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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@@ -1,214 +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 Rasmus Munk Larsen <rmlarsen@google.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_COST_MODEL_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_COST_MODEL_H
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-
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- namespace Eigen {
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-
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- /** \class TensorEvaluator
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief A cost model used to limit the number of threads used for evaluating
19
- * tensor expression.
20
- *
21
- */
22
-
23
- // Class storing the cost of evaluating a tensor expression in terms of the
24
- // estimated number of operand bytes loads, bytes stored, and compute cycles.
25
- class TensorOpCost {
26
- public:
27
- // TODO(rmlarsen): Fix the scalar op costs in Eigen proper. Even a simple
28
- // model based on minimal reciprocal throughput numbers from Intel or
29
- // Agner Fog's tables would be better than what is there now.
30
- template <typename ArgType>
31
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE int MulCost() {
32
- return internal::functor_traits<
33
- internal::scalar_product_op<ArgType, ArgType> >::Cost;
34
- }
35
- template <typename ArgType>
36
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE int AddCost() {
37
- return internal::functor_traits<internal::scalar_sum_op<ArgType> >::Cost;
38
- }
39
- template <typename ArgType>
40
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE int DivCost() {
41
- return internal::functor_traits<
42
- internal::scalar_quotient_op<ArgType, ArgType> >::Cost;
43
- }
44
- template <typename ArgType>
45
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE int ModCost() {
46
- return internal::functor_traits<internal::scalar_mod_op<ArgType> >::Cost;
47
- }
48
- template <typename SrcType, typename TargetType>
49
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE int CastCost() {
50
- return internal::functor_traits<
51
- internal::scalar_cast_op<SrcType, TargetType> >::Cost;
52
- }
53
-
54
- EIGEN_DEVICE_FUNC
55
- TensorOpCost() : bytes_loaded_(0), bytes_stored_(0), compute_cycles_(0) {}
56
- EIGEN_DEVICE_FUNC
57
- TensorOpCost(double bytes_loaded, double bytes_stored, double compute_cycles)
58
- : bytes_loaded_(bytes_loaded),
59
- bytes_stored_(bytes_stored),
60
- compute_cycles_(compute_cycles) {}
61
-
62
- EIGEN_DEVICE_FUNC
63
- TensorOpCost(double bytes_loaded, double bytes_stored, double compute_cycles,
64
- bool vectorized, double packet_size)
65
- : bytes_loaded_(bytes_loaded),
66
- bytes_stored_(bytes_stored),
67
- compute_cycles_(vectorized ? compute_cycles / packet_size
68
- : compute_cycles) {
69
- eigen_assert(bytes_loaded >= 0 && (numext::isfinite)(bytes_loaded));
70
- eigen_assert(bytes_stored >= 0 && (numext::isfinite)(bytes_stored));
71
- eigen_assert(compute_cycles >= 0 && (numext::isfinite)(compute_cycles));
72
- }
73
-
74
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE double bytes_loaded() const {
75
- return bytes_loaded_;
76
- }
77
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE double bytes_stored() const {
78
- return bytes_stored_;
79
- }
80
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE double compute_cycles() const {
81
- return compute_cycles_;
82
- }
83
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE double total_cost(
84
- double load_cost, double store_cost, double compute_cost) const {
85
- return load_cost * bytes_loaded_ + store_cost * bytes_stored_ +
86
- compute_cost * compute_cycles_;
87
- }
88
-
89
- // Drop memory access component. Intended for cases when memory accesses are
90
- // sequential or are completely masked by computations.
91
- EIGEN_DEVICE_FUNC void dropMemoryCost() {
92
- bytes_loaded_ = 0;
93
- bytes_stored_ = 0;
94
- }
95
-
96
- // TODO(rmlarsen): Define min in terms of total cost, not elementwise.
97
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost cwiseMin(
98
- const TensorOpCost& rhs) const {
99
- double bytes_loaded = numext::mini(bytes_loaded_, rhs.bytes_loaded());
100
- double bytes_stored = numext::mini(bytes_stored_, rhs.bytes_stored());
101
- double compute_cycles = numext::mini(compute_cycles_, rhs.compute_cycles());
102
- return TensorOpCost(bytes_loaded, bytes_stored, compute_cycles);
103
- }
104
-
105
- // TODO(rmlarsen): Define max in terms of total cost, not elementwise.
