sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.19__cp310-cp310-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.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +107 -5
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp310-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  13. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  15. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  17. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  18. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  19. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  20. sequenzo/multidomain/cat.py +0 -53
  21. sequenzo/multidomain/idcd.py +0 -1
  22. sequenzo/openmp_setup.py +233 -0
  23. sequenzo/visualization/plot_transition_matrix.py +21 -22
  24. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  25. sequenzo-0.1.19.dist-info/RECORD +272 -0
  26. sequenzo/dissimilarity_measures/setup.py +0 -35
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  169. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  171. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  172. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  173. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  174. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  175. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  176. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  177. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  178. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  179. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  180. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  181. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  182. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  183. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  184. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  185. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  186. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  187. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  188. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  189. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  190. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  191. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  192. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  197. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  198. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  199. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  200. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  201. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  202. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  203. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  206. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  207. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  208. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  209. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  210. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  211. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  212. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
  213. sequenzo/dissimilarity_measures/src/eigen/test/gpu_common.h +0 -176
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  395. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
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@@ -1,191 +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_FORWARD_DECLARATIONS_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_FORWARD_DECLARATIONS_H
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-
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- namespace Eigen {
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-
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- // MakePointer class is used as a container of the address space of the pointer
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- // on the host and on the device. From the host side it generates the T* pointer
17
- // and when EIGEN_USE_SYCL is used it construct a buffer with a map_allocator to
18
- // T* m_data on the host. It is always called on the device.
19
- // Specialisation of MakePointer class for creating the sycl buffer with
20
- // map_allocator.
21
- template<typename T> struct MakePointer {
22
- typedef T* Type;
23
- typedef const T* ConstType;
24
- };
25
-
26
- template <typename T>
27
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T* constCast(const T* data) {
28
- return const_cast<T*>(data);
29
- }
30
-
31
- // The StorageMemory class is a container of the device specific pointer
32
- // used for refering to a Pointer on TensorEvaluator class. While the TensorExpression
33
- // is a device-agnostic type and need MakePointer class for type conversion,
34
- // the TensorEvaluator class can be specialized for a device, hence it is possible
35
- // to construct different types of temproray storage memory in TensorEvaluator
36
- // for different devices by specializing the following StorageMemory class.
37
- template<typename T, typename device> struct StorageMemory: MakePointer <T> {};
38
-
39
- namespace internal{
40
- template<typename A, typename B> struct Pointer_type_promotion {
41
- static const bool val=false;
42
- };
43
- template<typename A> struct Pointer_type_promotion<A, A> {
44
- static const bool val = true;
45
- };
46
- template<typename A, typename B> struct TypeConversion {
47
- typedef A* type;
48
- };
49
- }
50
-
51
-
52
- template<typename PlainObjectType, int Options_ = Unaligned, template <class> class MakePointer_ = MakePointer> class TensorMap;
