multipers 2.2.3__cp311-cp311-win_amd64.whl → 2.3.1__cp311-cp311-win_amd64.whl

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Files changed (182) hide show
  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
multipers/grids.pyx CHANGED
@@ -1,350 +1,350 @@
1
-
2
- from libc.stdint cimport intptr_t, int32_t, int64_t
3
- from libcpp cimport bool,int,long, 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
-
13
-
14
- available_strategies = ["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
15
- Lstrategies = Literal["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
16
-
17
- ctypedef fused some_int:
18
- int32_t
19
- int64_t
20
- int
21
- long
22
-
23
- ctypedef fused some_float:
24
- float
25
- double
26
-
27
-
28
- def compute_grid(
29
- x,
30
- resolution:Optional[int|Iterable[int]]=None,
31
- strategy:Lstrategies="exact",
32
- bool unique=True,
33
- some_float _q_factor=1.,
34
- drop_quantiles=[0,0],
35
- bool dense = False,
36
- ):
37
- """
38
- Computes a grid from filtration values, using some strategy.
39
-
40
- Input
41
- -----
42
-
43
- - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
44
- where `filtration_of_parameter` is a array[float, ndim=1]
45
- - `resolution`:Optional[int|tuple[int]]
46
- - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
47
- - `unique`: if true, doesn't repeat values in the output grid.
48
- - `drop_quantiles` : drop some filtration values according to these quantiles
49
- Output
50
- ------
51
-
52
- Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
53
- """
54
-
55
- from multipers.slicer import is_slicer
56
- from multipers.simplex_tree_multi import is_simplextree_multi
57
- from multipers.mma_structures import is_mma
58
-
59
- if resolution is not None and strategy == "exact":
60
- raise ValueError("The 'exact' strategy does not support resolution.")
61
- if strategy != "exact":
62
- assert resolution is not None, "A resolution is required for non-exact strategies"
63
-
64
-
65
- cdef bool is_numpy_compatible = True
66
- if is_slicer(x):
67
- initial_grid = x.get_filtrations_values().T
68
- elif is_simplextree_multi(x):
69
- initial_grid = x.get_filtration_grid()
70
- elif is_mma(x):
71
- initial_grid = x.get_filtration_values()
72
- elif isinstance(x, np.ndarray):
73
- initial_grid = x
74
- else:
75
- x = tuple(x)
76
- if len(x) == 0: return []
77
- first = x[0]
78
- ## is_sm, i.e., iterable tuple(pts,weights)
79
- if isinstance(x[0], tuple) and getattr(x[0][0], "shape", None) is not None:
80
- initial_grid = tuple(f[0].T for f in x)
81
- if isinstance(initial_grid[0], np.ndarray):
82
- initial_grid = np.concatenate(initial_grid, axis=1)
83
- else:
84
- is_numpy_compatbile = False
85
- import torch
86
- assert isinstance(first[0], torch.Tensor), "Only numpy and torch are supported ftm."
87
- initial_grid = torch.cat(initial_grid, axis=1)
88
- ## is grid-like (num_params, num_pts)
89
- elif isinstance(first,list) or isinstance(first, tuple) or isinstance(first, np.ndarray):
90
- initial_grid = tuple(f for f in x)
91
- else:
92
- is_numpy_compatible = False
93
- import torch
94
- assert isinstance(first, torch.Tensor), "Only numpy and torch are supported ftm."
95
- initial_grid = x
96
- if is_numpy_compatible:
97
- return _compute_grid_numpy(
98
- initial_grid,
99
- resolution=resolution,
100
- strategy = strategy,
101
- unique = unique,
102
- _q_factor=_q_factor,
103
- drop_quantiles=drop_quantiles,
104
- dense = dense,
105
- )
106
- from multipers.torch.diff_grids import get_grid
107
- return get_grid(strategy)(initial_grid,resolution)
108
-
109
-
110
-
111
-
112
-
113
-
114
- def _compute_grid_numpy(
115
- filtrations_values,
116
- resolution=None,
117
- strategy:Lstrategies="exact",
118
- bool unique=True,
119
- some_float _q_factor=1.,
120
- drop_quantiles=[0,0],
121
- bool dense = False,
122
- ):
123
- """
124
- Computes a grid from filtration values, using some strategy.
