multipers 2.2.3__cp312-cp312-win_amd64.whl → 2.3.1__cp312-cp312-win_amd64.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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- multipers/__init__.py +33 -31
- multipers/_signed_measure_meta.py +430 -430
- multipers/_slicer_meta.py +211 -212
- multipers/data/MOL2.py +458 -458
- multipers/data/UCR.py +18 -18
- multipers/data/graphs.py +466 -466
- multipers/data/immuno_regions.py +27 -27
- multipers/data/pytorch2simplextree.py +90 -90
- multipers/data/shape3d.py +101 -101
- multipers/data/synthetic.py +113 -111
- multipers/distances.py +198 -198
- multipers/filtration_conversions.pxd.tp +84 -84
- multipers/filtrations/__init__.py +18 -0
- multipers/{ml/convolutions.py → filtrations/density.py} +563 -520
- multipers/filtrations/filtrations.py +289 -0
- multipers/filtrations.pxd +224 -224
- multipers/function_rips.cp312-win_amd64.pyd +0 -0
- multipers/function_rips.pyx +105 -105
- multipers/grids.cp312-win_amd64.pyd +0 -0
- multipers/grids.pyx +350 -350
- multipers/gudhi/Persistence_slices_interface.h +132 -132
- multipers/gudhi/Simplex_tree_interface.h +239 -245
- multipers/gudhi/Simplex_tree_multi_interface.h +516 -561
- multipers/gudhi/cubical_to_boundary.h +59 -59
- multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -450
- multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -1070
- multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -579
- multipers/gudhi/gudhi/Debug_utils.h +45 -45
- multipers/gudhi/gudhi/Fields/Multi_field.h +484 -484
- multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -455
- multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -450
- multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -531
- multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -507
- multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -531
- multipers/gudhi/gudhi/Fields/Z2_field.h +355 -355
- multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -376
- multipers/gudhi/gudhi/Fields/Zp_field.h +420 -420
- multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -400
- multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -418
- multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -337
- multipers/gudhi/gudhi/Matrix.h +2107 -2107
- multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -1038
- multipers/gudhi/gudhi/Multi_persistence/Box.h +171 -171
- multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -282
- multipers/gudhi/gudhi/Off_reader.h +173 -173
- multipers/gudhi/gudhi/One_critical_filtration.h +1433 -1431
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -769
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -686
- multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -842
- multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -1350
- multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -1105
- multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -859
- multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -910
- multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -139
- multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -230
- multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -211
- multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -60
- multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -60
- multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -136
- multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -190
- multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -616
- multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -150
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -106
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -219
- multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -327
- multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -1140
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -934
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -934
- multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -980
- multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -1092
- multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -192
- multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -921
- multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -1093
- multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -1012
- multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -1244
- multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -186
- multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -164
- multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -156
- multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -376
- multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -540
- multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -118
- multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -173
- multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -128
- multipers/gudhi/gudhi/Persistent_cohomology.h +745 -745
- multipers/gudhi/gudhi/Points_off_io.h +171 -171
- multipers/gudhi/gudhi/Simple_object_pool.h +69 -69
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -463
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -83
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -106
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -277
- multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -62
- multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -27
- multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -62
- multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -157
- multipers/gudhi/gudhi/Simplex_tree.h +2794 -2794
- multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -163
- multipers/gudhi/gudhi/distance_functions.h +62 -62
- multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -104
- multipers/gudhi/gudhi/persistence_interval.h +253 -253
- multipers/gudhi/gudhi/persistence_matrix_options.h +170 -170
- multipers/gudhi/gudhi/reader_utils.h +367 -367
- multipers/gudhi/mma_interface_coh.h +256 -255
- multipers/gudhi/mma_interface_h0.h +223 -231
- multipers/gudhi/mma_interface_matrix.h +291 -282
- multipers/gudhi/naive_merge_tree.h +536 -575
- multipers/gudhi/scc_io.h +310 -289
- multipers/gudhi/truc.h +957 -888
- multipers/io.cp312-win_amd64.pyd +0 -0
- multipers/io.pyx +714 -711
- multipers/ml/accuracies.py +90 -90
- multipers/ml/invariants_with_persistable.py +79 -79
- multipers/ml/kernels.py +176 -176
- multipers/ml/mma.py +713 -714
- multipers/ml/one.py +472 -472
- multipers/ml/point_clouds.py +352 -346
- multipers/ml/signed_measures.py +1589 -1589
- multipers/ml/sliced_wasserstein.py +461 -461
- multipers/ml/tools.py +113 -113
- multipers/mma_structures.cp312-win_amd64.pyd +0 -0
- multipers/mma_structures.pxd +127 -127
- multipers/mma_structures.pyx +4 -8
- multipers/mma_structures.pyx.tp +1083 -1085
- multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -93
- multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -97
- multipers/multi_parameter_rank_invariant/function_rips.h +322 -322
- multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -769
- multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -148
- multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -369
- multipers/multiparameter_edge_collapse.py +41 -41
- multipers/multiparameter_module_approximation/approximation.h +2298 -2295
- multipers/multiparameter_module_approximation/combinatory.h +129 -129
- multipers/multiparameter_module_approximation/debug.h +107 -107
- multipers/multiparameter_module_approximation/format_python-cpp.h +286 -286
- multipers/multiparameter_module_approximation/heap_column.h +238 -238
- multipers/multiparameter_module_approximation/images.h +79 -79
- multipers/multiparameter_module_approximation/list_column.h +174 -174
- multipers/multiparameter_module_approximation/list_column_2.h +232 -232