106
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost cwiseMax(
107
- const TensorOpCost& rhs) const {
108
- double bytes_loaded = numext::maxi(bytes_loaded_, rhs.bytes_loaded());
109
- double bytes_stored = numext::maxi(bytes_stored_, rhs.bytes_stored());
110
- double compute_cycles = numext::maxi(compute_cycles_, rhs.compute_cycles());
111
- return TensorOpCost(bytes_loaded, bytes_stored, compute_cycles);
112
- }
113
-
114
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost& operator+=(
115
- const TensorOpCost& rhs) {
116
- bytes_loaded_ += rhs.bytes_loaded();
117
- bytes_stored_ += rhs.bytes_stored();
118
- compute_cycles_ += rhs.compute_cycles();
119
- return *this;
120
- }
121
-
122
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost& operator*=(double rhs) {
123
- bytes_loaded_ *= rhs;
124
- bytes_stored_ *= rhs;
125
- compute_cycles_ *= rhs;
126
- return *this;
127
- }
128
-
129
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE friend TensorOpCost operator+(
130
- TensorOpCost lhs, const TensorOpCost& rhs) {
131
- lhs += rhs;
132
- return lhs;
133
- }
134
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE friend TensorOpCost operator*(
135
- TensorOpCost lhs, double rhs) {
136
- lhs *= rhs;
137
- return lhs;
138
- }
139
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE friend TensorOpCost operator*(
140
- double lhs, TensorOpCost rhs) {
141
- rhs *= lhs;
142
- return rhs;
143
- }
144
-
145
- friend std::ostream& operator<<(std::ostream& os, const TensorOpCost& tc) {
146
- return os << "[bytes_loaded = " << tc.bytes_loaded()
147
- << ", bytes_stored = " << tc.bytes_stored()
148
- << ", compute_cycles = " << tc.compute_cycles() << "]";
149
- }
150
-
151
- private:
152
- double bytes_loaded_;
153
- double bytes_stored_;
154
- double compute_cycles_;
155
- };
156
-
157
- // TODO(rmlarsen): Implement a policy that chooses an "optimal" number of theads
158
- // in [1:max_threads] instead of just switching multi-threading off for small
159
- // work units.
160
- template <typename Device>
161
- class TensorCostModel {
162
- public:
163
- // Scaling from Eigen compute cost to device cycles.
164
- static const int kDeviceCyclesPerComputeCycle = 1;
165
-
166
- // Costs in device cycles.
167
- static const int kStartupCycles = 100000;
168
- static const int kPerThreadCycles = 100000;
169
- static const int kTaskSize = 40000;
170
-
171
- // Returns the number of threads in [1:max_threads] to use for
172
- // evaluating an expression with the given output size and cost per
173
- // coefficient.
174
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE int numThreads(
175
- double output_size, const TensorOpCost& cost_per_coeff, int max_threads) {
176
- double cost = totalCost(output_size, cost_per_coeff);
177
- double threads = (cost - kStartupCycles) / kPerThreadCycles + 0.9;
178
- // Make sure we don't invoke undefined behavior when we convert to an int.
179
- threads = numext::mini<double>(threads, GenericNumTraits<int>::highest());
180
- return numext::mini(max_threads,
181
- numext::maxi<int>(1, static_cast<int>(threads)));
182
- }
183
-
184
- // taskSize assesses parallel task size.
185
- // Value of 1.0 means ideal parallel task size. Values < 1.0 mean that task
186
- // granularity needs to be increased to mitigate parallelization overheads.
187
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE double taskSize(
188
- double output_size, const TensorOpCost& cost_per_coeff) {
189
- return totalCost(output_size, cost_per_coeff) / kTaskSize;
190
- }
191
-
192
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE double totalCost(
193
- double output_size, const TensorOpCost& cost_per_coeff) {
194
- // Cost of memory fetches from L2 cache. 64 is typical cache line size.
195
- // 11 is L2 cache latency on Haswell.
