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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@@ -1,669 +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) 2015 Jianwei Cui <thucjw@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_FFT_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_FFT_H
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-
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- namespace Eigen {
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-
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- /** \class TensorFFT
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor FFT class.
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- *
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- * TODO:
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- * Vectorize the Cooley Tukey and the Bluestein algorithm
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- * Add support for multithreaded evaluation
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- * Improve the performance on GPU
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- */
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-
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- template <bool NeedUprade> struct MakeComplex {
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- template <typename T>
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- EIGEN_DEVICE_FUNC
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- T operator() (const T& val) const { return val; }
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- };
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-
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- template <> struct MakeComplex<true> {
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- template <typename T>
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- EIGEN_DEVICE_FUNC
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- std::complex<T> operator() (const T& val) const { return std::complex<T>(val, 0); }
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- };
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-
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- template <> struct MakeComplex<false> {
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- template <typename T>
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- EIGEN_DEVICE_FUNC
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- std::complex<T> operator() (const std::complex<T>& val) const { return val; }
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- };
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-
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- template <int ResultType> struct PartOf {
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- template <typename T> T operator() (const T& val) const { return val; }
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- };
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-
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- template <> struct PartOf<RealPart> {
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- template <typename T> T operator() (const std::complex<T>& val) const { return val.real(); }
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- };
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-
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- template <> struct PartOf<ImagPart> {
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- template <typename T> T operator() (const std::complex<T>& val) const { return val.imag(); }
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- };
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-
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- namespace internal {
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- template <typename FFT, typename XprType, int FFTResultType, int FFTDir>
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- struct traits<TensorFFTOp<FFT, XprType, FFTResultType, FFTDir> > : public traits<XprType> {
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- typedef traits<XprType> XprTraits;
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- typedef typename NumTraits<typename XprTraits::Scalar>::Real RealScalar;
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- typedef typename std::complex<RealScalar> ComplexScalar;
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- typedef typename XprTraits::Scalar InputScalar;
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- typedef typename conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
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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 traits<XprType>::PointerType PointerType;
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- };
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-
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- template <typename FFT, typename XprType, int FFTResultType, int FFTDirection>
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- struct eval<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>, Eigen::Dense> {
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- typedef const TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>& type;
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- };
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-
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- template <typename FFT, typename XprType, int FFTResultType, int FFTDirection>
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- struct nested<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>, 1, typename eval<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection> >::type> {
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- typedef TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection> 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 FFT, typename XprType, int FFTResultType, int FFTDir>
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- class TensorFFTOp : public TensorBase<TensorFFTOp<FFT, XprType, FFTResultType, FFTDir>, ReadOnlyAccessors> {
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- public:
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- typedef typename Eigen::internal::traits<TensorFFTOp>::Scalar Scalar;
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- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
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- typedef typename std::complex<RealScalar> ComplexScalar;