53
- template<typename Scalar_, int NumIndices_, int Options_ = 0, typename IndexType = DenseIndex> class Tensor;
54
- template<typename Scalar_, typename Dimensions, int Options_ = 0, typename IndexType = DenseIndex> class TensorFixedSize;
55
- template<typename PlainObjectType> class TensorRef;
56
- template<typename Derived, int AccessLevel> class TensorBase;
57
-
58
- template<typename NullaryOp, typename PlainObjectType> class TensorCwiseNullaryOp;
59
- template<typename UnaryOp, typename XprType> class TensorCwiseUnaryOp;
60
- template<typename BinaryOp, typename LeftXprType, typename RightXprType> class TensorCwiseBinaryOp;
61
- template<typename TernaryOp, typename Arg1XprType, typename Arg2XprType, typename Arg3XprType> class TensorCwiseTernaryOp;
62
- template<typename IfXprType, typename ThenXprType, typename ElseXprType> class TensorSelectOp;
63
- template<typename Op, typename Dims, typename XprType, template <class> class MakePointer_ = MakePointer > class TensorReductionOp;
64
- template<typename XprType> class TensorIndexTupleOp;
65
- template<typename ReduceOp, typename Dims, typename XprType> class TensorTupleReducerOp;
66
- template<typename Axis, typename LeftXprType, typename RightXprType> class TensorConcatenationOp;
67
- template<typename Dimensions, typename LeftXprType, typename RightXprType, typename OutputKernelType> class TensorContractionOp;
68
- template<typename TargetType, typename XprType> class TensorConversionOp;
69
- template<typename Dimensions, typename InputXprType, typename KernelXprType> class TensorConvolutionOp;
70
- template<typename FFT, typename XprType, int FFTDataType, int FFTDirection> class TensorFFTOp;
71
- template<typename PatchDim, typename XprType> class TensorPatchOp;
72
- template<DenseIndex Rows, DenseIndex Cols, typename XprType> class TensorImagePatchOp;
73
- template<DenseIndex Planes, DenseIndex Rows, DenseIndex Cols, typename XprType> class TensorVolumePatchOp;
74
- template<typename Broadcast, typename XprType> class TensorBroadcastingOp;
75
- template<DenseIndex DimId, typename XprType> class TensorChippingOp;
76
- template<typename NewDimensions, typename XprType> class TensorReshapingOp;
77
- template<typename XprType> class TensorLayoutSwapOp;
78
- template<typename StartIndices, typename Sizes, typename XprType> class TensorSlicingOp;
79
- template<typename ReverseDimensions, typename XprType> class TensorReverseOp;
80
- template<typename PaddingDimensions, typename XprType> class TensorPaddingOp;
81
- template<typename Shuffle, typename XprType> class TensorShufflingOp;
82
- template<typename Strides, typename XprType> class TensorStridingOp;
83
- template<typename StartIndices, typename StopIndices, typename Strides, typename XprType> class TensorStridingSlicingOp;
84
- template<typename Strides, typename XprType> class TensorInflationOp;
85
- template<typename Generator, typename XprType> class TensorGeneratorOp;
86
- template<typename LeftXprType, typename RightXprType> class TensorAssignOp;
87
- template<typename Op, typename XprType> class TensorScanOp;
88
- template<typename Dims, typename XprType> class TensorTraceOp;
89
-
90
- template<typename CustomUnaryFunc, typename XprType> class TensorCustomUnaryOp;
91
- template<typename CustomBinaryFunc, typename LhsXprType, typename RhsXprType> class TensorCustomBinaryOp;
92
-
93
- template<typename XprType, template <class> class MakePointer_ = MakePointer> class TensorEvalToOp;
94
- template<typename XprType> class TensorForcedEvalOp;
95
-
96
- template<typename ExpressionType, typename DeviceType> class TensorDevice;
97
- template<typename ExpressionType, typename DeviceType, typename DoneCallback> class TensorAsyncDevice;
98
- template<typename Derived, typename Device> struct TensorEvaluator;
99
-
100
- struct NoOpOutputKernel;
101
-
102
- struct DefaultDevice;
103
- struct ThreadPoolDevice;
104
- struct GpuDevice;
105
- struct SyclDevice;
106
-
107
- #ifdef EIGEN_USE_SYCL
108
-
109
- template <typename T> struct MakeSYCLPointer {
110
- typedef Eigen::TensorSycl::internal::RangeAccess<cl::sycl::access::mode::read_write, T> Type;
111
- };
112
-
113
- template <typename T>
114
- EIGEN_STRONG_INLINE const Eigen::TensorSycl::internal::RangeAccess<cl::sycl::access::mode::read_write, T>&
115
- constCast(const Eigen::TensorSycl::internal::RangeAccess<cl::sycl::access::mode::read_write, T>& data) {
116
- return data;
117
- }
118
-
119
- template <typename T>
120
- struct StorageMemory<T, SyclDevice> : MakeSYCLPointer<T> {};
121
- template <typename T>
122
- struct StorageMemory<T, const SyclDevice> : StorageMemory<T, SyclDevice> {};
123
-
124
- namespace TensorSycl {
125
- namespace internal{
126
- template <typename Evaluator, typename Op> class GenericNondeterministicReducer;
127
- }
128
- }
129
- #endif
130
-
131
-
132
- enum FFTResultType {
133
- RealPart = 0,
134
- ImagPart = 1,
135
- BothParts = 2
136
- };
137
-
138
- enum FFTDirection {
139
- FFT_FORWARD = 0,
140
- FFT_REVERSE = 1
141
- };
142
-
143
-
144
- namespace internal {
145
-
146
- template <typename Device, typename Expression>
147
- struct IsVectorizable {
148
- static const bool value = TensorEvaluator<Expression, Device>::PacketAccess;
149
- };
150
-
151
- template <typename Expression>
152
- struct IsVectorizable<GpuDevice, Expression> {
153
- static const bool value = TensorEvaluator<Expression, GpuDevice>::PacketAccess &&
154
- TensorEvaluator<Expression, GpuDevice>::IsAligned;
155
- };
156
-
157
- // Tiled evaluation strategy.
