sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.20__cp39-cp39-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/hierarchical_clustering.py +108 -6
  6. sequenzo/define_sequence_data.py +10 -1
  7. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  8. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  9. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  11. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  12. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  14. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  16. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  18. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  19. sequenzo/multidomain/cat.py +0 -53
  20. sequenzo/multidomain/dat.py +11 -3
  21. sequenzo/multidomain/idcd.py +0 -3
  22. sequenzo/multidomain/linked_polyad.py +0 -1
  23. sequenzo/openmp_setup.py +233 -0
  24. sequenzo/visualization/plot_transition_matrix.py +21 -22
  25. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  26. sequenzo-0.1.20.dist-info/RECORD +215 -0
  27. sequenzo/dissimilarity_measures/setup.py +0 -35
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  171. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  172. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  173. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  174. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  175. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  176. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  177. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  178. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  179. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  180. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  181. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  182. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  183. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  184. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  185. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  186. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  187. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  188. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  189. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  190. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  191. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  192. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  193. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  194. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  195. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  196. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  197. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  198. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  199. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  200. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  201. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  202. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  203. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  204. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  205. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  206. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  207. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  208. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  209. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
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  359. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,575 +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) 2014 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_TENSOR_CONTRACTION_MAPPER_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_CONTRACTION_MAPPER_H
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-
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- namespace Eigen {
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-
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- namespace internal {
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-
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- enum {
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- Rhs = 0,
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- Lhs = 1
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- };
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-
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- /*
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- * Implementation of the Eigen blas_data_mapper class for tensors.
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- */
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- /// The make pointer class is used by sycl in order to build the mapper class on the device. For other platform the default make pointer is used which
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- /// is scalar * for CoeffLoader.
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- template <typename Tensor, bool HasRawAccess, template <class> class MakePointer_ = MakePointer>
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- struct CoeffLoader;
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-
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- template <typename Scalar, typename Index, int side, typename Tensor,
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- typename nocontract_t, typename contract_t, int packet_size,
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- bool inner_dim_contiguous, bool inner_dim_reordered, int Alignment,
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- template <class> class MakePointer_ = MakePointer>
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- class BaseTensorContractionMapper;
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-
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- template <typename Tensor, bool HasRawAccess, template <class> class MakePointer_>
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- struct CoeffLoader {
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- enum {
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- DirectOffsets = false
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- };
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE CoeffLoader(const Tensor& tensor) : m_tensor(tensor) { }
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void offsetBuffer(typename Tensor::Index) {
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- eigen_assert(false && "unsupported");
