multipers 2.3.3b6__cp312-cp312-manylinux_2_39_x86_64.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.
Potentially problematic release.
This version of multipers might be problematic. Click here for more details.
- multipers/__init__.py +33 -0
- multipers/_signed_measure_meta.py +453 -0
- multipers/_slicer_meta.py +211 -0
- multipers/array_api/__init__.py +45 -0
- multipers/array_api/numpy.py +41 -0
- multipers/array_api/torch.py +58 -0
- multipers/data/MOL2.py +458 -0
- multipers/data/UCR.py +18 -0
- multipers/data/__init__.py +1 -0
- multipers/data/graphs.py +466 -0
- multipers/data/immuno_regions.py +27 -0
- multipers/data/minimal_presentation_to_st_bf.py +0 -0
- multipers/data/pytorch2simplextree.py +91 -0
- multipers/data/shape3d.py +101 -0
- multipers/data/synthetic.py +113 -0
- multipers/distances.py +202 -0
- multipers/filtration_conversions.pxd +229 -0
- multipers/filtration_conversions.pxd.tp +84 -0
- multipers/filtrations/__init__.py +18 -0
- multipers/filtrations/density.py +574 -0
- multipers/filtrations/filtrations.py +361 -0
- multipers/filtrations.pxd +224 -0
- multipers/function_rips.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/function_rips.pyx +105 -0
- multipers/grids.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/grids.pyx +433 -0
- multipers/gudhi/Persistence_slices_interface.h +132 -0
- multipers/gudhi/Simplex_tree_interface.h +239 -0
- multipers/gudhi/Simplex_tree_multi_interface.h +551 -0
- multipers/gudhi/cubical_to_boundary.h +59 -0
- multipers/gudhi/gudhi/Bitmap_cubical_complex.h +450 -0
- multipers/gudhi/gudhi/Bitmap_cubical_complex_base.h +1070 -0
- multipers/gudhi/gudhi/Bitmap_cubical_complex_periodic_boundary_conditions_base.h +579 -0
- multipers/gudhi/gudhi/Debug_utils.h +45 -0
- multipers/gudhi/gudhi/Fields/Multi_field.h +484 -0
- multipers/gudhi/gudhi/Fields/Multi_field_operators.h +455 -0
- multipers/gudhi/gudhi/Fields/Multi_field_shared.h +450 -0
- multipers/gudhi/gudhi/Fields/Multi_field_small.h +531 -0
- multipers/gudhi/gudhi/Fields/Multi_field_small_operators.h +507 -0
- multipers/gudhi/gudhi/Fields/Multi_field_small_shared.h +531 -0
- multipers/gudhi/gudhi/Fields/Z2_field.h +355 -0
- multipers/gudhi/gudhi/Fields/Z2_field_operators.h +376 -0
- multipers/gudhi/gudhi/Fields/Zp_field.h +420 -0
- multipers/gudhi/gudhi/Fields/Zp_field_operators.h +400 -0
- multipers/gudhi/gudhi/Fields/Zp_field_shared.h +418 -0
- multipers/gudhi/gudhi/Flag_complex_edge_collapser.h +337 -0
- multipers/gudhi/gudhi/Matrix.h +2107 -0
- multipers/gudhi/gudhi/Multi_critical_filtration.h +1038 -0
- multipers/gudhi/gudhi/Multi_persistence/Box.h +174 -0
- multipers/gudhi/gudhi/Multi_persistence/Line.h +282 -0
- multipers/gudhi/gudhi/Off_reader.h +173 -0
- multipers/gudhi/gudhi/One_critical_filtration.h +1441 -0
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix.h +769 -0
- multipers/gudhi/gudhi/Persistence_matrix/Base_matrix_with_column_compression.h +686 -0
- multipers/gudhi/gudhi/Persistence_matrix/Boundary_matrix.h +842 -0
- multipers/gudhi/gudhi/Persistence_matrix/Chain_matrix.h +1350 -0
- multipers/gudhi/gudhi/Persistence_matrix/Id_to_index_overlay.h +1105 -0
- multipers/gudhi/gudhi/Persistence_matrix/Position_to_index_overlay.h +859 -0
