sequenzo 0.1.18__cp311-cp311-macosx_10_9_universal2.whl → 0.1.20__cp311-cp311-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-311-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-311-darwin.so +0 -0
  11. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  12. sequenzo/dissimilarity_measures/utils/seqconc.cpython-311-darwin.so +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  14. sequenzo/dissimilarity_measures/utils/seqdss.cpython-311-darwin.so +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  16. sequenzo/dissimilarity_measures/utils/seqdur.cpython-311-darwin.so +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  18. sequenzo/dissimilarity_measures/utils/seqlength.cpython-311-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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@@ -1,216 +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_LAYOUT_SWAP_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_LAYOUT_SWAP_H
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-
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- namespace Eigen {
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-
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- /** \class TensorLayoutSwap
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Swap the layout from col-major to row-major, or row-major
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- * to col-major, and invert the order of the dimensions.
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- *
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- * Beware: the dimensions are reversed by this operation. If you want to
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- * preserve the ordering of the dimensions, you need to combine this
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- * operation with a shuffle.
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- *
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- * \example:
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- * Tensor<float, 2, ColMajor> input(2, 4);
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- * Tensor<float, 2, RowMajor> output = input.swap_layout();
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- * eigen_assert(output.dimension(0) == 4);
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- * eigen_assert(output.dimension(1) == 2);
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- *
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- * array<int, 2> shuffle(1, 0);
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- * output = input.swap_layout().shuffle(shuffle);
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- * eigen_assert(output.dimension(0) == 2);
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- * eigen_assert(output.dimension(1) == 4);
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- *
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- */
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- namespace internal {
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- template<typename XprType>
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- struct traits<TensorLayoutSwapOp<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 = traits<XprType>::NumDimensions;
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- static const int Layout = (traits<XprType>::Layout == ColMajor) ? RowMajor : ColMajor;
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- typedef typename XprTraits::PointerType PointerType;
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- };
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-
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- template<typename XprType>
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- struct eval<TensorLayoutSwapOp<XprType>, Eigen::Dense>
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- {
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- typedef const TensorLayoutSwapOp<XprType>& type;
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- };
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-
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- template<typename XprType>
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- struct nested<TensorLayoutSwapOp<XprType>, 1, typename eval<TensorLayoutSwapOp<XprType> >::type>
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- {
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- typedef TensorLayoutSwapOp<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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-
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-
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- template<typename XprType>
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- class TensorLayoutSwapOp : public TensorBase<TensorLayoutSwapOp<XprType>, WriteAccessors>
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- {
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- public:
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- typedef TensorBase<TensorLayoutSwapOp<XprType>, WriteAccessors> Base;
