sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.20__cp310-cp310-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 +155 -155
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-310-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 +155 -155
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-310-darwin.so +0 -0
  11. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  12. sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  14. sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  16. sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  18. sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-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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@@ -1,465 +0,0 @@
1
- // 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 Navdeep Jaitly <ndjaitly@google.com>
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- // 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_REVERSE_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_REVERSE_H
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- namespace Eigen {
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-
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- /** \class TensorReverse
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor reverse elements class.
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- *
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- */
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- namespace internal {
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- template<typename ReverseDimensions, typename XprType>
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- struct traits<TensorReverseOp<ReverseDimensions,
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- XprType> > : public traits<XprType>
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- {
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- typedef typename XprType::Scalar Scalar;
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- typedef traits<XprType> XprTraits;
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- typedef typename XprTraits::StorageKind StorageKind;
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- typedef typename XprTraits::Index Index;
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- typedef typename XprType::Nested Nested;
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- typedef typename remove_reference<Nested>::type _Nested;
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- static const int NumDimensions = XprTraits::NumDimensions;
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- static const int Layout = XprTraits::Layout;
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- typedef typename XprTraits::PointerType PointerType;
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- };
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-
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- template<typename ReverseDimensions, typename XprType>
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- struct eval<TensorReverseOp<ReverseDimensions, XprType>, Eigen::Dense>
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- {
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- typedef const TensorReverseOp<ReverseDimensions, XprType>& type;
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- };
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-
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- template<typename ReverseDimensions, typename XprType>
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- struct nested<TensorReverseOp<ReverseDimensions, XprType>, 1,
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- typename eval<TensorReverseOp<ReverseDimensions, XprType> >::type>
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- {
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- typedef TensorReverseOp<ReverseDimensions, XprType> type;
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- };
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-
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- } // end namespace internal
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-
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- template<typename ReverseDimensions, typename XprType>
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- class TensorReverseOp : public TensorBase<TensorReverseOp<ReverseDimensions,
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- XprType>, WriteAccessors>
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- {
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- public:
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- typedef TensorBase<TensorReverseOp<ReverseDimensions, XprType>, WriteAccessors>Base;
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- typedef typename Eigen::internal::traits<TensorReverseOp>::Scalar Scalar;
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- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
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- typedef typename XprType::CoeffReturnType CoeffReturnType;
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- typedef typename Eigen::internal::nested<TensorReverseOp>::type Nested;
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- typedef typename Eigen::internal::traits<TensorReverseOp>::StorageKind
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- StorageKind;
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- typedef typename Eigen::internal::traits<TensorReverseOp>::Index Index;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorReverseOp(
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- const XprType& expr, const ReverseDimensions& reverse_dims)
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- : m_xpr(expr), m_reverse_dims(reverse_dims) { }
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-
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- EIGEN_DEVICE_FUNC
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- const ReverseDimensions& reverse() const { return m_reverse_dims; }
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-
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- EIGEN_DEVICE_FUNC
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- const typename internal::remove_all<typename XprType::Nested>::type&
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- expression() const { return m_xpr; }
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-
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- EIGEN_TENSOR_INHERIT_ASSIGNMENT_OPERATORS(TensorReverseOp)
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-
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-
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- protected:
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- typename XprType::Nested m_xpr;
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- const ReverseDimensions m_reverse_dims;
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- };
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-
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- // Eval as rvalue
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- template<typename ReverseDimensions, typename ArgType, typename Device>
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- struct TensorEvaluator<const TensorReverseOp<ReverseDimensions, ArgType>, Device>
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- {
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- typedef TensorReverseOp<ReverseDimensions, ArgType> XprType;
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- typedef typename XprType::Index Index;
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- static const int NumDims = internal::array_size<ReverseDimensions>::value;
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- typedef DSizes<Index, NumDims> Dimensions;
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- typedef typename XprType::Scalar Scalar;
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- typedef typename XprType::CoeffReturnType CoeffReturnType;
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- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
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- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
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- typedef StorageMemory<CoeffReturnType, Device> Storage;
98
- typedef typename Storage::Type EvaluatorPointerType;
99
-
100
- enum {
101
- IsAligned = false,
102
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
103
- BlockAccess = NumDims > 0,
104
- PreferBlockAccess = true,
105
- Layout = TensorEvaluator<ArgType, Device>::Layout,
106
- CoordAccess = false, // to be implemented
107
- RawAccess = false
108
- };
109
-
110
- typedef internal::TensorIntDivisor<Index> IndexDivisor;
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 TensorEvaluator<const ArgType, Device>::TensorBlock
117
- ArgTensorBlock;
118
-
119
- typedef typename internal::TensorMaterializedBlock<CoeffReturnType, NumDims,
120
- Layout, Index>
121
- TensorBlock;
122
- //===--------------------------------------------------------------------===//
123
-
124
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
125
- : m_impl(op.expression(), device),
126
- m_reverse(op.reverse()),
127
- m_device(device)
128
- {
129
- // Reversing a scalar isn't supported yet. It would be a no-op anyway.