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE const typename MakePointer_<const typename Tensor::Scalar>::Type
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- data() const {
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- eigen_assert(false && "unsupported");
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- return NULL;
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE typename Tensor::Scalar coeff(typename Tensor::Index index) const { return m_tensor.coeff(index); }
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-
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- template<int LoadMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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- typename Tensor::PacketReturnType packet(typename Tensor::Index index) const
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- {
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- return m_tensor.template packet<LoadMode>(index);
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- }
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-
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- #ifdef EIGEN_USE_SYCL
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- // The placeholder accessors require to be bound to a command group handler for SYCL
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
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- m_tensor.bind(cgh);
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- }
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- #endif
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-
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- private:
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- const Tensor m_tensor;
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- };
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-
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- template <typename Tensor, template <class> class MakePointer_>
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- struct CoeffLoader<Tensor, true, MakePointer_> {
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- enum {
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- DirectOffsets = true
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- };
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE CoeffLoader(const Tensor& tensor) : m_data(tensor.data()) {}
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void offsetBuffer(typename Tensor::Index offset) {
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- m_data += offset;
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE const typename MakePointer_<const typename Tensor::Scalar>::Type
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- data() const {
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- return m_data;
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE typename Tensor::Scalar coeff(typename Tensor::Index index) const { return loadConstant(m_data+index); }
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-
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- template<int LoadMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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- typename Tensor::PacketReturnType packet(typename Tensor::Index index) const
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- {
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- return internal::ploadt_ro<typename Tensor::PacketReturnType, LoadMode>(m_data + index);
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- }
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-
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- #ifdef EIGEN_USE_SYCL
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- // The placeholder accessors require to be bound to a command group handler for SYCL
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
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- m_data.bind(cgh);
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- }
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- #endif
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- private:
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- typedef typename Tensor::Scalar Scalar;
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-
107
- typename MakePointer_<const Scalar>::Type m_data;
108
- };
109
-
110
- template<typename Scalar, typename Index, int side,
111
- typename Tensor,
112
- typename nocontract_t, typename contract_t,
113
- int packet_size, bool inner_dim_contiguous, int Alignment, template <class> class MakePointer_ = MakePointer>
114
- class SimpleTensorContractionMapper {
115
- public:
116
- EIGEN_DEVICE_FUNC
117
- SimpleTensorContractionMapper(const Tensor& tensor,
118
- const nocontract_t& nocontract_strides,
119
- const nocontract_t& ij_strides,
120
- const contract_t& contract_strides,
121
- const contract_t& k_strides) :
122
- m_tensor(tensor),
123
- m_nocontract_strides(nocontract_strides),
124
- m_ij_strides(ij_strides),
125
- m_contract_strides(contract_strides),
126
- m_k_strides(k_strides) { }
127
-
128
- enum {
129
- DirectOffsets = CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_>::DirectOffsets
130
- };
131
-
132
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void offsetBuffer(typename Tensor::Index offset) {
133
- m_tensor.offsetBuffer(offset);
134
- }
135
-
136
- EIGEN_DEVICE_FUNC
137
- EIGEN_STRONG_INLINE void prefetch(Index /*i*/) { }
138
-
139
- EIGEN_DEVICE_FUNC
140
- EIGEN_STRONG_INLINE Scalar operator()(Index row) const {
141
- // column major assumption
142
- return operator()(row, 0);
143
- }
144
-
145
- EIGEN_DEVICE_FUNC
146
- EIGEN_STRONG_INLINE Scalar operator()(Index row, Index col) const {
147
- return m_tensor.coeff(computeIndex(row, col));
148
- }
149
-
150
- EIGEN_DEVICE_FUNC
151
- EIGEN_STRONG_INLINE Index computeIndex(Index row, Index col) const {
152
- const bool left = (side == Lhs);
153
- EIGEN_UNUSED_VARIABLE(left); // annoying bug in g++8.1: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85963
154
- Index nocontract_val = left ? row : col;
155
- Index linidx = 0;
156
- EIGEN_UNROLL_LOOP
157
- for (int i = static_cast<int>(array_size<nocontract_t>::value) - 1; i > 0; i--) {
158
- const Index idx = nocontract_val / m_ij_strides[i];
159
- linidx += idx * m_nocontract_strides[i];
160
- nocontract_val -= idx * m_ij_strides[i];
161
- }
162
- if (array_size<typename Tensor::Dimensions>::value > array_size<contract_t>::value) {
163
- if (side == Lhs && inner_dim_contiguous) {
164
- eigen_assert(m_nocontract_strides[0] == 1);
165
- linidx += nocontract_val;
166
- } else {
