multipers 2.3.3__cp312-cp312-manylinux_2_39_x86_64.whl

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  1. multipers/__init__.py +33 -0
  2. multipers/_signed_measure_meta.py +450 -0
  3. multipers/_slicer_meta.py +211 -0
  4. multipers/array_api/__init__.py +62 -0
  5. multipers/array_api/numpy.py +104 -0
  6. multipers/array_api/torch.py +117 -0
  7. multipers/data/MOL2.py +458 -0
  8. multipers/data/UCR.py +18 -0
  9. multipers/data/__init__.py +1 -0
  10. multipers/data/graphs.py +466 -0
  11. multipers/data/immuno_regions.py +27 -0
  12. multipers/data/minimal_presentation_to_st_bf.py +0 -0
  13. multipers/data/pytorch2simplextree.py +91 -0
  14. multipers/data/shape3d.py +101 -0
  15. multipers/data/synthetic.py +113 -0
  16. multipers/distances.py +202 -0
  17. multipers/filtration_conversions.pxd +229 -0
  18. multipers/filtration_conversions.pxd.tp +84 -0
  19. multipers/filtrations/__init__.py +18 -0
  20. multipers/filtrations/density.py +533 -0
  21. multipers/filtrations/filtrations.py +361 -0
  22. multipers/filtrations.pxd +224 -0
  23. multipers/function_rips.cpython-312-x86_64-linux-gnu.so +0 -0
  24. multipers/function_rips.pyx +105 -0
  25. multipers/grids.cpython-312-x86_64-linux-gnu.so +0 -0
  26. multipers/grids.pyx +481 -0
  27. multipers/gudhi/Persistence_slices_interface.h +132 -0
  28. multipers/gudhi/Simplex_tree_interface.h +239 -0
  29. multipers/gudhi/Simplex_tree_multi_interface.h +551 -0
  30. multipers/gudhi/cubical_to_boundary.h +59 -0
  31. multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -0
  32. multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -0
  33. multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -0
  34. multipers/gudhi/gudhi/Debug_utils.h +45 -0
  35. multipers/gudhi/gudhi/Fields/Multi_field.h +484 -0
  36. multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -0
  37. multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -0
  38. multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -0
  39. multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -0
  40. multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -0
  41. multipers/gudhi/gudhi/Fields/Z2_field.h +355 -0
  42. multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -0
  43. multipers/gudhi/gudhi/Fields/Zp_field.h +420 -0
  44. multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -0
  45. multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -0
  46. multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -0
  47. multipers/gudhi/gudhi/Matrix.h +2107 -0
  48. multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -0
  49. multipers/gudhi/gudhi/Multi_persistence/Box.h +174 -0
  50. multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -0
  51. multipers/gudhi/gudhi/Off_reader.h +173 -0
  52. multipers/gudhi/gudhi/One_critical_filtration.h +1441 -0
  53. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -0
  54. multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -0
  55. multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -0
  56. multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -0
  57. multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -0
  58. multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -0
  59. multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -0
  60. multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -0
  61. multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -0
  62. multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -0
  63. multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -0
  64. multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -0
  65. multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -0
  66. multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -0
  67. multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -0
  68. multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -0
  69. multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -0
  70. multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -0
  71. multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -0
  72. multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -0
  73. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -0
  74. multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -0
  75. multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -0
  76. multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -0
  77. multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -0
  78. multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -0
  79. multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -0
  80. multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -0
  81. multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -0
  82. multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -0
  83. multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -0
  84. multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -0
  85. multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -0
  86. multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -0
  87. multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -0
  88. multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -0
  89. multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -0
  90. multipers/gudhi/gudhi/Persistent_cohomology.h +745 -0
  91. multipers/gudhi/gudhi/Points_off_io.h +171 -0
  92. multipers/gudhi/gudhi/Simple_object_pool.h +69 -0
  93. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -0
  94. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -0
  95. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -0
  96. multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -0
  97. multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -0
  98. multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -0
  99. multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -0
  100. multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -0
  101. multipers/gudhi/gudhi/Simplex_tree.h +2794 -0