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- typedef typename Eigen::internal::traits<TensorLayoutSwapOp>::Scalar Scalar;
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- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
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- typedef typename internal::remove_const<typename XprType::CoeffReturnType>::type CoeffReturnType;
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- typedef typename Eigen::internal::nested<TensorLayoutSwapOp>::type Nested;
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- typedef typename Eigen::internal::traits<TensorLayoutSwapOp>::StorageKind StorageKind;
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- typedef typename Eigen::internal::traits<TensorLayoutSwapOp>::Index Index;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorLayoutSwapOp(const XprType& expr)
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- : m_xpr(expr) {}
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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(TensorLayoutSwapOp)
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- protected:
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- typename XprType::Nested m_xpr;
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- };
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-
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-
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- // Eval as rvalue
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- template<typename ArgType, typename Device>
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- struct TensorEvaluator<const TensorLayoutSwapOp<ArgType>, Device>
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- {
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- typedef TensorLayoutSwapOp<ArgType> XprType;
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- typedef typename XprType::Index Index;
99
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
100
- typedef DSizes<Index, NumDims> Dimensions;
101
-
102
- enum {
103
- IsAligned = TensorEvaluator<ArgType, Device>::IsAligned,
104
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
105
- BlockAccess = false,
106
- PreferBlockAccess = TensorEvaluator<ArgType, Device>::PreferBlockAccess,
107
- Layout = (static_cast<int>(TensorEvaluator<ArgType, Device>::Layout) == static_cast<int>(ColMajor)) ? RowMajor : ColMajor,
108
- CoordAccess = false, // to be implemented
109
- RawAccess = TensorEvaluator<ArgType, Device>::RawAccess
110
- };
111
-
112
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
113
- typedef internal::TensorBlockNotImplemented TensorBlock;
114
- //===--------------------------------------------------------------------===//
115
-
116
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
117
- : m_impl(op.expression(), device)
118
- {
119
- for(int i = 0; i < NumDims; ++i) {
120
- m_dimensions[i] = m_impl.dimensions()[NumDims-1-i];
121
- }
122
- }
123
-
124
- #ifdef EIGEN_USE_SYCL
125
- // binding placeholder accessors to a command group handler for SYCL
126
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
127
- m_impl.bind(cgh);
128
- }
129
- #endif
130
-
131
- typedef typename XprType::Scalar Scalar;
132
- typedef typename XprType::CoeffReturnType CoeffReturnType;
133
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
134
- typedef StorageMemory<CoeffReturnType, Device> Storage;
135
- typedef typename Storage::Type EvaluatorPointerType;
136
-
137
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
138
-
139
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType data) {
140
- return m_impl.evalSubExprsIfNeeded(data);
141
- }
142
- EIGEN_STRONG_INLINE void cleanup() {
143
- m_impl.cleanup();
144
- }
145
-
146
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
147
- {
148
- return m_impl.coeff(index);
149
- }
150
-
151
- template<int LoadMode>
152
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
153
- {
154
- return m_impl.template packet<LoadMode>(index);
155
- }
156
-
157
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
158
- return m_impl.costPerCoeff(vectorized);
159
- }
160
-
161
- EIGEN_DEVICE_FUNC typename Storage::Type data() const {
162
- return constCast(m_impl.data());
163
- }
164
-
165
- const TensorEvaluator<ArgType, Device>& impl() const { return m_impl; }
166
-
167
- protected:
168
- TensorEvaluator<ArgType, Device> m_impl;
169
- Dimensions m_dimensions;
170
- };
171
-
172
-
173
- // Eval as lvalue
174
- template<typename ArgType, typename Device>
175
- struct TensorEvaluator<TensorLayoutSwapOp<ArgType>, Device>
176
- : public TensorEvaluator<const TensorLayoutSwapOp<ArgType>, Device>
177
- {
178
- typedef TensorEvaluator<const TensorLayoutSwapOp<ArgType>, Device> Base;
179
- typedef TensorLayoutSwapOp<ArgType> XprType;
180
-
181
- enum {
182
- IsAligned = TensorEvaluator<ArgType, Device>::IsAligned,
183
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
184
- BlockAccess = false,
185
- PreferBlockAccess = TensorEvaluator<ArgType, Device>::PreferBlockAccess,
186