- multipers/multiparameter_module_approximation/ru_matrix.h +347 -347
- multipers/multiparameter_module_approximation/set_column.h +135 -135
- multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -36
- multipers/multiparameter_module_approximation/unordered_set_column.h +166 -166
- multipers/multiparameter_module_approximation/utilities.h +403 -419
- multipers/multiparameter_module_approximation/vector_column.h +223 -223
- multipers/multiparameter_module_approximation/vector_matrix.h +331 -331
- multipers/multiparameter_module_approximation/vineyards.h +464 -464
- multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -649
- multipers/multiparameter_module_approximation.cp312-win_amd64.pyd +0 -0
- multipers/multiparameter_module_approximation.pyx +218 -217
- multipers/pickle.py +90 -53
- multipers/plots.py +342 -334
- multipers/point_measure.cp312-win_amd64.pyd +0 -0
- multipers/point_measure.pyx +322 -320
- multipers/simplex_tree_multi.cp312-win_amd64.pyd +0 -0
- multipers/simplex_tree_multi.pxd +133 -133
- multipers/simplex_tree_multi.pyx +115 -48
- multipers/simplex_tree_multi.pyx.tp +1947 -1935
- multipers/slicer.cp312-win_amd64.pyd +0 -0
- multipers/slicer.pxd +281 -100
- multipers/slicer.pxd.tp +218 -214
- multipers/slicer.pyx +1570 -507
- multipers/slicer.pyx.tp +931 -914
- multipers/tensor/tensor.h +672 -672
- multipers/tensor.pxd +13 -13
- multipers/test.pyx +44 -44
- multipers/tests/__init__.py +57 -57
- multipers/torch/diff_grids.py +217 -217
- multipers/torch/rips_density.py +310 -304
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/LICENSE +21 -21
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/METADATA +21 -11
- multipers-2.3.1.dist-info/RECORD +182 -0
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/WHEEL +1 -1
- multipers/tests/test_diff_helper.py +0 -73
- multipers/tests/test_hilbert_function.py +0 -82
- multipers/tests/test_mma.py +0 -83
- multipers/tests/test_point_clouds.py +0 -49
- multipers/tests/test_python-cpp_conversion.py +0 -82
- multipers/tests/test_signed_betti.py +0 -181
- multipers/tests/test_signed_measure.py +0 -89
- multipers/tests/test_simplextreemulti.py +0 -221
- multipers/tests/test_slicer.py +0 -221
- multipers-2.2.3.dist-info/RECORD +0 -189
- {multipers-2.2.3.dist-info → multipers-2.3.1.dist-info}/top_level.txt +0 -0
multipers/grids.pyx
CHANGED
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from libc.stdint cimport intptr_t, int32_t, int64_t
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from libcpp cimport bool,int,long, float
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import numpy as np
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available_strategies = ["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
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Lstrategies = Literal["regular","regular_closest", "regular_left", "partition", "quantile", "precomputed"]
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ctypedef fused some_int:
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initial_grid = x.get_filtration_grid()
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elif resolution is not None:
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try:
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int(resolution)
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resolution = [resolution]*num_parameters
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except:
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pass
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try:
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a,b=drop_quantiles
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except:
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a,b=drop_quantiles,drop_quantiles
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if a != 0 or b != 0:
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|
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boxes = np.asarray([np.quantile(filtration, [a, b], axis=1, method='closest_observation') for filtration in filtrations_values])
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min_filtration, max_filtration = np.min(boxes, axis=(0,1)), np.max(boxes, axis=(0,1)) # box, birth/death, filtration
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filtrations_values = [
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filtration[(m<filtration) * (filtration <M)]
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for filtration, m,M in zip(filtrations_values, min_filtration, max_filtration)
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]
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to_unique = lambda f : np.unique(f) if isinstance(f,np.ndarray) else f.unique()
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## match doesn't work with cython BUG
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if strategy == "exact":
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F=tuple(to_unique(f) for f in filtrations_values)
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elif strategy == "quantile":
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F = tuple(to_unique(f) for f in filtrations_values)
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max_resolution = [min(len(f),r) for f,r in zip(F,resolution)]
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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) )
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if unique:
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F = tuple(to_unique(f) for f in F)
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if np.all(np.asarray(max_resolution) > np.asarray([len(f) for f in F])):
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return _compute_grid_numpy(filtrations_values=filtrations_values, resolution=resolution, strategy="quantile",_q_factor=1.5*_q_factor)
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elif strategy == "regular":
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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))
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elif strategy == "regular_closest":
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F = tuple(_todo_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
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|
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elif strategy == "regular_left":
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F = tuple(_todo_regular_left(f,r, unique) for f,r in zip(filtrations_values, resolution))
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|
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elif strategy == "torch_regular_closest":
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F = tuple(_torch_regular_closest(f,r, unique) for f,r in zip(filtrations_values, resolution))
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|
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elif strategy == "partition":
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|
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F = tuple(_todo_partition(f,r, unique) for f,r in zip(filtrations_values, resolution))
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|
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elif strategy == "precomputed":
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F=filtrations_values
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|
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else:
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|
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raise ValueError(f"Invalid strategy {strategy}. Pick something in {available_strategies}.")
