sequenzo 0.1.17__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +155 -155
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-312-darwin.so +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-312-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-312-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-312-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-312-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-312-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-312-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
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  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,471 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_SHUFFLING_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_SHUFFLING_H
12
-
13
- namespace Eigen {
14
-
15
- /** \class TensorShuffling
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor shuffling class.
19
- *
20
- *
21
- */
22
- namespace internal {
23
- template<typename Shuffle, typename XprType>
24
- struct traits<TensorShufflingOp<Shuffle, XprType> > : public traits<XprType>
25
- {
26
- typedef typename XprType::Scalar Scalar;
27
- typedef traits<XprType> XprTraits;
28
- typedef typename XprTraits::StorageKind StorageKind;
29
- typedef typename XprTraits::Index Index;
30
- typedef typename XprType::Nested Nested;
31
- typedef typename remove_reference<Nested>::type _Nested;
32
- static const int NumDimensions = XprTraits::NumDimensions;
33
- static const int Layout = XprTraits::Layout;
34
- typedef typename XprTraits::PointerType PointerType;
35
- };
36
-
37
- template<typename Shuffle, typename XprType>
38
- struct eval<TensorShufflingOp<Shuffle, XprType>, Eigen::Dense>
39
- {
40
- typedef const TensorShufflingOp<Shuffle, XprType>& type;
41
- };
42
-
43
- template<typename Shuffle, typename XprType>
44
- struct nested<TensorShufflingOp<Shuffle, XprType>, 1, typename eval<TensorShufflingOp<Shuffle, XprType> >::type>
45
- {
46
- typedef TensorShufflingOp<Shuffle, XprType> type;
47
- };
48
-
49
- } // end namespace internal
50
-
51
-
52
-
53
- template<typename Shuffle, typename XprType>
54
- class TensorShufflingOp : public TensorBase<TensorShufflingOp<Shuffle, XprType> >
55
- {
56
- public:
57
- typedef TensorBase<TensorShufflingOp<Shuffle, XprType> > Base;
58
- typedef typename Eigen::internal::traits<TensorShufflingOp>::Scalar Scalar;
59
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
60
- typedef typename XprType::CoeffReturnType CoeffReturnType;
61
- typedef typename Eigen::internal::nested<TensorShufflingOp>::type Nested;
62
- typedef typename Eigen::internal::traits<TensorShufflingOp>::StorageKind StorageKind;
63
- typedef typename Eigen::internal::traits<TensorShufflingOp>::Index Index;
64
-
65
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorShufflingOp(const XprType& expr, const Shuffle& shfl)
66
- : m_xpr(expr), m_shuffle(shfl) {}
67
-
68
- EIGEN_DEVICE_FUNC
69
- const Shuffle& shufflePermutation() const { return m_shuffle; }
70
-
71
- EIGEN_DEVICE_FUNC
72
- const typename internal::remove_all<typename XprType::Nested>::type&
73
- expression() const { return m_xpr; }
74
-
75
- EIGEN_TENSOR_INHERIT_ASSIGNMENT_OPERATORS(TensorShufflingOp)
76
-
77
-
78
- protected:
79
- typename XprType::Nested m_xpr;
80
- const Shuffle m_shuffle;
81
- };
82
-
83
-
84
- // Eval as rvalue
85
- template<typename Shuffle, typename ArgType, typename Device>
86
- struct TensorEvaluator<const TensorShufflingOp<Shuffle, ArgType>, Device>
87
- {
88
- typedef TensorEvaluator<const TensorShufflingOp<Shuffle, ArgType>, Device> Self;
89
- typedef TensorShufflingOp<Shuffle, ArgType> XprType;
90
- typedef typename XprType::Index Index;
91
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
92
- typedef DSizes<Index, NumDims> Dimensions;
93
- typedef typename XprType::Scalar Scalar;
94
- typedef typename XprType::CoeffReturnType CoeffReturnType;
95
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
96
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
97
- typedef StorageMemory<CoeffReturnType, Device> Storage;
98
- typedef typename Storage::Type EvaluatorPointerType;
99
-
100
- enum {
101
- IsAligned = false,
102
- PacketAccess = (PacketType<CoeffReturnType, Device>::size > 1),
103
- BlockAccess = TensorEvaluator<ArgType, Device>::RawAccess,
104
- PreferBlockAccess = true,
105
- Layout = TensorEvaluator<ArgType, Device>::Layout,
106
- CoordAccess = false, // to be implemented
107
- RawAccess = false
108
- };
109
-
110
- typedef typename internal::remove_const<Scalar>::type ScalarNoConst;
111
-
112
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
113
- typedef internal::TensorBlockDescriptor<NumDims, Index> TensorBlockDesc;
114
- typedef internal::TensorBlockScratchAllocator<Device> TensorBlockScratch;