125
-
126
- Input
127
- -----
128
- - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
129
- where `filtration_of_parameter` is a array[float, ndim=1]
130
- - `resolution`:Optional[int|tuple[int]]
131
- - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
132
- - `unique`: if true, doesn't repeat values in the output grid.
133
- - `drop_quantiles` : drop some filtration values according to these quantiles
134
- Output
135
- ------
136
- Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
137
- """
138
- num_parameters = len(filtrations_values)
139
- if resolution is None and strategy not in ["exact", "precomputed"]:
140
- raise ValueError("Resolution must be provided for this strategy.")
141
- elif resolution is not None:
142
- try:
143
- int(resolution)
144
- resolution = [resolution]*num_parameters
145
- except:
146
- pass
147
- try:
148
- a,b=drop_quantiles
149
- except:
150
- a,b=drop_quantiles,drop_quantiles
151
-
152
- if a != 0 or b != 0:
153
- boxes = np.asarray([np.quantile(filtration, [a, b], axis=1, method='closest_observation') for filtration in filtrations_values])
154
- min_filtration, max_filtration = np.min(boxes, axis=(0,1)), np.max(boxes, axis=(0,1)) # box, birth/death, filtration
155
- filtrations_values = [
156
- filtration[(m<filtration) * (filtration <M)]
157
- for filtration, m,M in zip(filtrations_values, min_filtration, max_filtration)
158
- ]
159
-
160
- to_unique = lambda f : np.unique(f) if isinstance(f,np.ndarray) else f.unique()
161
- ## match doesn't work with cython BUG
162
- if strategy == "exact":
163
- F=tuple(to_unique(f) for f in filtrations_values)
164
- elif strategy == "quantile":
165
- F = tuple(to_unique(f) for f in filtrations_values)
166
- max_resolution = [min(len(f),r) for f,r in zip(F,resolution)]
167
- F = tuple( np.quantile(f, q=np.linspace(0,1,num=int(r*_q_factor)), axis=0, method='closest_observation') for f,r in zip(F, resolution) )
168
- if unique:
169
- F = tuple(to_unique(f) for f in F)
170
- if np.all(np.asarray(max_resolution) > np.asarray([len(f) for f in F])):
171
- return _compute_grid_numpy(filtrations_values=filtrations_values, resolution=resolution, strategy="quantile",_q_factor=1.5*_q_factor)
172
- elif strategy == "regular":
173
- F = tuple(np.linspace(np.min(f),np.max(f),num=r, dtype=np.asarray(f).dtype) for f,r in zip(filtrations_values, resolution))
174
- elif strategy == "regular_closest":
175
- F = tuple(_todo_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
176
- elif strategy == "regular_left":
177
- F = tuple(_todo_regular_left(f,r, unique) for f,r in zip(filtrations_values, resolution))
178
- elif strategy == "torch_regular_closest":
179
- F = tuple(_torch_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
180
- elif strategy == "partition":
181
- F = tuple(_todo_partition(f,r, unique) for f,r in zip(filtrations_values, resolution))
182
- elif strategy == "precomputed":
183
- F=filtrations_values
184
- else:
185
- raise ValueError(f"Invalid strategy {strategy}. Pick something in {available_strategies}.")
186
- if dense:
187
- return todense(F)
188
- return F
189
-
190
- def todense(grid, bool product_order=False):
191
- if len(grid) == 0:
192
- return np.empty(0)
193
- if not isinstance(grid[0], np.ndarray):
194
- import torch
195
- assert isinstance(grid[0], torch.Tensor)
196
- from multipers.torch.diff_grids import todense
197
- return todense(grid)
198
- dtype = grid[0].dtype
199
- if product_order:
200
- return np.fromiter(product(*grid), dtype=np.dtype((dtype, len(grid))), count=np.prod([len(f) for f in grid]))
201
- mesh = np.meshgrid(*grid)
202
- coordinates = np.concatenate(tuple(stuff.ravel()[:,None] for stuff in mesh), axis=1, dtype=dtype)
203
- return coordinates
204
-
205
-
206
-
207
- ## TODO : optimize. Pykeops ?