- Layout = (static_cast<int>(TensorEvaluator<ArgType, Device>::Layout) == static_cast<int>(ColMajor)) ? RowMajor : ColMajor,
187
- CoordAccess = false // to be implemented
188
- };
189
-
190
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
191
- typedef internal::TensorBlockNotImplemented TensorBlock;
192
- //===--------------------------------------------------------------------===//
193
-
194
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
195
- : Base(op, device)
196
- { }
197
-
198
- typedef typename XprType::Index Index;
199
- typedef typename XprType::Scalar Scalar;
200
- typedef typename XprType::CoeffReturnType CoeffReturnType;
201
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
202
-
203
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType& coeffRef(Index index)
204
- {
205
- return this->m_impl.coeffRef(index);
206
- }
207
- template <int StoreMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
208
- void writePacket(Index index, const PacketReturnType& x)
209
- {
210
- this->m_impl.template writePacket<StoreMode>(index, x);
211
- }
212
- };
213
-
214
- } // end namespace Eigen
215
-
216
- #endif // EIGEN_CXX11_TENSOR_TENSOR_LAYOUT_SWAP_H
@@ -1,98 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2015 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_META_MACROS_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_META_MACROS_H
12
-
13
-
14
- /** use this macro in sfinae selection in templated functions
15
- *
16
- * template<typename T,
17
- * typename std::enable_if< isBanana<T>::value , int >::type = 0
18
- * >
19
- * void foo(){}
20
- *
21
- * becomes =>
22
- *
23
- * template<typename TopoType,
24
- * SFINAE_ENABLE_IF( isBanana<T>::value )
25
- * >
26
- * void foo(){}
27
- */
28
-
29
- // SFINAE requires variadic templates
30
- #if !defined(EIGEN_GPUCC)
31
- #if EIGEN_HAS_VARIADIC_TEMPLATES
32
- // SFINAE doesn't work for gcc <= 4.7
33
- #ifdef EIGEN_COMP_GNUC
34
- #if EIGEN_GNUC_AT_LEAST(4,8)
35
- #define EIGEN_HAS_SFINAE
36
- #endif
37
- #else
38
- #define EIGEN_HAS_SFINAE
39
- #endif
40
- #endif
41
- #endif
42
-
43
- #define EIGEN_SFINAE_ENABLE_IF( __condition__ ) \
44
- typename internal::enable_if< ( __condition__ ) , int >::type = 0
45
-
46
- // Define a macro to use a reference on the host but a value on the device
47
- #if defined(SYCL_DEVICE_ONLY)
48
- #define EIGEN_DEVICE_REF
49
- #else
50
- #define EIGEN_DEVICE_REF &
51
- #endif
52
-
53
- // Define a macro for catching SYCL exceptions if exceptions are enabled
54
- #define EIGEN_SYCL_TRY_CATCH(X) \
55
- do { \
56
- EIGEN_TRY {X;} \
57
- EIGEN_CATCH(const cl::sycl::exception& e) { \
58
- EIGEN_THROW_X(std::runtime_error("SYCL exception at " + \
59
- std::string(__FILE__) + ":" + \
60
- std::to_string(__LINE__) + "\n" + \
61
- e.what())); \
62
- } \
63
- } while (false)
64
-
65
- // Define a macro if local memory flags are unset or one of them is set
66
- // Setting both flags is the same as unsetting them
67
- #if (!defined(EIGEN_SYCL_LOCAL_MEM) && !defined(EIGEN_SYCL_NO_LOCAL_MEM)) || \
68
- (defined(EIGEN_SYCL_LOCAL_MEM) && defined(EIGEN_SYCL_NO_LOCAL_MEM))
69
- #define EIGEN_SYCL_LOCAL_MEM_UNSET_OR_ON 1
70
- #define EIGEN_SYCL_LOCAL_MEM_UNSET_OR_OFF 1
71
- #elif defined(EIGEN_SYCL_LOCAL_MEM) && !defined(EIGEN_SYCL_NO_LOCAL_MEM)
72
- #define EIGEN_SYCL_LOCAL_MEM_UNSET_OR_ON 1
73
- #elif !defined(EIGEN_SYCL_LOCAL_MEM) && defined(EIGEN_SYCL_NO_LOCAL_MEM)
74
- #define EIGEN_SYCL_LOCAL_MEM_UNSET_OR_OFF 1
75
- #endif
76
-
77
- #if EIGEN_COMP_CLANG // workaround clang bug (see http://forum.kde.org/viewtopic.php?f=74&t=102653)
78
- #define EIGEN_TENSOR_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) \
79
- using Base::operator =; \
80
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const Derived& other) { Base::operator=(other); return *this; } \
81
- template <typename OtherDerived> \
82
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const OtherDerived& other) { Base::operator=(other); return *this; }
83
- #else
84
- #define EIGEN_TENSOR_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) \
85
- EIGEN_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived)
86
- #endif
87
-
88
- /** \internal
89
- * \brief Macro to manually inherit assignment operators.
90
- * This is necessary, because the implicitly defined assignment operator gets deleted when a custom operator= is defined.
91
- * This also inherits template<OtherDerived> operator=(const OtherDerived&) assignments.
92
- * With C++11 or later this also default-implements the copy-constructor
93
- */
94
- #define EIGEN_TENSOR_INHERIT_ASSIGNMENT_OPERATORS(Derived) \
95
- EIGEN_TENSOR_INHERIT_ASSIGNMENT_EQUAL_OPERATOR(Derived) \
96
- EIGEN_DEFAULT_COPY_CONSTRUCTOR(Derived)
97
-
98
- #endif
@@ -1,327 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_MAP_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_MAP_H
12
-
13
- namespace Eigen {
14
-
15
- // FIXME use proper doxygen documentation (e.g. \tparam MakePointer_)
16
-
17
- /** \class TensorMap
18
- * \ingroup CXX11_Tensor_Module
19
- *
20
- * \brief A tensor expression mapping an existing array of data.