167
- linidx += nocontract_val * m_nocontract_strides[0];
168
- }
169
- }
170
-
171
- Index contract_val = left ? col : row;
172
- if(array_size<contract_t>::value > 0) {
173
- EIGEN_UNROLL_LOOP
174
- for (int i = static_cast<int>(array_size<contract_t>::value) - 1; i > 0; i--) {
175
- const Index idx = contract_val / m_k_strides[i];
176
- linidx += idx * m_contract_strides[i];
177
- contract_val -= idx * m_k_strides[i];
178
- }
179
-
180
- if (side == Rhs && inner_dim_contiguous) {
181
- eigen_assert(m_contract_strides[0] == 1);
182
- linidx += contract_val;
183
- } else {
184
- linidx += contract_val * m_contract_strides[0];
185
- }
186
- }
187
-
188
- return linidx;
189
- }
190
-
191
- EIGEN_DEVICE_FUNC
192
- EIGEN_STRONG_INLINE IndexPair<Index> computeIndexPair(Index row, Index col, const Index distance) const {
193
- const bool left = (side == Lhs);
194
- EIGEN_UNUSED_VARIABLE(left); // annoying bug in g++8.1: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85963
195
- Index nocontract_val[2] = {left ? row : col, left ? row + distance : col};
196
- Index linidx[2] = {0, 0};
197
- if (array_size<typename Tensor::Dimensions>::value > array_size<contract_t>::value) {
198
- EIGEN_UNROLL_LOOP
199
- for (int i = static_cast<int>(array_size<nocontract_t>::value) - 1; i > 0; i--) {
200
- const Index idx0 = nocontract_val[0] / m_ij_strides[i];
201
- const Index idx1 = nocontract_val[1] / m_ij_strides[i];
202
- linidx[0] += idx0 * m_nocontract_strides[i];
203
- linidx[1] += idx1 * m_nocontract_strides[i];
204
- nocontract_val[0] -= idx0 * m_ij_strides[i];
205
- nocontract_val[1] -= idx1 * m_ij_strides[i];
206
- }
207
- if (side == Lhs && inner_dim_contiguous) {
208
- eigen_assert(m_nocontract_strides[0] == 1);
209
- linidx[0] += nocontract_val[0];
210
- linidx[1] += nocontract_val[1];
211
- } else {
212
- linidx[0] += nocontract_val[0] * m_nocontract_strides[0];
213
- linidx[1] += nocontract_val[1] * m_nocontract_strides[0];
214
- }
215
- }
216
-
217
- Index contract_val[2] = {left ? col : row, left ? col : row + distance};
218
- if (array_size<contract_t>::value> 0) {
219
- EIGEN_UNROLL_LOOP
220
- for (int i = static_cast<int>(array_size<contract_t>::value) - 1; i > 0; i--) {
221
- const Index idx0 = contract_val[0] / m_k_strides[i];
222
- const Index idx1 = contract_val[1] / m_k_strides[i];
223
- linidx[0] += idx0 * m_contract_strides[i];
224
- linidx[1] += idx1 * m_contract_strides[i];
225
- contract_val[0] -= idx0 * m_k_strides[i];
226
- contract_val[1] -= idx1 * m_k_strides[i];
227
- }
228
-
229
- if (side == Rhs && inner_dim_contiguous) {
230
- eigen_assert(m_contract_strides[0] == 1);
231
- linidx[0] += contract_val[0];
232
- linidx[1] += contract_val[1];
233
- } else {
234
- linidx[0] += contract_val[0] * m_contract_strides[0];
235
- linidx[1] += contract_val[1] * m_contract_strides[0];
236
- }
237
- }
238
- return IndexPair<Index>(linidx[0], linidx[1]);
239
- }
240
-
241
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Index firstAligned(Index size) const {
242
- // Only claim alignment when we can compute the actual stride (ie when we're
243
- // dealing with the lhs with inner_dim_contiguous. This is because the
244
- // matrix-vector product relies on the stride when dealing with aligned inputs.
245
- return (Alignment == Aligned) && (side == Lhs) && inner_dim_contiguous ? 0 : size;
246
- }
247
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Index stride() const {
248
- return ((side == Lhs) && inner_dim_contiguous && array_size<contract_t>::value > 0) ? m_contract_strides[0] : 1;
249
- }
250
-
251
- #ifdef EIGEN_USE_SYCL
252
- // The placeholder accessors require to be bound to a command group handler for SYCL
253
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
254
- m_tensor.bind(cgh);
255
- }
256
- #endif
257
-
258
- const CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_>& tensor() const {
259
- return m_tensor;
260
- }
261
-
262
- const nocontract_t& nocontract_strides() const {
263
- return m_nocontract_strides;
264
- }
265
- const nocontract_t& ij_strides() const { return m_ij_strides; }
266
- const contract_t& contract_strides() const { return m_contract_strides; }
267
- const contract_t& k_strides() const { return m_k_strides; }
268
-
269
- protected:
270
- CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_> m_tensor;
271
- const nocontract_t m_nocontract_strides;
272
- const nocontract_t m_ij_strides;
273
- const contract_t m_contract_strides;
274
- const contract_t m_k_strides;
275
- };
276
-
277
- template<typename Scalar, typename Index, int side,
278
- typename Tensor,
279
- typename nocontract_t, typename contract_t,
280
- int packet_size, bool inner_dim_contiguous,
281
- bool inner_dim_reordered, int Alignment, template <class> class MakePointer_>
282
- class BaseTensorContractionMapper : public SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, Alignment, MakePointer_>
283
- {
284
- public:
285
- typedef SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, Alignment, MakePointer_> ParentMapper;
286
-
287
- EIGEN_DEVICE_FUNC
288
- BaseTensorContractionMapper(const Tensor& tensor,
289
- const nocontract_t& nocontract_strides,
290
- const nocontract_t& ij_strides,
291
- const contract_t& contract_strides,
292
- const contract_t& k_strides) :
293
- ParentMapper(tensor, nocontract_strides, ij_strides, contract_strides, k_strides) { }
294
-
295
- template <typename PacketT,int AlignmentType>
296
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
297
- typename internal::enable_if<internal::unpacket_traits<PacketT>::size==packet_size,PacketT>::type
298
- load(Index i, Index j) const
299
- {
300
- // whole method makes column major assumption
301
-
302
- // don't need to add offsets for now (because operator handles that)
303
- // current code assumes packet size must be a multiple of 2
304
- EIGEN_STATIC_ASSERT(packet_size % 2 == 0, YOU_MADE_A_PROGRAMMING_MISTAKE);
305
-
306
- if (Tensor::PacketAccess && inner_dim_contiguous && !inner_dim_reordered) {
307
- const Index index = this->computeIndex(i, j);
308
- eigen_assert(this->computeIndex(i+packet_size-1, j) == index + packet_size-1);
309
- return this->m_tensor.template packet<AlignmentType>(index);
310
- }
311
-
312
- const IndexPair<Index> indexPair = this->computeIndexPair(i, j, packet_size - 1);
313
- const Index first = indexPair.first;
314
- const Index lastIdx = indexPair.second;
315
-
316
- // We can always do optimized packet reads from left hand side right now, because
317
- // the vertical matrix dimension on the left hand side is never contracting.