  102. multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -0
  103. multipers/gudhi/gudhi/distance_functions.h +62 -0
  104. multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -0
  105. multipers/gudhi/gudhi/persistence_interval.h +253 -0
  106. multipers/gudhi/gudhi/persistence_matrix_options.h +170 -0
  107. multipers/gudhi/gudhi/reader_utils.h +367 -0
  108. multipers/gudhi/mma_interface_coh.h +256 -0
  109. multipers/gudhi/mma_interface_h0.h +223 -0
  110. multipers/gudhi/mma_interface_matrix.h +293 -0
  111. multipers/gudhi/naive_merge_tree.h +536 -0
  112. multipers/gudhi/scc_io.h +310 -0
  113. multipers/gudhi/truc.h +1403 -0
  114. multipers/io.cpython-312-x86_64-linux-gnu.so +0 -0
  115. multipers/io.pyx +644 -0
  116. multipers/ml/__init__.py +0 -0
  117. multipers/ml/accuracies.py +90 -0
  118. multipers/ml/invariants_with_persistable.py +79 -0
  119. multipers/ml/kernels.py +176 -0
  120. multipers/ml/mma.py +713 -0
  121. multipers/ml/one.py +472 -0
  122. multipers/ml/point_clouds.py +352 -0
  123. multipers/ml/signed_measures.py +1667 -0
  124. multipers/ml/sliced_wasserstein.py +461 -0
  125. multipers/ml/tools.py +113 -0
  126. multipers/mma_structures.cpython-312-x86_64-linux-gnu.so +0 -0
  127. multipers/mma_structures.pxd +128 -0
  128. multipers/mma_structures.pyx +2786 -0
  129. multipers/mma_structures.pyx.tp +1094 -0
  130. multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -0
  131. multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -0
  132. multipers/multi_parameter_rank_invariant/function_rips.h +322 -0
  133. multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -0
  134. multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -0
  135. multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -0
  136. multipers/multiparameter_edge_collapse.py +41 -0
  137. multipers/multiparameter_module_approximation/approximation.h +2330 -0
  138. multipers/multiparameter_module_approximation/combinatory.h +129 -0
  139. multipers/multiparameter_module_approximation/debug.h +107 -0
  140. multipers/multiparameter_module_approximation/euler_curves.h +0 -0
  141. multipers/multiparameter_module_approximation/format_python-cpp.h +286 -0
  142. multipers/multiparameter_module_approximation/heap_column.h +238 -0
  143. multipers/multiparameter_module_approximation/images.h +79 -0
  144. multipers/multiparameter_module_approximation/list_column.h +174 -0
  145. multipers/multiparameter_module_approximation/list_column_2.h +232 -0
  146. multipers/multiparameter_module_approximation/ru_matrix.h +347 -0
  147. multipers/multiparameter_module_approximation/set_column.h +135 -0
  148. multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -0
  149. multipers/multiparameter_module_approximation/unordered_set_column.h +166 -0
  150. multipers/multiparameter_module_approximation/utilities.h +403 -0
  151. multipers/multiparameter_module_approximation/vector_column.h +223 -0
  152. multipers/multiparameter_module_approximation/vector_matrix.h +331 -0
  153. multipers/multiparameter_module_approximation/vineyards.h +464 -0
  154. multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -0
  155. multipers/multiparameter_module_approximation.cpython-312-x86_64-linux-gnu.so +0 -0
  156. multipers/multiparameter_module_approximation.pyx +235 -0
  157. multipers/pickle.py +90 -0
  158. multipers/plots.py +470 -0
  159. multipers/point_measure.cpython-312-x86_64-linux-gnu.so +0 -0
  160. multipers/point_measure.pyx +395 -0
  161. multipers/simplex_tree_multi.cpython-312-x86_64-linux-gnu.so +0 -0
  162. multipers/simplex_tree_multi.pxd +134 -0
  163. multipers/simplex_tree_multi.pyx +10980 -0
  164. multipers/simplex_tree_multi.pyx.tp +2007 -0
  165. multipers/slicer.cpython-312-x86_64-linux-gnu.so +0 -0
  166. multipers/slicer.pxd +3034 -0
  167. multipers/slicer.pxd.tp +234 -0
  168. multipers/slicer.pyx +20481 -0
  169. multipers/slicer.pyx.tp +1088 -0
  170. multipers/tensor/tensor.h +672 -0
  171. multipers/tensor.pxd +13 -0
  172. multipers/test.pyx +44 -0
  173. multipers/tests/__init__.py +62 -0
  174. multipers/torch/__init__.py +1 -0
  175. multipers/torch/diff_grids.py +240 -0
  176. multipers/torch/rips_density.py +310 -0
  177. multipers-2.3.3.dist-info/METADATA +128 -0
  178. multipers-2.3.3.dist-info/RECORD +182 -0
  179. multipers-2.3.3.dist-info/WHEEL +5 -0
  180. multipers-2.3.3.dist-info/licenses/LICENSE +21 -0
  181. multipers-2.3.3.dist-info/top_level.txt +1 -0
  182. multipers.libs/libtbb-ca48af5c.so.12.16 +0 -0
multipers/grids.pyx ADDED
@@ -0,0 +1,481 @@
1
+
2
+ from libc.stdint cimport intptr_t, int32_t, int64_t
3
+ from libcpp cimport bool,int, float
4
+
5
+ cimport numpy as cnp
6
+ import numpy as np
7
+ cnp.import_array()
8
+
9
+
10
+ from typing import Iterable,Literal,Optional
11
+ from itertools import product
12
+ from multipers.array_api import api_from_tensor, api_from_tensors
13
+ from multipers.array_api import numpy as npapi
14
+ from multipers.array_api import check_keops
15
+
16
+ available_strategies = ["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
17
+ Lstrategies = Literal["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
18
+
19
+ ctypedef fused some_int:
20
+ int32_t
21
+ int64_t
22
+
23
+ ctypedef fused some_float:
24
+ float
25
+ double
26
+
27
+ def sanitize_grid(grid, bool numpyfy=False):
28
+ if len(grid) == 0:
29
+ raise ValueError("empty filtration grid")
30
+ api = api_from_tensors(*grid)
31
+ if numpyfy:
32
+ grid = tuple(api.asnumpy(g) for g in grid)
33
+ else:
34
+ # copy here may not be necessary, but cheap
35
+ grid = tuple(api.astensor(g) for g in grid)
36
+ assert np.all([g.ndim==1 for g in grid])
37
+ return grid
38
+
39
+ def compute_grid(
40
+ x,
41
+ resolution:Optional[int|Iterable[int]]=None,
42
+ strategy:Lstrategies="exact",
43
+ bool unique=True,
44
+ some_float _q_factor=1.,
45
+ drop_quantiles=[0,0],
46
+ bool dense = False,
47
+ ):
48
+ """
49
+ Computes a grid from filtration values, using some strategy.