21
- *
22
- */
23
- /// `template <class> class MakePointer_` is added to convert the host pointer to the device pointer.
24
- /// It is added due to the fact that for our device compiler `T*` is not allowed.
25
- /// If we wanted to use the same Evaluator functions we have to convert that type to our pointer `T`.
26
- /// This is done through our `MakePointer_` class. By default the Type in the `MakePointer_<T>` is `T*` .
27
- /// Therefore, by adding the default value, we managed to convert the type and it does not break any
28
- /// existing code as its default value is `T*`.
29
- template<typename PlainObjectType, int Options_, template <class> class MakePointer_> class TensorMap : public TensorBase<TensorMap<PlainObjectType, Options_, MakePointer_> >
30
- {
31
- public:
32
- typedef TensorMap<PlainObjectType, Options_, MakePointer_> Self;
33
- typedef TensorBase<TensorMap<PlainObjectType, Options_, MakePointer_> > Base;
34
- #ifdef EIGEN_USE_SYCL
35
- typedef typename Eigen::internal::remove_reference<typename Eigen::internal::nested<Self>::type>::type Nested;
36
- #else
37
- typedef typename Eigen::internal::nested<Self>::type Nested;
38
- #endif
39
- typedef typename internal::traits<PlainObjectType>::StorageKind StorageKind;
40
- typedef typename internal::traits<PlainObjectType>::Index Index;
41
- typedef typename internal::traits<PlainObjectType>::Scalar Scalar;
42
- typedef typename NumTraits<Scalar>::Real RealScalar;
43
- typedef typename PlainObjectType::Base::CoeffReturnType CoeffReturnType;
44
-
45
- typedef typename MakePointer_<Scalar>::Type PointerType;
46
- typedef typename MakePointer_<Scalar>::ConstType PointerConstType;
47
-
48
- // WARN: PointerType still can be a pointer to const (const Scalar*), for
49
- // example in TensorMap<Tensor<const Scalar, ...>> expression. This type of
50
- // expression should be illegal, but adding this restriction is not possible
51
- // in practice (see https://bitbucket.org/eigen/eigen/pull-requests/488).
52
- typedef typename internal::conditional<
53
- bool(internal::is_lvalue<PlainObjectType>::value),
54
- PointerType, // use simple pointer in lvalue expressions
55
- PointerConstType // use const pointer in rvalue expressions
56
- >::type StoragePointerType;
57
-
58
- // If TensorMap was constructed over rvalue expression (e.g. const Tensor),
59
- // we should return a reference to const from operator() (and others), even
60
- // if TensorMap itself is not const.
61
- typedef typename internal::conditional<
62
- bool(internal::is_lvalue<PlainObjectType>::value),
63
- Scalar&,
64
- const Scalar&
65
- >::type StorageRefType;
66
-
67
- static const int Options = Options_;
68
-
69
- static const Index NumIndices = PlainObjectType::NumIndices;
70
- typedef typename PlainObjectType::Dimensions Dimensions;
71
-
72
- enum {
73
- IsAligned = ((int(Options_)&Aligned)==Aligned),
74
- Layout = PlainObjectType::Layout,
75
- CoordAccess = true,
76
- RawAccess = true
77
- };
78
-
79
- EIGEN_DEVICE_FUNC
80
- EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr) : m_data(dataPtr), m_dimensions() {
81
- // The number of dimensions used to construct a tensor must be equal to the rank of the tensor.
82
- EIGEN_STATIC_ASSERT((0 == NumIndices || NumIndices == Dynamic), YOU_MADE_A_PROGRAMMING_MISTAKE)
83
- }
84
-
85
- #if EIGEN_HAS_VARIADIC_TEMPLATES
86
- template<typename... IndexTypes> EIGEN_DEVICE_FUNC
87
- EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, Index firstDimension, IndexTypes... otherDimensions) : m_data(dataPtr), m_dimensions(firstDimension, otherDimensions...) {
88
- // The number of dimensions used to construct a tensor must be equal to the rank of the tensor.
