi_interface<_multifiltration>;
18
+ using interface_multi = _multist;
19
+
20
+
21
+ std::pair<std::map<value_type, unsigned int>, std::vector<value_type>>
22
+ inline radius_to_coordinate(Simplex_tree_std &st) {
23
+ unsigned int count = 0;
24
+ std::map<value_type, unsigned int> out;
25
+ std::vector<value_type> filtration_values;
26
+ filtration_values.reserve(st.num_simplices());
27
+ for (auto sh : st.filtration_simplex_range()) { // ordered by filtration, so
28
+ // should be sorted
29
+ auto filtration = st.filtration(sh);
30
+ if (!out.contains(filtration)) {
31
+ out[filtration] = count;
32
+ filtration_values.push_back(filtration);
33
+ count++;
34
+ }
35
+ }
36
+ return {out, filtration_values};
37
+ }
38
+
39
+ // Takes a standard simplextree and turn it into a simplextreemulti, whose first
40
+ // axis is the rips, and the others are the filtrations of the node at each
41
+ // degree in degrees Assumes that the degrees are sorted, and unique
42
+
43
+ std::tuple<_multist,
44
+ std::vector<value_type>, int>
45
+ inline get_degree_filtrations( // also return max_degree,filtration_values
46
+ python_interface::interface_std &st, const std::vector<int> &degrees) {
47
+ constexpr const bool verbose = false;
48
+ using filtration_lists = std::vector<std::vector<value_type>>;
49
+
50
+ assert(st.dimension() ==
51
+ 1); // the st slices will be expanded + collapsed after being filled.
52
+ _multist st_multi;
53
+ std::vector<value_type> rips_filtration_values = {
54
+ 0}; // vector that will hold the used filtration values
55
+ rips_filtration_values.reserve(st.num_simplices());
56
+ int max_st_degree = 0;
57
+
58
+ int num_degrees = degrees.size();
59
+ Gudhi::multi_persistence::multify(st, st_multi, 0); // puts the st filtration in axis 0 + fitrations for
60
+ // each degrees afterward
61
+ // preprocess
62
+ filtration_lists edge_filtration_of_nodes(st.num_vertices());
63
+ for (auto sh : st.complex_simplex_range()) {
64
+ if (st.dimension() == 0)
65
+ continue;
66
+ value_type filtration = st.filtration(sh);
67
+ for (auto node : st.simplex_vertex_range(sh)) {
68
+ edge_filtration_of_nodes[node].push_back(filtration);
69
+ }
70
+ }
71
+
72
+ for (auto &filtrations : edge_filtration_of_nodes) { // todo : parallel ?
73
+ std::sort(filtrations.begin(), filtrations.end());
74
+ int node_degree = filtrations.size();
75
+ max_st_degree = std::max(node_degree, max_st_degree);
76
+ filtrations.resize(std::max(num_degrees, node_degree));
77
+ if constexpr (verbose)
78
+ std::cout << "Filtration of node ";
79
+ for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
80
+ if (degrees[degree_index] < node_degree)
81
+ filtrations[degree_index] = filtrations[degrees[degree_index]];
82
+ else
83
+ filtrations[degree_index] = std::numeric_limits<value_type>::infinity();
84
+ if constexpr (verbose)
85
+ std::cout << filtrations[degree_index] << " ";
86
+ }
87
+ filtrations.resize(num_degrees);
88
+ std::reverse(filtrations.begin(),
89
+ filtrations.end()); // degree is in opposite direction
90
+ for (value_type filtration_value : filtrations)
91
+ rips_filtration_values.push_back(
92
+ filtration_value); // we only do that here to have a smaller grid.