115
-
116
- typedef typename internal::TensorMaterializedBlock<ScalarNoConst, NumDims,
117
- Layout, Index>
118
- TensorBlock;
119
- //===--------------------------------------------------------------------===//
120
-
121
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
122
- : m_device(device),
123
- m_impl(op.expression(), device)
124
- {
125
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
126
- const Shuffle& shuffle = op.shufflePermutation();
127
- m_is_identity = true;
128
- for (int i = 0; i < NumDims; ++i) {
129
- m_shuffle[i] = static_cast<int>(shuffle[i]);
130
- m_dimensions[i] = input_dims[shuffle[i]];
131
- m_inverseShuffle[shuffle[i]] = i;
132
- if (m_is_identity && shuffle[i] != i) {
133
- m_is_identity = false;
134
- }
135
- }
136
-
137
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
138
- m_unshuffledInputStrides[0] = 1;
139
- m_outputStrides[0] = 1;
140
-
141
- for (int i = 1; i < NumDims; ++i) {
142
- m_unshuffledInputStrides[i] =
143
- m_unshuffledInputStrides[i - 1] * input_dims[i - 1];
144
- m_outputStrides[i] = m_outputStrides[i - 1] * m_dimensions[i - 1];
145
- m_fastOutputStrides[i] = internal::TensorIntDivisor<Index>(
146
- m_outputStrides[i] > 0 ? m_outputStrides[i] : Index(1));
147
- }
148
- } else {
149
- m_unshuffledInputStrides[NumDims - 1] = 1;
150
- m_outputStrides[NumDims - 1] = 1;
151
- for (int i = NumDims - 2; i >= 0; --i) {
152
- m_unshuffledInputStrides[i] =
153
- m_unshuffledInputStrides[i + 1] * input_dims[i + 1];
154
- m_outputStrides[i] = m_outputStrides[i + 1] * m_dimensions[i + 1];
155
- m_fastOutputStrides[i] = internal::TensorIntDivisor<Index>(
156
- m_outputStrides[i] > 0 ? m_outputStrides[i] : Index(1));
157
- }
158
- }
159
-
160
- for (int i = 0; i < NumDims; ++i) {
161
- m_inputStrides[i] = m_unshuffledInputStrides[shuffle[i]];
162
- }
163
- }
164
-
165
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
166
-
167
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType /*data*/) {
168
- m_impl.evalSubExprsIfNeeded(NULL);
169
- return true;
170
- }
171
-
172
- #ifdef EIGEN_USE_THREADS
173
- template <typename EvalSubExprsCallback>
174
- EIGEN_STRONG_INLINE void evalSubExprsIfNeededAsync(
175
- EvaluatorPointerType, EvalSubExprsCallback done) {
176
- m_impl.evalSubExprsIfNeededAsync(nullptr, [done](bool) { done(true); });
177
- }
178
- #endif // EIGEN_USE_THREADS
179
-
180
- EIGEN_STRONG_INLINE void cleanup() {
181
- m_impl.cleanup();
182
- }
183
-
184
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
185
- {
186
- if (m_is_identity) {
187
- return m_impl.coeff(index);
188
- } else {
189
- return m_impl.coeff(srcCoeff(index));
190
- }
191
- }
192
-
193
- template <int LoadMode, typename Self, bool ImplPacketAccess>
194
- struct PacketLoader {
195
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
196
- static PacketReturnType Run(const Self& self, Index index) {
197
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
198
- EIGEN_UNROLL_LOOP
199
- for (int i = 0; i < PacketSize; ++i) {
200
- values[i] = self.coeff(index + i);
201
- }
202
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
203
- return rslt;
204
- }
205
- };
206
-
207
- template<int LoadMode, typename Self>
208
- struct PacketLoader<LoadMode, Self, true> {
209
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
210
- static PacketReturnType Run(const Self& self, Index index) {
211
- if (self.m_is_identity) {
212
- return self.m_impl.template packet<LoadMode>(index);
213
- } else {
214
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
215
- EIGEN_UNROLL_LOOP
216
- for (int i = 0; i < PacketSize; ++i) {
217
- values[i] = self.coeff(index + i);
218
- }
219
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
220
- return rslt;
221
- }
222
- }
223
- };
224
-
225
- template<int LoadMode>
226
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
227
- {
228
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
229
- eigen_assert(index + PacketSize - 1 < dimensions().TotalSize());
230
- return PacketLoader<LoadMode, Self, TensorEvaluator<ArgType, Device>::PacketAccess>::Run(*this, index);
231
- }
232
-
233
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
234
- internal::TensorBlockResourceRequirements getResourceRequirements() const {
235
- static const int inner_dim =
236
- Layout == static_cast<int>(ColMajor) ? 0 : NumDims - 1;
237
-
238
- const size_t target_size = m_device.firstLevelCacheSize();
239
- const bool inner_dim_shuffled = m_shuffle[inner_dim] != inner_dim;
240
-
241
- // Shuffled inner dimensions leads to a random memory access, which is not
242
- // captured by default cost model bytes loaded/stored. We add this cost
243
- // explicitly. The number of cycles picked based on the benchmarks.