130
- EIGEN_STATIC_ASSERT((NumDims > 0), YOU_MADE_A_PROGRAMMING_MISTAKE);
131
-
132
- // Compute strides
133
- m_dimensions = m_impl.dimensions();
134
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
135
- m_strides[0] = 1;
136
- for (int i = 1; i < NumDims; ++i) {
137
- m_strides[i] = m_strides[i-1] * m_dimensions[i-1];
138
- if (m_strides[i] > 0) m_fastStrides[i] = IndexDivisor(m_strides[i]);
139
- }
140
- } else {
141
- m_strides[NumDims-1] = 1;
142
- for (int i = NumDims - 2; i >= 0; --i) {
143
- m_strides[i] = m_strides[i+1] * m_dimensions[i+1];
144
- if (m_strides[i] > 0) m_fastStrides[i] = IndexDivisor(m_strides[i]);
145
- }
146
- }
147
- }
148
-
149
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
150
- const Dimensions& dimensions() const { return m_dimensions; }
151
-
152
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType) {
153
- m_impl.evalSubExprsIfNeeded(NULL);
154
- return true;
155
- }
156
-
157
- #ifdef EIGEN_USE_THREADS
158
- template <typename EvalSubExprsCallback>
159
- EIGEN_STRONG_INLINE void evalSubExprsIfNeededAsync(
160
- EvaluatorPointerType, EvalSubExprsCallback done) {
161
- m_impl.evalSubExprsIfNeededAsync(nullptr, [done](bool) { done(true); });
162
- }
163
- #endif // EIGEN_USE_THREADS
164
-
165
- EIGEN_STRONG_INLINE void cleanup() {
166
- m_impl.cleanup();
167
- }
168
-
169
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index reverseIndex(
170
- Index index) const {
171
- eigen_assert(index < dimensions().TotalSize());
172
- Index inputIndex = 0;
173
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
174
- EIGEN_UNROLL_LOOP
175
- for (int i = NumDims - 1; i > 0; --i) {
176
- Index idx = index / m_fastStrides[i];
177
- index -= idx * m_strides[i];
178
- if (m_reverse[i]) {
179
- idx = m_dimensions[i] - idx - 1;
180
- }
181
- inputIndex += idx * m_strides[i] ;
182
- }
183
- if (m_reverse[0]) {
184
- inputIndex += (m_dimensions[0] - index - 1);
185
- } else {
186
- inputIndex += index;
187
- }
188
- } else {
189
- EIGEN_UNROLL_LOOP
190
- for (int i = 0; i < NumDims - 1; ++i) {
191
- Index idx = index / m_fastStrides[i];
192
- index -= idx * m_strides[i];
193
- if (m_reverse[i]) {
194
- idx = m_dimensions[i] - idx - 1;
195
- }
196
- inputIndex += idx * m_strides[i] ;
197
- }
198
- if (m_reverse[NumDims-1]) {
199
- inputIndex += (m_dimensions[NumDims-1] - index - 1);
200
- } else {
201
- inputIndex += index;
202
- }
203
- }
204
- return inputIndex;
205
- }
206
-
207
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(
208
- Index index) const {
209
- return m_impl.coeff(reverseIndex(index));
210
- }
211
-
212
- template<int LoadMode>
213
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
214
- PacketReturnType packet(Index index) const
215
- {
216
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
217
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
218
-
219
- // TODO(ndjaitly): write a better packing routine that uses
220
- // local structure.
221
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type
222
- values[PacketSize];
223
- EIGEN_UNROLL_LOOP
224
- for (int i = 0; i < PacketSize; ++i) {
225
- values[i] = coeff(index+i);
226
- }
227
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
228
- return rslt;
229
- }
230
-
231
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
232
- internal::TensorBlockResourceRequirements getResourceRequirements() const {
233
- const size_t target_size = m_device.lastLevelCacheSize();
234
- // Block evaluation reads underlying memory in reverse order, and default
235
- // cost model does not properly catch this in bytes stored/loaded.