196
- // We don't know whether data is in L1, L2 or L3. But we are most interested
197
- // in single-threaded computational time around 100us-10ms (smaller time
198
- // is too small for parallelization, larger time is not interesting
199
- // either because we are probably using all available threads already).
200
- // And for the target time range, L2 seems to be what matters. Data set
201
- // fitting into L1 is too small to take noticeable time. Data set fitting
202
- // only into L3 presumably will take more than 10ms to load and process.
203
- const double kLoadCycles = 1.0 / 64 * 11;
204
- const double kStoreCycles = 1.0 / 64 * 11;
205
- // Scaling from Eigen compute cost to device cycles.
206
- return output_size *
207
- cost_per_coeff.total_cost(kLoadCycles, kStoreCycles,
208
- kDeviceCyclesPerComputeCycle);
209
- }
210
- };
211
-
212
- } // namespace Eigen
213
-
214
- #endif // EIGEN_CXX11_TENSOR_TENSOR_COST_MODEL_H
@@ -1,347 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_CUSTOM_OP_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_CUSTOM_OP_H
12
-
13
- namespace Eigen {
14
-
15
- /** \class TensorCustomUnaryOp
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor custom class.
19
- *
20
- *
21
- */
22
- namespace internal {
23
- template<typename CustomUnaryFunc, typename XprType>
24
- struct traits<TensorCustomUnaryOp<CustomUnaryFunc, XprType> >
25
- {
26
- typedef typename XprType::Scalar Scalar;
27
- typedef typename XprType::StorageKind StorageKind;
28
- typedef typename XprType::Index Index;
29
- typedef typename XprType::Nested Nested;
30
- typedef typename remove_reference<Nested>::type _Nested;
31
- static const int NumDimensions = traits<XprType>::NumDimensions;
32
- static const int Layout = traits<XprType>::Layout;
33
- typedef typename traits<XprType>::PointerType PointerType;
34
- };
35
-
36
- template<typename CustomUnaryFunc, typename XprType>
37
- struct eval<TensorCustomUnaryOp<CustomUnaryFunc, XprType>, Eigen::Dense>
38
- {
39
- typedef const TensorCustomUnaryOp<CustomUnaryFunc, XprType>EIGEN_DEVICE_REF type;
40
- };
41
-
42
- template<typename CustomUnaryFunc, typename XprType>
43
- struct nested<TensorCustomUnaryOp<CustomUnaryFunc, XprType> >
44
- {
45
- typedef TensorCustomUnaryOp<CustomUnaryFunc, XprType> type;
46
- };
47
-
48
- } // end namespace internal
49
-
50
-
51
-
52
- template<typename CustomUnaryFunc, typename XprType>
53
- class TensorCustomUnaryOp : public TensorBase<TensorCustomUnaryOp<CustomUnaryFunc, XprType>, ReadOnlyAccessors>
54
- {
55
- public:
56
- typedef typename internal::traits<TensorCustomUnaryOp>::Scalar Scalar;
57
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
58
- typedef typename XprType::CoeffReturnType CoeffReturnType;
59
- typedef typename internal::nested<TensorCustomUnaryOp>::type Nested;
60
- typedef typename internal::traits<TensorCustomUnaryOp>::StorageKind StorageKind;
61
- typedef typename internal::traits<TensorCustomUnaryOp>::Index Index;
62
-
63
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorCustomUnaryOp(const XprType& expr, const CustomUnaryFunc& func)
64
- : m_expr(expr), m_func(func) {}
65
-
66
- EIGEN_DEVICE_FUNC
67
- const CustomUnaryFunc& func() const { return m_func; }
68
-
69
- EIGEN_DEVICE_FUNC
70
- const typename internal::remove_all<typename XprType::Nested>::type&
71
- expression() const { return m_expr; }
72
-
73
- protected:
74
- typename XprType::Nested m_expr;
75
- const CustomUnaryFunc m_func;
76
- };
77
-
78
-
79
- // Eval as rvalue
80
- template<typename CustomUnaryFunc, typename XprType, typename Device>