93
+ if constexpr (verbose)
94
+ std::cout << "\n";
95
+ }
96
+ // sort + unique the filtration values
97
+ std::sort(rips_filtration_values.begin(), rips_filtration_values.end());
98
+ rips_filtration_values.erase(
99
+ std::unique(rips_filtration_values.begin(), rips_filtration_values.end()),
100
+ rips_filtration_values.end());
101
+
102
+ // fills the degree_rips simplextree with lower star
103
+ auto sh_standard =
104
+ st.complex_simplex_range()
105
+ .begin(); // waiting for c++23 & zip to remove this garbage
106
+ auto _end = st.complex_simplex_range().end();
107
+ auto sh_multi = st_multi.complex_simplex_range().begin();
108
+ for (; sh_standard != _end; ++sh_multi, ++sh_standard) {
109
+ if (st.dimension(*sh_standard) == 0) // only fill using the node
110
+ continue; // will be filled afterward
111
+ // dimension is 1 by assumption. fill using the node + rips value
112
+ value_type edge_filtration = st.filtration(*sh_standard);
113
+ _multifiltration &edge_degree_rips_filtration =
114
+ st_multi.filtration_mutable(*sh_multi); // the filtration vector to fill
115
+ edge_degree_rips_filtration.resize(num_degrees);
116
+ for (auto degree_index = 0; degree_index < num_degrees; degree_index++) {
117
+ value_type edge_filtration_of_degree =
118
+ edge_filtration; // copy as we do the max with edges of degree index
119
+ for (int node : st.simplex_vertex_range(*sh_standard)) {
120
+ edge_filtration_of_degree =
121
+ std::max(edge_filtration_of_degree,
122
+ edge_filtration_of_nodes[node][degree_index]);
123
+ }
124
+ edge_degree_rips_filtration[degree_index] =
125
+ edge_filtration_of_degree; // fills the correct value in the edge
126
+ // filtration
127
+ }
128
+ }
129
+
130
+ // fills the dimension 0 simplices
131
+ { // scope for count;
132
+ for (auto vertex :
133
+ st_multi.complex_vertex_range()) { // should be in increasing order
134
+ auto &vertex_filtration =
135
+ st_multi.filtration_mutable(st_multi.find({vertex}));
136
+ if constexpr (verbose) {
137
+ std::cout << "Setting filtration of node " << vertex << " to ";
138
+ for (auto degree_index = 0u; degree_index < num_degrees;
139
+ degree_index++) {
140
+ std::cout << edge_filtration_of_nodes[vertex][degree_index] << " ";
141
+ }
142
+ std::cout << "\n";
143
+ }
144
+ vertex_filtration.swap(edge_filtration_of_nodes[vertex]);
145
+ }
146
+ }
147
+
148
+ return {st_multi, rips_filtration_values, max_st_degree};
149
+ }
150
+
151
+ // assumes that the degree is 1
152
+ inline void fill_st_slice(Simplex_tree_std &st_container,
153
+ _multist &degree_rips_st, int degree) {
154
+ auto sh_std = st_container.complex_simplex_range().begin();
155
+ auto sh_multi = degree_rips_st.complex_simplex_range().begin();
156
+ auto sh_end = st_container.complex_simplex_range().end();
157
+ for (; sh_std != sh_end; ++sh_std, ++sh_multi) {
158
+ value_type splx_filtration =
159
+ degree_rips_st.filtration_mutable(*sh_multi)[degree];
160
+ st_container.assign_filtration(*sh_std, splx_filtration);
161
+ }
162
+ return;
163
+ }
164
+
165
+ template <typename dtype, typename index_type>
166
+ inline void
167
+ compute_2d_function_rips(_multist &st_multi, // Function rips
168
+ // Simplex_tree_std &_st,
169
+ const tensor::static_tensor_view<dtype, index_type>
170
+ &out, // assumes its a zero tensor
171
+ const std::vector<index_type> degrees, index_type I,
172
+ index_type J, // grid_shape
173
+ bool mobius_inverion, bool zero_pad) {
174
+ constexpr bool verbose = false;
175
+ if constexpr (verbose)
176
+ std::cout << "Grid shape : " << I << " " << J << std::endl;
177
+
178
+ // inits default simplextrees
179
+ Simplex_tree_std _st;
180
+ Gudhi::multi_persistence::flatten(_st, st_multi,
181
+ -1); // copies the st_multi to a standard 1-pers simplextree
182
+ tbb::enumerable_thread_specific<Simplex_tree_std> thread_simplex_tree(_st);
183
+ int max_simplex_dimension =
184
+ *std::max_element(degrees.begin(), degrees.end()) + 1;
185
+ tbb::parallel_for(0, J, [&](index_type function_value) {
186
+ auto &st_std = thread_simplex_tree.local();
187
+ fill_st_slice(st_std, st_multi, function_value);
188
+ constexpr int num_collapses = 10;
189
+ const std::vector<Barcode> barcodes =
190
+ compute_dgms(st_std, degrees, num_collapses, max_simplex_dimension);
191
+
192
+ index_type degree_index = 0;
193
+ for (const auto &barcode : barcodes) { // TODO range view cartesian product
194
+ // coordinates_container[0] = degree_index;
195
+ for (const auto &bar : barcode) {
196
+ auto birth = bar.first; // float
197
+ auto death = bar.second;
198
+ if (birth > I) // some birth can be infinite
199
+ continue;
200
+
201
+ if (!mobius_inverion) {
202
+ index_type shift_value =
203
+ out.get_cum_resolution()[1]; // degree, x coord, y coord
204
+ index_type border = I;
205
+ // index_type border = out.get_resolution()[i+1];
206
+ // dtype* ptr = &out[coordinates_container];
207
+ dtype *ptr = &out[{degree_index, static_cast<index_type>(birth),
208
+ function_value}];
209
+ auto stop_value = death > static_cast<value_type>(border)
210
+ ? border
211
+ : static_cast<index_type>(death);
212
+ // Warning : for some reason linux static casts float inf to -min_int
213
+ // so min doesnt work.