- multipers/gudhi/gudhi/Persistence_matrix/RU_matrix.h +910 -0
- multipers/gudhi/gudhi/Persistence_matrix/allocators/entry_constructors.h +139 -0
- multipers/gudhi/gudhi/Persistence_matrix/base_pairing.h +230 -0
- multipers/gudhi/gudhi/Persistence_matrix/base_swap.h +211 -0
- multipers/gudhi/gudhi/Persistence_matrix/boundary_cell_position_to_id_mapper.h +60 -0
- multipers/gudhi/gudhi/Persistence_matrix/boundary_face_position_to_id_mapper.h +60 -0
- multipers/gudhi/gudhi/Persistence_matrix/chain_pairing.h +136 -0
- multipers/gudhi/gudhi/Persistence_matrix/chain_rep_cycles.h +190 -0
- multipers/gudhi/gudhi/Persistence_matrix/chain_vine_swap.h +616 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/chain_column_extra_properties.h +150 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_dimension_holder.h +106 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/column_utilities.h +219 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/entry_types.h +327 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/heap_column.h +1140 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_list_column.h +934 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/intrusive_set_column.h +934 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/list_column.h +980 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/naive_vector_column.h +1092 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/row_access.h +192 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/set_column.h +921 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/small_vector_column.h +1093 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/unordered_set_column.h +1012 -0
- multipers/gudhi/gudhi/Persistence_matrix/columns/vector_column.h +1244 -0
- multipers/gudhi/gudhi/Persistence_matrix/matrix_dimension_holders.h +186 -0
- multipers/gudhi/gudhi/Persistence_matrix/matrix_row_access.h +164 -0
- multipers/gudhi/gudhi/Persistence_matrix/ru_pairing.h +156 -0
- multipers/gudhi/gudhi/Persistence_matrix/ru_rep_cycles.h +376 -0
- multipers/gudhi/gudhi/Persistence_matrix/ru_vine_swap.h +540 -0
- multipers/gudhi/gudhi/Persistent_cohomology/Field_Zp.h +118 -0
- multipers/gudhi/gudhi/Persistent_cohomology/Multi_field.h +173 -0
- multipers/gudhi/gudhi/Persistent_cohomology/Persistent_cohomology_column.h +128 -0
- multipers/gudhi/gudhi/Persistent_cohomology.h +745 -0
- multipers/gudhi/gudhi/Points_off_io.h +171 -0
- multipers/gudhi/gudhi/Simple_object_pool.h +69 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_iterators.h +463 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_node_explicit_storage.h +83 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_siblings.h +106 -0
- multipers/gudhi/gudhi/Simplex_tree/Simplex_tree_star_simplex_iterators.h +277 -0
- multipers/gudhi/gudhi/Simplex_tree/hooks_simplex_base.h +62 -0
- multipers/gudhi/gudhi/Simplex_tree/indexing_tag.h +27 -0
- multipers/gudhi/gudhi/Simplex_tree/serialization_utils.h +62 -0
- multipers/gudhi/gudhi/Simplex_tree/simplex_tree_options.h +157 -0
- multipers/gudhi/gudhi/Simplex_tree.h +2794 -0
- multipers/gudhi/gudhi/Simplex_tree_multi.h +152 -0
- multipers/gudhi/gudhi/distance_functions.h +62 -0
- multipers/gudhi/gudhi/graph_simplicial_complex.h +104 -0