81
- struct TensorEvaluator<const TensorCustomUnaryOp<CustomUnaryFunc, XprType>, Device>
82
- {
83
- typedef TensorCustomUnaryOp<CustomUnaryFunc, XprType> ArgType;
84
- typedef typename internal::traits<ArgType>::Index Index;
85
- static const int NumDims = internal::traits<ArgType>::NumDimensions;
86
- typedef DSizes<Index, NumDims> Dimensions;
87
- typedef typename internal::remove_const<typename ArgType::Scalar>::type Scalar;
88
- typedef typename internal::remove_const<typename XprType::CoeffReturnType>::type CoeffReturnType;
89
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
90
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
91
- typedef typename Eigen::internal::traits<XprType>::PointerType TensorPointerType;
92
- typedef StorageMemory<CoeffReturnType, Device> Storage;
93
- typedef typename Storage::Type EvaluatorPointerType;
94
-
95
- enum {
96
- IsAligned = false,
97
- PacketAccess = (PacketType<CoeffReturnType, Device>::size > 1),
98
- BlockAccess = false,
99
- PreferBlockAccess = false,
100
- Layout = TensorEvaluator<XprType, Device>::Layout,
101
- CoordAccess = false, // to be implemented
102
- RawAccess = false
103
- };
104
-
105
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
106
- typedef internal::TensorBlockNotImplemented TensorBlock;
107
- //===--------------------------------------------------------------------===//
108
-
109
- EIGEN_STRONG_INLINE TensorEvaluator(const ArgType& op, const Device& device)
110
- : m_op(op), m_device(device), m_result(NULL)
111
- {
112
- m_dimensions = op.func().dimensions(op.expression());
113
- }
114
-
115
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
116
-
117
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType data) {
118
- if (data) {
119
- evalTo(data);
120
- return false;
121
- } else {
122
- m_result = static_cast<EvaluatorPointerType>(m_device.get( (CoeffReturnType*)
123
- m_device.allocate_temp(dimensions().TotalSize() * sizeof(Scalar))));
124
- evalTo(m_result);
125
- return true;
126
- }
127
- }
128
-
129
- EIGEN_STRONG_INLINE void cleanup() {
130
- if (m_result) {
131
- m_device.deallocate_temp(m_result);
132
- m_result = NULL;
133
- }
134
- }
135
-
136
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const {
137
- return m_result[index];
138
- }
139
-
140
- template<int LoadMode>
141
- EIGEN_DEVICE_FUNC PacketReturnType packet(Index index) const {
142
- return internal::ploadt<PacketReturnType, LoadMode>(m_result + index);
143
- }
144
-
145
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
146
- // TODO(rmlarsen): Extend CustomOp API to return its cost estimate.
147
- return TensorOpCost(sizeof(CoeffReturnType), 0, 0, vectorized, PacketSize);
148
- }
149
-
150
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return m_result; }
151
-
152
- #ifdef EIGEN_USE_SYCL
153
- // binding placeholder accessors to a command group handler for SYCL
154
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
155
- m_result.bind(cgh);
156
- }
157
- #endif
158
-
159
- protected:
160
- void evalTo(EvaluatorPointerType data) {
161
- TensorMap<Tensor<CoeffReturnType, NumDims, Layout, Index> > result(m_device.get(data), m_dimensions);
162
- m_op.func().eval(m_op.expression(), result, m_device);
163
- }
164
-
165
- Dimensions m_dimensions;
166
- const ArgType m_op;
167
- const Device EIGEN_DEVICE_REF m_device;
168
- EvaluatorPointerType m_result;
169
- };
170
-
171
-
172
-
173
- /** \class TensorCustomBinaryOp
174
- * \ingroup CXX11_Tensor_Module
175
- *
176
- * \brief Tensor custom class.
