sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/hierarchical_clustering.py +107 -5
  6. sequenzo/define_sequence_data.py +10 -1
  7. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  8. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  9. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  10. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  11. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  13. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  15. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  17. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  18. sequenzo/multidomain/cat.py +0 -53
  19. sequenzo/multidomain/idcd.py +0 -1
  20. sequenzo/openmp_setup.py +233 -0
  21. sequenzo/visualization/plot_transition_matrix.py +21 -22
  22. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  23. sequenzo-0.1.19.dist-info/RECORD +215 -0
  24. sequenzo/dissimilarity_measures/setup.py +0 -35
  25. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  26. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  167. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  168. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  169. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  170. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  171. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  172. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  173. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  174. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  175. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  176. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  177. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  178. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  179. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  180. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  181. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  182. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  183. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  184. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  185. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  186. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  187. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  188. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  189. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  190. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  191. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  192. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  193. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  194. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  195. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  196. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  197. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  198. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  199. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  200. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  201. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  202. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  203. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  204. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  205. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  206. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  207. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
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@@ -1,357 +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) 2016 Eugene Brevdo <ebrevdo@gmail.com>
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- // Copyright (C) 2016 Gael Guennebaud <gael.guennebaud@inria.fr>
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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_BESSELFUNCTIONS_FUNCTORS_H
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- #define EIGEN_BESSELFUNCTIONS_FUNCTORS_H
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-
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- namespace Eigen {
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-
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- namespace internal {
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-
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- /** \internal
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- * \brief Template functor to compute the modified Bessel function of the first
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- * kind of order zero.
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- * \sa class CwiseUnaryOp, Cwise::bessel_i0()
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- */
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- template <typename Scalar>
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- struct scalar_bessel_i0_op {
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- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_i0_op)
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
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- using numext::bessel_i0;
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- return bessel_i0(x);
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- }
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- typedef typename packet_traits<Scalar>::type Packet;
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
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- return internal::pbessel_i0(x);
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- }
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- };
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- template <typename Scalar>
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- struct functor_traits<scalar_bessel_i0_op<Scalar> > {
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- enum {
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- // On average, a Chebyshev polynomial of order N=20 is computed.
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- // The cost is N multiplications and 2N additions. We also add
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- // the cost of an additional exp over i0e.
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- Cost = 28 * NumTraits<Scalar>::MulCost + 48 * NumTraits<Scalar>::AddCost,
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- PacketAccess = packet_traits<Scalar>::HasBessel
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- };
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- };
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-
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- /** \internal
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- * \brief Template functor to compute the exponentially scaled modified Bessel
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- * function of the first kind of order zero
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- * \sa class CwiseUnaryOp, Cwise::bessel_i0e()
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- */
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- template <typename Scalar>
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- struct scalar_bessel_i0e_op {
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- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_i0e_op)
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
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- using numext::bessel_i0e;
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- return bessel_i0e(x);
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- }
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- typedef typename packet_traits<Scalar>::type Packet;
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
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- return internal::pbessel_i0e(x);
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- }
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- };
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- template <typename Scalar>
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- struct functor_traits<scalar_bessel_i0e_op<Scalar> > {
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- enum {
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- // On average, a Chebyshev polynomial of order N=20 is computed.
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- // The cost is N multiplications and 2N additions.
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- Cost = 20 * NumTraits<Scalar>::MulCost + 40 * NumTraits<Scalar>::AddCost,
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- PacketAccess = packet_traits<Scalar>::HasBessel
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- };
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- };
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-
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- /** \internal
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- * \brief Template functor to compute the modified Bessel function of the first
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- * kind of order one
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- * \sa class CwiseUnaryOp, Cwise::bessel_i1()
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- */
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- template <typename Scalar>
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- struct scalar_bessel_i1_op {
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- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_i1_op)
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
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- using numext::bessel_i1;
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- return bessel_i1(x);
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- }
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- typedef typename packet_traits<Scalar>::type Packet;
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
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- return internal::pbessel_i1(x);
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- }
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- };
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- template <typename Scalar>
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- struct functor_traits<scalar_bessel_i1_op<Scalar> > {
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- enum {
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- // On average, a Chebyshev polynomial of order N=20 is computed.
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- // The cost is N multiplications and 2N additions. We also add
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- // the cost of an additional exp over i1e.