244
- // TODO(ezhulenev): This number was picked based on a very questionable
245
- // benchmarks, add benchmarks that are representative of real workloads.
246
- using BlockRequirements = internal::TensorBlockResourceRequirements;
247
- if (inner_dim_shuffled) {
248
- return BlockRequirements::uniform<Scalar>(target_size)
249
- .addCostPerCoeff({0, 0, NumDims * 28});
250
- } else {
251
- return BlockRequirements::skewed<Scalar>(target_size);
252
- }
253
- }
254
-
255
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorBlock
256
- block(TensorBlockDesc& desc, TensorBlockScratch& scratch,
257
- bool root_of_expr_ast = false) const {
258
- assert(m_impl.data() != NULL);
259
-
260
- typedef internal::TensorBlockIO<ScalarNoConst, Index, NumDims, Layout>
261
- TensorBlockIO;
262
- typedef typename TensorBlockIO::Dst TensorBlockIODst;
263
- typedef typename TensorBlockIO::Src TensorBlockIOSrc;
264
-
265
- const typename TensorBlock::Storage block_storage =
266
- TensorBlock::prepareStorage(
267
- desc, scratch, /*allow_strided_storage=*/root_of_expr_ast);
268
-
269
- typename TensorBlockIO::Dimensions input_strides(m_unshuffledInputStrides);
270
- TensorBlockIOSrc src(input_strides, m_impl.data(), srcCoeff(desc.offset()));
271
-
272
- TensorBlockIODst dst(block_storage.dimensions(), block_storage.strides(),
273
- block_storage.data());
274
-
275
- typename TensorBlockIO::DimensionsMap dst_to_src_dim_map(m_shuffle);
276
- TensorBlockIO::Copy(dst, src, dst_to_src_dim_map);
277
-
278
- return block_storage.AsTensorMaterializedBlock();
279
- }
280
-
281
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
282
- const double compute_cost = m_is_identity ? TensorOpCost::AddCost<Index>() :
283
- NumDims * (2 * TensorOpCost::AddCost<Index>() +
284
- 2 * TensorOpCost::MulCost<Index>() +
285
- TensorOpCost::DivCost<Index>());
286
- return m_impl.costPerCoeff(vectorized) +
287
- TensorOpCost(0, 0, compute_cost, m_is_identity /* vectorized */, PacketSize);
288
- }
289
-
290
- EIGEN_DEVICE_FUNC typename Storage::Type data() const { return NULL; }
291
-
292
- #ifdef EIGEN_USE_SYCL
293
- // binding placeholder accessors to a command group handler for SYCL
294
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
295
- m_impl.bind(cgh);
296
- }
297
- #endif
298
- protected:
299
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index GetBlockOutputIndex(
300
- Index input_index,
301
- const DSizes<Index, NumDims>& input_block_strides,
302
- const DSizes<Index, NumDims>& output_block_strides,
303
- const DSizes<internal::TensorIntDivisor<Index>, NumDims>& fast_input_block_strides) const {
304
- Index output_index = 0;
305
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
306
- for (int i = NumDims - 1; i > 0; --i) {
307
- const Index idx = input_index / fast_input_block_strides[i];
308
- output_index += idx * output_block_strides[m_inverseShuffle[i]];
309
- input_index -= idx * input_block_strides[i];
310
- }
311
- return output_index + input_index *
312
- output_block_strides[m_inverseShuffle[0]];
313
- } else {
314
- for (int i = 0; i < NumDims - 1; ++i) {
315
- const Index idx = input_index / fast_input_block_strides[i];
316
- output_index += idx * output_block_strides[m_inverseShuffle[i]];
317
- input_index -= idx * input_block_strides[i];
318
- }
319
- return output_index + input_index *
320
- output_block_strides[m_inverseShuffle[NumDims - 1]];
321
- }
322
- }
323
-
324
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index srcCoeff(Index index) const {
325
- Index inputIndex = 0;
326
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
327
- for (int i = NumDims - 1; i > 0; --i) {
328
- const Index idx = index / m_fastOutputStrides[i];
329
