sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp312-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp312-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp312-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp312-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp312-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp312-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp312-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp312-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,291 +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_PATCH_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_PATCH_H
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-
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- namespace Eigen {
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-
15
- /** \class TensorPatch
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor patch class.
19
- *
20
- *
21
- */
22
- namespace internal {
23
- template<typename PatchDim, typename XprType>
24
- struct traits<TensorPatchOp<PatchDim, XprType> > : public traits<XprType>
25
- {
26
- typedef typename XprType::Scalar Scalar;
27
- typedef traits<XprType> XprTraits;
28
- typedef typename XprTraits::StorageKind StorageKind;
29
- typedef typename XprTraits::Index Index;
30
- typedef typename XprType::Nested Nested;
31
- typedef typename remove_reference<Nested>::type _Nested;
32
- static const int NumDimensions = XprTraits::NumDimensions + 1;
33
- static const int Layout = XprTraits::Layout;
34
- typedef typename XprTraits::PointerType PointerType;
35
- };
36
-
37
- template<typename PatchDim, typename XprType>
38
- struct eval<TensorPatchOp<PatchDim, XprType>, Eigen::Dense>
39
- {
40
- typedef const TensorPatchOp<PatchDim, XprType>& type;
41
- };
42
-
43
- template<typename PatchDim, typename XprType>
44
- struct nested<TensorPatchOp<PatchDim, XprType>, 1, typename eval<TensorPatchOp<PatchDim, XprType> >::type>
45
- {
46
- typedef TensorPatchOp<PatchDim, XprType> type;
47
- };
48
-
49
- } // end namespace internal
50
-
51
-
52
-
53
- template<typename PatchDim, typename XprType>
54
- class TensorPatchOp : public TensorBase<TensorPatchOp<PatchDim, XprType>, ReadOnlyAccessors>
55
- {
56
- public:
57
- typedef typename Eigen::internal::traits<TensorPatchOp>::Scalar Scalar;
58
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
59
- typedef typename XprType::CoeffReturnType CoeffReturnType;
60
- typedef typename Eigen::internal::nested<TensorPatchOp>::type Nested;
61
- typedef typename Eigen::internal::traits<TensorPatchOp>::StorageKind StorageKind;
62
- typedef typename Eigen::internal::traits<TensorPatchOp>::Index Index;
63
-
64
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorPatchOp(const XprType& expr, const PatchDim& patch_dims)
65
- : m_xpr(expr), m_patch_dims(patch_dims) {}
66
-
67
- EIGEN_DEVICE_FUNC
68
- const PatchDim& patch_dims() const { return m_patch_dims; }
69
-
70
- EIGEN_DEVICE_FUNC
71
- const typename internal::remove_all<typename XprType::Nested>::type&
72
- expression() const { return m_xpr; }
73
-
74
- protected:
75
- typename XprType::Nested m_xpr;
76
- const PatchDim m_patch_dims;
77
- };
78
-
79
-
80
- // Eval as rvalue
81
- template<typename PatchDim, typename ArgType, typename Device>
82
- struct TensorEvaluator<const TensorPatchOp<PatchDim, ArgType>, Device>
83
- {