50
+
51
+ Input
52
+ -----
53
+
54
+ - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
55
+ where `filtration_of_parameter` is a array[float, ndim=1]
56
+ - `resolution`:Optional[int|tuple[int]]
57
+ - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
58
+ - `unique`: if true, doesn't repeat values in the output grid.
59
+ - `drop_quantiles` : drop some filtration values according to these quantiles
60
+ Output
61
+ ------
62
+
63
+ Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
64
+ """
65
+
66
+ from multipers.slicer import is_slicer
67
+ from multipers.simplex_tree_multi import is_simplextree_multi
68
+ from multipers.mma_structures import is_mma
69
+
70
+ if resolution is not None and strategy == "exact":
71
+ raise ValueError("The 'exact' strategy does not support resolution.")
72
+ if strategy != "exact":
73
+ assert resolution is not None, "A resolution is required for non-exact strategies"
74
+
75
+
76
+ cdef bool is_numpy_compatible = True
77
+ if (is_slicer(x) or is_simplextree_multi(x)) and x.is_squeezed:
78
+ initial_grid = x.filtration_grid
79
+ api = api_from_tensors(*initial_grid)
80
+ elif is_slicer(x):
81
+ initial_grid = x.get_filtrations_values().T
82
+ api = npapi
83
+ elif is_simplextree_multi(x):
84
+ initial_grid = x.get_filtration_grid()
85
+ api = npapi
86
+ elif is_mma(x):
87
+ initial_grid = x.get_filtration_values()
88
+ api = npapi
89
+ elif isinstance(x, np.ndarray):
90
+ initial_grid = x
91
+ api = npapi
92
+ else:
93
+ x = tuple(x)
94
+ if len(x) == 0: return []
95
+ first = x[0]
96
+ ## is_sm, i.e., iterable tuple(pts,weights)
97
+ if isinstance(first, tuple) and getattr(first[0], "shape", None) is not None:
98
+ initial_grid = tuple(f[0].T for f in x)
99
+ api = api_from_tensors(*initial_grid)
100
+ initial_grid = api.cat(initial_grid, axis=1)
101
+ # if isinstance(initial_grid[0], np.ndarray):
102
+ # initial_grid = np.concatenate(initial_grid, axis=1)
103
+ # else:
104
+ # is_numpy_compatible = False
105
+ # import torch
106
+ # assert isinstance(first[0], torch.Tensor), "Only numpy and torch are supported ftm."
107
+ # initial_grid = torch.cat(initial_grid, axis=1)
108
+ ## is grid-like (num_params, num_pts)
109
+ else:
110
+ api = api_from_tensors(*x)
111
+ initial_grid = tuple(api.astensor(f) for f in x)
112
+ # elif isinstance(first,list) or isinstance(first, tuple) or isinstance(first, np.ndarray):
113
+ # initial_grid = tuple(f for f in x)
114
+ # else:
115
+ # is_numpy_compatible = False
116
+ # import torch
117
+ # assert isinstance(first, torch.Tensor), "Only numpy and torch are supported ftm."
118
+ # initial_grid = x
119
+
120
+ num_parameters = len(initial_grid)
121
+ try:
122
+ int(resolution)
123
+ resolution = [resolution]*num_parameters
124
+ except TypeError:
125
+ pass
126
+
127
+ grid = _compute_grid_numpy(
128
+ initial_grid,
129
+ resolution=resolution,
130
+ strategy = strategy,
131
+ unique = unique,
132
+ _q_factor=_q_factor,
133
+ drop_quantiles=drop_quantiles,
134
+ dense = dense,
135
+ )
136
+ # from multipers.torch.diff_grids import get_grid
137
+ # grid = get_grid(strategy)(initial_grid,resolution)
138
+ if dense:
139
+ grid = todense(grid)
140
+ return grid
141
+
142
+
143
+
144
+
145
+
146
+ def _compute_grid_numpy(
147
+ filtrations_values,
148
+ resolution=None,
149
+ strategy:Lstrategies="exact",
150
+ bool unique=True,
151
+ some_float _q_factor=1.,
152
+ drop_quantiles=[0,0],
153
+ bool dense = False,
154
+ ):
155
+ """
156
+ Computes a grid from filtration values, using some strategy.