158
- enum TiledEvaluation {
159
- Off = 0, // tiled evaluation is not supported
160
- On = 1, // still work in progress (see TensorBlock.h)
161
- };
162
-
163
- template <typename Device, typename Expression>
164
- struct IsTileable {
165
- // Check that block evaluation is supported and it's a preferred option (at
166
- // least one sub-expression has much faster block evaluation, e.g.
167
- // broadcasting).
168
- static const bool BlockAccess =
169
- TensorEvaluator<Expression, Device>::BlockAccess &&
170
- TensorEvaluator<Expression, Device>::PreferBlockAccess;
171
-
172
- static const TiledEvaluation value =
173
- BlockAccess ? TiledEvaluation::On : TiledEvaluation::Off;
174
- };
175
-
176
- template <typename Expression, typename Device,
177
- bool Vectorizable = IsVectorizable<Device, Expression>::value,
178
- TiledEvaluation Tiling = IsTileable<Device, Expression>::value>
179
- class TensorExecutor;
180
-
181
- template <typename Expression, typename Device, typename DoneCallback,
182
- bool Vectorizable = IsVectorizable<Device, Expression>::value,
183
- TiledEvaluation Tiling = IsTileable<Device, Expression>::value>
184
- class TensorAsyncExecutor;
185
-
186
-
187
- } // end namespace internal
188
-
189
- } // end namespace Eigen
190
-
191
- #endif // EIGEN_CXX11_TENSOR_TENSOR_FORWARD_DECLARATIONS_H
@@ -1,488 +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_FUNCTORS_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_FUNCTORS_H
12
-
13
- namespace Eigen {
14
- namespace internal {
15
-
16
-
17
- /** \internal
18
- * \brief Template functor to compute the modulo between an array and a scalar.
19
- */
20
- template <typename Scalar>
21
- struct scalar_mod_op {
22
- EIGEN_DEVICE_FUNC scalar_mod_op(const Scalar& divisor) : m_divisor(divisor) {}
23
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar operator() (const Scalar& a) const { return a % m_divisor; }
24
- const Scalar m_divisor;
25
- };
26
- template <typename Scalar>
27
- struct functor_traits<scalar_mod_op<Scalar> >
28
- { enum { Cost = scalar_div_cost<Scalar,false>::value, PacketAccess = false }; };
29
-
30
-
31
- /** \internal
32
- * \brief Template functor to compute the modulo between 2 arrays.
33
- */
34
- template <typename Scalar>
35
- struct scalar_mod2_op {
36
- EIGEN_EMPTY_STRUCT_CTOR(scalar_mod2_op)
37
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar operator() (const Scalar& a, const Scalar& b) const { return a % b; }
38
- };
39
- template <typename Scalar>
40
- struct functor_traits<scalar_mod2_op<Scalar> >
41
- { enum { Cost = scalar_div_cost<Scalar,false>::value, PacketAccess = false }; };
42
-
43
- template <typename Scalar>
44
- struct scalar_fmod_op {
45
- EIGEN_EMPTY_STRUCT_CTOR(scalar_fmod_op)
46
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar
47
- operator()(const Scalar& a, const Scalar& b) const {
48
- return numext::fmod(a, b);
49
- }
50
- };
51
- template <typename Scalar>
52
- struct functor_traits<scalar_fmod_op<Scalar> > {
53
- enum { Cost = 13, // Reciprocal throughput of FPREM on Haswell.