- multipers/gudhi/gudhi/persistence_interval.h +253 -0
- multipers/gudhi/gudhi/persistence_matrix_options.h +170 -0
- multipers/gudhi/gudhi/reader_utils.h +367 -0
- multipers/gudhi/mma_interface_coh.h +256 -0
- multipers/gudhi/mma_interface_h0.h +223 -0
- multipers/gudhi/mma_interface_matrix.h +293 -0
- multipers/gudhi/naive_merge_tree.h +536 -0
- multipers/gudhi/scc_io.h +310 -0
- multipers/gudhi/truc.h +1403 -0
- multipers/io.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/io.pyx +644 -0
- multipers/ml/__init__.py +0 -0
- multipers/ml/accuracies.py +90 -0
- multipers/ml/invariants_with_persistable.py +79 -0
- multipers/ml/kernels.py +176 -0
- multipers/ml/mma.py +713 -0
- multipers/ml/one.py +472 -0
- multipers/ml/point_clouds.py +352 -0
- multipers/ml/signed_measures.py +1589 -0
- multipers/ml/sliced_wasserstein.py +461 -0
- multipers/ml/tools.py +113 -0
- multipers/mma_structures.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/mma_structures.pxd +128 -0
- multipers/mma_structures.pyx +2786 -0
- multipers/mma_structures.pyx.tp +1094 -0
- multipers/multi_parameter_rank_invariant/diff_helpers.h +84 -0
- multipers/multi_parameter_rank_invariant/euler_characteristic.h +97 -0
- multipers/multi_parameter_rank_invariant/function_rips.h +322 -0
- multipers/multi_parameter_rank_invariant/hilbert_function.h +769 -0
- multipers/multi_parameter_rank_invariant/persistence_slices.h +148 -0
- multipers/multi_parameter_rank_invariant/rank_invariant.h +369 -0
- multipers/multiparameter_edge_collapse.py +41 -0
- multipers/multiparameter_module_approximation/approximation.h +2330 -0
- multipers/multiparameter_module_approximation/combinatory.h +129 -0
- multipers/multiparameter_module_approximation/debug.h +107 -0
- multipers/multiparameter_module_approximation/euler_curves.h +0 -0
- multipers/multiparameter_module_approximation/format_python-cpp.h +286 -0
- multipers/multiparameter_module_approximation/heap_column.h +238 -0
- multipers/multiparameter_module_approximation/images.h +79 -0
- multipers/multiparameter_module_approximation/list_column.h +174 -0
- multipers/multiparameter_module_approximation/list_column_2.h +232 -0
- multipers/multiparameter_module_approximation/ru_matrix.h +347 -0
- multipers/multiparameter_module_approximation/set_column.h +135 -0
- multipers/multiparameter_module_approximation/structure_higher_dim_barcode.h +36 -0
- multipers/multiparameter_module_approximation/unordered_set_column.h +166 -0
- multipers/multiparameter_module_approximation/utilities.h +403 -0
- multipers/multiparameter_module_approximation/vector_column.h +223 -0
- multipers/multiparameter_module_approximation/vector_matrix.h +331 -0
- multipers/multiparameter_module_approximation/vineyards.h +464 -0
- multipers/multiparameter_module_approximation/vineyards_trajectories.h +649 -0
- multipers/multiparameter_module_approximation.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/multiparameter_module_approximation.pyx +235 -0
- multipers/pickle.py +90 -0
- multipers/plots.py +456 -0
- multipers/point_measure.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/point_measure.pyx +395 -0
- multipers/simplex_tree_multi.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/simplex_tree_multi.pxd +134 -0