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- typedef typename internal::conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
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- typedef OutputScalar CoeffReturnType;
93
- typedef typename Eigen::internal::nested<TensorFFTOp>::type Nested;
94
- typedef typename Eigen::internal::traits<TensorFFTOp>::StorageKind StorageKind;
95
- typedef typename Eigen::internal::traits<TensorFFTOp>::Index Index;
96
-
97
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorFFTOp(const XprType& expr, const FFT& fft)
98
- : m_xpr(expr), m_fft(fft) {}
99
-
100
- EIGEN_DEVICE_FUNC
101
- const FFT& fft() const { return m_fft; }
102
-
103
- EIGEN_DEVICE_FUNC
104
- const typename internal::remove_all<typename XprType::Nested>::type& expression() const {
105
- return m_xpr;
106
- }
107
-
108
- protected:
109
- typename XprType::Nested m_xpr;
110
- const FFT m_fft;
111
- };
112
-
113
- // Eval as rvalue
114
- template <typename FFT, typename ArgType, typename Device, int FFTResultType, int FFTDir>
115
- struct TensorEvaluator<const TensorFFTOp<FFT, ArgType, FFTResultType, FFTDir>, Device> {
116
- typedef TensorFFTOp<FFT, ArgType, FFTResultType, FFTDir> XprType;
117
- typedef typename XprType::Index Index;
118
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
119
- typedef DSizes<Index, NumDims> Dimensions;
120
- typedef typename XprType::Scalar Scalar;
121
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
122
- typedef typename std::complex<RealScalar> ComplexScalar;
123
- typedef typename TensorEvaluator<ArgType, Device>::Dimensions InputDimensions;
124
- typedef internal::traits<XprType> XprTraits;
125
- typedef typename XprTraits::Scalar InputScalar;
126
- typedef typename internal::conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
127
- typedef OutputScalar CoeffReturnType;
128
- typedef typename PacketType<OutputScalar, Device>::type PacketReturnType;
129
- static const int PacketSize = internal::unpacket_traits<PacketReturnType>::size;
130
- typedef StorageMemory<CoeffReturnType, Device> Storage;
131
- typedef typename Storage::Type EvaluatorPointerType;
132
-
133
- enum {
134
- IsAligned = false,
135
- PacketAccess = true,
136
- BlockAccess = false,
137
- PreferBlockAccess = false,
138
- Layout = TensorEvaluator<ArgType, Device>::Layout,
139
- CoordAccess = false,
140
- RawAccess = false
141
- };
142
-
143
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
144
- typedef internal::TensorBlockNotImplemented TensorBlock;
145
- //===--------------------------------------------------------------------===//
146
-
147
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device) : m_fft(op.fft()), m_impl(op.expression(), device), m_data(NULL), m_device(device) {
148
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
149
- for (int i = 0; i < NumDims; ++i) {
150
- eigen_assert(input_dims[i] > 0);
151
- m_dimensions[i] = input_dims[i];
152
- }
153
-
154
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
155
- m_strides[0] = 1;
156
- for (int i = 1; i < NumDims; ++i) {
157
- m_strides[i] = m_strides[i - 1] * m_dimensions[i - 1];
158
- }
159
- } else {
160
- m_strides[NumDims - 1] = 1;
161
- for (int i = NumDims - 2; i >= 0; --i) {
162
- m_strides[i] = m_strides[i + 1] * m_dimensions[i + 1];
163
- }
164
- }
165
- m_size = m_dimensions.TotalSize();
166
- }
167
-
168
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const {
169
- return m_dimensions;
170
- }
171
-
172
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType data) {
173
- m_impl.evalSubExprsIfNeeded(NULL);
174
- if (data) {
175
- evalToBuf(data);
176
- return false;
177
- } else {
178
- m_data = (EvaluatorPointerType)m_device.get((CoeffReturnType*)(m_device.allocate_temp(sizeof(CoeffReturnType) * m_size)));
179
- evalToBuf(m_data);
180
- return true;
181
- }
182
- }
183
-
184
- EIGEN_STRONG_INLINE void cleanup() {
185
- if (m_data) {
186
- m_device.deallocate(m_data);
187
- m_data = NULL;
188
- }
189
- m_impl.cleanup();
190
- }
191
-
192
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE CoeffReturnType coeff(Index index) const {
193
- return m_data[index];
194
- }
195
-
196
- template <int LoadMode>
197
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketReturnType
198
- packet(Index index) const {
199
- return internal::ploadt<PacketReturnType, LoadMode>(m_data + index);
200
- }
201
-
202
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
203
- costPerCoeff(bool vectorized) const {
204
- return TensorOpCost(sizeof(CoeffReturnType), 0, 0, vectorized, PacketSize);
205
- }
206
-
207
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return m_data; }
208
- #ifdef EIGEN_USE_SYCL
209
- // binding placeholder accessors to a command group handler for SYCL
210
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
211
- m_data.bind(cgh);
212
- }
213
- #endif
214
-
215
- private:
216
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalToBuf(EvaluatorPointerType data) {
217
- const bool write_to_out = internal::is_same<OutputScalar, ComplexScalar>::value;
218
- ComplexScalar* buf = write_to_out ? (ComplexScalar*)data : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * m_size);
219
-
220
- for (Index i = 0; i < m_size; ++i) {
221
- buf[i] = MakeComplex<internal::is_same<InputScalar, RealScalar>::value>()(m_impl.coeff(i));
222
- }
223
-
224
- for (size_t i = 0; i < m_fft.size(); ++i) {
225
- Index dim = m_fft[i];
226
- eigen_assert(dim >= 0 && dim < NumDims);
227
- Index line_len = m_dimensions[dim];
228
- eigen_assert(line_len >= 1);
229
- ComplexScalar* line_buf = (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * line_len);
230
- const bool is_power_of_two = isPowerOfTwo(line_len);
231
- const Index good_composite = is_power_of_two ? 0 : findGoodComposite(line_len);
232
- const Index log_len = is_power_of_two ? getLog2(line_len) : getLog2(good_composite);
233
-
234
- ComplexScalar* a = is_power_of_two ? NULL : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * good_composite);
235
- ComplexScalar* b = is_power_of_two ? NULL : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * good_composite);
236
- ComplexScalar* pos_j_base_powered = is_power_of_two ? NULL : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * (line_len + 1));
237
- if (!is_power_of_two) {
238
- // Compute twiddle factors
239
- // t_n = exp(sqrt(-1) * pi * n^2 / line_len)
240
- // for n = 0, 1,..., line_len-1.