84
- typedef TensorPatchOp<PatchDim, ArgType> XprType;
85
- typedef typename XprType::Index Index;
86
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value + 1;
87
- typedef DSizes<Index, NumDims> Dimensions;
88
- typedef typename XprType::Scalar Scalar;
89
- typedef typename XprType::CoeffReturnType CoeffReturnType;
90
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
91
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
92
- typedef StorageMemory<CoeffReturnType, Device> Storage;
93
- typedef typename Storage::Type EvaluatorPointerType;
94
-
95
-
96
- enum {
97
- IsAligned = false,
98
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
99
- BlockAccess = false,
100
- PreferBlockAccess = TensorEvaluator<ArgType, Device>::PreferBlockAccess,
101
- Layout = TensorEvaluator<ArgType, Device>::Layout,
102
- CoordAccess = false,
103
- RawAccess = false
104
- };
105
-
106
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
107
- typedef internal::TensorBlockNotImplemented TensorBlock;
108
- //===--------------------------------------------------------------------===//
109
-
110
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
111
- : m_impl(op.expression(), device)
112
- {
113
- Index num_patches = 1;
114
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
115
- const PatchDim& patch_dims = op.patch_dims();
116
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
117
- for (int i = 0; i < NumDims-1; ++i) {
118
- m_dimensions[i] = patch_dims[i];
119
- num_patches *= (input_dims[i] - patch_dims[i] + 1);
120
- }
121
- m_dimensions[NumDims-1] = num_patches;
122
-
123
- m_inputStrides[0] = 1;
124
- m_patchStrides[0] = 1;
125
- for (int i = 1; i < NumDims-1; ++i) {
126
- m_inputStrides[i] = m_inputStrides[i-1] * input_dims[i-1];
127
- m_patchStrides[i] = m_patchStrides[i-1] * (input_dims[i-1] - patch_dims[i-1] + 1);
128
- }
129
- m_outputStrides[0] = 1;
130
- for (int i = 1; i < NumDims; ++i) {
131
- m_outputStrides[i] = m_outputStrides[i-1] * m_dimensions[i-1];
132
- }
133
- } else {
134
- for (int i = 0; i < NumDims-1; ++i) {
135
- m_dimensions[i+1] = patch_dims[i];
136
- num_patches *= (input_dims[i] - patch_dims[i] + 1);
137
- }
138
- m_dimensions[0] = num_patches;
139
-
140
- m_inputStrides[NumDims-2] = 1;
141
- m_patchStrides[NumDims-2] = 1;
142
- for (int i = NumDims-3; i >= 0; --i) {
143
- m_inputStrides[i] = m_inputStrides[i+1] * input_dims[i+1];
144
- m_patchStrides[i] = m_patchStrides[i+1] * (input_dims[i+1] - patch_dims[i+1] + 1);
145
- }
146
- m_outputStrides[NumDims-1] = 1;
147
- for (int i = NumDims-2; i >= 0; --i) {
148
- m_outputStrides[i] = m_outputStrides[i+1] * m_dimensions[i+1];
149
- }
150
- }
151
- }
152
-
153
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
154
-
155
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType /*data*/) {
156
- m_impl.evalSubExprsIfNeeded(NULL);
157
- return true;
158
- }
159
-
160
- EIGEN_STRONG_INLINE void cleanup() {
161
- m_impl.cleanup();
162
- }
163
-
164
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
165
- {
166
- Index output_stride_index = (static_cast<int>(Layout) == static_cast<int>(ColMajor)) ? NumDims - 1 : 0;
167
- // Find the location of the first element of the patch.
168
- Index patchIndex = index / m_outputStrides[output_stride_index];
169
- // Find the offset of the element wrt the location of the first element.