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- Cost = 28 * NumTraits<Scalar>::MulCost + 48 * NumTraits<Scalar>::AddCost,
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- PacketAccess = packet_traits<Scalar>::HasBessel
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- };
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- };
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-
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- /** \internal
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- * \brief Template functor to compute the exponentially scaled modified Bessel
103
- * function of the first kind of order zero
104
- * \sa class CwiseUnaryOp, Cwise::bessel_i1e()
105
- */
106
- template <typename Scalar>
107
- struct scalar_bessel_i1e_op {
108
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_i1e_op)
109
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
110
- using numext::bessel_i1e;
111
- return bessel_i1e(x);
112
- }
113
- typedef typename packet_traits<Scalar>::type Packet;
114
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
115
- return internal::pbessel_i1e(x);
116
- }
117
- };
118
- template <typename Scalar>
119
- struct functor_traits<scalar_bessel_i1e_op<Scalar> > {
120
- enum {
121
- // On average, a Chebyshev polynomial of order N=20 is computed.
122
- // The cost is N multiplications and 2N additions.
123
- Cost = 20 * NumTraits<Scalar>::MulCost + 40 * NumTraits<Scalar>::AddCost,
124
- PacketAccess = packet_traits<Scalar>::HasBessel
125
- };
126
- };
127
-
128
- /** \internal
129
- * \brief Template functor to compute the Bessel function of the second kind of
130
- * order zero
131
- * \sa class CwiseUnaryOp, Cwise::bessel_j0()
132
- */
133
- template <typename Scalar>
134
- struct scalar_bessel_j0_op {
135
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_j0_op)
136
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
137
- using numext::bessel_j0;
138
- return bessel_j0(x);
139
- }
140
- typedef typename packet_traits<Scalar>::type Packet;
141
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
142
- return internal::pbessel_j0(x);
143
- }
144
- };
145
- template <typename Scalar>
146
- struct functor_traits<scalar_bessel_j0_op<Scalar> > {
147
- enum {
148
- // 6 polynomial of order ~N=8 is computed.
149
- // The cost is N multiplications and N additions each, along with a
150
- // sine, cosine and rsqrt cost.
151
- Cost = 63 * NumTraits<Scalar>::MulCost + 48 * NumTraits<Scalar>::AddCost,
152
- PacketAccess = packet_traits<Scalar>::HasBessel
153
- };
154
- };
155
-
156
- /** \internal
157
- * \brief Template functor to compute the Bessel function of the second kind of
158
- * order zero
159
- * \sa class CwiseUnaryOp, Cwise::bessel_y0()
160
- */
161
- template <typename Scalar>
162
- struct scalar_bessel_y0_op {
163
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_y0_op)
164
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
165
- using numext::bessel_y0;
166
- return bessel_y0(x);
167
- }
168
- typedef typename packet_traits<Scalar>::type Packet;
169
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
170
- return internal::pbessel_y0(x);
171
- }
172
- };
173
- template <typename Scalar>
174
- struct functor_traits<scalar_bessel_y0_op<Scalar> > {
175
- enum {
176
- // 6 polynomial of order ~N=8 is computed.
177
- // The cost is N multiplications and N additions each, along with a
178
- // sine, cosine, rsqrt and j0 cost.
179
- Cost = 126 * NumTraits<Scalar>::MulCost + 96 * NumTraits<Scalar>::AddCost,
180
- PacketAccess = packet_traits<Scalar>::HasBessel
181
- };
182
- };
183
-
184
- /** \internal
185
- * \brief Template functor to compute the Bessel function of the first kind of
186
- * order one
187
- * \sa class CwiseUnaryOp, Cwise::bessel_j1()
188
- */
189
- template <typename Scalar>
190
- struct scalar_bessel_j1_op {
191
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_j1_op)
192
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
193
- using numext::bessel_j1;
194
- return bessel_j1(x);
195
- }
196
- typedef typename packet_traits<Scalar>::type Packet;
197
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
198
- return internal::pbessel_j1(x);
199
- }
200
- };
201
- template <typename Scalar>
202
- struct functor_traits<scalar_bessel_j1_op<Scalar> > {
203
- enum {
204
- // 6 polynomial of order ~N=8 is computed.
205
- // The cost is N multiplications and N additions each, along with a
206
- // sine, cosine and rsqrt cost.