241
- // For n > 2 we use the recurrence t_n = t_{n-1}^2 / t_{n-2} * t_1^2
242
-
243
- // The recurrence is correct in exact arithmetic, but causes
244
- // numerical issues for large transforms, especially in
245
- // single-precision floating point.
246
- //
247
- // pos_j_base_powered[0] = ComplexScalar(1, 0);
248
- // if (line_len > 1) {
249
- // const ComplexScalar pos_j_base = ComplexScalar(
250
- // numext::cos(M_PI / line_len), numext::sin(M_PI / line_len));
251
- // pos_j_base_powered[1] = pos_j_base;
252
- // if (line_len > 2) {
253
- // const ComplexScalar pos_j_base_sq = pos_j_base * pos_j_base;
254
- // for (int i = 2; i < line_len + 1; ++i) {
255
- // pos_j_base_powered[i] = pos_j_base_powered[i - 1] *
256
- // pos_j_base_powered[i - 1] /
257
- // pos_j_base_powered[i - 2] *
258
- // pos_j_base_sq;
259
- // }
260
- // }
261
- // }
262
- // TODO(rmlarsen): Find a way to use Eigen's vectorized sin
263
- // and cosine functions here.
264
- for (int j = 0; j < line_len + 1; ++j) {
265
- double arg = ((EIGEN_PI * j) * j) / line_len;
266
- std::complex<double> tmp(numext::cos(arg), numext::sin(arg));
267
- pos_j_base_powered[j] = static_cast<ComplexScalar>(tmp);
268
- }
269
- }
270
-
271
- for (Index partial_index = 0; partial_index < m_size / line_len; ++partial_index) {
272
- const Index base_offset = getBaseOffsetFromIndex(partial_index, dim);
273
-
274
- // get data into line_buf
275
- const Index stride = m_strides[dim];
276
- if (stride == 1) {
277
- m_device.memcpy(line_buf, &buf[base_offset], line_len*sizeof(ComplexScalar));
278
- } else {
279
- Index offset = base_offset;
280
- for (int j = 0; j < line_len; ++j, offset += stride) {
281
- line_buf[j] = buf[offset];
282
- }
283
- }
284
-
285
- // process the line
286
- if (is_power_of_two) {
287
- processDataLineCooleyTukey(line_buf, line_len, log_len);
288
- }
289
- else {
290
- processDataLineBluestein(line_buf, line_len, good_composite, log_len, a, b, pos_j_base_powered);
291
- }
292
-
293
- // write back
294
- if (FFTDir == FFT_FORWARD && stride == 1) {
295
- m_device.memcpy(&buf[base_offset], line_buf, line_len*sizeof(ComplexScalar));
296
- } else {
297
- Index offset = base_offset;
298
- const ComplexScalar div_factor = ComplexScalar(1.0 / line_len, 0);
299
- for (int j = 0; j < line_len; ++j, offset += stride) {
300
- buf[offset] = (FFTDir == FFT_FORWARD) ? line_buf[j] : line_buf[j] * div_factor;
301
- }
302
- }
303
- }
304
- m_device.deallocate(line_buf);
305
- if (!is_power_of_two) {
306
- m_device.deallocate(a);
307
- m_device.deallocate(b);
308
- m_device.deallocate(pos_j_base_powered);
309
- }
310
- }
311
-
312
- if(!write_to_out) {
313
- for (Index i = 0; i < m_size; ++i) {
314
- data[i] = PartOf<FFTResultType>()(buf[i]);
315
- }
316
- m_device.deallocate(buf);
317
- }
318
- }
319
-
320
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static bool isPowerOfTwo(Index x) {
321
- eigen_assert(x > 0);
322
- return !(x & (x - 1));
323
- }
324
-
325
- // The composite number for padding, used in Bluestein's FFT algorithm