157
+
158
+ Input
159
+ -----
160
+ - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
161
+ where `filtration_of_parameter` is a array[float, ndim=1]
162
+ - `resolution`:Optional[int|tuple[int]]
163
+ - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
164
+ - `unique`: if true, doesn't repeat values in the output grid.
165
+ - `drop_quantiles` : drop some filtration values according to these quantiles
166
+ Output
167
+ ------
168
+ Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
169
+ """
170
+ num_parameters = len(filtrations_values)
171
+ api = api_from_tensors(*filtrations_values)
172
+ try:
173
+ a,b=drop_quantiles
174
+ except:
175
+ a,b=drop_quantiles,drop_quantiles
176
+
177
+ if a != 0 or b != 0:
178
+ boxes = api.astensor([api.quantile_closest(filtration, [a, b], axis=1) for filtration in filtrations_values])
179
+ min_filtration, max_filtration = api.minvalues(boxes, axis=(0,1)), api.maxvalues(boxes, axis=(0,1)) # box, birth/death, filtration
180
+ filtrations_values = [
181
+ filtration[(m<filtration) * (filtration <M)]
182
+ for filtration, m,M in zip(filtrations_values, min_filtration, max_filtration)
183
+ ]
184
+
185
+ ## match doesn't work with cython BUG
186
+ if strategy == "exact":
187
+ F=tuple(api.unique(f) for f in filtrations_values)
188
+ elif strategy == "quantile":
189
+ F = tuple(api.unique(f) for f in filtrations_values)
190
+ max_resolution = [min(len(f),r) for f,r in zip(F,resolution)]
191
+ F = tuple( api.quantile_closest(f, q=api.linspace(0,1,int(r*_q_factor)), axis=0) for f,r in zip(F, resolution) )
192
+ if unique:
193
+ F = tuple(api.unique(f) for f in F)
194
+ if np.all(np.asarray(max_resolution) > np.asarray([len(f) for f in F])):
195
+ return _compute_grid_numpy(filtrations_values=filtrations_values, resolution=resolution, strategy="quantile",_q_factor=1.5*_q_factor)
196
+ elif strategy == "regular":
197
+ F = tuple(_todo_regular(f,r,api) for f,r in zip(filtrations_values, resolution))
198
+ elif strategy == "regular_closest":
199
+ F = tuple(_todo_regular_closest(f,r, unique,api) for f,r in zip(filtrations_values, resolution))
200
+ elif strategy == "regular_left":
201
+ F = tuple(_todo_regular_left(f,r, unique,api) for f,r in zip(filtrations_values, resolution))
202
+ # elif strategy == "torch_regular_closest":
203
+ # F = tuple(_torch_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
204
+ elif strategy == "partition":
205
+ F = tuple(_todo_partition(f,r, unique, api) for f,r in zip(filtrations_values, resolution))
206
+ elif strategy == "precomputed":
207
+ F=filtrations_values
208
+ else:
209
+ raise ValueError(f"Invalid strategy {strategy}. Pick something in {available_strategies}.")
210
+ if dense:
211
+ return todense(F)
212
+ return F
213
+
214
+ def todense(grid, bool product_order=False):
215
+ if len(grid) == 0:
216
+ return np.empty(0)
217
+ api = api_from_tensors(*grid)
218
+ # if product_order:
219
+ # if not api.backend ==np:
220
+ # raise NotImplementedError("only numpy here.")
221
+ # return np.fromiter(product(*grid), dtype=np.dtype((dtype, len(grid))), count=np.prod([len(f) for f in grid]))
222
+ return api.cartesian_product(*grid)
223
+ # if not isinstance(grid[0], np.ndarray):
224
+ # import torch
225
+ # assert isinstance(grid[0], torch.Tensor)
226
+ # from multipers.torch.diff_grids import todense
227
+ # return todense(grid)
228
+ # dtype = grid[0].dtype
229
+ # if product_order:
230
+ # return np.fromiter(product(*grid), dtype=np.dtype((dtype, len(grid))), count=np.prod([len(f) for f in grid]))
231
+ # mesh = np.meshgrid(*grid)
232
+ # coordinates = np.stack(mesh, axis=-1).reshape(-1, len(grid)).astype(dtype)
233
+ # return coordinates
234
+
235
+
236
+
237
+ def _todo_regular(f, int r, api):
238
+ if api.has_grad(f):
239
+ from warnings import warn
240
+ warn("`strategy=regular` is not differentiable. Removing grad.")