89
- EIGEN_STATIC_ASSERT((sizeof...(otherDimensions) + 1 == NumIndices || NumIndices == Dynamic), YOU_MADE_A_PROGRAMMING_MISTAKE)
90
- }
91
- #else
92
- EIGEN_DEVICE_FUNC
93
- EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, Index firstDimension) : m_data(dataPtr), m_dimensions(firstDimension) {
94
- // The number of dimensions used to construct a tensor must be equal to the rank of the tensor.
95
- EIGEN_STATIC_ASSERT((1 == NumIndices || NumIndices == Dynamic), YOU_MADE_A_PROGRAMMING_MISTAKE)
96
- }
97
- EIGEN_DEVICE_FUNC
98
- EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, Index dim1, Index dim2) : m_data(dataPtr), m_dimensions(dim1, dim2) {
99
- EIGEN_STATIC_ASSERT(2 == NumIndices || NumIndices == Dynamic, YOU_MADE_A_PROGRAMMING_MISTAKE)
100
- }
101
- EIGEN_DEVICE_FUNC
102
- EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, Index dim1, Index dim2, Index dim3) : m_data(dataPtr), m_dimensions(dim1, dim2, dim3) {
103
- EIGEN_STATIC_ASSERT(3 == NumIndices || NumIndices == Dynamic, YOU_MADE_A_PROGRAMMING_MISTAKE)
104
- }
105
- EIGEN_DEVICE_FUNC
106
- EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, Index dim1, Index dim2, Index dim3, Index dim4) : m_data(dataPtr), m_dimensions(dim1, dim2, dim3, dim4) {
107
- EIGEN_STATIC_ASSERT(4 == NumIndices || NumIndices == Dynamic, YOU_MADE_A_PROGRAMMING_MISTAKE)
108
- }
109
- EIGEN_DEVICE_FUNC
110
- EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, Index dim1, Index dim2, Index dim3, Index dim4, Index dim5) : m_data(dataPtr), m_dimensions(dim1, dim2, dim3, dim4, dim5) {
111
- EIGEN_STATIC_ASSERT(5 == NumIndices || NumIndices == Dynamic, YOU_MADE_A_PROGRAMMING_MISTAKE)
112
- }
113
- #endif
114
-
115
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, const array<Index, NumIndices>& dimensions)
116
- : m_data(dataPtr), m_dimensions(dimensions)
117
- { }
118
-
119
- template <typename Dimensions>
120
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorMap(StoragePointerType dataPtr, const Dimensions& dimensions)
121
- : m_data(dataPtr), m_dimensions(dimensions)
122
- { }
123
-
124
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorMap(PlainObjectType& tensor)
125
- : m_data(tensor.data()), m_dimensions(tensor.dimensions())
126
- { }
127
-
128
- EIGEN_DEVICE_FUNC
129
- EIGEN_STRONG_INLINE Index rank() const { return m_dimensions.rank(); }
130
- EIGEN_DEVICE_FUNC
131
- EIGEN_STRONG_INLINE Index dimension(Index n) const { return m_dimensions[n]; }
132
- EIGEN_DEVICE_FUNC
133
- EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
134
- EIGEN_DEVICE_FUNC
135
- EIGEN_STRONG_INLINE Index size() const { return m_dimensions.TotalSize(); }
136
- EIGEN_DEVICE_FUNC
137
- EIGEN_STRONG_INLINE StoragePointerType data() { return m_data; }
138
- EIGEN_DEVICE_FUNC
139
- EIGEN_STRONG_INLINE StoragePointerType data() const { return m_data; }
140
-
141
- EIGEN_DEVICE_FUNC
142
- EIGEN_STRONG_INLINE StorageRefType operator()(const array<Index, NumIndices>& indices) const
143
- {
144
- // eigen_assert(checkIndexRange(indices));
145
- if (PlainObjectType::Options&RowMajor) {
146
- const Index index = m_dimensions.IndexOfRowMajor(indices);
147
- return m_data[index];
148
- } else {
149
- const Index index = m_dimensions.IndexOfColMajor(indices);
150
- return m_data[index];
151
- }
152
- }
153
-
154
- EIGEN_DEVICE_FUNC
155