236
- return internal::TensorBlockResourceRequirements::skewed<Scalar>(
237
- target_size)
238
- .addCostPerCoeff({0, 0, 24});
239
- }
240
-
241
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorBlock
242
- block(TensorBlockDesc& desc, TensorBlockScratch& scratch,
243
- bool /*root_of_expr_ast*/ = false) const {
244
- // TODO(ezhulenev): If underlying tensor expression supports and prefers
245
- // block evaluation we must use it. Currently we use coeff and packet
246
- // access into the underlying tensor expression.
247
- // static const bool useBlockAccessForArgType =
248
- // TensorEvaluator<ArgType, Device>::BlockAccess &&
249
- // TensorEvaluator<ArgType, Device>::PreferBlockAccess;
250
-
251
- static const bool isColMajor =
252
- static_cast<int>(Layout) == static_cast<int>(ColMajor);
253
-
254
- static const Index inner_dim_idx = isColMajor ? 0 : NumDims - 1;
255
- const bool inner_dim_reversed = m_reverse[inner_dim_idx];
256
-
257
- // Offset in the output block.
258
- Index block_offset = 0;
259
-
260
- // Offset in the input Tensor.
261
- Index input_offset = reverseIndex(desc.offset());
262
-
263
- // Initialize output block iterator state. Dimension in this array are
264
- // always in inner_most -> outer_most order (col major layout).
265
- array<BlockIteratorState, NumDims> it;
266
- for (int i = 0; i < NumDims; ++i) {
267
- const int dim = isColMajor ? i : NumDims - 1 - i;
268
- it[i].size = desc.dimension(dim);
269
- it[i].count = 0;
270
- it[i].reverse = m_reverse[dim];
271
-
272
- it[i].block_stride =
273
- i == 0 ? 1 : (it[i - 1].size * it[i - 1].block_stride);
274
- it[i].block_span = it[i].block_stride * (it[i].size - 1);
275
-
276
- it[i].input_stride = m_strides[dim];
277
- it[i].input_span = it[i].input_stride * (it[i].size - 1);
278
-
279
- if (it[i].reverse) {
280
- it[i].input_stride = -1 * it[i].input_stride;
281
- it[i].input_span = -1 * it[i].input_span;
282
- }
283
- }
284
-
285
- // If multiple inner dimensions have the same reverse flag, check if we can
286
- // merge them into a single virtual inner dimension.
287
- int effective_inner_dim = 0;
288
- for (int i = 1; i < NumDims; ++i) {
289
- if (it[i].reverse != it[effective_inner_dim].reverse) break;
290
- if (it[i].block_stride != it[effective_inner_dim].size) break;
291
- if (it[i].block_stride != numext::abs(it[i].input_stride)) break;
292
-
293
- it[i].size = it[effective_inner_dim].size * it[i].size;
294
-
295
- it[i].block_stride = 1;
296
- it[i].input_stride = (inner_dim_reversed ? -1 : 1);
297
-
298
- it[i].block_span = it[i].block_stride * (it[i].size - 1);
299
- it[i].input_span = it[i].input_stride * (it[i].size - 1);
300
-
301
- effective_inner_dim = i;
302
- }
303
-
304
- eigen_assert(it[effective_inner_dim].block_stride == 1);
305
- eigen_assert(it[effective_inner_dim].input_stride ==
306
- (inner_dim_reversed ? -1 : 1));
307
-
308
- const Index inner_dim_size = it[effective_inner_dim].size;
309
-
310
- // Prepare storage for the materialized reverse result.
311
- const typename TensorBlock::Storage block_storage =
312
- TensorBlock::prepareStorage(desc, scratch);
313
- CoeffReturnType* block_buffer = block_storage.data();
314
-
315
- while (it[NumDims - 1].count < it[NumDims - 1].size) {
316
- // Copy inner-most dimension data from reversed location in input.
317
- Index dst = block_offset;
318
- Index src = input_offset;
319
-
320
- // NOTE(ezhulenev): Adding vectorized path with internal::preverse showed
321
- // worse results in benchmarks than a simple coefficient loop.
322
- if (inner_dim_reversed) {
323
- for (Index i = 0; i < inner_dim_size; ++i) {
324
- block_buffer[dst] = m_impl.coeff(src);
325
- ++dst;
326
- --src;
327
- }
328
- } else {
329
- for (Index i = 0; i < inner_dim_size; ++i) {
330
- block_buffer[dst] = m_impl.coeff(src);
331
- ++dst;
332
- ++src;
333
- }
334
- }
335
-
336
- // For the 1d tensor we need to generate only one inner-most dimension.
337
- if ((NumDims - effective_inner_dim) == 1) break;
338
-
339
- // Update offset.