207
- Cost = 63 * NumTraits<Scalar>::MulCost + 48 * NumTraits<Scalar>::AddCost,
208
- PacketAccess = packet_traits<Scalar>::HasBessel
209
- };
210
- };
211
-
212
- /** \internal
213
- * \brief Template functor to compute the Bessel function of the second kind of
214
- * order one
215
- * \sa class CwiseUnaryOp, Cwise::bessel_j1e()
216
- */
217
- template <typename Scalar>
218
- struct scalar_bessel_y1_op {
219
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_y1_op)
220
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
221
- using numext::bessel_y1;
222
- return bessel_y1(x);
223
- }
224
- typedef typename packet_traits<Scalar>::type Packet;
225
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
226
- return internal::pbessel_y1(x);
227
- }
228
- };
229
- template <typename Scalar>
230
- struct functor_traits<scalar_bessel_y1_op<Scalar> > {
231
- enum {
232
- // 6 polynomial of order ~N=8 is computed.
233
- // The cost is N multiplications and N additions each, along with a
234
- // sine, cosine, rsqrt and j1 cost.
235
- Cost = 126 * NumTraits<Scalar>::MulCost + 96 * NumTraits<Scalar>::AddCost,
236
- PacketAccess = packet_traits<Scalar>::HasBessel
237
- };
238
- };
239
-
240
- /** \internal
241
- * \brief Template functor to compute the modified Bessel function of the second
242
- * kind of order zero
243
- * \sa class CwiseUnaryOp, Cwise::bessel_k0()
244
- */
245
- template <typename Scalar>
246
- struct scalar_bessel_k0_op {
247
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_k0_op)
248
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
249
- using numext::bessel_k0;
250
- return bessel_k0(x);
251
- }
252
- typedef typename packet_traits<Scalar>::type Packet;
253
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
254
- return internal::pbessel_k0(x);
255
- }
256
- };
257
- template <typename Scalar>
258
- struct functor_traits<scalar_bessel_k0_op<Scalar> > {
259
- enum {
260
- // On average, a Chebyshev polynomial of order N=10 is computed.
261
- // The cost is N multiplications and 2N additions. In addition we compute
262
- // i0, a log, exp and prsqrt and sin and cos.
263
- Cost = 68 * NumTraits<Scalar>::MulCost + 88 * NumTraits<Scalar>::AddCost,
264
- PacketAccess = packet_traits<Scalar>::HasBessel
265
- };
266
- };
267
-
268
- /** \internal
269
- * \brief Template functor to compute the exponentially scaled modified Bessel
270
- * function of the second kind of order zero
271
- * \sa class CwiseUnaryOp, Cwise::bessel_k0e()
272
- */
273
- template <typename Scalar>
274
- struct scalar_bessel_k0e_op {
275
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_k0e_op)
276
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
277
- using numext::bessel_k0e;
278
- return bessel_k0e(x);
279
- }
280
- typedef typename packet_traits<Scalar>::type Packet;
281
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
282
- return internal::pbessel_k0e(x);
283
- }
284
- };
285
- template <typename Scalar>
286
- struct functor_traits<scalar_bessel_k0e_op<Scalar> > {
287
- enum {
288
- // On average, a Chebyshev polynomial of order N=10 is computed.
289
- // The cost is N multiplications and 2N additions. In addition we compute
290
- // i0, a log, exp and prsqrt and sin and cos.
291
- Cost = 68 * NumTraits<Scalar>::MulCost + 88 * NumTraits<Scalar>::AddCost,
292
- PacketAccess = packet_traits<Scalar>::HasBessel
293
- };
294
- };
295
-
296
- /** \internal
297
- * \brief Template functor to compute the modified Bessel function of the
298
- * second kind of order one
299
- * \sa class CwiseUnaryOp, Cwise::bessel_k1()
300
- */
301
- template <typename Scalar>
302
- struct scalar_bessel_k1_op {
303
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_k1_op)
304
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
305
- using numext::bessel_k1;
306
- return bessel_k1(x);
307
- }
308
- typedef typename packet_traits<Scalar>::type Packet;
309
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
310
- return internal::pbessel_k1(x);
311
- }
312
- };
313
- template <typename Scalar>
314
- struct functor_traits<scalar_bessel_k1_op<Scalar> > {
315
- enum {
316
- // On average, a Chebyshev polynomial of order N=10 is computed.
317
- // The cost is N multiplications and 2N additions. In addition we compute
318
- // i1, a log, exp and prsqrt and sin and cos.