326
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static Index findGoodComposite(Index n) {
327
- Index i = 2;
328
- while (i < 2 * n - 1) i *= 2;
329
- return i;
330
- }
331
-
332
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static Index getLog2(Index m) {
333
- Index log2m = 0;
334
- while (m >>= 1) log2m++;
335
- return log2m;
336
- }
337
-
338
- // Call Cooley Tukey algorithm directly, data length must be power of 2
339
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void processDataLineCooleyTukey(ComplexScalar* line_buf, Index line_len, Index log_len) {
340
- eigen_assert(isPowerOfTwo(line_len));
341
- scramble_FFT(line_buf, line_len);
342
- compute_1D_Butterfly<FFTDir>(line_buf, line_len, log_len);
343
- }
344
-
345
- // Call Bluestein's FFT algorithm, m is a good composite number greater than (2 * n - 1), used as the padding length
346
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void processDataLineBluestein(ComplexScalar* line_buf, Index line_len, Index good_composite, Index log_len, ComplexScalar* a, ComplexScalar* b, const ComplexScalar* pos_j_base_powered) {
347
- Index n = line_len;
348
- Index m = good_composite;
349
- ComplexScalar* data = line_buf;
350
-
351
- for (Index i = 0; i < n; ++i) {
352
- if(FFTDir == FFT_FORWARD) {
353
- a[i] = data[i] * numext::conj(pos_j_base_powered[i]);
354
- }
355
- else {
356
- a[i] = data[i] * pos_j_base_powered[i];
357
- }
358
- }
359
- for (Index i = n; i < m; ++i) {
360
- a[i] = ComplexScalar(0, 0);
361
- }
362
-
363
- for (Index i = 0; i < n; ++i) {
364
- if(FFTDir == FFT_FORWARD) {
365
- b[i] = pos_j_base_powered[i];
366
- }
367
- else {
368
- b[i] = numext::conj(pos_j_base_powered[i]);
369
- }
370
- }
371
- for (Index i = n; i < m - n; ++i) {
372
- b[i] = ComplexScalar(0, 0);
373
- }
374
- for (Index i = m - n; i < m; ++i) {
375
- if(FFTDir == FFT_FORWARD) {
376
- b[i] = pos_j_base_powered[m-i];
377
- }
378
- else {
379
- b[i] = numext::conj(pos_j_base_powered[m-i]);
380
- }
381
- }
382
-
383
- scramble_FFT(a, m);
384
- compute_1D_Butterfly<FFT_FORWARD>(a, m, log_len);
385
-
386
- scramble_FFT(b, m);
387
- compute_1D_Butterfly<FFT_FORWARD>(b, m, log_len);
388
-
389
- for (Index i = 0; i < m; ++i) {
390
- a[i] *= b[i];
391
- }
392
-
393
- scramble_FFT(a, m);
394
- compute_1D_Butterfly<FFT_REVERSE>(a, m, log_len);
395
-
396
- //Do the scaling after ifft
397
- for (Index i = 0; i < m; ++i) {
398
- a[i] /= m;
399
- }
400
-
401
- for (Index i = 0; i < n; ++i) {
402
- if(FFTDir == FFT_FORWARD) {
403
- data[i] = a[i] * numext::conj(pos_j_base_powered[i]);
404
- }
405
- else {
406
- data[i] = a[i] * pos_j_base_powered[i];
407
- }
408
- }
409
- }
410
-
411
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static void scramble_FFT(ComplexScalar* data, Index n) {
412
- eigen_assert(isPowerOfTwo(n));
413
- Index j = 1;
414
- for (Index i = 1; i < n; ++i){
415
- if (j > i) {
416
- std::swap(data[j-1], data[i-1]);
417
- }
418
- Index m = n >> 1;
419
- while (m >= 2 && j > m) {
420
- j -= m;
421
- m >>= 1;