340
- for (Index i = effective_inner_dim + 1; i < NumDims; ++i) {
341
- if (++it[i].count < it[i].size) {
342
- block_offset += it[i].block_stride;
343
- input_offset += it[i].input_stride;
344
- break;
345
- }
346
- if (i != NumDims - 1) it[i].count = 0;
347
- block_offset -= it[i].block_span;
348
- input_offset -= it[i].input_span;
349
- }
350
- }
351
-
352
- return block_storage.AsTensorMaterializedBlock();
353
- }
354
-
355
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
356
- double compute_cost = NumDims * (2 * TensorOpCost::AddCost<Index>() +
357
- 2 * TensorOpCost::MulCost<Index>() +
358
- TensorOpCost::DivCost<Index>());
359
- for (int i = 0; i < NumDims; ++i) {
360
- if (m_reverse[i]) {
361
- compute_cost += 2 * TensorOpCost::AddCost<Index>();
362
- }
363
- }
364
- return m_impl.costPerCoeff(vectorized) +
365
- TensorOpCost(0, 0, compute_cost, false /* vectorized */, PacketSize);
366
- }
367
-
368
- EIGEN_DEVICE_FUNC typename Storage::Type data() const { return NULL; }
369
-
370
- #ifdef EIGEN_USE_SYCL
371
- // binding placeholder accessors to a command group handler for SYCL
372
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
373
- m_impl.bind(cgh);
374
- }
375
- #endif
376
-
377
- protected:
378
- Dimensions m_dimensions;
379
- array<Index, NumDims> m_strides;
380
- array<IndexDivisor, NumDims> m_fastStrides;
381
- TensorEvaluator<ArgType, Device> m_impl;
382
- ReverseDimensions m_reverse;
383
- const Device EIGEN_DEVICE_REF m_device;
384
-
385
- private:
386
- struct BlockIteratorState {
387
- BlockIteratorState()
388
- : size(0),
389
- count(0),
390
- reverse(false),
391
- block_stride(0),
392
- block_span(0),
393
- input_stride(0),
394
- input_span(0) {}
395
-
396
- Index size;
397
- Index count;
398
- bool reverse;
399
- Index block_stride;
400
- Index block_span;
401
- Index input_stride;
402
- Index input_span;
403
- };
404
- };
405
-
406
- // Eval as lvalue
407
-
408
- template <typename ReverseDimensions, typename ArgType, typename Device>
409
- struct TensorEvaluator<TensorReverseOp<ReverseDimensions, ArgType>, Device>
410
- : public TensorEvaluator<const TensorReverseOp<ReverseDimensions, ArgType>,
411
- Device> {
412
- typedef TensorEvaluator<const TensorReverseOp<ReverseDimensions, ArgType>,
413
- Device> Base;
414
- typedef TensorReverseOp<ReverseDimensions, ArgType> XprType;
415
- typedef typename XprType::Index Index;
416
- static const int NumDims = internal::array_size<ReverseDimensions>::value;
417
- typedef DSizes<Index, NumDims> Dimensions;
418
-
419
- enum {
420
- IsAligned = false,
421
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
422
- BlockAccess = false,
423
- PreferBlockAccess = false,
424
- Layout = TensorEvaluator<ArgType, Device>::Layout,
425
- CoordAccess = false, // to be implemented
426
- RawAccess = false
427
- };
428
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
429
- : Base(op, device) {}
430
-
431
- typedef typename XprType::Scalar Scalar;
432
- typedef typename XprType::CoeffReturnType CoeffReturnType;
433
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
434
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
435
-
436
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
437
- typedef internal::TensorBlockNotImplemented TensorBlock;
438
- //===--------------------------------------------------------------------===//
439
-
440
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
441
- const Dimensions& dimensions() const { return this->m_dimensions; }
442
-
443
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& coeffRef(Index index) {
444
- return this->m_impl.coeffRef(this->reverseIndex(index));
445
- }
446
-
447
- template <int StoreMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
448
- void writePacket(Index index, const PacketReturnType& x) {
449
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
450
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
451
-
452
- // This code is pilfered from TensorMorphing.h
453
- EIGEN_ALIGN_MAX CoeffReturnType values[PacketSize];
454
- internal::pstore<CoeffReturnType, PacketReturnType>(values, x);
455
- EIGEN_UNROLL_LOOP
456
- for (int i = 0; i < PacketSize; ++i) {
457
- this->coeffRef(index+i) = values[i];
458
- }
459
- }
460
- };
461
-
462
-
463
- } // end namespace Eigen
464
-
465
- #endif // EIGEN_CXX11_TENSOR_TENSOR_REVERSE_H