- multipers/simplex_tree_multi.pyx +10840 -0
- multipers/simplex_tree_multi.pyx.tp +2009 -0
- multipers/slicer.cpython-312-x86_64-linux-gnu.so +0 -0
- multipers/slicer.pxd +3034 -0
- multipers/slicer.pxd.tp +234 -0
- multipers/slicer.pyx +20481 -0
- multipers/slicer.pyx.tp +1088 -0
- multipers/tensor/tensor.h +672 -0
- multipers/tensor.pxd +13 -0
- multipers/test.pyx +44 -0
- multipers/tests/__init__.py +62 -0
- multipers/torch/__init__.py +1 -0
- multipers/torch/diff_grids.py +240 -0
- multipers/torch/rips_density.py +310 -0
- multipers-2.3.3b6.dist-info/METADATA +128 -0
- multipers-2.3.3b6.dist-info/RECORD +182 -0
- multipers-2.3.3b6.dist-info/WHEEL +5 -0
- multipers-2.3.3b6.dist-info/licenses/LICENSE +21 -0
- multipers-2.3.3b6.dist-info/top_level.txt +1 -0
- multipers.libs/libtbb-ca48af5c.so.12.16 +0 -0
|
@@ -0,0 +1,192 @@
|
|
|
1
|
+
/* This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
|
|
2
|
+
* See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
|
|
3
|
+
* Author(s): Hannah Schreiber
|
|
4
|
+
*
|
|
5
|
+
* Copyright (C) 2022-24 Inria
|
|
6
|
+
*
|
|
7
|
+
* Modification(s):
|
|
8
|
+
* - YYYY/MM Author: Description of the modification
|
|
9
|
+
*/
|
|
10
|
+
|
|
11
|
+
/**
|
|
12
|
+
* @file row_access.h
|
|
13
|
+
* @author Hannah Schreiber
|
|
14
|
+
* @brief Contains the @ref Gudhi::persistence_matrix::Row_access class and
|
|
15
|
+
* @ref Gudhi::persistence_matrix::Dummy_row_access structure.
|
|
16
|
+
*/
|
|
17
|
+
|
|
18
|
+
#ifndef PM_ROW_ACCESS_H
|
|
19
|
+
#define PM_ROW_ACCESS_H
|
|
20
|
+
|
|
21
|
+
#include <utility> //std::swap
|
|
22
|
+
|
|
23
|
+
namespace Gudhi {
|
|
24
|
+
namespace persistence_matrix {
|
|
25
|
+
|
|
26
|
+
/**
|
|
27
|
+
* @ingroup persistence_matrix
|
|
28
|
+
*
|
|
29
|
+
* @brief Empty structure.
|
|
30
|
+
* Inherited instead of @ref Row_access, if the row access is not enabled.
|
|
31
|
+
*/
|
|
32
|
+
struct Dummy_row_access
|
|
33
|
+
{
|
|
34
|
+
friend void swap([[maybe_unused]] Dummy_row_access& d1, [[maybe_unused]] Dummy_row_access& d2) {}
|
|
35
|
+
|
|
36
|
+
Dummy_row_access() {}
|
|
37
|
+
template <typename Index, class Row_container>
|
|
38
|
+
Dummy_row_access([[maybe_unused]] Index columnIndex, [[maybe_unused]] Row_container& rows) {}
|
|
39
|
+
};
|
|
40
|
+
|
|
41
|
+
/**
|
|
42
|
+
* @class Row_access row_access.h gudhi/Persistence_matrix/columns/row_access.h
|
|
43
|
+
* @ingroup persistence_matrix
|
|
44
|
+
*
|
|
45
|
+
* @brief Class managing the row access for the columns.
|
|
46
|
+
*
|
|
47
|
+
* @tparam Master_matrix An instantiation of @ref Matrix from which all types and options are deduced.
|
|
48
|
+
*/
|
|
49
|
+
template <class Master_matrix>
|
|
50
|
+
class Row_access
|
|
51
|
+
{
|
|
52
|
+
public:
|
|
53
|
+
using Index = typename Master_matrix::Index; /**< @ref MatIdx index type. */
|
|
54
|
+
using ID_index = typename Master_matrix::ID_index; /**< @ref IDIdx index type. */
|
|
55
|
+
using Matrix_entry = typename Master_matrix::Matrix_entry; /**< @ref Entry. */
|
|
56
|
+
using Row_container = typename Master_matrix::Row_container; /**< Type of the row container. */
|
|
57
|
+
|
|
58
|
+
/**
|
|
59
|
+
* @brief Default constructor. Sets the column index to -1 and the row container to nullptr.