177
- *
178
- *
179
- */
180
- namespace internal {
181
- template<typename CustomBinaryFunc, typename LhsXprType, typename RhsXprType>
182
- struct traits<TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType> >
183
- {
184
- typedef typename internal::promote_storage_type<typename LhsXprType::Scalar,
185
- typename RhsXprType::Scalar>::ret Scalar;
186
- typedef typename internal::promote_storage_type<typename LhsXprType::CoeffReturnType,
187
- typename RhsXprType::CoeffReturnType>::ret CoeffReturnType;
188
- typedef typename promote_storage_type<typename traits<LhsXprType>::StorageKind,
189
- typename traits<RhsXprType>::StorageKind>::ret StorageKind;
190
- typedef typename promote_index_type<typename traits<LhsXprType>::Index,
191
- typename traits<RhsXprType>::Index>::type Index;
192
- typedef typename LhsXprType::Nested LhsNested;
193
- typedef typename RhsXprType::Nested RhsNested;
194
- typedef typename remove_reference<LhsNested>::type _LhsNested;
195
- typedef typename remove_reference<RhsNested>::type _RhsNested;
196
- static const int NumDimensions = traits<LhsXprType>::NumDimensions;
197
- static const int Layout = traits<LhsXprType>::Layout;
198
- typedef typename conditional<Pointer_type_promotion<typename LhsXprType::Scalar, Scalar>::val,
199
- typename traits<LhsXprType>::PointerType, typename traits<RhsXprType>::PointerType>::type PointerType;
200
- };
201
-
202
- template<typename CustomBinaryFunc, typename LhsXprType, typename RhsXprType>
203
- struct eval<TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType>, Eigen::Dense>
204
- {
205
- typedef const TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType>& type;
206
- };
207
-
208
- template<typename CustomBinaryFunc, typename LhsXprType, typename RhsXprType>
209
- struct nested<TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType> >
210
- {
211
- typedef TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType> type;
212
- };
213
-
214
- } // end namespace internal
215
-
216
-
217
-
218
- template<typename CustomBinaryFunc, typename LhsXprType, typename RhsXprType>
219
- class TensorCustomBinaryOp : public TensorBase<TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType>, ReadOnlyAccessors>
220
- {
221
- public:
222
- typedef typename internal::traits<TensorCustomBinaryOp>::Scalar Scalar;
223
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
224
- typedef typename internal::traits<TensorCustomBinaryOp>::CoeffReturnType CoeffReturnType;
225
- typedef typename internal::nested<TensorCustomBinaryOp>::type Nested;
226
- typedef typename internal::traits<TensorCustomBinaryOp>::StorageKind StorageKind;
227
- typedef typename internal::traits<TensorCustomBinaryOp>::Index Index;
228
-
229
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorCustomBinaryOp(const LhsXprType& lhs, const RhsXprType& rhs, const CustomBinaryFunc& func)
230
-
231
- : m_lhs_xpr(lhs), m_rhs_xpr(rhs), m_func(func) {}
232
-
233
- EIGEN_DEVICE_FUNC
234
- const CustomBinaryFunc& func() const { return m_func; }
235
-
236
- EIGEN_DEVICE_FUNC
237
- const typename internal::remove_all<typename LhsXprType::Nested>::type&
238
- lhsExpression() const { return m_lhs_xpr; }
239
-
240
- EIGEN_DEVICE_FUNC
241
- const typename internal::remove_all<typename RhsXprType::Nested>::type&
242
- rhsExpression() const { return m_rhs_xpr; }
243
-
244
- protected:
245
- typename LhsXprType::Nested m_lhs_xpr;
246
- typename RhsXprType::Nested m_rhs_xpr;
247
- const CustomBinaryFunc m_func;
248
- };
249
-
250
-
251
- // Eval as rvalue
252
- template<typename CustomBinaryFunc, typename LhsXprType, typename RhsXprType, typename Device>
253
- struct TensorEvaluator<const TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType>, Device>
254
- {
255
- typedef TensorCustomBinaryOp<CustomBinaryFunc, LhsXprType, RhsXprType> XprType;
256
- typedef typename internal::traits<XprType>::Index Index;
257
- static const int NumDims = internal::traits<XprType>::NumDimensions;
258
- typedef DSizes<Index, NumDims> Dimensions;
259
- typedef typename XprType::Scalar Scalar;
260
- typedef typename internal::remove_const<typename XprType::CoeffReturnType>::type CoeffReturnType;
261
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
262
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
263
-
264
- typedef typename Eigen::internal::traits<XprType>::PointerType TensorPointerType;
265
- typedef StorageMemory<CoeffReturnType, Device> Storage;
266
- typedef typename Storage::Type EvaluatorPointerType;
267
-
268
- enum {
269
- IsAligned = false,
270
- PacketAccess = (PacketType<CoeffReturnType, Device>::size > 1),
271
- BlockAccess = false,
272
- PreferBlockAccess = false,
273
- Layout = TensorEvaluator<LhsXprType, Device>::Layout,
274
- CoordAccess = false, // to be implemented
275
- RawAccess = false
276
- };
277
-
278
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
279