208
- def _todo_regular_closest(some_float[:] f, int r, bool unique):
209
- f_array = np.asarray(f)
210
- f_regular = np.linspace(np.min(f), np.max(f),num=r, dtype=f_array.dtype)
211
- f_regular_closest = np.asarray([f[<long>np.argmin(np.abs(f_array-f_regular[i]))] for i in range(r)])
212
- if unique: f_regular_closest = np.unique(f_regular_closest)
213
- return f_regular_closest
214
-
215
- def _todo_regular_left(some_float[:] f, int r, bool unique):
216
- sorted_f = np.sort(f)
217
- f_regular = np.linspace(sorted_f[0],sorted_f[-1],num=r, dtype=sorted_f.dtype)
218
- f_regular_closest = sorted_f[np.searchsorted(sorted_f,f_regular)]
219
- if unique: f_regular_closest = np.unique(f_regular_closest)
220
- return f_regular_closest
221
-
222
- def _torch_regular_closest(f, int r, bool unique=True):
223
- import torch
224
- f_regular = torch.linspace(f.min(),f.max(), r, dtype=f.dtype)
225
- f_regular_closest =torch.tensor([f[(f-x).abs().argmin()] for x in f_regular])
226
- if unique: f_regular_closest = f_regular_closest.unique()
227
- return f_regular_closest
228
-
229
- def _todo_partition(some_float[:] data,int resolution, bool unique):
230
- if data.shape[0] < resolution: resolution=data.shape[0]
231
- k = data.shape[0] // resolution
232
- partitions = np.partition(data, k)
233
- f = partitions[[i*k for i in range(resolution)]]
234
- if unique: f= np.unique(f)
235
- return f
236
-
237
-
238
- def compute_bounding_box(stuff, inflate = 0.):
239
- r"""
240
- Returns a array of shape (2, num_parameters)
241
- such that for any filtration value $y$ of something in stuff,
242
- then if (x,z) is the output of this function, we have
243
- $x\le y \le z$.
244
- """
245
- box = np.array(compute_grid(stuff,strategy="regular",resolution=2)).T
246
- if inflate:
247
- box[0] -= inflate
248
- box[1] += inflate
249
- return box
250
-
251
- def push_to_grid(some_float[:,:] points, grid, bool return_coordinate=False):
252
- """
253
- Given points and a grid (list of one parameter grids),
254
- pushes the points onto the grid.
255
- """
256
- num_points, num_parameters = points.shape[0], points.shape[1]
257
- cdef cnp.ndarray[long,ndim=2] coordinates = np.empty((num_points, num_parameters),dtype=np.int64)
258
- for parameter in range(num_parameters):
259
- coordinates[:,parameter] = np.searchsorted(grid[parameter],points[:,parameter])
260
- if return_coordinate:
261
- return coordinates
262
- out = np.empty((num_points,num_parameters), grid[0].dtype)
263
- for parameter in range(num_parameters):
264
- out[:,parameter] = grid[parameter][coordinates[:,parameter]]
265
- return out
266
-
267
-
268
- def coarsen_points(some_float[:,:] points, strategy="exact", int resolution=-1, bool coordinate=False):
269
- grid = _compute_grid_numpy(points.T, strategy=strategy, resolution=resolution)
270
- if coordinate:
271
- return push_to_grid(points, grid, coordinate), grid
272
- return push_to_grid(points, grid, coordinate)
273
-
274
-
275
-
276
- def evaluate_in_grid(pts, grid, mass_default=None):
277
- """
278
- Input
279
- -----
280
- - pts: of the form array[int, ndim=2]
281
- - grid of the form Iterable[array[float, ndim=1]]
282
- """
283
- first_filtration = grid[0]
284
- dtype = first_filtration.dtype
285
- if isinstance(first_filtration, np.ndarray):
286
- if mass_default is not None:
287
- grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
288
- def empty_like(x):
289
- return np.empty_like(x, dtype=dtype)
290
- else:
291
- import torch
292
- # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
293
- if mass_default is not None:
294
- grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
295
- def empty_like(x):
296
- return torch.empty(x.shape,dtype=dtype)
297
-
298
- coords= empty_like(pts)
299
- for i in range(coords.shape[1]):
300
- coords[:,i] = grid[i][pts[:,i]]
301
- return coords
302
-
303
- def sm_in_grid(pts, weights, grid, int num_parameters=-1, mass_default=None):
304
- """Given a measure whose points are coordinates,
305
- pushes this measure in this grid.