- EIGEN_STRONG_INLINE StorageRefType operator()() const
156
- {
157
- EIGEN_STATIC_ASSERT(NumIndices == 0, YOU_MADE_A_PROGRAMMING_MISTAKE)
158
- return m_data[0];
159
- }
160
-
161
- EIGEN_DEVICE_FUNC
162
- EIGEN_STRONG_INLINE StorageRefType operator()(Index index) const
163
- {
164
- eigen_internal_assert(index >= 0 && index < size());
165
- return m_data[index];
166
- }
167
-
168
- #if EIGEN_HAS_VARIADIC_TEMPLATES
169
- template<typename... IndexTypes> EIGEN_DEVICE_FUNC
170
- EIGEN_STRONG_INLINE StorageRefType operator()(Index firstIndex, Index secondIndex, IndexTypes... otherIndices) const
171
- {
172
- EIGEN_STATIC_ASSERT(sizeof...(otherIndices) + 2 == NumIndices, YOU_MADE_A_PROGRAMMING_MISTAKE)
173
- eigen_assert(internal::all((Eigen::NumTraits<Index>::highest() >= otherIndices)...));
174
- if (PlainObjectType::Options&RowMajor) {
175
- const Index index = m_dimensions.IndexOfRowMajor(array<Index, NumIndices>{{firstIndex, secondIndex, otherIndices...}});
176
- return m_data[index];
177
- } else {
178
- const Index index = m_dimensions.IndexOfColMajor(array<Index, NumIndices>{{firstIndex, secondIndex, otherIndices...}});
179
- return m_data[index];
180
- }
181
- }
182
- #else
183
- EIGEN_DEVICE_FUNC
184
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1) const
185
- {
186
- if (PlainObjectType::Options&RowMajor) {
187
- const Index index = i1 + i0 * m_dimensions[1];
188
- return m_data[index];
189
- } else {
190
- const Index index = i0 + i1 * m_dimensions[0];
191
- return m_data[index];
192
- }
193
- }
194
- EIGEN_DEVICE_FUNC
195
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1, Index i2) const
196
- {
197
- if (PlainObjectType::Options&RowMajor) {
198
- const Index index = i2 + m_dimensions[2] * (i1 + m_dimensions[1] * i0);
199
- return m_data[index];
200
- } else {
201
- const Index index = i0 + m_dimensions[0] * (i1 + m_dimensions[1] * i2);
202
- return m_data[index];
203
- }
204
- }
205
- EIGEN_DEVICE_FUNC
206
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1, Index i2, Index i3) const
207
- {
208
- if (PlainObjectType::Options&RowMajor) {
209
- const Index index = i3 + m_dimensions[3] * (i2 + m_dimensions[2] * (i1 + m_dimensions[1] * i0));
210
- return m_data[index];
211
- } else {
212
- const Index index = i0 + m_dimensions[0] * (i1 + m_dimensions[1] * (i2 + m_dimensions[2] * i3));
213
- return m_data[index];
214
- }
215
- }
216
- EIGEN_DEVICE_FUNC
217
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1, Index i2, Index i3, Index i4) const
218
- {
219
- if (PlainObjectType::Options&RowMajor) {
220
- const Index index = i4 + m_dimensions[4] * (i3 + m_dimensions[3] * (i2 + m_dimensions[2] * (i1 + m_dimensions[1] * i0)));
221
- return m_data[index];
222
- } else {
223
- const Index index = i0 + m_dimensions[0] * (i1 + m_dimensions[1] * (i2 + m_dimensions[2] * (i3 + m_dimensions[3] * i4)));
224
- return m_data[index];
225
- }
226
- }
227
- #endif
228
-
229
- EIGEN_DEVICE_FUNC
230
- EIGEN_STRONG_INLINE StorageRefType operator()(const array<Index, NumIndices>& indices)
231
- {
232
- // eigen_assert(checkIndexRange(indices));
233
- if (PlainObjectType::Options&RowMajor) {
234
- const Index index = m_dimensions.IndexOfRowMajor(indices);
235
- return m_data[index];
236
- } else {
237
- const Index index = m_dimensions.IndexOfColMajor(indices);
238
- return m_data[index];