170
- Index patchOffset = index - patchIndex * m_outputStrides[output_stride_index];
171
- Index inputIndex = 0;
172
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
173
- EIGEN_UNROLL_LOOP
174
- for (int i = NumDims - 2; i > 0; --i) {
175
- const Index patchIdx = patchIndex / m_patchStrides[i];
176
- patchIndex -= patchIdx * m_patchStrides[i];
177
- const Index offsetIdx = patchOffset / m_outputStrides[i];
178
- patchOffset -= offsetIdx * m_outputStrides[i];
179
- inputIndex += (patchIdx + offsetIdx) * m_inputStrides[i];
180
- }
181
- } else {
182
- EIGEN_UNROLL_LOOP
183
- for (int i = 0; i < NumDims - 2; ++i) {
184
- const Index patchIdx = patchIndex / m_patchStrides[i];
185
- patchIndex -= patchIdx * m_patchStrides[i];
186
- const Index offsetIdx = patchOffset / m_outputStrides[i+1];
187
- patchOffset -= offsetIdx * m_outputStrides[i+1];
188
- inputIndex += (patchIdx + offsetIdx) * m_inputStrides[i];
189
- }
190
- }
191
- inputIndex += (patchIndex + patchOffset);
192
- return m_impl.coeff(inputIndex);
193
- }
194
-
195
- template<int LoadMode>
196
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
197
- {
198
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
199
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
200
-
201
- Index output_stride_index = (static_cast<int>(Layout) == static_cast<int>(ColMajor)) ? NumDims - 1 : 0;
202
- Index indices[2] = {index, index + PacketSize - 1};
203
- Index patchIndices[2] = {indices[0] / m_outputStrides[output_stride_index],
204
- indices[1] / m_outputStrides[output_stride_index]};
205
- Index patchOffsets[2] = {indices[0] - patchIndices[0] * m_outputStrides[output_stride_index],
206
- indices[1] - patchIndices[1] * m_outputStrides[output_stride_index]};
207
-
208
- Index inputIndices[2] = {0, 0};
209
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
210
- EIGEN_UNROLL_LOOP
211
- for (int i = NumDims - 2; i > 0; --i) {
212
- const Index patchIdx[2] = {patchIndices[0] / m_patchStrides[i],
213
- patchIndices[1] / m_patchStrides[i]};
214
- patchIndices[0] -= patchIdx[0] * m_patchStrides[i];
215
- patchIndices[1] -= patchIdx[1] * m_patchStrides[i];
216
-
217
- const Index offsetIdx[2] = {patchOffsets[0] / m_outputStrides[i],
218
- patchOffsets[1] / m_outputStrides[i]};
219
- patchOffsets[0] -= offsetIdx[0] * m_outputStrides[i];
220
- patchOffsets[1] -= offsetIdx[1] * m_outputStrides[i];
221
-
222
- inputIndices[0] += (patchIdx[0] + offsetIdx[0]) * m_inputStrides[i];
223
- inputIndices[1] += (patchIdx[1] + offsetIdx[1]) * m_inputStrides[i];
224
- }
225
- } else {
226
- EIGEN_UNROLL_LOOP
227
- for (int i = 0; i < NumDims - 2; ++i) {
228
- const Index patchIdx[2] = {patchIndices[0] / m_patchStrides[i],
229
- patchIndices[1] / m_patchStrides[i]};
230
- patchIndices[0] -= patchIdx[0] * m_patchStrides[i];
231
- patchIndices[1] -= patchIdx[1] * m_patchStrides[i];
232
-
233
- const Index offsetIdx[2] = {patchOffsets[0] / m_outputStrides[i+1],
234
- patchOffsets[1] / m_outputStrides[i+1]};
235
- patchOffsets[0] -= offsetIdx[0] * m_outputStrides[i+1];
236
- patchOffsets[1] -= offsetIdx[1] * m_outputStrides[i+1];
237
-
238
- inputIndices[0] += (patchIdx[0] + offsetIdx[0]) * m_inputStrides[i];
239
- inputIndices[1] += (patchIdx[1] + offsetIdx[1]) * m_inputStrides[i];
240
- }
241
- }
242
- inputIndices[0] += (patchIndices[0] + patchOffsets[0]);
243
- inputIndices[1] += (patchIndices[1] + patchOffsets[1]);
244
-
245
- if (inputIndices[1] - inputIndices[0] == PacketSize - 1) {
246
- PacketReturnType rslt = m_impl.template packet<Unaligned>(inputIndices[0]);
247
- return rslt;
248
- }
249
- else {
250
- EIGEN_ALIGN_MAX CoeffReturnType values[PacketSize];
251
- values[0] = m_impl.coeff(inputIndices[0]);
252
- values[PacketSize-1] = m_impl.coeff(inputIndices[1]);
253
- EIGEN_UNROLL_LOOP
254
- for (int i = 1; i < PacketSize-1; ++i) {
255
- values[i] = coeff(index+i);
256
- }
257