318
- // On the right hand side we need to check if the contracting dimensions may have
319
- // been shuffled first.
320
- if (Tensor::PacketAccess &&
321
- (side == Lhs || internal::array_size<contract_t>::value <= 1 || !inner_dim_reordered) &&
322
- (lastIdx - first) == (packet_size - 1)) {
323
-
324
- return this->m_tensor.template packet<AlignmentType>(first);
325
- }
326
-
327
- EIGEN_ALIGN_MAX Scalar data[packet_size];
328
-
329
- data[0] = this->m_tensor.coeff(first);
330
- EIGEN_UNROLL_LOOP
331
- for (Index k = 1; k < packet_size - 1; k += 2) {
332
- const IndexPair<Index> internal_pair = this->computeIndexPair(i + k, j, 1);
333
- data[k] = this->m_tensor.coeff(internal_pair.first);
334
- data[k + 1] = this->m_tensor.coeff(internal_pair.second);
335
- }
336
- data[packet_size - 1] = this->m_tensor.coeff(lastIdx);
337
-
338
- return pload<PacketT>(data);
339
- }
340
-
341
- template <typename PacketT,int AlignmentType>
342
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
343
- typename internal::enable_if<internal::unpacket_traits<PacketT>::size!=packet_size,PacketT>::type
344
- load(Index i, Index j) const
345
- {
346
- const Index requested_packet_size = internal::unpacket_traits<PacketT>::size;
347
- EIGEN_ALIGN_MAX Scalar data[requested_packet_size];
348
-
349
- const IndexPair<Index> indexPair = this->computeIndexPair(i, j, requested_packet_size - 1);
350
- const Index first = indexPair.first;
351
- const Index lastIdx = indexPair.second;
352
-
353
- data[0] = this->m_tensor.coeff(first);
354
- for (Index k = 1; k < requested_packet_size - 1; k += 2) {
355
- const IndexPair<Index> internal_pair = this->computeIndexPair(i + k, j, 1);
356
- data[k] = this->m_tensor.coeff(internal_pair.first);
357
- data[k + 1] = this->m_tensor.coeff(internal_pair.second);
358
- }
359
- data[requested_packet_size - 1] = this->m_tensor.coeff(lastIdx);
360
-
361
- return pload<PacketT>(data);
362
- }
363
-
364
- template <typename PacketT,int AlignmentType>
365
- EIGEN_DEVICE_FUNC
366
- EIGEN_STRONG_INLINE PacketT loadPacket(Index i, Index j) const {
367
- return this->load<PacketT,AlignmentType>(i,j);
368
- }
369
- };
370
-
371
-
372
- template<typename Scalar, typename Index, int side,
373
- typename Tensor,
374
- typename nocontract_t, typename contract_t,
375
- bool inner_dim_contiguous,
376
- bool inner_dim_reordered, int Alignment, template <class> class MakePointer_>
377
- class BaseTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, 1, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_>
378
- : public SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, 1, inner_dim_contiguous, Alignment, MakePointer_>
379
- {
380
- public:
381
- typedef SimpleTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, 1, inner_dim_contiguous, Alignment, MakePointer_> ParentMapper;
382
-
383
- EIGEN_DEVICE_FUNC
384
- BaseTensorContractionMapper(const Tensor& tensor,
385
- const nocontract_t& nocontract_strides,
386
- const nocontract_t& ij_strides,
387
- const contract_t& contract_strides,
388
- const contract_t& k_strides) :
389
- ParentMapper(tensor, nocontract_strides, ij_strides, contract_strides, k_strides) { }
390
-
391
- template <typename PacketT,int> EIGEN_DEVICE_FUNC
392
- EIGEN_STRONG_INLINE PacketT loadPacket(Index i, Index j) const {
393
- EIGEN_ALIGN_MAX Scalar data[1];
394
- data[0] = this->m_tensor.coeff(this->computeIndex(i, j));
395
- return pload<PacketT>(data);
396
- }
397
- template <typename PacketT,int> EIGEN_DEVICE_FUNC
398
- EIGEN_STRONG_INLINE PacketT load(Index i, Index j) const {
399
- EIGEN_ALIGN_MAX Scalar data[1];
400
- data[0] = this->m_tensor.coeff(this->computeIndex(i, j));
401
- return pload<PacketT>(data);
402
- }
403
- };
404
-
405
-
406