319
- Cost = 68 * NumTraits<Scalar>::MulCost + 88 * NumTraits<Scalar>::AddCost,
320
- PacketAccess = packet_traits<Scalar>::HasBessel
321
- };
322
- };
323
-
324
- /** \internal
325
- * \brief Template functor to compute the exponentially scaled modified Bessel
326
- * function of the second kind of order one
327
- * \sa class CwiseUnaryOp, Cwise::bessel_k1e()
328
- */
329
- template <typename Scalar>
330
- struct scalar_bessel_k1e_op {
331
- EIGEN_EMPTY_STRUCT_CTOR(scalar_bessel_k1e_op)
332
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar operator()(const Scalar& x) const {
333
- using numext::bessel_k1e;
334
- return bessel_k1e(x);
335
- }
336
- typedef typename packet_traits<Scalar>::type Packet;
337
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet packetOp(const Packet& x) const {
338
- return internal::pbessel_k1e(x);
339
- }
340
- };
341
- template <typename Scalar>
342
- struct functor_traits<scalar_bessel_k1e_op<Scalar> > {
343
- enum {
344
- // On average, a Chebyshev polynomial of order N=10 is computed.
345
- // The cost is N multiplications and 2N additions. In addition we compute
346
- // i1, a log, exp and prsqrt and sin and cos.
347
- Cost = 68 * NumTraits<Scalar>::MulCost + 88 * NumTraits<Scalar>::AddCost,
348
- PacketAccess = packet_traits<Scalar>::HasBessel
349
- };
350
- };
351
-
352
-
353
- } // end namespace internal
354
-
355
- } // end namespace Eigen
356
-
357
- #endif // EIGEN_BESSELFUNCTIONS_FUNCTORS_H
@@ -1,66 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // This Source Code Form is subject to the terms of the Mozilla
5
- // Public License v. 2.0. If a copy of the MPL was not distributed
6
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
7
-
8
- #ifndef EIGEN_BESSELFUNCTIONS_HALF_H
9
- #define EIGEN_BESSELFUNCTIONS_HALF_H
10
-
11
- namespace Eigen {
12
- namespace numext {
13
-
14
- #if EIGEN_HAS_C99_MATH
15
- template <>
16
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_i0(const Eigen::half& x) {
17
- return Eigen::half(Eigen::numext::bessel_i0(static_cast<float>(x)));
18
- }
19
- template <>
20
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_i0e(const Eigen::half& x) {
21
- return Eigen::half(Eigen::numext::bessel_i0e(static_cast<float>(x)));
22
- }
23
- template <>
24
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_i1(const Eigen::half& x) {
25
- return Eigen::half(Eigen::numext::bessel_i1(static_cast<float>(x)));
26
- }
27
- template <>
28
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_i1e(const Eigen::half& x) {
29
- return Eigen::half(Eigen::numext::bessel_i1e(static_cast<float>(x)));
30
- }
31
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_j0(const Eigen::half& x) {
32
- return Eigen::half(Eigen::numext::bessel_j0(static_cast<float>(x)));
33
- }
34
- template <>
35
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_j1(const Eigen::half& x) {
36
- return Eigen::half(Eigen::numext::bessel_j1(static_cast<float>(x)));
37
- }
38
- template <>
39
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_y0(const Eigen::half& x) {
40
- return Eigen::half(Eigen::numext::bessel_y0(static_cast<float>(x)));
41
- }
42
- template <>
43
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_y1(const Eigen::half& x) {
44
- return Eigen::half(Eigen::numext::bessel_y1(static_cast<float>(x)));
45
- }
46
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_k0(const Eigen::half& x) {
47
- return Eigen::half(Eigen::numext::bessel_k0(static_cast<float>(x)));
48
- }
49
- template <>
50
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_k0e(const Eigen::half& x) {
51
- return Eigen::half(Eigen::numext::bessel_k0e(static_cast<float>(x)));
52
- }
53
- template <>
54
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_k1(const Eigen::half& x) {
55
- return Eigen::half(Eigen::numext::bessel_k1(static_cast<float>(x)));
56
- }
57
- template <>
58
- EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC Eigen::half bessel_k1e(const Eigen::half& x) {
59
- return Eigen::half(Eigen::numext::bessel_k1e(static_cast<float>(x)));
60
- }
61
- #endif
62
-
63
- } // end namespace numext
64
- } // end namespace Eigen
65
-
66
- #endif // EIGEN_BESSELFUNCTIONS_HALF_H