241
+ with api.no_grad():
242
+ return api.linspace(api.min(f), api.max(f), r)
243
+
244
+ def _project_on_1d_grid(f,grid, bool unique, api):
245
+ # api=api_from_tensors(f,grid)
246
+ if f.ndim != 1:
247
+ raise ValueError(f"Got ndim!=1. {f=}")
248
+ f = api.unique(f)
249
+ with api.no_grad():
250
+ _f = api.LazyTensor(f[:, None, None])
251
+ _f_reg = api.LazyTensor(grid[None, :, None])
252
+ indices = (_f - _f_reg).abs().argmin(0).ravel()
253
+ f = api.cat([f, api.tensor([api.inf], dtype=f.dtype)])
254
+ f_proj = f[indices]
255
+ if unique:
256
+ f_proj = api.unique(f_proj)
257
+ return f_proj
258
+
259
+ def _todo_regular_closest_keops(f, int r, bool unique, api):
260
+ f = api.astensor(f)
261
+ with api.no_grad():
262
+ f_regular = api.linspace(api.min(f), api.max(f), r, device = api.device(f),dtype=f.dtype)
263
+ return _project_on_1d_grid(f,f_regular,unique,api)
264
+
265
+ def _todo_regular_closest_old(some_float[:] f, int r, bool unique, api=None):
266
+ f_array = np.asarray(f)
267
+ f_regular = np.linspace(np.min(f), np.max(f),num=r, dtype=f_array.dtype)
268
+ f_regular_closest = np.asarray([f[<int64_t>np.argmin(np.abs(f_array-f_regular[i]))] for i in range(r)], dtype=f_array.dtype)
269
+ if unique: f_regular_closest = np.unique(f_regular_closest)
270
+ return f_regular_closest
271
+
272
+ def _todo_regular_left(f, int r, bool unique,api):
273
+ sorted_f = api.sort(f)
274
+ with api.no_grad():
275
+ f_regular = api.linspace(sorted_f[0],sorted_f[-1],r, dtype=sorted_f.dtype, device=api.device(sorted_f))
276
+ idx=api.searchsorted(sorted_f,f_regular)
277
+ f_regular_closest = sorted_f[idx]
278
+ if unique: f_regular_closest = api.unique(f_regular_closest)
279
+ return f_regular_closest
280
+
281
+ def _todo_regular_left_old(some_float[:] f, int r, bool unique):
282
+ sorted_f = np.sort(f)
283
+ f_regular = np.linspace(sorted_f[0],sorted_f[-1],num=r, dtype=sorted_f.dtype)
284
+ f_regular_closest = sorted_f[np.searchsorted(sorted_f,f_regular)]
285
+ if unique: f_regular_closest = np.unique(f_regular_closest)
286
+ return f_regular_closest
287
+
288
+ def _todo_partition(x, int resolution, bool unique, api):
289
+ if api.has_grad(x):
290
+ from warnings import warn
291
+ warn("`strategy=partition` is not differentiable. Removing grad.")
292
+ out = _todo_partition_(api.asnumpy(x), resolution, unique)
293
+ return api.from_numpy(out)
294
+
295
+ def _todo_partition_(some_float[:] data,int resolution, bool unique):
296
+ if data.shape[0] < resolution: resolution=data.shape[0]
297
+ k = data.shape[0] // resolution
298
+ partitions = np.partition(data, k)
299
+ f = partitions[[i*k for i in range(resolution)]]
300
+ if unique: f= np.unique(f)
301
+ return f
302
+
303
+
304
+ if check_keops():
305
+ _todo_regular_closest = _todo_regular_closest_keops
306
+ else:
307
+ _todo_regular_closest = _todo_regular_closest_old
308
+
309
+
310
+ def compute_bounding_box(stuff, inflate = 0.):
311
+ r"""
312
+ Returns a array of shape (2, num_parameters)
313
+ such that for any filtration value $y$ of something in stuff,
314
+ then if (x,z) is the output of this function, we have
315
+ $x\le y \le z$.
316
+ """
317
+ box = np.array(compute_grid(stuff,strategy="regular",resolution=2)).T
318
+ if inflate:
319
+ box[0] -= inflate
320
+ box[1] += inflate
321
+ return box
322
+
323
+ def push_to_grid(some_float[:,:] points, grid, bool return_coordinate=False):
324
+ """
325
+ Given points and a grid (list of one parameter grids),
326
+ pushes the points onto the grid.