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
258
- return rslt;
259
- }
260
- }
261
-
262
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
263
- const double compute_cost = NumDims * (TensorOpCost::DivCost<Index>() +
264
- TensorOpCost::MulCost<Index>() +
265
- 2 * TensorOpCost::AddCost<Index>());
266
- return m_impl.costPerCoeff(vectorized) +
267
- TensorOpCost(0, 0, compute_cost, vectorized, PacketSize);
268
- }
269
-
270
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return NULL; }
271
-
272
- #ifdef EIGEN_USE_SYCL
273
- // binding placeholder accessors to a command group handler for SYCL
274
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
275
- m_impl.bind(cgh);
276
- }
277
- #endif
278
-
279
- protected:
280
- Dimensions m_dimensions;
281
- array<Index, NumDims> m_outputStrides;
282
- array<Index, NumDims-1> m_inputStrides;
283
- array<Index, NumDims-1> m_patchStrides;
284
-
285
- TensorEvaluator<ArgType, Device> m_impl;
286
-
287
- };
288
-
289
- } // end namespace Eigen
290
-
291
- #endif // EIGEN_CXX11_TENSOR_TENSOR_PATCH_H
@@ -1,322 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2016 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- // Copyright (C) 2018 Mehdi Goli <eigen@codeplay.com> Codeplay Software Ltd.
6
- //
7
- // This Source Code Form is subject to the terms of the Mozilla
8
- // Public License v. 2.0. If a copy of the MPL was not distributed
9
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
-
11
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_RANDOM_H
12
- #define EIGEN_CXX11_TENSOR_TENSOR_RANDOM_H
13
-
14
- namespace Eigen {
15
- namespace internal {
16
-
17
- namespace {
18
-
19
- EIGEN_DEVICE_FUNC uint64_t get_random_seed() {
20
- #if defined(EIGEN_GPU_COMPILE_PHASE)
21
- // We don't support 3d kernels since we currently only use 1 and
22
- // 2d kernels.
23
- gpu_assert(threadIdx.z == 0);
24
- return blockIdx.x * blockDim.x + threadIdx.x
25
- + gridDim.x * blockDim.x * (blockIdx.y * blockDim.y + threadIdx.y);
26
- #else
27
- // Rely on Eigen's random implementation.
28
- return random<uint64_t>();
29
- #endif
30
- }
31
-
32
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE unsigned PCG_XSH_RS_generator(uint64_t* state, uint64_t stream) {
33
- // TODO: Unify with the implementation in the non blocking thread pool.
34
- uint64_t current = *state;
35
- // Update the internal state
36
- *state = current * 6364136223846793005ULL + (stream << 1 | 1);
37
- // Generate the random output (using the PCG-XSH-RS scheme)
38
- return static_cast<unsigned>((current ^ (current >> 22)) >> (22 + (current >> 61)));
39
- }
40
-
41
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE uint64_t PCG_XSH_RS_state(uint64_t seed) {
42
- seed = seed ? seed : get_random_seed();
43
- return seed * 6364136223846793005ULL + 0xda3e39cb94b95bdbULL;
44
- }
45
-
46
- } // namespace
47
-
48
-
49
- template <typename T> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
50
- T RandomToTypeUniform(uint64_t* state, uint64_t stream) {
51
- unsigned rnd = PCG_XSH_RS_generator(state, stream);
52
- return static_cast<T>(rnd);
53
- }
54
-
55
-
56
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
57
- Eigen::half RandomToTypeUniform<Eigen::half>(uint64_t* state, uint64_t stream) {
58
- // Generate 10 random bits for the mantissa, merge with exponent.
59
- unsigned rnd = PCG_XSH_RS_generator(state, stream);
60
- const uint16_t half_bits = static_cast<uint16_t>(rnd & 0x3ffu) | (static_cast<uint16_t>(15) << 10);
61
- Eigen::half result = Eigen::numext::bit_cast<Eigen::half>(half_bits);
62
- // Return the final result
63
- return result - Eigen::half(1.0f);
64
- }
65
-
66
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
67
- Eigen::bfloat16 RandomToTypeUniform<Eigen::bfloat16>(uint64_t* state, uint64_t stream) {
68
-
69
- // Generate 7 random bits for the mantissa, merge with exponent.
