sequenzo 0.1.18__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 +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +155 -155
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-312-darwin.so +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/hierarchical_clustering.py +107 -5
  6. sequenzo/define_sequence_data.py +10 -1
  7. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  8. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
  9. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-312-darwin.so +0 -0
  10. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  11. sequenzo/dissimilarity_measures/utils/seqconc.cpython-312-darwin.so +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  13. sequenzo/dissimilarity_measures/utils/seqdss.cpython-312-darwin.so +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  15. sequenzo/dissimilarity_measures/utils/seqdur.cpython-312-darwin.so +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  17. sequenzo/dissimilarity_measures/utils/seqlength.cpython-312-darwin.so +0 -0
  18. sequenzo/multidomain/cat.py +0 -53
  19. sequenzo/multidomain/idcd.py +0 -1
  20. sequenzo/openmp_setup.py +233 -0
  21. sequenzo/visualization/plot_transition_matrix.py +21 -22
  22. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  23. sequenzo-0.1.19.dist-info/RECORD +215 -0
  24. sequenzo/dissimilarity_measures/setup.py +0 -35
  25. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  26. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  167. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  168. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  169. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  170. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  171. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  172. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  173. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  174. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  175. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  176. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  177. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  178. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  179. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  180. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  181. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  182. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  183. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  184. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  185. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  186. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  187. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  188. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  189. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  190. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  191. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  192. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  193. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  194. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  195. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  196. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  197. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  198. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  199. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  200. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  201. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  202. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  203. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  204. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  205. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  206. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  207. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
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  356. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
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@@ -1,377 +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_CONCATENATION_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_CONCATENATION_H
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-
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- namespace Eigen {
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-
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- /** \class TensorConcatenationOp
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor concatenation class.
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- *
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- *
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- */
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- namespace internal {
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- template<typename Axis, typename LhsXprType, typename RhsXprType>
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- struct traits<TensorConcatenationOp<Axis, LhsXprType, RhsXprType> >
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- {
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- // Type promotion to handle the case where the types of the lhs and the rhs are different.
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- typedef typename promote_storage_type<typename LhsXprType::Scalar,
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- typename RhsXprType::Scalar>::ret Scalar;
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- typedef typename promote_storage_type<typename traits<LhsXprType>::StorageKind,
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- typename traits<RhsXprType>::StorageKind>::ret StorageKind;
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- typedef typename promote_index_type<typename traits<LhsXprType>::Index,
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- typename traits<RhsXprType>::Index>::type Index;
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- typedef typename LhsXprType::Nested LhsNested;
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- typedef typename RhsXprType::Nested RhsNested;
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- typedef typename remove_reference<LhsNested>::type _LhsNested;
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- typedef typename remove_reference<RhsNested>::type _RhsNested;
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- static const int NumDimensions = traits<LhsXprType>::NumDimensions;
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- static const int Layout = traits<LhsXprType>::Layout;
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- enum { Flags = 0 };
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- typedef typename conditional<Pointer_type_promotion<typename LhsXprType::Scalar, Scalar>::val,
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- typename traits<LhsXprType>::PointerType, typename traits<RhsXprType>::PointerType>::type PointerType;
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- };
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-
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- template<typename Axis, typename LhsXprType, typename RhsXprType>
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- struct eval<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, Eigen::Dense>
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- {
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- typedef const TensorConcatenationOp<Axis, LhsXprType, RhsXprType>& type;