327
+ """
328
+ num_points, num_parameters = points.shape[0], points.shape[1]
329
+ cdef cnp.ndarray[int64_t,ndim=2] coordinates = np.empty((num_points, num_parameters),dtype=np.int64)
330
+ for parameter in range(num_parameters):
331
+ coordinates[:,parameter] = np.searchsorted(grid[parameter],points[:,parameter])
332
+ if return_coordinate:
333
+ return coordinates
334
+ out = np.empty((num_points,num_parameters), grid[0].dtype)
335
+ for parameter in range(num_parameters):
336
+ out[:,parameter] = grid[parameter][coordinates[:,parameter]]
337
+ return out
338
+
339
+
340
+ def coarsen_points(some_float[:,:] points, strategy="exact", int resolution=-1, bool coordinate=False):
341
+ grid = _compute_grid_numpy(points.T, strategy=strategy, resolution=resolution)
342
+ if coordinate:
343
+ return push_to_grid(points, grid, coordinate), grid
344
+ return push_to_grid(points, grid, coordinate)
345
+
346
+ def _inf_value(array):
347
+ if isinstance(array, type|np.dtype):
348
+ dtype = np.dtype(array) # torch types are not types
349
+ elif isinstance(array, np.ndarray):
350
+ dtype = np.dtype(array.dtype)
351
+ else:
352
+ import torch
353
+ if isinstance(array, torch.Tensor):
354
+ dtype=array.dtype
355
+ elif isinstance(array, torch.dtype):
356
+ dtype=array
357
+ else:
358
+ raise ValueError(f"unknown input of type {type(array)=} {array=}")
359
+
360
+ if isinstance(dtype, np.dtype):
361
+ if dtype.kind == 'f':
362
+ return np.asarray(np.inf,dtype=dtype)
363
+ if dtype.kind == 'i':
364
+ return np.iinfo(dtype).max
365
+ # torch only here.
366
+ if dtype.is_floating_point:
367
+ return torch.tensor(torch.inf, dtype=dtype)
368
+ else:
369
+ return torch.iinfo(dtype).max
370
+ raise ValueError(f"Dtype must be integer or floating like (got {dtype})")
371
+
372
+ def evaluate_in_grid(pts, grid, mass_default=None):
373
+ """
374
+ Input
375
+ -----
376
+ - pts: of the form array[int, ndim=2]
377
+ - grid of the form Iterable[array[float, ndim=1]]
378
+ """
379
+ assert pts.ndim == 2
380
+ first_filtration = grid[0]
381
+ dtype = first_filtration.dtype
382
+ if isinstance(first_filtration, np.ndarray):
383
+ if mass_default is not None:
384
+ grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
385
+ def empty_like(x):
386
+ return np.empty_like(x, dtype=dtype)
387
+ else:
388
+ import torch
389
+ # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
390
+ if mass_default is not None:
391
+ grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
392
+ def empty_like(x):
393
+ return torch.empty(x.shape,dtype=dtype)
394
+
395
+ coords=empty_like(pts)
396
+ cdef int dim = coords.shape[1]
397
+ pts_inf = _inf_value(pts)
398
+ coords_inf = _inf_value(coords)
399
+ idx = np.argwhere(pts == pts_inf)
400
+ pts[idx] == 0
401
+ for i in range(dim):
402
+ coords[:,i] = grid[i][pts[:,i]]
403
+ coords[idx] = coords_inf
404
+ return coords
405
+
406
+ def sm_in_grid(pts, weights, grid, mass_default=None):
407
+ """Given a measure whose points are coordinates,
408
+ pushes this measure in this grid.
409
+ Input
410
+ -----
411
+ - pts: of the form array[int, ndim=2]
412
+ - weights: array[int, ndim=1]
413
+ - grid of the form Iterable[array[float, ndim=1]]
414
+ - num_parameters: number of parameters
415
+ """
416
+ if pts.ndim != 2:
417
+ raise ValueError(f"invalid dirac locations. got {pts.ndim=} != 2")
418
+ if len(grid) == 0:
419
+ raise ValueError(f"Empty grid given. Got {grid=}")
420
+ cdef int num_parameters = pts.shape[1]
421
+ if mass_default is None:
422
+ api = api_from_tensors(*grid)
423
+ else:
424
+ api = api_from_tensors(*grid, mass_default)
425
+
426
+ _grid = list(grid)
427
+ _mass_default = None if mass_default is None else api.astensor(mass_default)
428
+ while len(_grid) < num_parameters:
429
+ _grid += [api.cat([
430
+ (gt:=api.astensor(g))[1:],
431
+ api.astensor(_inf_value(api.asnumpy(gt))).reshape(1)
432
+ ]) for g in grid]
433
+ if mass_default is not None:
434
+ _mass_default = api.cat([_mass_default,mass_default])
435
+ grid = tuple(_grid)
436
+ mass_default = _mass_default
437
+
438
+ coords = evaluate_in_grid(np.asarray(pts, dtype=int), grid, mass_default)
439
+ return (coords, weights)
440
+
441
+ # TODO : optimize with memoryviews / typing
442
+ def sms_in_grid(sms, grid, mass_default=None):
443
+ """Given a measure whose points are coordinates,
444
+ pushes this measure in this grid.