214
+ if constexpr (verbose) {
215
+ std::cout << "Adding : (";
216
+ // for (auto stuff : coordinates_container) std::cout << stuff << ",
217
+ // ";
218
+ std::cout << ") With death " << death << " casted at "
219
+ << static_cast<index_type>(death) << "with threshold at"
220
+ << stop_value << " with " << border << std::endl;
221
+ }
222
+ for (index_type b = birth; b < stop_value; b++) {
223
+ (*ptr)++; // adds one to the vector
224
+ ptr += shift_value; // shift the pointer to the next element in the
225
+ // segment [birth, death]
226
+ }
227
+ } else {
228
+ // adds birth
229
+ out[{degree_index, static_cast<index_type>(birth), function_value}]++;
230
+ if constexpr (verbose) {
231
+ std::cout << "Coordinate : ";
232
+ // for (auto c : coordinates_container) std::cout << c << ", ";
233
+ std::cout << std::endl;
234
+ std::cout << "axis, death, resolution : " << 1 << ", "
235
+ << std::to_string(death) << ", "
236
+ << out.get_resolution()[1];
237
+ std::cout << std::endl;
238
+ }
239
+ // removes death
240
+ if (death < I) {
241
+ out[{degree_index, static_cast<index_type>(death),
242
+ function_value}]--;
243
+ } else if (zero_pad) {
244
+ out[{degree_index, I - 1, function_value}]--;
245
+ }
246
+ }
247
+ }
248
+ degree_index++;
249
+ }
250
+ });
251
+ }
252
+
253
+ // python interface
254
+
255
+ std::pair<std::vector<value_type>, int>
256
+ inline get_degree_rips_st_python(const intptr_t simplextree_ptr,
257
+ const intptr_t st_multi_ptr,
258
+ const std::vector<int> &degrees) {
259
+ auto &st_std = python_interface::get_simplextree_from_pointer<python_interface::interface_std>(simplextree_ptr);
260
+ auto &st_multi_python_container =
261
+ python_interface::get_simplextree_from_pointer<_multist>(st_multi_ptr);
262
+ auto [st_multi, rips_filtration_values, max_node_degree] =
263
+ get_degree_filtrations(st_std, degrees);
264
+ st_multi_python_container = std::move(st_multi);
265
+ return {rips_filtration_values, max_node_degree};
266
+ }
267
+
268
+ template <typename dtype, typename indices_type>
269
+ void compute_function_rips_surface_python(
270
+ const intptr_t st_multi_ptr, dtype *data_ptr,
271
+ const std::vector<indices_type> degrees, indices_type I, indices_type J,
272
+ const bool mobius_inversion = false, const bool zero_pad = false,
273
+ indices_type n_jobs = 0) {
274
+ if (degrees.size() == 0)
275
+ return;
276
+ // const bool verbose = false;
277
+ auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
278
+ tensor::static_tensor_view<dtype, indices_type> container(
279
+ data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
280
+ if (zero_pad) {
281
+ I--;
282
+ J--;
283
+ }
284
+
285
+ oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
286
+ arena.execute([&] {
287
+ compute_2d_function_rips(st_multi, container, degrees, I, J,
288
+ mobius_inversion, zero_pad);
289
+ });
290
+ if (mobius_inversion)
291
+ container.differentiate(2); // degree,x axis (already inversed), y axis
292
+ }
293
+
294
+ template <typename dtype, typename indices_type>
295
+ std::pair<std::vector<std::vector<indices_type>>, std::vector<dtype>>
296
+ compute_function_rips_signed_measure_python(
297
+ const intptr_t st_multi_ptr, dtype *data_ptr,
298
+ const std::vector<indices_type> degrees, indices_type I, indices_type J,
299
+ const bool mobius_inversion = false, const bool zero_pad = false,
300
+ indices_type n_jobs = 0) {
301
+ if (degrees.size() == 0)
302
+ return {{}, {}};
303
+ // const bool verbose = false;
304
+ auto &st_multi = python_interface::get_simplextree_from_pointer<interface_multi>(st_multi_ptr);
305
+ tensor::static_tensor_view<dtype, indices_type> container(
306
+ data_ptr, {static_cast<indices_type>(degrees.size()), I, J});
307
+ if (zero_pad) {
308
+ I--;
309
+ J--;
310
+ }
311
+
312
+ oneapi::tbb::task_arena arena(n_jobs); // limits the number of threads
313
+ arena.execute([&] {
314
+ compute_2d_function_rips(st_multi, container, degrees, I, J,
315
+ mobius_inversion, zero_pad);
316
+ });
317
+ if (mobius_inversion)
318
+ container.differentiate(2); // degree,x axis (already inversed), y axis
319
+ return container.sparsify();
320
+ }
321
+
322
+ }}} // namespace Gudhi::multiparameter::function_rips