|
|
60
|
+
* Should only be used by dummy columns.
|
|
61
|
+
*/
|
|
62
|
+
Row_access();
|
|
63
|
+
/**
|
|
64
|
+
* @brief Constructor setting the column index and the row container by the given values.
|
|
65
|
+
*
|
|
66
|
+
* @param columnIndex Column index to store.
|
|
67
|
+
* @param rows Pointer to the row container.
|
|
68
|
+
*/
|
|
69
|
+
Row_access(Index columnIndex, Row_container* rows);
|
|
70
|
+
/**
|
|
71
|
+
* @brief Move constructor.
|
|
72
|
+
*
|
|
73
|
+
* @param other Column to move.
|
|
74
|
+
*/
|
|
75
|
+
Row_access(Row_access&& other) noexcept;
|
|
76
|
+
|
|
77
|
+
/**
|
|
78
|
+
* @brief Inserts the given entry at the given row index.
|
|
79
|
+
*
|
|
80
|
+
* @param rowIndex @ref rowindex "Row index" of the entry.
|
|
81
|
+
* @param entry Pointer to the entry to insert.
|
|
82
|
+
*/
|
|
83
|
+
void insert_entry(ID_index rowIndex, Matrix_entry* entry);
|
|
84
|
+
/**
|
|
85
|
+
* @brief Removes the given entry from its row.
|
|
86
|
+
*
|
|
87
|
+
* @param entry Pointer to the entry to remove.
|
|
88
|
+
*/
|
|
89
|
+
void unlink(Matrix_entry* entry);
|
|
90
|
+
/**
|
|
91
|
+
* @brief If @ref PersistenceMatrixOptions::has_intrusive_rows is false, updates the copy of the entry in its row.
|
|
92
|
+
* Otherwise does nothing.
|
|
93
|
+
*
|
|
94
|
+
* If the rows are intrusive, only a pointer of the entry is stored and therefore any update on the entry (value
|
|
95
|
+
* or column index) is automatically forwarded. But for non intrusive rows, any update has to be pushed explicitly.
|
|
96
|
+
*
|
|
97
|
+
* @param entry Entry to update.
|
|
98
|
+
*/
|
|
99
|
+
void update_entry(const Matrix_entry& entry);
|
|
100
|
+
/**
|
|
101
|
+
* @brief Returns the @ref MatIdx column index.
|
|
102
|
+
*
|
|
103
|
+
* @return The @ref MatIdx column index.
|
|
104
|
+
*/
|
|
105
|
+
Index get_column_index() const;
|
|
106
|
+
|
|
107
|
+
/**
|
|
108
|
+
* @brief Swap operator.