445
+ Input
446
+ -----
447
+ - sms: of the form (signed_measure_like for num_measures)
448
+ where signed_measure_like = tuple(array[int, ndim=2], array[int])
449
+ - grid of the form Iterable[array[float, ndim=1]]
450
+ """
451
+ sms = tuple(sm_in_grid(pts,weights,grid=grid, mass_default=mass_default) for pts,weights in sms)
452
+ return sms
453
+
454
+
455
+ def _push_pts_to_line(pts, basepoint, direction=None):
456
+ api = api_from_tensors(pts, basepoint)
457
+ pts = api.astensor(pts)
458
+ basepoint = api.astensor(basepoint)
459
+ num_parameters = basepoint.shape[0]
460
+ if direction is not None:
461
+ if not api.is_promotable(direction):
462
+ raise ValueError(f"Incompatible input types. Got {type(pts)=}, {type(basepoint)=}, {type(direction)=}")
463
+
464
+ direction = api.astensor(direction)
465
+ ok_idx = direction > 0
466
+ if ok_idx.sum() == 0:
467
+ raise ValueError(f"Got invalid direction {direction}")
468
+ zero_idx = None if ok_idx.all() else direction == 0
469
+ else:
470
+ direction = api.tensor([1], dtype=int)
471
+ ok_idx = slice(None)
472
+ zero_idx = None
473
+ xa = api.maxvalues(
474
+ (pts[:, ok_idx] - basepoint[ok_idx]) / direction[ok_idx], axis=1, keepdims=True
475
+ )
476
+ if zero_idx is not None:
477
+ xb = api.where(pts[:, zero_idx] <= basepoint[zero_idx], -np.inf, np.inf)
478
+ xs = api.maxvalues(api.cat([xa, xb], axis=1), axis=1, keepdims=True)
479
+ else:
480
+ xs = xa
481
+ return xs.squeeze()
@@ -0,0 +1,132 @@
1
+ #pragma once
2
+
3
+ #include "mma_interface_h0.h"
4
+ #include "mma_interface_matrix.h"
5
+ #include "mma_interface_coh.h"
6
+ #include <type_traits> // For static_assert
7
+ #include "truc.h"
8
+ #include <gudhi/Simplex_tree_multi.h>
9
+ #include <gudhi/One_critical_filtration.h>
10
+ #include <gudhi/Multi_critical_filtration.h>
11
+
12
+ template <typename Filtration>
13
+ using SimplexTreeMultiOptions = Gudhi::multi_persistence::Simplex_tree_options_multidimensional_filtration<Filtration>;
14
+
15
+ enum Column_types_strs { LIST, SET, HEAP, VECTOR, NAIVE_VECTOR, UNORDERED_SET, INTRUSIVE_LIST, INTRUSIVE_SET };
16
+
17
+ using Available_columns = Gudhi::persistence_matrix::Column_types;
18
+
19
+ template <Available_columns col>
20
+ using BackendOptionsWithVine = Gudhi::multiparameter::truc_interface::Multi_persistence_options<col>;
21
+ template <Available_columns col>
22
+ using BackendOptionsWithoutVine = Gudhi::multiparameter::truc_interface::No_vine_multi_persistence_options<col>;
23
+
24
+ template <Available_columns col>
25
+ using ClementBackendOptionsWithVine = Gudhi::multiparameter::truc_interface::Multi_persistence_Clement_options<col>;
26
+
27
+ using SimplicialStructure = Gudhi::multiparameter::truc_interface::SimplicialStructure;
28
+ using PresentationStructure = Gudhi::multiparameter::truc_interface::PresentationStructure;
29
+
30
+ template <Available_columns col, class Structure = SimplicialStructure>
31
+ using MatrixBackendNoVine =
32
+ Gudhi::multiparameter::truc_interface::Persistence_backend_matrix<BackendOptionsWithoutVine<col>, Structure>;
33
+
34
+ template <Available_columns col, class Structure = SimplicialStructure>
35
+ using MatrixBackendVine =
36
+ Gudhi::multiparameter::truc_interface::Persistence_backend_matrix<BackendOptionsWithVine<col>, Structure>;
37
+
38
+ template <Available_columns col, class Structure = SimplicialStructure>
39
+ using ClementMatrixBackendVine =
40
+ Gudhi::multiparameter::truc_interface::Persistence_backend_matrix<ClementBackendOptionsWithVine<col>, Structure>;
41
+ using GraphBackendVine = Gudhi::multiparameter::truc_interface::Persistence_backend_h0<SimplicialStructure>;
42
+
43
+ using Filtration_value = Gudhi::multi_filtration::One_critical_filtration<float>;
44
+
45
+ template <Available_columns col = Available_columns::INTRUSIVE_SET>
46
+ using SimplicialNoVineMatrixTruc =
47
+ Gudhi::multiparameter::truc_interface::Truc<MatrixBackendNoVine<col>, SimplicialStructure, Filtration_value>;
48
+
49
+ template <Available_columns col = Available_columns::INTRUSIVE_SET>
50
+ using GeneralVineTruc = Gudhi::multiparameter::truc_interface::
51
+ Truc<MatrixBackendVine<col, PresentationStructure>, PresentationStructure, Filtration_value>;