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- };
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-
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- template<typename Axis, typename LhsXprType, typename RhsXprType>
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- struct nested<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, 1, typename eval<TensorConcatenationOp<Axis, LhsXprType, RhsXprType> >::type>
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- {
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- typedef TensorConcatenationOp<Axis, LhsXprType, RhsXprType> type;
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- };
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-
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- } // end namespace internal
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-
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-
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- template<typename Axis, typename LhsXprType, typename RhsXprType>
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- class TensorConcatenationOp : public TensorBase<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, WriteAccessors>
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- {
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- public:
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- typedef TensorBase<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, WriteAccessors> Base;
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- typedef typename internal::traits<TensorConcatenationOp>::Scalar Scalar;
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- typedef typename internal::traits<TensorConcatenationOp>::StorageKind StorageKind;
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- typedef typename internal::traits<TensorConcatenationOp>::Index Index;
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- typedef typename internal::nested<TensorConcatenationOp>::type Nested;
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- typedef typename internal::promote_storage_type<typename LhsXprType::CoeffReturnType,
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- typename RhsXprType::CoeffReturnType>::ret CoeffReturnType;
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- typedef typename NumTraits<Scalar>::Real RealScalar;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorConcatenationOp(const LhsXprType& lhs, const RhsXprType& rhs, Axis axis)
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- : m_lhs_xpr(lhs), m_rhs_xpr(rhs), m_axis(axis) {}
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-
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- EIGEN_DEVICE_FUNC
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- const typename internal::remove_all<typename LhsXprType::Nested>::type&
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- lhsExpression() const { return m_lhs_xpr; }
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-
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- EIGEN_DEVICE_FUNC
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- const typename internal::remove_all<typename RhsXprType::Nested>::type&
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- rhsExpression() const { return m_rhs_xpr; }
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-
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- EIGEN_DEVICE_FUNC const Axis& axis() const { return m_axis; }
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-
85
- EIGEN_TENSOR_INHERIT_ASSIGNMENT_OPERATORS(TensorConcatenationOp)
86
- protected:
87
- typename LhsXprType::Nested m_lhs_xpr;
88
- typename RhsXprType::Nested m_rhs_xpr;
89
- const Axis m_axis;
90
- };
91
-
92
-
93
- // Eval as rvalue
94
- template<typename Axis, typename LeftArgType, typename RightArgType, typename Device>
95
- struct TensorEvaluator<const TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device>
96
- {
97
- typedef TensorConcatenationOp<Axis, LeftArgType, RightArgType> XprType;
98
- typedef typename XprType::Index Index;
99
- static const int NumDims = internal::array_size<typename TensorEvaluator<LeftArgType, Device>::Dimensions>::value;
100
- static const int RightNumDims = internal::array_size<typename TensorEvaluator<RightArgType, Device>::Dimensions>::value;
101
- typedef DSizes<Index, NumDims> Dimensions;
102
- typedef typename XprType::Scalar Scalar;
103
- typedef typename XprType::CoeffReturnType CoeffReturnType;
104
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
105
- typedef StorageMemory<CoeffReturnType, Device> Storage;
106
- typedef typename Storage::Type EvaluatorPointerType;
107
- enum {
108
- IsAligned = false,
109
- PacketAccess = TensorEvaluator<LeftArgType, Device>::PacketAccess &&
110
- TensorEvaluator<RightArgType, Device>::PacketAccess,
111
- BlockAccess = false,
112
- PreferBlockAccess = TensorEvaluator<LeftArgType, Device>::PreferBlockAccess ||
113
- TensorEvaluator<RightArgType, Device>::PreferBlockAccess,
114
- Layout = TensorEvaluator<LeftArgType, Device>::Layout,
115
- RawAccess = false
116
- };
117
-
118
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
119
- typedef internal::TensorBlockNotImplemented TensorBlock;
120
- //===--------------------------------------------------------------------===//
121
-
122
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
123
- : m_leftImpl(op.lhsExpression(), device), m_rightImpl(op.rhsExpression(), device), m_axis(op.axis())
124
- {
125
- EIGEN_STATIC_ASSERT((static_cast<int>(TensorEvaluator<LeftArgType, Device>::Layout) == static_cast<int>(TensorEvaluator<RightArgType, Device>::Layout) || NumDims == 1), YOU_MADE_A_PROGRAMMING_MISTAKE);
126
- EIGEN_STATIC_ASSERT((NumDims == RightNumDims), YOU_MADE_A_PROGRAMMING_MISTAKE);
127
- EIGEN_STATIC_ASSERT((NumDims > 0), YOU_MADE_A_PROGRAMMING_MISTAKE);
128
-
129
- eigen_assert(0 <= m_axis && m_axis < NumDims);
130
- const Dimensions& lhs_dims = m_leftImpl.dimensions();
131
- const Dimensions& rhs_dims = m_rightImpl.dimensions();
132
- {
133
- int i = 0;
134
- for (; i < m_axis; ++i) {
135
- eigen_assert(lhs_dims[i] > 0);
136
- eigen_assert(lhs_dims[i] == rhs_dims[i]);
137
- m_dimensions[i] = lhs_dims[i];
138
- }
139
- eigen_assert(lhs_dims[i] > 0); // Now i == m_axis.
140
- eigen_assert(rhs_dims[i] > 0);
141
- m_dimensions[i] = lhs_dims[i] + rhs_dims[i];
142
- for (++i; i < NumDims; ++i) {
143
- eigen_assert(lhs_dims[i] > 0);
144
- eigen_assert(lhs_dims[i] == rhs_dims[i]);
145
- m_dimensions[i] = lhs_dims[i];
146
- }
147
- }
148
-
149
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
150
- m_leftStrides[0] = 1;
151
- m_rightStrides[0] = 1;
152
- m_outputStrides[0] = 1;
153
-
154
- for (int j = 1; j < NumDims; ++j) {
155
- m_leftStrides[j] = m_leftStrides[j-1] * lhs_dims[j-1];
156
- m_rightStrides[j] = m_rightStrides[j-1] * rhs_dims[j-1];
157
- m_outputStrides[j] = m_outputStrides[j-1] * m_dimensions[j-1];
158
- }
159
- } else {
160
- m_leftStrides[NumDims - 1] = 1;
161
- m_rightStrides[NumDims - 1] = 1;
162
- m_outputStrides[NumDims - 1] = 1;
163
-
164
- for (int j = NumDims - 2; j >= 0; --j) {
165
- m_leftStrides[j] = m_leftStrides[j+1] * lhs_dims[j+1];
166
- m_rightStrides[j] = m_rightStrides[j+1] * rhs_dims[j+1];
167
- m_outputStrides[j] = m_outputStrides[j+1] * m_dimensions[j+1];
168
- }
169
- }
170
- }
171
-
172
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
173
-
174
- // TODO(phli): Add short-circuit memcpy evaluation if underlying data are linear?