- inputIndex += idx * m_inputStrides[i];
330
- index -= idx * m_outputStrides[i];
331
- }
332
- return inputIndex + index * m_inputStrides[0];
333
- } else {
334
- for (int i = 0; i < NumDims - 1; ++i) {
335
- const Index idx = index / m_fastOutputStrides[i];
336
- inputIndex += idx * m_inputStrides[i];
337
- index -= idx * m_outputStrides[i];
338
- }
339
- return inputIndex + index * m_inputStrides[NumDims - 1];
340
- }
341
- }
342
-
343
- Dimensions m_dimensions;
344
- bool m_is_identity;
345
- array<int, NumDims> m_shuffle;
346
- array<Index, NumDims> m_inverseShuffle; // TODO(ezhulenev): Make it int type.
347
- array<Index, NumDims> m_outputStrides;
348
- array<internal::TensorIntDivisor<Index>, NumDims> m_fastOutputStrides;
349
- array<Index, NumDims> m_inputStrides;
350
- array<Index, NumDims> m_unshuffledInputStrides;
351
-
352
- const Device EIGEN_DEVICE_REF m_device;
353
- TensorEvaluator<ArgType, Device> m_impl;
354
- };
355
-
356
-
357
- // Eval as lvalue
358
- template<typename Shuffle, typename ArgType, typename Device>
359
- struct TensorEvaluator<TensorShufflingOp<Shuffle, ArgType>, Device>
360
- : public TensorEvaluator<const TensorShufflingOp<Shuffle, ArgType>, Device>
361
- {
362
- typedef TensorEvaluator<const TensorShufflingOp<Shuffle, ArgType>, Device> Base;
363
-
364
- typedef TensorShufflingOp<Shuffle, ArgType> XprType;
365
- typedef typename XprType::Index Index;
366
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
367
- typedef DSizes<Index, NumDims> Dimensions;
368
- typedef typename XprType::Scalar Scalar;
369
- typedef typename XprType::CoeffReturnType CoeffReturnType;
370
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
371
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
372
-
373
- enum {
374
- IsAligned = false,
375
- PacketAccess = (PacketType<CoeffReturnType, Device>::size > 1),
376
- BlockAccess = TensorEvaluator<ArgType, Device>::RawAccess,
377
- PreferBlockAccess = true,
378
- Layout = TensorEvaluator<ArgType, Device>::Layout,
379
- RawAccess = false
380
- };
381
-
382
- typedef typename internal::remove_const<Scalar>::type ScalarNoConst;
383
-
384
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
385
- typedef internal::TensorBlockDescriptor<NumDims, Index> TensorBlockDesc;
386
- //===--------------------------------------------------------------------===//
387
-
388
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
389
- : Base(op, device)
390
- { }
391
-
392
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType& coeffRef(Index index)
393
- {
394
- return this->m_impl.coeffRef(this->srcCoeff(index));
395
- }
396
-
397
- template <int StoreMode> EIGEN_STRONG_INLINE
398
- void writePacket(Index index, const PacketReturnType& x)
399
- {
400
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
401
-
402
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
403
- internal::pstore<CoeffReturnType, PacketReturnType>(values, x);
404
- EIGEN_UNROLL_LOOP
405
- for (int i = 0; i < PacketSize; ++i) {
406
- this->coeffRef(index+i) = values[i];
407
- }
408
- }
409
-
410
- template <typename TensorBlock>
411
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void writeBlock(
412
- const TensorBlockDesc& desc, const TensorBlock& block) {
413
- eigen_assert(this->m_impl.data() != NULL);
414
-
415
- typedef internal::TensorBlockIO<ScalarNoConst, Index, NumDims, Layout>
416
- TensorBlockIO;
417
- typedef typename TensorBlockIO::Dst TensorBlockIODst;
418
- typedef typename TensorBlockIO::Src TensorBlockIOSrc;
419
-
420
- const Scalar* block_buffer = block.data();
421
-
422
- // TODO(ezhulenev): TensorBlockIO should be able to read from any Eigen
423
- // expression with coefficient and packet access as `src`.