- typedef internal::TensorBlockNotImplemented TensorBlock;
280
- //===--------------------------------------------------------------------===//
281
-
282
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
283
- : m_op(op), m_device(device), m_result(NULL)
284
- {
285
- m_dimensions = op.func().dimensions(op.lhsExpression(), op.rhsExpression());
286
- }
287
-
288
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
289
-
290
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType data) {
291
- if (data) {
292
- evalTo(data);
293
- return false;
294
- } else {
295
- m_result = static_cast<EvaluatorPointerType>(m_device.get( (CoeffReturnType*)
296
- m_device.allocate_temp(dimensions().TotalSize() * sizeof(CoeffReturnType))));
297
- evalTo(m_result);
298
- return true;
299
- }
300
- }
301
-
302
- EIGEN_STRONG_INLINE void cleanup() {
303
- if (m_result != NULL) {
304
- m_device.deallocate_temp(m_result);
305
- m_result = NULL;
306
- }
307
- }
308
-
309
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const {
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- return m_result[index];
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- }
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-
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- template<int LoadMode>
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- EIGEN_DEVICE_FUNC PacketReturnType packet(Index index) const {
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- return internal::ploadt<PacketReturnType, LoadMode>(m_result + index);
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
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- // TODO(rmlarsen): Extend CustomOp API to return its cost estimate.
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- return TensorOpCost(sizeof(CoeffReturnType), 0, 0, vectorized, PacketSize);
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- }
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-
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- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return m_result; }
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-
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- #ifdef EIGEN_USE_SYCL
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- // binding placeholder accessors to a command group handler for SYCL
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
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- m_result.bind(cgh);
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- }
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- #endif
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-
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- protected:
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- void evalTo(EvaluatorPointerType data) {
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- TensorMap<Tensor<CoeffReturnType, NumDims, Layout> > result(m_device.get(data), m_dimensions);
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- m_op.func().eval(m_op.lhsExpression(), m_op.rhsExpression(), result, m_device);
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- }
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-
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- Dimensions m_dimensions;
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- const XprType m_op;
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- const Device EIGEN_DEVICE_REF m_device;
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- EvaluatorPointerType m_result;
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- };
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-
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-
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- } // end namespace Eigen
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-
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- #endif // EIGEN_CXX11_TENSOR_TENSOR_CUSTOM_OP_H
@@ -1,137 +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_DEVICE_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_DEVICE_H
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-
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- namespace Eigen {
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-
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- /** \class TensorDevice
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Pseudo expression providing an operator = that will evaluate its argument
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- * on the specified computing 'device' (GPU, thread pool, ...)
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- *
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- * Example:
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- * C.device(EIGEN_GPU) = A + B;
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- *
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- * Todo: operator *= and /=.