422
- }
423
- j += m;
424
- }
425
- }
426
-
427
- template <int Dir>
428
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_2(ComplexScalar* data) {
429
- ComplexScalar tmp = data[1];
430
- data[1] = data[0] - data[1];
431
- data[0] += tmp;
432
- }
433
-
434
- template <int Dir>
435
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_4(ComplexScalar* data) {
436
- ComplexScalar tmp[4];
437
- tmp[0] = data[0] + data[1];
438
- tmp[1] = data[0] - data[1];
439
- tmp[2] = data[2] + data[3];
440
- if (Dir == FFT_FORWARD) {
441
- tmp[3] = ComplexScalar(0.0, -1.0) * (data[2] - data[3]);
442
- } else {
443
- tmp[3] = ComplexScalar(0.0, 1.0) * (data[2] - data[3]);
444
- }
445
- data[0] = tmp[0] + tmp[2];
446
- data[1] = tmp[1] + tmp[3];
447
- data[2] = tmp[0] - tmp[2];
448
- data[3] = tmp[1] - tmp[3];
449
- }
450
-
451
- template <int Dir>
452
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_8(ComplexScalar* data) {
453
- ComplexScalar tmp_1[8];
454
- ComplexScalar tmp_2[8];
455
-
456
- tmp_1[0] = data[0] + data[1];
457
- tmp_1[1] = data[0] - data[1];
458
- tmp_1[2] = data[2] + data[3];
459
- if (Dir == FFT_FORWARD) {
460
- tmp_1[3] = (data[2] - data[3]) * ComplexScalar(0, -1);
461
- } else {
462
- tmp_1[3] = (data[2] - data[3]) * ComplexScalar(0, 1);
463
- }
464
- tmp_1[4] = data[4] + data[5];
465
- tmp_1[5] = data[4] - data[5];
466
- tmp_1[6] = data[6] + data[7];
467
- if (Dir == FFT_FORWARD) {
468
- tmp_1[7] = (data[6] - data[7]) * ComplexScalar(0, -1);
469
- } else {
470
- tmp_1[7] = (data[6] - data[7]) * ComplexScalar(0, 1);
471
- }
472
- tmp_2[0] = tmp_1[0] + tmp_1[2];
473
- tmp_2[1] = tmp_1[1] + tmp_1[3];
474
- tmp_2[2] = tmp_1[0] - tmp_1[2];
475
- tmp_2[3] = tmp_1[1] - tmp_1[3];
476
- tmp_2[4] = tmp_1[4] + tmp_1[6];
477
- // SQRT2DIV2 = sqrt(2)/2
478
- #define SQRT2DIV2 0.7071067811865476
479
- if (Dir == FFT_FORWARD) {
480
- tmp_2[5] = (tmp_1[5] + tmp_1[7]) * ComplexScalar(SQRT2DIV2, -SQRT2DIV2);
481
- tmp_2[6] = (tmp_1[4] - tmp_1[6]) * ComplexScalar(0, -1);
482
- tmp_2[7] = (tmp_1[5] - tmp_1[7]) * ComplexScalar(-SQRT2DIV2, -SQRT2DIV2);
483
- } else {
484
- tmp_2[5] = (tmp_1[5] + tmp_1[7]) * ComplexScalar(SQRT2DIV2, SQRT2DIV2);
485
- tmp_2[6] = (tmp_1[4] - tmp_1[6]) * ComplexScalar(0, 1);
486
- tmp_2[7] = (tmp_1[5] - tmp_1[7]) * ComplexScalar(-SQRT2DIV2, SQRT2DIV2);
487
- }
488
- data[0] = tmp_2[0] + tmp_2[4];
489
- data[1] = tmp_2[1] + tmp_2[5];
490
- data[2] = tmp_2[2] + tmp_2[6];
491
- data[3] = tmp_2[3] + tmp_2[7];
492
- data[4] = tmp_2[0] - tmp_2[4];
493
- data[5] = tmp_2[1] - tmp_2[5];
494
- data[6] = tmp_2[2] - tmp_2[6];
495
- data[7] = tmp_2[3] - tmp_2[7];
496
- }
497
-
498
- template <int Dir>
499
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_1D_merge(
500
- ComplexScalar* data, Index n, Index n_power_of_2) {
501
- // Original code:
502
- // RealScalar wtemp = std::sin(M_PI/n);
503
- // RealScalar wpi = -std::sin(2 * M_PI/n);
504
- const RealScalar wtemp = m_sin_PI_div_n_LUT[n_power_of_2];
505
- const RealScalar wpi = (Dir == FFT_FORWARD)
506