|
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|
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if dense:
|
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|
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return todense(F)
|
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|
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return F
|
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|
-
|
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190
|
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def todense(grid, bool product_order=False):
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|
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if len(grid) == 0:
|
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|
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return np.empty(0)
|
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|
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if not isinstance(grid[0], np.ndarray):
|
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|
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import torch
|
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195
|
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assert isinstance(grid[0], torch.Tensor)
|
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|
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from multipers.torch.diff_grids import todense
|
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|
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return todense(grid)
|
|
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|
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dtype = grid[0].dtype
|
|
199
|
-
if product_order:
|
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200
|
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return np.fromiter(product(*grid), dtype=np.dtype((dtype, len(grid))), count=np.prod([len(f) for f in grid]))
|
|
201
|
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mesh = np.meshgrid(*grid)
|
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202
|
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coordinates = np.concatenate(tuple(stuff.ravel()[:,None] for stuff in mesh), axis=1, dtype=dtype)
|
|
203
|
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return coordinates
|
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204
|
-
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205
|
-
|
|
206
|
-
|
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207
|
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## TODO : optimize. Pykeops ?
|
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208
|
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def _todo_regular_closest(some_float[:] f, int r, bool unique):
|
|
209
|
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f_array = np.asarray(f)
|
|
210
|
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f_regular = np.linspace(np.min(f), np.max(f),num=r, dtype=f_array.dtype)
|
|
211
|
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f_regular_closest = np.asarray([f[<long>np.argmin(np.abs(f_array-f_regular[i]))] for i in range(r)])
|
|
212
|
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if unique: f_regular_closest = np.unique(f_regular_closest)
|
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213
|
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return f_regular_closest
|
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214
|
-
|
|
215
|
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def _todo_regular_left(some_float[:] f, int r, bool unique):
|
|
216
|
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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
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85
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+
import torch
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86
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+
assert isinstance(first[0], torch.Tensor), "Only numpy and torch are supported ftm."
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87
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+
initial_grid = torch.cat(initial_grid, axis=1)
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88
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+
## is grid-like (num_params, num_pts)
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89
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+
elif isinstance(first,list) or isinstance(first, tuple) or isinstance(first, np.ndarray):
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90
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+
initial_grid = tuple(f for f in x)
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91
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+
else:
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92
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+
is_numpy_compatible = False
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93
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+
import torch
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94
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+
assert isinstance(first, torch.Tensor), "Only numpy and torch are supported ftm."
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95
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+
initial_grid = x
|
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96
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+
if is_numpy_compatible:
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97
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+
return _compute_grid_numpy(
|
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98
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+
initial_grid,
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99
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+
resolution=resolution,
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100
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strategy = strategy,
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unique = unique,
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+
_q_factor=_q_factor,
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drop_quantiles=drop_quantiles,
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104
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+
dense = dense,
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+
)
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106
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+
from multipers.torch.diff_grids import get_grid
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+
return get_grid(strategy)(initial_grid,resolution)
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108
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+
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109
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+
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110
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+
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111
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+
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112
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+
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113
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+
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114
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+
def _compute_grid_numpy(
|
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115
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+
filtrations_values,
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116
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+
resolution=None,
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117
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+
strategy:Lstrategies="exact",
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118
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bool unique=True,
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119
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+
some_float _q_factor=1.,
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120
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drop_quantiles=[0,0],
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121
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bool dense = False,
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+
):
|
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123
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+
"""
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124
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+
Computes a grid from filtration values, using some strategy.
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125
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+
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126
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+
Input
|
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127
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+
-----
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128
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- `filtrations_values`: `Iterable[filtration of parameter for parameter]`
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where `filtration_of_parameter` is a array[float, ndim=1]
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+
- `resolution`:Optional[int|tuple[int]]
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131
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+
- `strategy`: either exact, regular, regular_closest, regular_left, partition, quantile, or precomputed.
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+
- `unique`: if true, doesn't repeat values in the output grid.
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+
- `drop_quantiles` : drop some filtration values according to these quantiles
|
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134
|
+
Output
|
|
135
|
+
------
|
|
136
|
+
Iterable[array[float, ndim=1]] : the 1d-grid for each parameter.
|
|
137
|
+
"""
|
|
138
|
+
num_parameters = len(filtrations_values)
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|
139
|
+
if resolution is None and strategy not in ["exact", "precomputed"]:
|
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140
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+
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
|