- template<typename Scalar, typename Index, int side,
407
- typename Tensor,
408
- typename nocontract_t, typename contract_t,
409
- int packet_size,
410
- bool inner_dim_contiguous, bool inner_dim_reordered, int Alignment, template <class> class MakePointer_=MakePointer>
411
- class TensorContractionSubMapper {
412
- public:
413
-
414
- typedef BaseTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> ParentMapper;
415
- typedef TensorContractionSubMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> Self;
416
- typedef Self LinearMapper;
417
-
418
- enum {
419
- // We can use direct offsets iff the parent mapper supports then and we can compute the strides.
420
- // TODO: we should also enable direct offsets for the Rhs case.
421
- UseDirectOffsets = ParentMapper::DirectOffsets && (side == Lhs) && inner_dim_contiguous && (array_size<contract_t>::value > 0)
422
- };
423
-
424
- EIGEN_DEVICE_FUNC TensorContractionSubMapper(const ParentMapper& base_mapper, Index vert_offset, Index horiz_offset)
425
- : m_base_mapper(base_mapper), m_vert_offset(vert_offset), m_horiz_offset(horiz_offset) {
426
- // Bake the offsets into the buffer used by the base mapper whenever possible. This avoids the need to recompute
427
- // this offset every time we attempt to access a coefficient.
428
- if (UseDirectOffsets) {
429
- Index stride = m_base_mapper.stride();
430
- m_base_mapper.offsetBuffer(vert_offset + horiz_offset * stride);
431
- }
432
- }
433
-
434
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Scalar operator()(Index i) const {
435
- if (UseDirectOffsets) {
436
- return m_base_mapper(i, 0);
437
- }
438
- return m_base_mapper(i + m_vert_offset, m_horiz_offset);
439
- }
440
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE Scalar operator()(Index i, Index j) const {
441
- if (UseDirectOffsets) {
442
- return m_base_mapper(i, j);
443
- }
444
- return m_base_mapper(i + m_vert_offset, j + m_horiz_offset);
445
- }
446
-
447
- template <typename PacketT>
448
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT loadPacket(Index i) const {
449
- if (UseDirectOffsets) {
450
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i, 0);
451
- }
452
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i + m_vert_offset, m_horiz_offset);
453
- }
454
-
455
- template <typename PacketT>
456
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT loadPacket(Index i, Index j) const {
457
- if (UseDirectOffsets) {
458
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i, j);
459
- }
460
- return m_base_mapper.template loadPacket<PacketT,Alignment>(i + m_vert_offset, j + m_horiz_offset);
461
- }
462
-
463
- template <typename PacketT, int AlignmentType>
464
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT loadPacket(Index i, Index j) const {
465
- if (UseDirectOffsets) {
466
- return m_base_mapper.template load<PacketT,AlignmentType>(i, j);
467
- }
468
- return m_base_mapper.template loadPacket<PacketT,AlignmentType>(i + m_vert_offset, j + m_horiz_offset);
469
- }
470
-
471
- template <typename PacketT>
472
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE void storePacket(Index i, const PacketT& p) const {
473
- if (UseDirectOffsets) {
474
- m_base_mapper.storePacket(i, 0, p);
475
- }
476
- m_base_mapper.storePacket(i + m_vert_offset, m_horiz_offset, p);
477
- }
478
-
479
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE LinearMapper getLinearMapper(Index i, Index j) const {
480
- if (UseDirectOffsets) {
481
- return LinearMapper(m_base_mapper, i, j);
482
- }
483
- return LinearMapper(m_base_mapper, i + m_vert_offset, j + m_horiz_offset);
484
- }
485
-
486
- template <typename PacketT, int AlignmentType>
487
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketT load(Index i) const {