424
- void* mem = NULL;
425
- if (block_buffer == NULL) {
426
- mem = this->m_device.allocate(desc.size() * sizeof(Scalar));
427
- ScalarNoConst* buf = static_cast<ScalarNoConst*>(mem);
428
-
429
- typedef internal::TensorBlockAssignment<
430
- ScalarNoConst, NumDims, typename TensorBlock::XprType, Index>
431
- TensorBlockAssignment;
432
-
433
- TensorBlockAssignment::Run(
434
- TensorBlockAssignment::target(
435
- desc.dimensions(), internal::strides<Layout>(desc.dimensions()),
436
- buf),
437
- block.expr());
438
-
439
- block_buffer = buf;
440
- }
441
-
442
- // Read from block.
443
- TensorBlockIOSrc src(internal::strides<Layout>(desc.dimensions()),
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- block_buffer);
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-
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- // Write to the output buffer.
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- typename TensorBlockIO::Dimensions output_strides(
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- this->m_unshuffledInputStrides);
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- typename TensorBlockIO::Dimensions output_dimensions;
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- for (int i = 0; i < NumDims; ++i) {
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- output_dimensions[this->m_shuffle[i]] = desc.dimension(i);
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- }
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- TensorBlockIODst dst(output_dimensions, output_strides, this->m_impl.data(),
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- this->srcCoeff(desc.offset()));
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-
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- // Reorder dimensions according to the shuffle.
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- typename TensorBlockIO::DimensionsMap dst_to_src_dim_map;
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- for (int i = 0; i < NumDims; ++i) {
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- dst_to_src_dim_map[i] = static_cast<int>(this->m_inverseShuffle[i]);
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- }
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- TensorBlockIO::Copy(dst, src, dst_to_src_dim_map);
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-
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- // Deallocate temporary buffer used for the block materialization.
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- if (mem != NULL) this->m_device.deallocate(mem);
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- }
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- };
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-
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-
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- } // end namespace Eigen
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-
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- #endif // EIGEN_CXX11_TENSOR_TENSOR_SHUFFLING_H
@@ -1,161 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2013 Christian Seiler <christian@iwakd.de>
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- // Copyright (C) 2014-2015 Benoit Steiner <benoit.steiner.goog@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_CXX11_TENSOR_TENSORSTORAGE_H
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- #define EIGEN_CXX11_TENSOR_TENSORSTORAGE_H
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-
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- #ifdef EIGEN_TENSOR_STORAGE_CTOR_PLUGIN
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- #define EIGEN_INTERNAL_TENSOR_STORAGE_CTOR_PLUGIN EIGEN_TENSOR_STORAGE_CTOR_PLUGIN;
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- #else
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- #define EIGEN_INTERNAL_TENSOR_STORAGE_CTOR_PLUGIN
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- #endif
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-
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- namespace Eigen {
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-
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- /** \internal
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- *
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- * \class TensorStorage
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Stores the data of a tensor
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- *
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- * This class stores the data of fixed-size, dynamic-size or mixed tensors
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- * in a way as compact as possible.
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- *
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- * \sa Tensor
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- */
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- template<typename T, typename Dimensions, int Options> class TensorStorage;
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-
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-
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- // Pure fixed-size storage
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- template<typename T, typename FixedDimensions, int Options_>
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- class TensorStorage
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- {
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- private:
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- static const std::size_t Size = FixedDimensions::total_size;
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-
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- // Allocate an array of size at least one to prevent compiler warnings.