70
- unsigned rnd = PCG_XSH_RS_generator(state, stream);
71
- const uint16_t half_bits = static_cast<uint16_t>(rnd & 0x7fu) | (static_cast<uint16_t>(127) << 7);
72
- Eigen::bfloat16 result = Eigen::numext::bit_cast<Eigen::bfloat16>(half_bits);
73
- // Return the final result
74
- return result - Eigen::bfloat16(1.0f);
75
- }
76
-
77
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
78
- float RandomToTypeUniform<float>(uint64_t* state, uint64_t stream) {
79
- typedef union {
80
- uint32_t raw;
81
- float fp;
82
- } internal;
83
- internal result;
84
- // Generate 23 random bits for the mantissa mantissa
85
- const unsigned rnd = PCG_XSH_RS_generator(state, stream);
86
- result.raw = rnd & 0x7fffffu;
87
- // Set the exponent
88
- result.raw |= (static_cast<uint32_t>(127) << 23);
89
- // Return the final result
90
- return result.fp - 1.0f;
91
- }
92
-
93
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
94
- double RandomToTypeUniform<double>(uint64_t* state, uint64_t stream) {
95
- typedef union {
96
- uint64_t raw;
97
- double dp;
98
- } internal;
99
- internal result;
100
- result.raw = 0;
101
- // Generate 52 random bits for the mantissa
102
- // First generate the upper 20 bits
103
- unsigned rnd1 = PCG_XSH_RS_generator(state, stream) & 0xfffffu;
104
- // The generate the lower 32 bits
105
- unsigned rnd2 = PCG_XSH_RS_generator(state, stream);
106
- result.raw = (static_cast<uint64_t>(rnd1) << 32) | rnd2;
107
- // Set the exponent
108
- result.raw |= (static_cast<uint64_t>(1023) << 52);
109
- // Return the final result
110
- return result.dp - 1.0;
111
- }
112
-
113
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
114
- std::complex<float> RandomToTypeUniform<std::complex<float> >(uint64_t* state, uint64_t stream) {
115
- return std::complex<float>(RandomToTypeUniform<float>(state, stream),
116
- RandomToTypeUniform<float>(state, stream));
117
- }
118
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
119
- std::complex<double> RandomToTypeUniform<std::complex<double> >(uint64_t* state, uint64_t stream) {
120
- return std::complex<double>(RandomToTypeUniform<double>(state, stream),
121
- RandomToTypeUniform<double>(state, stream));
122
- }
123
-
124
- template <typename T> class UniformRandomGenerator {
125
- public:
126
- static const bool PacketAccess = true;
127
-
128
- // Uses the given "seed" if non-zero, otherwise uses a random seed.
129
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE UniformRandomGenerator(
130
- uint64_t seed = 0) {
131
- m_state = PCG_XSH_RS_state(seed);
132
- #ifdef EIGEN_USE_SYCL
133
- // In SYCL it is not possible to build PCG_XSH_RS_state in one step.
134
- // Therefor, we need two step to initializate the m_state.
135
- // IN SYCL, the constructor of the functor is s called on the CPU
136
- // and we get the clock seed here from the CPU. However, This seed is
137
- //the same for all the thread. As unlike CUDA, the thread.ID, BlockID, etc is not a global function.
138
- // and only available on the Operator() function (which is called on the GPU).
139
- // Thus for CUDA (((CLOCK + global_thread_id)* 6364136223846793005ULL) + 0xda3e39cb94b95bdbULL) is passed to each thread
140
- // but for SYCL ((CLOCK * 6364136223846793005ULL) + 0xda3e39cb94b95bdbULL) is passed to each thread and each thread adds
141
- // the (global_thread_id* 6364136223846793005ULL) for itself only once, in order to complete the construction
142
- // similar to CUDA Therefore, the thread Id injection is not available at this stage.