488
- EIGEN_STATIC_ASSERT((internal::is_same<PacketT, PacketT>::value), YOU_MADE_A_PROGRAMMING_MISTAKE);
489
- const int ActualAlignment = (AlignmentType == Aligned) && (Alignment == Aligned) ? Aligned : Unaligned;
490
- if (UseDirectOffsets) {
491
- return m_base_mapper.template loadPacket<PacketT,ActualAlignment>(i, 0);
492
- }
493
- return m_base_mapper.template loadPacket<PacketT,ActualAlignment>(i + m_vert_offset, m_horiz_offset);
494
- }
495
-
496
- template <typename PacketT>
497
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool aligned(Index) const {
498
- return false;
499
- }
500
-
501
- #ifdef EIGEN_USE_SYCL
502
- // The placeholder accessors require to be bound to a command group handler for SYCL
503
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
504
- m_base_mapper.bind(cgh);
505
- }
506
- #endif
507
-
508
- const ParentMapper& base_mapper() const { return m_base_mapper; }
509
- Index vert_offset() const { return m_vert_offset; }
510
- Index horiz_offset() const { return m_horiz_offset; }
511
-
512
- private:
513
- ParentMapper m_base_mapper;
514
- const Index m_vert_offset;
515
- const Index m_horiz_offset;
516
- };
517
-
518
-
519
- template<typename Scalar_, typename Index, int side,
520
- typename Tensor,
521
- typename nocontract_t, typename contract_t,
522
- int packet_size,
523
- bool inner_dim_contiguous, bool inner_dim_reordered, int Alignment, template <class> class MakePointer_=MakePointer>
524
- class TensorContractionInputMapper
525
- : public BaseTensorContractionMapper<Scalar_, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> {
526
-
527
- public:
528
- typedef Scalar_ Scalar;
529
- typedef BaseTensorContractionMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> Base;
530
- typedef TensorContractionSubMapper<Scalar, Index, side, Tensor, nocontract_t, contract_t, packet_size, inner_dim_contiguous, inner_dim_reordered, Alignment, MakePointer_> SubMapper;
531
- typedef SubMapper VectorMapper;
532
-
533
- EIGEN_DEVICE_FUNC TensorContractionInputMapper(const Tensor& tensor,
534
- const nocontract_t& nocontract_strides,
535
- const nocontract_t& ij_strides,
536
- const contract_t& contract_strides,
537
- const contract_t& k_strides)
538
- : Base(tensor, nocontract_strides, ij_strides, contract_strides, k_strides) { }
539
-
540
- EIGEN_DEVICE_FUNC
541
- EIGEN_STRONG_INLINE SubMapper getSubMapper(Index i, Index j) const {
542
- return SubMapper(*this, i, j);
543
- }
544
-
545
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE VectorMapper getVectorMapper(Index i, Index j) const {
546
- return VectorMapper(*this, i, j);
547
- }
548
-
549
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE const CoeffLoader<Tensor, Tensor::RawAccess, MakePointer_>& get_tensor() const {
550
- return Base::m_tensor;
551
- }
552
- };
553
-
554
-
555
- template <typename T> struct TensorContractionInputMapperTrait;
556
-
557
- template<typename Scalar_, typename Index_, int side_,
558
- typename Tensor_,
559
- typename nocontract_t_, typename contract_t_,
560
- int packet_size_,
561
- bool inner_dim_contiguous_, bool inner_dim_reordered_, int Alignment_, template <class> class MakePointer_>
562
- struct TensorContractionInputMapperTrait<TensorContractionInputMapper<Scalar_, Index_, side_, Tensor_,
563
- nocontract_t_, contract_t_, packet_size_, inner_dim_contiguous_,
564
- inner_dim_reordered_, Alignment_, MakePointer_> > {
565
-
566
- typedef Tensor_ XprType;
567
- static const bool inner_dim_contiguous = inner_dim_contiguous_;
568
- static const bool inner_dim_reordered = inner_dim_reordered_;
569
- };
570
-
571
-
572
- } // end namespace internal
573
- } // end namespace Eigen
574
-
575
- #endif // EIGEN_CXX11_TENSOR_TENSOR_CONTRACTION_MAPPER_H