175
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType)
176
- {
177
- m_leftImpl.evalSubExprsIfNeeded(NULL);
178
- m_rightImpl.evalSubExprsIfNeeded(NULL);
179
- return true;
180
- }
181
-
182
- EIGEN_STRONG_INLINE void cleanup()
183
- {
184
- m_leftImpl.cleanup();
185
- m_rightImpl.cleanup();
186
- }
187
-
188
- // TODO(phli): attempt to speed this up. The integer divisions and modulo are slow.
189
- // See CL/76180724 comments for more ideas.
190
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
191
- {
192
- // Collect dimension-wise indices (subs).
193
- array<Index, NumDims> subs;
194
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
195
- for (int i = NumDims - 1; i > 0; --i) {
196
- subs[i] = index / m_outputStrides[i];
197
- index -= subs[i] * m_outputStrides[i];
198
- }
199
- subs[0] = index;
200
- } else {
201
- for (int i = 0; i < NumDims - 1; ++i) {
202
- subs[i] = index / m_outputStrides[i];
203
- index -= subs[i] * m_outputStrides[i];
204
- }
205
- subs[NumDims - 1] = index;
206
- }
207
-
208
- const Dimensions& left_dims = m_leftImpl.dimensions();
209
- if (subs[m_axis] < left_dims[m_axis]) {
210
- Index left_index;
211
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
212
- left_index = subs[0];
213
- EIGEN_UNROLL_LOOP
214
- for (int i = 1; i < NumDims; ++i) {
215
- left_index += (subs[i] % left_dims[i]) * m_leftStrides[i];
216
- }
217
- } else {
218
- left_index = subs[NumDims - 1];
219
- EIGEN_UNROLL_LOOP
220
- for (int i = NumDims - 2; i >= 0; --i) {
221
- left_index += (subs[i] % left_dims[i]) * m_leftStrides[i];
222
- }
223
- }
224
- return m_leftImpl.coeff(left_index);
225
- } else {
226
- subs[m_axis] -= left_dims[m_axis];
227
- const Dimensions& right_dims = m_rightImpl.dimensions();
228
- Index right_index;
229
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
230
- right_index = subs[0];
231
- EIGEN_UNROLL_LOOP
232
- for (int i = 1; i < NumDims; ++i) {
233
- right_index += (subs[i] % right_dims[i]) * m_rightStrides[i];
234
- }
235
- } else {
236
- right_index = subs[NumDims - 1];
237
- EIGEN_UNROLL_LOOP
238
- for (int i = NumDims - 2; i >= 0; --i) {
239
- right_index += (subs[i] % right_dims[i]) * m_rightStrides[i];
240
- }
241
- }
242
- return m_rightImpl.coeff(right_index);
243
- }
244
- }
245
-
246
- // TODO(phli): Add a real vectorization.