143
- //However when the operator() is called the thread ID will be avilable. So inside the opeator,
144
- // we add the thrreadID, BlockId,... (which is equivalent of i)
145
- //to the seed and construct the unique m_state per thead similar to cuda.
146
- m_exec_once =false;
147
- #endif
148
- }
149
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE UniformRandomGenerator(
150
- const UniformRandomGenerator& other) {
151
- m_state = other.m_state;
152
- #ifdef EIGEN_USE_SYCL
153
- m_exec_once =other.m_exec_once;
154
- #endif
155
- }
156
-
157
- template<typename Index> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
158
- T operator()(Index i) const {
159
- #ifdef EIGEN_USE_SYCL
160
- if(!m_exec_once) {
161
- // This is the second stage of adding thread Id to the CPU clock seed and build unique seed per thread
162
- // The (i * 6364136223846793005ULL) is the remaining part of the PCG_XSH_RS_state on the GPU side
163
- m_state += (i * 6364136223846793005ULL);
164
- m_exec_once =true;
165
- }
166
- #endif
167
- T result = RandomToTypeUniform<T>(&m_state, i);
168
- return result;
169
- }
170
-
171
- template<typename Packet, typename Index> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
172
- Packet packetOp(Index i) const {
173
- const int packetSize = internal::unpacket_traits<Packet>::size;
174
- EIGEN_ALIGN_MAX T values[packetSize];
175
- #ifdef EIGEN_USE_SYCL
176
- if(!m_exec_once) {
177
- // This is the second stage of adding thread Id to the CPU clock seed and build unique seed per thread
178
- m_state += (i * 6364136223846793005ULL);
179
- m_exec_once =true;
180
- }
181
- #endif
182
- EIGEN_UNROLL_LOOP
183
- for (int j = 0; j < packetSize; ++j) {
184
- values[j] = RandomToTypeUniform<T>(&m_state, i);
185
- }
186
- return internal::pload<Packet>(values);
187
- }
188
-
189
- private:
190
- mutable uint64_t m_state;
191
- #ifdef EIGEN_USE_SYCL
192
- mutable bool m_exec_once;
193
- #endif
194
- };
195
-
196
- template <typename Scalar>
197
- struct functor_traits<UniformRandomGenerator<Scalar> > {
198
- enum {
199
- // Rough estimate for floating point, multiplied by ceil(sizeof(T) / sizeof(float)).
200
- Cost = 12 * NumTraits<Scalar>::AddCost *
201
- ((sizeof(Scalar) + sizeof(float) - 1) / sizeof(float)),
202
- PacketAccess = UniformRandomGenerator<Scalar>::PacketAccess
203
- };
204
- };
205
-
206
-
207
-
208
- template <typename T> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
209
- T RandomToTypeNormal(uint64_t* state, uint64_t stream) {
210
- // Use the ratio of uniform method to generate numbers following a normal
211
- // distribution. See for example Numerical Recipes chapter 7.3.9 for the
212
- // details.
213
- T u, v, q;
214
- do {
215
- u = RandomToTypeUniform<T>(state, stream);
216
- v = T(1.7156) * (RandomToTypeUniform<T>(state, stream) - T(0.5));
217
- const T x = u - T(0.449871);
218
- const T y = numext::abs(v) + T(0.386595);
219
- q = x*x + y * (T(0.196)*y - T(0.25472)*x);
220
- } while (q > T(0.27597) &&
221
- (q > T(0.27846) || v*v > T(-4) * numext::log(u) * u*u));
222
-
223
- return v/u;
224
- }
225
-
226
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
227
- std::complex<float> RandomToTypeNormal<std::complex<float> >(uint64_t* state, uint64_t stream) {
228
- return std::complex<float>(RandomToTypeNormal<float>(state, stream),
229
- RandomToTypeNormal<float>(state, stream));
230
- }
231
- template <> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
232
- std::complex<double> RandomToTypeNormal<std::complex<double> >(uint64_t* state, uint64_t stream) {
233
- return std::complex<double>(RandomToTypeNormal<double>(state, stream),
234
- RandomToTypeNormal<double>(state, stream));
235
- }
236
-
237
-
238
- template <typename T> class NormalRandomGenerator {
239
- public:
240
- static const bool PacketAccess = true;
241
-
242
- // Uses the given "seed" if non-zero, otherwise uses a random seed.