306
- Input
307
- -----
308
- - pts: of the form array[int, ndim=2]
309
- - weights: array[int, ndim=1]
310
- - grid of the form Iterable[array[float, ndim=1]]
311
- - num_parameters: number of parameters
312
- """
313
- first_filtration = grid[0]
314
- dtype = first_filtration.dtype
315
- def to_int(x):
316
- return np.asarray(x,dtype=np.int64)
317
- if isinstance(first_filtration, np.ndarray):
318
- if mass_default is not None:
319
- grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
320
- def empty_like(x, weights):
321
- return np.empty_like(x, dtype=dtype), np.asarray(weights)
322
- else:
323
- import torch
324
- # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
325
- if mass_default is not None:
326
- grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
327
- def empty_like(x, weights):
328
- return torch.empty(x.shape,dtype=dtype), torch.from_numpy(weights)
329
-
330
- pts = to_int(pts)
331
- coords,weights = empty_like(pts,weights)
332
- for i in range(coords.shape[1]):
333
- if num_parameters > 0:
334
- coords[:,i] = grid[i%num_parameters][pts[:,i]]
335
- else:
336
- coords[:,i] = grid[i][pts[:,i]]
337
- return (coords, weights)
338
-
339
- # TODO : optimize with memoryviews / typing
340
- def sms_in_grid(sms, grid, int num_parameters=-1, mass_default=None):
341
- """Given a measure whose points are coordinates,
342
- pushes this measure in this grid.
343
- Input
344
- -----
345
- - sms: of the form (signed_measure_like for num_measures)
346
- where signed_measure_like = tuple(array[int, ndim=2], array[int])
347
- - grid of the form Iterable[array[float, ndim=1]]
348
- """
349
- sms = tuple(sm_in_grid(pts,weights,grid=grid,num_parameters=num_parameters, mass_default=mass_default) for pts,weights in sms)
350
- return sms
1
+
2
+ from libc.stdint cimport intptr_t, int32_t, int64_t
3
+ from libcpp cimport bool,int,long, 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
+
13
+
14
+ available_strategies = ["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
15
+ Lstrategies = Literal["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
16
+
17
+ ctypedef fused some_int:
18
+ int32_t
19
+ int64_t
20
+ int
21
+ long
22
+
23
+ ctypedef fused some_float:
24
+ float
25
+ double
26
+
27
+
28
+ def compute_grid(
29
+ x,
30
+ resolution:Optional[int|Iterable[int]]=None,
31
+ strategy:Lstrategies="exact",
32
+ bool unique=True,
33
+ some_float _q_factor=1.,
34
+ drop_quantiles=[0,0],
35
+ bool dense = False,
36
+ ):
37
+ """
38
+ Computes a grid from filtration values, using some strategy.
39
+
40
+ Input
41
+ -----
42
+
43
+ - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
44
+ where `filtration_of_parameter` is a array[float, ndim=1]
45
+ - `resolution`:Optional[int|tuple[int]]
46
+ - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
47
+ - `unique`: if true, doesn't repeat values in the output grid.
48
+ - `drop_quantiles` : drop some filtration values according to these quantiles
49
+ Output
50
+ ------
51
+
52
+ Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
53
+ """
54
+
55
+ from multipers.slicer import is_slicer
56
+ from multipers.simplex_tree_multi import is_simplextree_multi
57
+ from multipers.mma_structures import is_mma
58
+
59
+ if resolution is not None and strategy == "exact":
60
+ raise ValueError("The 'exact' strategy does not support resolution.")
61
+ if strategy != "exact":
62
+ assert resolution is not None, "A resolution is required for non-exact strategies"
63
+
64
+
65
+ cdef bool is_numpy_compatible = True
66
+ if is_slicer(x):
67
+ initial_grid = x.get_filtrations_values().T
68
+ elif is_simplextree_multi(x):
69
+ initial_grid = x.get_filtration_grid()
70
+ elif is_mma(x):
71
+ initial_grid = x.get_filtration_values()
72
+ elif isinstance(x, np.ndarray):
73
+ initial_grid = x
74
+ else:
75
+ x = tuple(x)
76
+ if len(x) == 0: return []
77
+ first = x[0]
78
+ ## is_sm, i.e., iterable tuple(pts,weights)
79
+ if isinstance(x[0], tuple) and getattr(x[0][0], "shape", None) is not None:
80
+ initial_grid = tuple(f[0].T for f in x)
81
+ if isinstance(initial_grid[0], np.ndarray):
82
+ initial_grid = np.concatenate(initial_grid, axis=1)
83
+ else:
84
+ is_numpy_compatbile = False
85
+ import torch
86
+ assert isinstance(first[0], torch.Tensor), "Only numpy and torch are supported ftm."