52
+
53
+ template <Available_columns col = Available_columns::INTRUSIVE_SET>
54
+ using GeneralNoVineTruc = Gudhi::multiparameter::truc_interface::
55
+ Truc<MatrixBackendNoVine<col, PresentationStructure>, PresentationStructure, Filtration_value>;
56
+
57
+ template <Available_columns col = Available_columns::INTRUSIVE_SET>
58
+ using GeneralVineClementTruc = Gudhi::multiparameter::truc_interface::
59
+ Truc<ClementMatrixBackendVine<col, PresentationStructure>, PresentationStructure, Filtration_value>;
60
+
61
+ template <Available_columns col = Available_columns::INTRUSIVE_SET>
62
+ using SimplicialVineMatrixTruc =
63
+ Gudhi::multiparameter::truc_interface::Truc<MatrixBackendVine<col>, SimplicialStructure, Filtration_value>;
64
+ using SimplicialVineGraphTruc =
65
+ Gudhi::multiparameter::truc_interface::Truc<GraphBackendVine, SimplicialStructure, Filtration_value>;
66
+
67
+ // multicrititcal
68
+ using Multi_critical_filtrationValue = Gudhi::multi_filtration::Multi_critical_filtration<float>;
69
+ template <Available_columns col = Available_columns::INTRUSIVE_SET>
70
+ using KCriticalVineTruc = Gudhi::multiparameter::truc_interface::
71
+ Truc<MatrixBackendVine<col, PresentationStructure>, PresentationStructure, Multi_critical_filtrationValue>;
72
+
73
+ template <bool is_vine, Available_columns col = Available_columns::INTRUSIVE_SET>
74
+ using Matrix_interface = std::conditional_t<is_vine,
75
+ MatrixBackendVine<col, PresentationStructure>,
76
+ MatrixBackendNoVine<col, PresentationStructure>>;
77
+
78
+ template <bool is_kcritical, typename value_type>
79
+ using filtration_options = std::conditional_t<is_kcritical,
80
+ Gudhi::multi_filtration::Multi_critical_filtration<value_type>,
81
+ Gudhi::multi_filtration::One_critical_filtration<value_type>>;
82
+
83
+ template <bool is_vine,
84
+ bool is_kcritical,
85
+ typename value_type,
86
+ Available_columns col = Available_columns::INTRUSIVE_SET>
87
+ using MatrixTrucPythonInterface = Gudhi::multiparameter::truc_interface::
88
+ Truc<Matrix_interface<is_vine, col>, PresentationStructure, filtration_options<is_kcritical, value_type>>;
89
+
90
+ enum class BackendsEnum { Matrix, Graph, Clement, GudhiCohomology };
91
+
92
+ // Create a template metafunction to simplify the type selection
93
+ template <BackendsEnum backend, bool is_vine, Available_columns col>
94
+ struct PersBackendOptsImpl;
95
+
96
+ template <bool is_vine, Available_columns col>
97
+ struct PersBackendOptsImpl<BackendsEnum::Matrix, is_vine, col> {
98
+ using type = Matrix_interface<is_vine, col>;
99
+ };
100
+
101
+ template <bool is_vine, Available_columns col>
102
+ struct PersBackendOptsImpl<BackendsEnum::Clement, is_vine, col> {
103
+ static_assert(is_vine, "Clement is vine");
104
+ using type = ClementMatrixBackendVine<col, PresentationStructure>;
105
+ };
106
+
107
+ template <bool is_vine, Available_columns col>
108
+ struct PersBackendOptsImpl<BackendsEnum::GudhiCohomology, is_vine, col> {
109
+ static_assert(!is_vine, "Gudhi is not vine");
110
+ using type = Gudhi::multiparameter::truc_interface::Persistence_backend_cohomology<PresentationStructure>;
111
+ };
112
+
113
+ template <bool is_vine, Available_columns col>
114
+ struct PersBackendOptsImpl<BackendsEnum::Graph, is_vine, col> {
115
+ static_assert(is_vine, "Graph backend requires is_vine to be true");
116
+ using type = GraphBackendVine;
117
+ };
118
+
119
+ // Helper alias to extract the type
120
+ template <BackendsEnum backend, bool is_vine, Available_columns col>
121
+ using PersBackendOpts = typename PersBackendOptsImpl<backend, is_vine, col>::type;
122
+
123
+ template <BackendsEnum backend>
124
+ using StructureStuff = std::conditional_t<backend == BackendsEnum::Graph, SimplicialStructure, PresentationStructure>;
125
+
126
+ template <BackendsEnum backend,
127
+ bool is_vine,
128
+ bool is_kcritical,
129
+ typename value_type,
130
+ Available_columns col = Available_columns::INTRUSIVE_SET>
131
+ using TrucPythonInterface = Gudhi::multiparameter::truc_interface::
132
+ Truc<PersBackendOpts<backend, is_vine, col>, StructureStuff<backend>, filtration_options<is_kcritical, value_type>>;