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- static const std::size_t MinSize = max_n_1<Size>::size;
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- EIGEN_ALIGN_MAX T m_data[MinSize];
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-
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- public:
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE TensorStorage() {
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- }
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-
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE T *data() { return m_data; }
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const T *data() const { return m_data; }
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-
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- static EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const FixedDimensions& dimensions()
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- {
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- static const FixedDimensions* singleton_dimensions = new FixedDimensions();
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- return *singleton_dimensions;
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- }
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-
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE DenseIndex size() const { return Size; }
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- };
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-
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- // pure dynamic
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- template<typename T, typename IndexType, int NumIndices_, int Options_>
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- class TensorStorage<T, DSizes<IndexType, NumIndices_>, Options_>
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- {
73
- public:
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- typedef IndexType Index;
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- typedef DSizes<IndexType, NumIndices_> Dimensions;
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- typedef TensorStorage<T, DSizes<IndexType, NumIndices_>, Options_> Self;
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-
78
- EIGEN_DEVICE_FUNC TensorStorage() : m_data(0), m_dimensions() {
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- if (NumIndices_ == 0) {
80
- m_data = internal::conditional_aligned_new_auto<T,(Options_&DontAlign)==0>(1);
81
- }
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- }
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- EIGEN_DEVICE_FUNC TensorStorage(internal::constructor_without_unaligned_array_assert)
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- : m_data(0), m_dimensions(internal::template repeat<NumIndices_, Index>(0)) {}
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- EIGEN_DEVICE_FUNC TensorStorage(Index size, const array<Index, NumIndices_>& dimensions)
86
- : m_data(internal::conditional_aligned_new_auto<T,(Options_&DontAlign)==0>(size)), m_dimensions(dimensions)
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- { EIGEN_INTERNAL_TENSOR_STORAGE_CTOR_PLUGIN }
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-
89
- #if EIGEN_HAS_VARIADIC_TEMPLATES
90
- template <typename... DenseIndex>
91
- EIGEN_DEVICE_FUNC TensorStorage(DenseIndex... indices) : m_dimensions(indices...) {
92
- m_data = internal::conditional_aligned_new_auto<T,(Options_&DontAlign)==0>(internal::array_prod(m_dimensions));
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- }
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- #endif
95
-
96
- EIGEN_DEVICE_FUNC TensorStorage(const Self& other)
97
- : m_data(internal::conditional_aligned_new_auto<T,(Options_&DontAlign)==0>(internal::array_prod(other.m_dimensions)))
98
- , m_dimensions(other.m_dimensions)
99
- {
100
- internal::smart_copy(other.m_data, other.m_data+internal::array_prod(other.m_dimensions), m_data);
101
- }
102
- EIGEN_DEVICE_FUNC Self& operator=(const Self& other)
103
- {
104
- if (this != &other) {
105
- Self tmp(other);
106
- this->swap(tmp);
107
- }
108
- return *this;
109
- }
110
-
111
- #if EIGEN_HAS_RVALUE_REFERENCES
112
- EIGEN_DEVICE_FUNC TensorStorage(Self&& other) : TensorStorage()
113
- {
114
- *this = std::move(other);
115
- }
116
-
117
- EIGEN_DEVICE_FUNC Self& operator=(Self&& other)
118
- {
119
- numext::swap(m_data, other.m_data);
120
- numext::swap(m_dimensions, other.m_dimensions);
121
- return *this;
122
- }
123
- #endif
124
-
125
- EIGEN_DEVICE_FUNC ~TensorStorage() { internal::conditional_aligned_delete_auto<T,(Options_&DontAlign)==0>(m_data, internal::array_prod(m_dimensions)); }
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- EIGEN_DEVICE_FUNC void swap(Self& other)
127
- { numext::swap(m_data,other.m_data); numext::swap(m_dimensions,other.m_dimensions); }
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-
129
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const {return m_dimensions;}
130
-
131
- EIGEN_DEVICE_FUNC void resize(Index size, const array<Index, NumIndices_>& nbDimensions)
132
- {
133
- const Index currentSz = internal::array_prod(m_dimensions);
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- if(size != currentSz)
135
- {
136
- internal::conditional_aligned_delete_auto<T,(Options_&DontAlign)==0>(m_data, currentSz);
137
- if (size)
138
- m_data = internal::conditional_aligned_new_auto<T,(Options_&DontAlign)==0>(size);
139
- else if (NumIndices_ == 0) {
140
- m_data = internal::conditional_aligned_new_auto<T,(Options_&DontAlign)==0>(1);
141
- }
142
- else
143
- m_data = 0;
144
- EIGEN_INTERNAL_DENSE_STORAGE_CTOR_PLUGIN({})
145
- }
146
- m_dimensions = nbDimensions;
147
- }
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-
149
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T *data() { return m_data; }
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const T *data() const { return m_data; }
151
-
152
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index size() const { return m_dimensions.TotalSize(); }
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-
154
- private:
155
- T *m_data;
156
- Dimensions m_dimensions;
157
- };
158
-
159
- } // end namespace Eigen
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-
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- #endif // EIGEN_CXX11_TENSOR_TENSORSTORAGE_H