87
+ initial_grid = torch.cat(initial_grid, axis=1)
88
+ ## is grid-like (num_params, num_pts)
89
+ elif isinstance(first,list) or isinstance(first, tuple) or isinstance(first, np.ndarray):
90
+ initial_grid = tuple(f for f in x)
91
+ else:
92
+ is_numpy_compatible = False
93
+ import torch
94
+ assert isinstance(first, torch.Tensor), "Only numpy and torch are supported ftm."
95
+ initial_grid = x
96
+ if is_numpy_compatible:
97
+ return _compute_grid_numpy(
98
+ initial_grid,
99
+ resolution=resolution,
100
+ strategy = strategy,
101
+ unique = unique,
102
+ _q_factor=_q_factor,
103
+ drop_quantiles=drop_quantiles,
104
+ dense = dense,
105
+ )
106
+ from multipers.torch.diff_grids import get_grid
107
+ return get_grid(strategy)(initial_grid,resolution)
108
+
109
+
110
+
111
+
112
+
113
+
114
+ def _compute_grid_numpy(
115
+ filtrations_values,
116
+ resolution=None,
117
+ strategy:Lstrategies="exact",
118
+ bool unique=True,
119
+ some_float _q_factor=1.,
120
+ drop_quantiles=[0,0],
121
+ bool dense = False,
122
+ ):
123
+ """
124
+ Computes a grid from filtration values, using some strategy.
125
+
126
+ Input
127
+ -----
128
+ - `filtrations_values`: `Iterable[filtration of parameter for parameter]`
129
+ where `filtration_of_parameter` is a array[float, ndim=1]
130
+ - `resolution`:Optional[int|tuple[int]]
131
+ - `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
132
+ - `unique`: if true, doesn't repeat values in the output grid.
133
+ - `drop_quantiles` : drop some filtration values according to these quantiles
134
+ Output
135
+ ------
136
+ Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
137
+ """
138
+ num_parameters = len(filtrations_values)
139
+ if resolution is None and strategy not in ["exact", "precomputed"]:
140
+ raise ValueError("Resolution must be provided for this strategy.")
141
+ elif resolution is not None:
142
+ try:
143
+ int(resolution)
144
+ resolution = [resolution]*num_parameters
145
+ except:
146
+ pass
147
+ try:
148
+ a,b=drop_quantiles
149
+ except:
150
+ a,b=drop_quantiles,drop_quantiles
151
+
152
+ if a != 0 or b != 0:
153
+ boxes = np.asarray([np.quantile(filtration, [a, b], axis=1, method='closest_observation') for filtration in filtrations_values])
154
+ min_filtration, max_filtration = np.min(boxes, axis=(0,1)), np.max(boxes, axis=(0,1)) # box, birth/death, filtration
155
+ filtrations_values = [
156
+ filtration[(m<filtration) * (filtration <M)]
157
+ for filtration, m,M in zip(filtrations_values, min_filtration, max_filtration)
158
+ ]
159
+
160
+ to_unique = lambda f : np.unique(f) if isinstance(f,np.ndarray) else f.unique()
161
+ ## match doesn't work with cython BUG
162
+ if strategy == "exact":
163
+ F=tuple(to_unique(f) for f in filtrations_values)
164
+ elif strategy == "quantile":
165
+ F = tuple(to_unique(f) for f in filtrations_values)
166
+ max_resolution = [min(len(f),r) for f,r in zip(F,resolution)]
167
+ F = tuple( np.quantile(f, q=np.linspace(0,1,num=int(r*_q_factor)), axis=0, method='closest_observation') for f,r in zip(F, resolution) )
168
+ if unique:
169
+ F = tuple(to_unique(f) for f in F)
170
+ if np.all(np.asarray(max_resolution) > np.asarray([len(f) for f in F])):
171
+ return _compute_grid_numpy(filtrations_values=filtrations_values, resolution=resolution, strategy="quantile",_q_factor=1.5*_q_factor)
172
+ elif strategy == "regular":
173
+ F = tuple(np.linspace(np.min(f),np.max(f),num=r, dtype=np.asarray(f).dtype) for f,r in zip(filtrations_values, resolution))
174
+ elif strategy == "regular_closest":
175
+ F = tuple(_todo_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
176
+ elif strategy == "regular_left":
177
+ F = tuple(_todo_regular_left(f,r, unique) for f,r in zip(filtrations_values, resolution))
178
+ elif strategy == "torch_regular_closest":
179
+ F = tuple(_torch_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
180
+ elif strategy == "partition":
181
+ F = tuple(_todo_partition(f,r, unique) for f,r in zip(filtrations_values, resolution))
182
+ elif strategy == "precomputed":
183
+ F=filtrations_values
184
+ else:
185
+ raise ValueError(f"Invalid strategy {strategy}. Pick something in {available_strategies}.")