- ? m_minus_sin_2_PI_div_n_LUT[n_power_of_2]
507
- : -m_minus_sin_2_PI_div_n_LUT[n_power_of_2];
508
-
509
- const ComplexScalar wp(wtemp, wpi);
510
- const ComplexScalar wp_one = wp + ComplexScalar(1, 0);
511
- const ComplexScalar wp_one_2 = wp_one * wp_one;
512
- const ComplexScalar wp_one_3 = wp_one_2 * wp_one;
513
- const ComplexScalar wp_one_4 = wp_one_3 * wp_one;
514
- const Index n2 = n / 2;
515
- ComplexScalar w(1.0, 0.0);
516
- for (Index i = 0; i < n2; i += 4) {
517
- ComplexScalar temp0(data[i + n2] * w);
518
- ComplexScalar temp1(data[i + 1 + n2] * w * wp_one);
519
- ComplexScalar temp2(data[i + 2 + n2] * w * wp_one_2);
520
- ComplexScalar temp3(data[i + 3 + n2] * w * wp_one_3);
521
- w = w * wp_one_4;
522
-
523
- data[i + n2] = data[i] - temp0;
524
- data[i] += temp0;
525
-
526
- data[i + 1 + n2] = data[i + 1] - temp1;
527
- data[i + 1] += temp1;
528
-
529
- data[i + 2 + n2] = data[i + 2] - temp2;
530
- data[i + 2] += temp2;
531
-
532
- data[i + 3 + n2] = data[i + 3] - temp3;
533
- data[i + 3] += temp3;
534
- }
535
- }
536
-
537
- template <int Dir>
538
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void compute_1D_Butterfly(
539
- ComplexScalar* data, Index n, Index n_power_of_2) {
540
- eigen_assert(isPowerOfTwo(n));
541
- if (n > 8) {
542
- compute_1D_Butterfly<Dir>(data, n / 2, n_power_of_2 - 1);
543
- compute_1D_Butterfly<Dir>(data + n / 2, n / 2, n_power_of_2 - 1);
544
- butterfly_1D_merge<Dir>(data, n, n_power_of_2);
545
- } else if (n == 8) {
546
- butterfly_8<Dir>(data);
547
- } else if (n == 4) {
548
- butterfly_4<Dir>(data);
549
- } else if (n == 2) {
550
- butterfly_2<Dir>(data);
551
- }
552
- }
553
-
554
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index getBaseOffsetFromIndex(Index index, Index omitted_dim) const {
555
- Index result = 0;
556
-
557
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
558
- for (int i = NumDims - 1; i > omitted_dim; --i) {
559
- const Index partial_m_stride = m_strides[i] / m_dimensions[omitted_dim];
560
- const Index idx = index / partial_m_stride;
561
- index -= idx * partial_m_stride;
562
- result += idx * m_strides[i];
563
- }
564
- result += index;
565
- }
566
- else {
567
- for (Index i = 0; i < omitted_dim; ++i) {
568
- const Index partial_m_stride = m_strides[i] / m_dimensions[omitted_dim];
569
- const Index idx = index / partial_m_stride;
570
- index -= idx * partial_m_stride;
571
- result += idx * m_strides[i];
572
- }
573
- result += index;
574
- }
575
- // Value of index_coords[omitted_dim] is not determined to this step
576
- return result;
577
- }
578
-
579
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index getIndexFromOffset(Index base, Index omitted_dim, Index offset) const {
580
- Index result = base + offset * m_strides[omitted_dim] ;
581
- return result;
582
- }
583
-
584
- protected:
585
- Index m_size;
586
- const FFT EIGEN_DEVICE_REF m_fft;
587
- Dimensions m_dimensions;
588
- array<Index, NumDims> m_strides;
589
- TensorEvaluator<ArgType, Device> m_impl;
590
- EvaluatorPointerType m_data;
591