243
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE NormalRandomGenerator(uint64_t seed = 0) {
244
- m_state = PCG_XSH_RS_state(seed);
245
- #ifdef EIGEN_USE_SYCL
246
- // In SYCL it is not possible to build PCG_XSH_RS_state in one step.
247
- // Therefor, we need two steps to initializate the m_state.
248
- // IN SYCL, the constructor of the functor is s called on the CPU
249
- // and we get the clock seed here from the CPU. However, This seed is
250
- //the same for all the thread. As unlike CUDA, the thread.ID, BlockID, etc is not a global function.
251
- // and only available on the Operator() function (which is called on the GPU).
252
- // Therefore, the thread Id injection is not available at this stage. However when the operator()
253
- //is called the thread ID will be avilable. So inside the opeator,
254
- // we add the thrreadID, BlockId,... (which is equivalent of i)
255
- //to the seed and construct the unique m_state per thead similar to cuda.
256
- m_exec_once =false;
257
- #endif
258
- }
259
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE NormalRandomGenerator(
260
- const NormalRandomGenerator& other) {
261
- m_state = other.m_state;
262
- #ifdef EIGEN_USE_SYCL
263
- m_exec_once=other.m_exec_once;
264
- #endif
265
- }
266
-
267
- template<typename Index> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
268
- T operator()(Index i) const {
269
- #ifdef EIGEN_USE_SYCL
270
- if(!m_exec_once) {
271
- // This is the second stage of adding thread Id to the CPU clock seed and build unique seed per thread
272
- m_state += (i * 6364136223846793005ULL);
273
- m_exec_once =true;
274
- }
275
- #endif
276
- T result = RandomToTypeNormal<T>(&m_state, i);
277
- return result;
278
- }
279
-
280
- template<typename Packet, typename Index> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
281
- Packet packetOp(Index i) const {
282
- const int packetSize = internal::unpacket_traits<Packet>::size;
283
- EIGEN_ALIGN_MAX T values[packetSize];
284
- #ifdef EIGEN_USE_SYCL
285
- if(!m_exec_once) {
286
- // This is the second stage of adding thread Id to the CPU clock seed and build unique seed per thread
287
- m_state += (i * 6364136223846793005ULL);
288
- m_exec_once =true;
289
- }
290
- #endif
291
- EIGEN_UNROLL_LOOP
292
- for (int j = 0; j < packetSize; ++j) {
293
- values[j] = RandomToTypeNormal<T>(&m_state, i);
294
- }
295
- return internal::pload<Packet>(values);
296
- }
297
-
298
- private:
299
- mutable uint64_t m_state;
300
- #ifdef EIGEN_USE_SYCL
301
- mutable bool m_exec_once;
302
- #endif
303
- };
304
-
305
-
306
- template <typename Scalar>
307
- struct functor_traits<NormalRandomGenerator<Scalar> > {
308
- enum {
309
- // On average, we need to generate about 3 random numbers
310
- // 15 mul, 8 add, 1.5 logs
311
- Cost = 3 * functor_traits<UniformRandomGenerator<Scalar> >::Cost +
312
- 15 * NumTraits<Scalar>::AddCost + 8 * NumTraits<Scalar>::AddCost +
313
- 3 * functor_traits<scalar_log_op<Scalar> >::Cost / 2,
314
- PacketAccess = NormalRandomGenerator<Scalar>::PacketAccess
315
- };
316
- };
317
-
318
-
319
- } // end namespace internal
320
- } // end namespace Eigen
321
-
322
- #endif // EIGEN_CXX11_TENSOR_TENSOR_RANDOM_H