239
- }
240
- }
241
-
242
- EIGEN_DEVICE_FUNC
243
- EIGEN_STRONG_INLINE StorageRefType operator()()
244
- {
245
- EIGEN_STATIC_ASSERT(NumIndices == 0, YOU_MADE_A_PROGRAMMING_MISTAKE)
246
- return m_data[0];
247
- }
248
-
249
- EIGEN_DEVICE_FUNC
250
- EIGEN_STRONG_INLINE StorageRefType operator()(Index index)
251
- {
252
- eigen_internal_assert(index >= 0 && index < size());
253
- return m_data[index];
254
- }
255
-
256
- #if EIGEN_HAS_VARIADIC_TEMPLATES
257
- template<typename... IndexTypes> EIGEN_DEVICE_FUNC
258
- EIGEN_STRONG_INLINE StorageRefType operator()(Index firstIndex, Index secondIndex, IndexTypes... otherIndices)
259
- {
260
- static_assert(sizeof...(otherIndices) + 2 == NumIndices || NumIndices == Dynamic, "Number of indices used to access a tensor coefficient must be equal to the rank of the tensor.");
261
- eigen_assert(internal::all((Eigen::NumTraits<Index>::highest() >= otherIndices)...));
262
- const std::size_t NumDims = sizeof...(otherIndices) + 2;
263
- if (PlainObjectType::Options&RowMajor) {
264
- const Index index = m_dimensions.IndexOfRowMajor(array<Index, NumDims>{{firstIndex, secondIndex, otherIndices...}});
265
- return m_data[index];
266
- } else {
267
- const Index index = m_dimensions.IndexOfColMajor(array<Index, NumDims>{{firstIndex, secondIndex, otherIndices...}});
268
- return m_data[index];
269
- }
270
- }
271
- #else
272
- EIGEN_DEVICE_FUNC
273
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1)
274
- {
275
- if (PlainObjectType::Options&RowMajor) {
276
- const Index index = i1 + i0 * m_dimensions[1];
277
- return m_data[index];
278
- } else {
279
- const Index index = i0 + i1 * m_dimensions[0];
280
- return m_data[index];
281
- }
282
- }
283
- EIGEN_DEVICE_FUNC
284
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1, Index i2)
285
- {
286
- if (PlainObjectType::Options&RowMajor) {
287
- const Index index = i2 + m_dimensions[2] * (i1 + m_dimensions[1] * i0);
288
- return m_data[index];
289
- } else {
290
- const Index index = i0 + m_dimensions[0] * (i1 + m_dimensions[1] * i2);
291
- return m_data[index];
292
- }
293
- }
294
- EIGEN_DEVICE_FUNC
295
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1, Index i2, Index i3)
296
- {
297
- if (PlainObjectType::Options&RowMajor) {
298
- const Index index = i3 + m_dimensions[3] * (i2 + m_dimensions[2] * (i1 + m_dimensions[1] * i0));
299
- return m_data[index];
300
- } else {
301
- const Index index = i0 + m_dimensions[0] * (i1 + m_dimensions[1] * (i2 + m_dimensions[2] * i3));
302
- return m_data[index];
303
- }
304
- }
305
- EIGEN_DEVICE_FUNC
306
- EIGEN_STRONG_INLINE StorageRefType operator()(Index i0, Index i1, Index i2, Index i3, Index i4)
307
- {
308
- if (PlainObjectType::Options&RowMajor) {
309
- const Index index = i4 + m_dimensions[4] * (i3 + m_dimensions[3] * (i2 + m_dimensions[2] * (i1 + m_dimensions[1] * i0)));
310
- return m_data[index];
311
- } else {
312
- const Index index = i0 + m_dimensions[0] * (i1 + m_dimensions[1] * (i2 + m_dimensions[2] * (i3 + m_dimensions[3] * i4)));
313
- return m_data[index];
314
- }
315
- }
316
- #endif
317
-
318
- EIGEN_TENSOR_INHERIT_ASSIGNMENT_OPERATORS(TensorMap)
319
-
320
- private:
321
- StoragePointerType m_data;
322
- Dimensions m_dimensions;
323
- };
324
-
325
- } // end namespace Eigen
326
-
327
- #endif // EIGEN_CXX11_TENSOR_TENSOR_MAP_H