186
+ if dense:
187
+ return todense(F)
188
+ return F
189
+
190
+ def todense(grid, bool product_order=False):
191
+ if len(grid) == 0:
192
+ return np.empty(0)
193
+ if not isinstance(grid[0], np.ndarray):
194
+ import torch
195
+ assert isinstance(grid[0], torch.Tensor)
196
+ from multipers.torch.diff_grids import todense
197
+ return todense(grid)
198
+ dtype = grid[0].dtype
199
+ if product_order:
200
+ return np.fromiter(product(*grid), dtype=np.dtype((dtype, len(grid))), count=np.prod([len(f) for f in grid]))
201
+ mesh = np.meshgrid(*grid)
202
+ coordinates = np.concatenate(tuple(stuff.ravel()[:,None] for stuff in mesh), axis=1, dtype=dtype)
203
+ return coordinates
204
+
205
+
206
+
207
+ ## TODO : optimize. Pykeops ?
208
+ def _todo_regular_closest(some_float[:] f, int r, bool unique):
209
+ f_array = np.asarray(f)
210
+ f_regular = np.linspace(np.min(f), np.max(f),num=r, dtype=f_array.dtype)
211
+ f_regular_closest = np.asarray([f[<long>np.argmin(np.abs(f_array-f_regular[i]))] for i in range(r)])
212
+ if unique: f_regular_closest = np.unique(f_regular_closest)
213
+ return f_regular_closest
214
+
215
+ def _todo_regular_left(some_float[:] f, int r, bool unique):
216
+ sorted_f = np.sort(f)
217
+ f_regular = np.linspace(sorted_f[0],sorted_f[-1],num=r, dtype=sorted_f.dtype)
218
+ f_regular_closest = sorted_f[np.searchsorted(sorted_f,f_regular)]
219
+ if unique: f_regular_closest = np.unique(f_regular_closest)
220
+ return f_regular_closest
221
+
222
+ def _torch_regular_closest(f, int r, bool unique=True):
223
+ import torch
224
+ f_regular = torch.linspace(f.min(),f.max(), r, dtype=f.dtype)
225
+ f_regular_closest =torch.tensor([f[(f-x).abs().argmin()] for x in f_regular])
226
+ if unique: f_regular_closest = f_regular_closest.unique()
227
+ return f_regular_closest
228
+
229
+ def _todo_partition(some_float[:] data,int resolution, bool unique):
230
+ if data.shape[0] < resolution: resolution=data.shape[0]
231
+ k = data.shape[0] // resolution
232
+ partitions = np.partition(data, k)
233
+ f = partitions[[i*k for i in range(resolution)]]
234
+ if unique: f= np.unique(f)
235
+ return f
236
+
237
+
238
+ def compute_bounding_box(stuff, inflate = 0.):
239
+ r"""
240
+ Returns a array of shape (2, num_parameters)
241
+ such that for any filtration value $y$ of something in stuff,
242
+ then if (x,z) is the output of this function, we have
243
+ $x\le y \le z$.
244
+ """
245
+ box = np.array(compute_grid(stuff,strategy="regular",resolution=2)).T
246
+ if inflate:
247
+ box[0] -= inflate
248
+ box[1] += inflate
249
+ return box
250
+
251
+ def push_to_grid(some_float[:,:] points, grid, bool return_coordinate=False):
252
+ """
253
+ Given points and a grid (list of one parameter grids),
254
+ pushes the points onto the grid.