|
|
109
|
+
*/
|
|
110
|
+
friend void swap(Row_access& r1, Row_access& r2) {
|
|
111
|
+
std::swap(r1.rows_, r2.rows_);
|
|
112
|
+
std::swap(r1.columnIndex_, r2.columnIndex_);
|
|
113
|
+
}
|
|
114
|
+
|
|
115
|
+
protected:
|
|
116
|
+
Index columnIndex_; /**< Column index. */
|
|
117
|
+
Row_container* rows_; /**< Row container. Be careful to not destroy before the columns. */
|
|
118
|
+
|
|
119
|
+
private:
|
|
120
|
+
using Base_hook_matrix_row = typename Master_matrix::Base_hook_matrix_row;
|
|
121
|
+
};
|
|
122
|
+
|
|
123
|
+
template <class Master_matrix>
|
|
124
|
+
inline Row_access<Master_matrix>::Row_access() : columnIndex_(-1), rows_(nullptr)
|
|
125
|
+
{}
|
|
126
|
+
|
|
127
|
+
template <class Master_matrix>
|
|
128
|
+
inline Row_access<Master_matrix>::Row_access(Index columnIndex, Row_container* rows)
|
|
129
|
+
: columnIndex_(columnIndex), rows_(rows)
|
|
130
|
+
{}
|
|
131
|
+
|
|
132
|
+
template <class Master_matrix>
|
|
133
|
+
inline Row_access<Master_matrix>::Row_access(Row_access&& other) noexcept
|
|
134
|
+
: columnIndex_(std::exchange(other.columnIndex_, 0)), rows_(other.rows_)
|
|
135
|
+
{}
|
|
136
|
+
|
|
137
|
+
template <class Master_matrix>
|
|
138
|
+
inline void Row_access<Master_matrix>::insert_entry(ID_index rowIndex, Matrix_entry* entry)
|
|
139
|
+
{
|
|
140
|
+
if (rows_ == nullptr) return;
|
|
141
|
+
|
|
142
|
+
if constexpr (!Master_matrix::Option_list::has_removable_rows) {
|
|
143
|
+
if (rows_->size() < rowIndex + 1) rows_->resize(rowIndex + 1);
|
|
144
|
+
}
|
|
145
|
+
|
|
146
|
+
// if has_removable_rows should op[] create non existing entry? If not, use try_emplace()
|
|
147
|
+
if constexpr (Master_matrix::Option_list::has_intrusive_rows) {
|
|
148
|
+
rows_->operator[](rowIndex).push_back(*entry);
|
|
149
|
+
} else {
|
|
150
|
+
rows_->operator[](rowIndex).insert(*entry);
|
|
151
|
+
}
|
|
152
|
+
}
|
|
153
|
+
|
|
154
|
+
template <class Master_matrix>
|
|
155
|
+
inline void Row_access<Master_matrix>::unlink(Matrix_entry* entry)
|
|
156
|
+
{
|
|
157
|
+
if (rows_ == nullptr) return;
|
|
158
|
+
|
|
159
|
+
if constexpr (Master_matrix::Option_list::has_intrusive_rows) {
|
|
160
|
+
entry->Base_hook_matrix_row::unlink();
|
|
161
|
+
} else {
|
|
162
|
+
if constexpr (Master_matrix::Option_list::has_removable_rows) {
|
|
163
|
+
auto it = rows_->find(entry->get_row_index());
|
|
164
|
+
it->second.erase(*entry);
|
|
165
|
+
} else {
|
|
166
|
+
rows_->operator[](entry->get_row_index()).erase(*entry);
|
|
167
|
+
}
|
|
168
|
+
}
|
|
169
|
+
}
|
|
170
|
+
|
|
171
|
+
template <class Master_matrix>
|
|
172
|
+
inline void Row_access<Master_matrix>::update_entry(const Matrix_entry& entry)
|
|
173
|
+
{
|
|
174
|
+
if constexpr (!Master_matrix::Option_list::has_intrusive_rows) {
|
|
175
|
+
if (rows_ == nullptr) return;
|
|
176
|
+
auto& row = rows_->at(entry.get_row_index());
|
|
177
|
+
auto it = row.find(entry);
|
|
178
|
+
it = row.erase(it);
|
|
179
|
+
row.insert(it, entry);
|
|
180
|
+
}
|
|
181
|
+
}
|
|
182
|
+
|
|
183
|
+
template <class Master_matrix>
|
|
184
|
+
inline typename Row_access<Master_matrix>::Index Row_access<Master_matrix>::get_column_index() const
|
|
185
|
+
{
|
|
186
|
+
return columnIndex_;
|
|
187
|
+
}
|
|
188
|
+
|
|
189
|
+
} // namespace persistence_matrix
|
|
190
|
+
} // namespace Gudhi
|
|
191
|
+
|
|
192
|
+
#endif // PM_ROW_ACCESS_H
|