- const Device EIGEN_DEVICE_REF m_device;
592
-
593
- // This will support a maximum FFT size of 2^32 for each dimension
594
- // m_sin_PI_div_n_LUT[i] = (-2) * std::sin(M_PI / std::pow(2,i)) ^ 2;
595
- const RealScalar m_sin_PI_div_n_LUT[32] = {
596
- RealScalar(0.0),
597
- RealScalar(-2),
598
- RealScalar(-0.999999999999999),
599
- RealScalar(-0.292893218813453),
600
- RealScalar(-0.0761204674887130),
601
- RealScalar(-0.0192147195967696),
602
- RealScalar(-0.00481527332780311),
603
- RealScalar(-0.00120454379482761),
604
- RealScalar(-3.01181303795779e-04),
605
- RealScalar(-7.52981608554592e-05),
606
- RealScalar(-1.88247173988574e-05),
607
- RealScalar(-4.70619042382852e-06),
608
- RealScalar(-1.17654829809007e-06),
609
- RealScalar(-2.94137117780840e-07),
610
- RealScalar(-7.35342821488550e-08),
611
- RealScalar(-1.83835707061916e-08),
612
- RealScalar(-4.59589268710903e-09),
613
- RealScalar(-1.14897317243732e-09),
614
- RealScalar(-2.87243293150586e-10),
615
- RealScalar( -7.18108232902250e-11),
616
- RealScalar(-1.79527058227174e-11),
617
- RealScalar(-4.48817645568941e-12),
618
- RealScalar(-1.12204411392298e-12),
619
- RealScalar(-2.80511028480785e-13),
620
- RealScalar(-7.01277571201985e-14),
621
- RealScalar(-1.75319392800498e-14),
622
- RealScalar(-4.38298482001247e-15),
623
- RealScalar(-1.09574620500312e-15),
624
- RealScalar(-2.73936551250781e-16),
625
- RealScalar(-6.84841378126949e-17),
626
- RealScalar(-1.71210344531737e-17),
627
- RealScalar(-4.28025861329343e-18)
628
- };
629
-
630
- // m_minus_sin_2_PI_div_n_LUT[i] = -std::sin(2 * M_PI / std::pow(2,i));
631
- const RealScalar m_minus_sin_2_PI_div_n_LUT[32] = {
632
- RealScalar(0.0),
633
- RealScalar(0.0),
634
- RealScalar(-1.00000000000000e+00),
635
- RealScalar(-7.07106781186547e-01),
636
- RealScalar(-3.82683432365090e-01),
637
- RealScalar(-1.95090322016128e-01),
638
- RealScalar(-9.80171403295606e-02),
639
- RealScalar(-4.90676743274180e-02),
640
- RealScalar(-2.45412285229123e-02),
641
- RealScalar(-1.22715382857199e-02),
642
- RealScalar(-6.13588464915448e-03),
643
- RealScalar(-3.06795676296598e-03),
644
- RealScalar(-1.53398018628477e-03),
645
- RealScalar(-7.66990318742704e-04),
646
- RealScalar(-3.83495187571396e-04),
647
- RealScalar(-1.91747597310703e-04),
648
- RealScalar(-9.58737990959773e-05),
649
- RealScalar(-4.79368996030669e-05),
650
- RealScalar(-2.39684498084182e-05),
651
- RealScalar(-1.19842249050697e-05),
652
- RealScalar(-5.99211245264243e-06),
653
- RealScalar(-2.99605622633466e-06),
654
- RealScalar(-1.49802811316901e-06),
655
- RealScalar(-7.49014056584716e-07),
656
- RealScalar(-3.74507028292384e-07),
657
- RealScalar(-1.87253514146195e-07),
658
- RealScalar(-9.36267570730981e-08),
659
- RealScalar(-4.68133785365491e-08),
660
- RealScalar(-2.34066892682746e-08),
661
- RealScalar(-1.17033446341373e-08),
662
- RealScalar(-5.85167231706864e-09),
663
- RealScalar(-2.92583615853432e-09)
664
- };
665
- };
666
-
667
- } // end namespace Eigen
668
-
669
- #endif // EIGEN_CXX11_TENSOR_TENSOR_FFT_H