255
+ """
256
+ num_points, num_parameters = points.shape[0], points.shape[1]
257
+ cdef cnp.ndarray[long,ndim=2] coordinates = np.empty((num_points, num_parameters),dtype=np.int64)
258
+ for parameter in range(num_parameters):
259
+ coordinates[:,parameter] = np.searchsorted(grid[parameter],points[:,parameter])
260
+ if return_coordinate:
261
+ return coordinates
262
+ out = np.empty((num_points,num_parameters), grid[0].dtype)
263
+ for parameter in range(num_parameters):
264
+ out[:,parameter] = grid[parameter][coordinates[:,parameter]]
265
+ return out
266
+
267
+
268
+ def coarsen_points(some_float[:,:] points, strategy="exact", int resolution=-1, bool coordinate=False):
269
+ grid = _compute_grid_numpy(points.T, strategy=strategy, resolution=resolution)
270
+ if coordinate:
271
+ return push_to_grid(points, grid, coordinate), grid
272
+ return push_to_grid(points, grid, coordinate)
273
+
274
+
275
+
276
+ def evaluate_in_grid(pts, grid, mass_default=None):
277
+ """
278
+ Input
279
+ -----
280
+ - pts: of the form array[int, ndim=2]
281
+ - grid of the form Iterable[array[float, ndim=1]]
282
+ """
283
+ first_filtration = grid[0]
284
+ dtype = first_filtration.dtype
285
+ if isinstance(first_filtration, np.ndarray):
286
+ if mass_default is not None:
287
+ grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
288
+ def empty_like(x):
289
+ return np.empty_like(x, dtype=dtype)
290
+ else:
291
+ import torch
292
+ # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
293
+ if mass_default is not None:
294
+ grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
295
+ def empty_like(x):
296
+ return torch.empty(x.shape,dtype=dtype)
297
+
298
+ coords= empty_like(pts)
299
+ for i in range(coords.shape[1]):
300
+ coords[:,i] = grid[i][pts[:,i]]
301
+ return coords
302
+
303
+ def sm_in_grid(pts, weights, grid, int num_parameters=-1, mass_default=None):
304
+ """Given a measure whose points are coordinates,
305
+ pushes this measure in this grid.
306
+ Input
307
+ -----
308
+ - pts: of the form array[int, ndim=2]
309
+ - weights: array[int, ndim=1]
310
+ - grid of the form Iterable[array[float, ndim=1]]
311
+ - num_parameters: number of parameters
312
+ """
313
+ first_filtration = grid[0]
314
+ dtype = first_filtration.dtype
315
+ def to_int(x):
316
+ return np.asarray(x,dtype=np.int64)
317
+ if isinstance(first_filtration, np.ndarray):
318
+ if mass_default is not None:
319
+ grid = tuple(np.concatenate([g, [m]]) for g,m in zip(grid, mass_default))
320
+ def empty_like(x, weights):
321
+ return np.empty_like(x, dtype=dtype), np.asarray(weights)
322
+ else:
323
+ import torch
324
+ # assert isinstance(first_filtration, torch.Tensor), f"Invalid grid type. Got {type(grid[0])}, expected numpy or torch array."
325
+ if mass_default is not None:
326
+ grid = tuple(torch.cat([g, torch.tensor(m)[None]]) for g,m in zip(grid, mass_default))
327
+ def empty_like(x, weights):
328
+ return torch.empty(x.shape,dtype=dtype), torch.from_numpy(weights)
329
+
330
+ pts = to_int(pts)
331
+ coords,weights = empty_like(pts,weights)
332
+ for i in range(coords.shape[1]):
333
+ if num_parameters > 0:
334
+ coords[:,i] = grid[i%num_parameters][pts[:,i]]
335
+ else:
336
+ coords[:,i] = grid[i][pts[:,i]]
337
+ return (coords, weights)
338
+
339
+ # TODO : optimize with memoryviews / typing
340
+ def sms_in_grid(sms, grid, int num_parameters=-1, mass_default=None):
341
+ """Given a measure whose points are coordinates,
342
+ pushes this measure in this grid.
343
+ Input
344
+ -----
345
+ - sms: of the form (signed_measure_like for num_measures)
346
+ where signed_measure_like = tuple(array[int, ndim=2], array[int])
347
+ - grid of the form Iterable[array[float, ndim=1]]
348
+ """
349
+ sms = tuple(sm_in_grid(pts,weights,grid=grid,num_parameters=num_parameters, mass_default=mass_default) for pts,weights in sms)
350
+ return sms