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- */
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-
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- template <typename ExpressionType, typename DeviceType> class TensorDevice {
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- public:
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- TensorDevice(const DeviceType& device, ExpressionType& expression) : m_device(device), m_expression(expression) {}
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-
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- EIGEN_DEFAULT_COPY_CONSTRUCTOR(TensorDevice)
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-
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- template<typename OtherDerived>
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- EIGEN_STRONG_INLINE TensorDevice& operator=(const OtherDerived& other) {
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- typedef TensorAssignOp<ExpressionType, const OtherDerived> Assign;
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- Assign assign(m_expression, other);
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- internal::TensorExecutor<const Assign, DeviceType>::run(assign, m_device);
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- return *this;
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- }
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-
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- template<typename OtherDerived>
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- EIGEN_STRONG_INLINE TensorDevice& operator+=(const OtherDerived& other) {
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- typedef typename OtherDerived::Scalar Scalar;
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- typedef TensorCwiseBinaryOp<internal::scalar_sum_op<Scalar>, const ExpressionType, const OtherDerived> Sum;
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- Sum sum(m_expression, other);
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- typedef TensorAssignOp<ExpressionType, const Sum> Assign;
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- Assign assign(m_expression, sum);
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- internal::TensorExecutor<const Assign, DeviceType>::run(assign, m_device);
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- return *this;
50
- }
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-
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- template<typename OtherDerived>
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- EIGEN_STRONG_INLINE TensorDevice& operator-=(const OtherDerived& other) {
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- typedef typename OtherDerived::Scalar Scalar;
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- typedef TensorCwiseBinaryOp<internal::scalar_difference_op<Scalar>, const ExpressionType, const OtherDerived> Difference;
56
- Difference difference(m_expression, other);
57
- typedef TensorAssignOp<ExpressionType, const Difference> Assign;
58
- Assign assign(m_expression, difference);
59
- internal::TensorExecutor<const Assign, DeviceType>::run(assign, m_device);
60
- return *this;
61
- }
62
-
63
- protected:
64
- const DeviceType& m_device;
65
- ExpressionType& m_expression;
66
- };
67
-
68
- /** \class TensorAsyncDevice
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Pseudo expression providing an operator = that will evaluate its
72
- * argument asynchronously on the specified device. Currently only
73
- * ThreadPoolDevice implements proper asynchronous execution, while the default
74
- * and GPU devices just run the expression synchronously and call m_done() on
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- * completion..
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- *
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- * Example:
78
- * auto done = []() { ... expression evaluation done ... };
79
- * C.device(thread_pool_device, std::move(done)) = A + B;
80
- */
81
-
82
- template <typename ExpressionType, typename DeviceType, typename DoneCallback>
83
- class TensorAsyncDevice {
84
- public:
85
- TensorAsyncDevice(const DeviceType& device, ExpressionType& expression,
86
- DoneCallback done)
87
- : m_device(device), m_expression(expression), m_done(std::move(done)) {}
88
-
89
- template <typename OtherDerived>
90
- EIGEN_STRONG_INLINE TensorAsyncDevice& operator=(const OtherDerived& other) {
91
- typedef TensorAssignOp<ExpressionType, const OtherDerived> Assign;
92
- typedef internal::TensorExecutor<const Assign, DeviceType> Executor;
93
-
94
- Assign assign(m_expression, other);
95
- Executor::run(assign, m_device);
96
- m_done();
97
-
98
- return *this;
99
- }
100
-
101
- protected:
102
- const DeviceType& m_device;
103
- ExpressionType& m_expression;
104
- DoneCallback m_done;
105
- };
106
-
107
-
108
- #ifdef EIGEN_USE_THREADS
109
- template <typename ExpressionType, typename DoneCallback>
110
- class TensorAsyncDevice<ExpressionType, ThreadPoolDevice, DoneCallback> {
111
- public:
112
- TensorAsyncDevice(const ThreadPoolDevice& device, ExpressionType& expression,
113
- DoneCallback done)
114
- : m_device(device), m_expression(expression), m_done(std::move(done)) {}
115
-
116
- template <typename OtherDerived>
117
- EIGEN_STRONG_INLINE TensorAsyncDevice& operator=(const OtherDerived& other) {
118
- typedef TensorAssignOp<ExpressionType, const OtherDerived> Assign;
119
- typedef internal::TensorAsyncExecutor<const Assign, ThreadPoolDevice, DoneCallback> Executor;
120
-
121
- // WARNING: After assignment 'm_done' callback will be in undefined state.
122
- Assign assign(m_expression, other);
123
- Executor::runAsync(assign, m_device, std::move(m_done));
124
-
125
- return *this;
126
- }
127
-
128
- protected:
129
- const ThreadPoolDevice& m_device;
130
- ExpressionType& m_expression;
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- DoneCallback m_done;
132
- };
133
- #endif
134
-
135
- } // end namespace Eigen
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-
137
- #endif // EIGEN_CXX11_TENSOR_TENSOR_DEVICE_H