247
- template<int LoadMode>
248
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
249
- {
250
- const int packetSize = PacketType<CoeffReturnType, Device>::size;
251
- EIGEN_STATIC_ASSERT((packetSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
252
- eigen_assert(index + packetSize - 1 < dimensions().TotalSize());
253
-
254
- EIGEN_ALIGN_MAX CoeffReturnType values[packetSize];
255
- EIGEN_UNROLL_LOOP
256
- for (int i = 0; i < packetSize; ++i) {
257
- values[i] = coeff(index+i);
258
- }
259
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
260
- return rslt;
261
- }
262
-
263
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
264
- costPerCoeff(bool vectorized) const {
265
- const double compute_cost = NumDims * (2 * TensorOpCost::AddCost<Index>() +
266
- 2 * TensorOpCost::MulCost<Index>() +
267
- TensorOpCost::DivCost<Index>() +
268
- TensorOpCost::ModCost<Index>());
269
- const double lhs_size = m_leftImpl.dimensions().TotalSize();
270
- const double rhs_size = m_rightImpl.dimensions().TotalSize();
271
- return (lhs_size / (lhs_size + rhs_size)) *
272
- m_leftImpl.costPerCoeff(vectorized) +
273
- (rhs_size / (lhs_size + rhs_size)) *
274
- m_rightImpl.costPerCoeff(vectorized) +
275
- TensorOpCost(0, 0, compute_cost);
276
- }
277
-
278
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return NULL; }
279
-
280
- #ifdef EIGEN_USE_SYCL
281
- // binding placeholder accessors to a command group handler for SYCL
282
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
283
- m_leftImpl.bind(cgh);
284
- m_rightImpl.bind(cgh);
285
- }
286
- #endif
287
-
288
- protected:
289
- Dimensions m_dimensions;
290
- array<Index, NumDims> m_outputStrides;
291
- array<Index, NumDims> m_leftStrides;
292
- array<Index, NumDims> m_rightStrides;
293
- TensorEvaluator<LeftArgType, Device> m_leftImpl;
294
- TensorEvaluator<RightArgType, Device> m_rightImpl;
295
- const Axis m_axis;
296
- };
297
-
298
- // Eval as lvalue
299
- template<typename Axis, typename LeftArgType, typename RightArgType, typename Device>
300
- struct TensorEvaluator<TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device>
301
- : public TensorEvaluator<const TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device>
302
- {
303
- typedef TensorEvaluator<const TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device> Base;
304
- typedef TensorConcatenationOp<Axis, LeftArgType, RightArgType> XprType;
305
- typedef typename Base::Dimensions Dimensions;
306
- enum {
307
- IsAligned = false,
308
- PacketAccess = TensorEvaluator<LeftArgType, Device>::PacketAccess &&
309
- TensorEvaluator<RightArgType, Device>::PacketAccess,
310
- BlockAccess = false,
311
- PreferBlockAccess = TensorEvaluator<LeftArgType, Device>::PreferBlockAccess ||
312
- TensorEvaluator<RightArgType, Device>::PreferBlockAccess,
313
- Layout = TensorEvaluator<LeftArgType, Device>::Layout,
314
- RawAccess = false
315
- };
316
-
317
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
318
- typedef internal::TensorBlockNotImplemented TensorBlock;
319
- //===--------------------------------------------------------------------===//
320
-
321
- EIGEN_STRONG_INLINE TensorEvaluator(XprType& op, const Device& device)
322
- : Base(op, device)
323
- {
324
- EIGEN_STATIC_ASSERT((static_cast<int>(Layout) == static_cast<int>(ColMajor)), YOU_MADE_A_PROGRAMMING_MISTAKE);
325
- }
326
-
327
- typedef typename XprType::Index Index;
328
- typedef typename XprType::Scalar Scalar;
329
- typedef typename XprType::CoeffReturnType CoeffReturnType;
330
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
331
-
332
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType& coeffRef(Index index)
333
- {
334
- // Collect dimension-wise indices (subs).
335
- array<Index, Base::NumDims> subs;
336
- for (int i = Base::NumDims - 1; i > 0; --i) {
337
- subs[i] = index / this->m_outputStrides[i];
338
- index -= subs[i] * this->m_outputStrides[i];
339
- }
340
- subs[0] = index;
341
-
342
- const Dimensions& left_dims = this->m_leftImpl.dimensions();
343
- if (subs[this->m_axis] < left_dims[this->m_axis]) {
344
- Index left_index = subs[0];
345
- for (int i = 1; i < Base::NumDims; ++i) {
346
- left_index += (subs[i] % left_dims[i]) * this->m_leftStrides[i];
347
- }
348
- return this->m_leftImpl.coeffRef(left_index);
349
- } else {
350
- subs[this->m_axis] -= left_dims[this->m_axis];
351
- const Dimensions& right_dims = this->m_rightImpl.dimensions();
352
- Index right_index = subs[0];
353
- for (int i = 1; i < Base::NumDims; ++i) {
354
- right_index += (subs[i] % right_dims[i]) * this->m_rightStrides[i];
355
- }
356
- return this->m_rightImpl.coeffRef(right_index);
357
- }
358
- }
359
-
360
- template <int StoreMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
361
- void writePacket(Index index, const PacketReturnType& x)
362
- {
363
- const int packetSize = PacketType<CoeffReturnType, Device>::size;
364
- EIGEN_STATIC_ASSERT((packetSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
365
- eigen_assert(index + packetSize - 1 < this->dimensions().TotalSize());
366
-
367
- EIGEN_ALIGN_MAX CoeffReturnType values[packetSize];
368
- internal::pstore<CoeffReturnType, PacketReturnType>(values, x);
369
- for (int i = 0; i < packetSize; ++i) {
370
- coeffRef(index+i) = values[i];
371
- }
372
- }
373
- };
374
-
375
- } // end namespace Eigen
376
-
377
- #endif // EIGEN_CXX11_TENSOR_TENSOR_CONCATENATION_H