54
- PacketAccess = false };
55
- };
56
-
57
- template<typename Reducer, typename Device>
58
- struct reducer_traits {
59
- enum {
60
- Cost = 1,
61
- PacketAccess = false,
62
- IsStateful = false,
63
- IsExactlyAssociative = true
64
- };
65
- };
66
-
67
- // Standard reduction functors
68
- template <typename T> struct SumReducer
69
- {
70
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(const T t, T* accum) const {
71
- internal::scalar_sum_op<T> sum_op;
72
- *accum = sum_op(*accum, t);
73
- }
74
- template <typename Packet>
75
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reducePacket(const Packet& p, Packet* accum) const {
76
- (*accum) = padd<Packet>(*accum, p);
77
- }
78
-
79
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T initialize() const {
80
- internal::scalar_cast_op<int, T> conv;
81
- return conv(0);
82
- }
83
- template <typename Packet>
84
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet initializePacket() const {
85
- return pset1<Packet>(initialize());
86
- }
87
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalize(const T accum) const {
88
- return accum;
89
- }
90
- template <typename Packet>
91
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet finalizePacket(const Packet& vaccum) const {
92
- return vaccum;
93
- }
94
- template <typename Packet>
95
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalizeBoth(const T saccum, const Packet& vaccum) const {
96
- internal::scalar_sum_op<T> sum_op;
97
- return sum_op(saccum, predux(vaccum));
98
- }
99
- };
100
-
101
- template <typename T, typename Device>
102
- struct reducer_traits<SumReducer<T>, Device> {
103
- enum {
104
- Cost = NumTraits<T>::AddCost,
105
- PacketAccess = PacketType<T, Device>::HasAdd,
106
- IsStateful = false,
107
- IsExactlyAssociative = NumTraits<T>::IsInteger
108
- };
109
- };
110
-
111
- template <typename T> struct MeanReducer
112
- {
113
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
114
- MeanReducer() : scalarCount_(0), packetCount_(0) { }
115
-
116
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(const T t, T* accum) {
117
- internal::scalar_sum_op<T> sum_op;
118
- *accum = sum_op(*accum, t);
119
- scalarCount_++;
120
- }
121
- template <typename Packet>
122
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reducePacket(const Packet& p, Packet* accum) {
123
- (*accum) = padd<Packet>(*accum, p);
124
- packetCount_++;
125
- }
126
-
127
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T initialize() const {
128
- internal::scalar_cast_op<int, T> conv;
129
- return conv(0);
130
- }
131
- template <typename Packet>
132
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet initializePacket() const {
133
- return pset1<Packet>(initialize());
134
- }
135
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalize(const T accum) const {
136
- internal::scalar_quotient_op<T> quotient_op;
137
- return quotient_op(accum, T(scalarCount_));
138
- }
139
- template <typename Packet>
140
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet finalizePacket(const Packet& vaccum) const {
141
- return pdiv(vaccum, pset1<Packet>(T(packetCount_)));
142
- }
143
- template <typename Packet>
144
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalizeBoth(const T saccum, const Packet& vaccum) const {
145
- internal::scalar_sum_op<T> sum_op;
146
- internal::scalar_quotient_op<T> quotient_op;
147
- return quotient_op(
148
- sum_op(saccum, predux(vaccum)),
149
- T(scalarCount_ + packetCount_ * unpacket_traits<Packet>::size));
150
- }
151
-
152
- protected:
153
- DenseIndex scalarCount_;
154
- DenseIndex packetCount_;
155
- };
156
-
157
- template <typename T, typename Device>
158
- struct reducer_traits<MeanReducer<T>, Device> {
159
- enum {
160
- Cost = NumTraits<T>::AddCost,
161
- PacketAccess = PacketType<T, Device>::HasAdd &&
162
- PacketType<T, Device>::HasDiv && !NumTraits<T>::IsInteger,
163
- IsStateful = true,
164
- IsExactlyAssociative = NumTraits<T>::IsInteger
165
- };
166
- };
167
-
168
-
169
- template <typename T, bool IsMax = true, bool IsInteger = true>
170
- struct MinMaxBottomValue {
171
- EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE T bottom_value() {
172
- return Eigen::NumTraits<T>::lowest();
173
- }
174
- };
175
- template <typename T>
176
- struct MinMaxBottomValue<T, true, false> {
177
- EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE T bottom_value() {
178
- return -Eigen::NumTraits<T>::infinity();
179
- }
180
- };
181
- template <typename T>
182
- struct MinMaxBottomValue<T, false, true> {
183
- EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE T bottom_value() {
184
- return Eigen::NumTraits<T>::highest();
185
- }
186
- };
187
- template <typename T>
188
- struct MinMaxBottomValue<T, false, false> {
189
- EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE T bottom_value() {
190
- return Eigen::NumTraits<T>::infinity();
191
- }
192
- };
193
-
194
-
195
- template <typename T, int NaNPropagation=PropagateFast> struct MaxReducer
196
- {
197
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(const T t, T* accum) const {
198
- scalar_max_op<T, T, NaNPropagation> op;
199
- *accum = op(t, *accum);
200
- }
201
- template <typename Packet>
202
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reducePacket(const Packet& p, Packet* accum) const {
203
- scalar_max_op<T, T, NaNPropagation> op;
204
- (*accum) = op.packetOp(*accum, p);
205
- }
206
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T initialize() const {
207
- return MinMaxBottomValue<T, /*IsMax=*/true, Eigen::NumTraits<T>::IsInteger>::bottom_value();
208
- }
209
- template <typename Packet>
210
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet initializePacket() const {
211
- return pset1<Packet>(initialize());
212
- }
213
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalize(const T accum) const {
214
- return accum;
215
- }
216
- template <typename Packet>
217
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet finalizePacket(const Packet& vaccum) const {
218
- return vaccum;
219
- }
220
- template <typename Packet>
221
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalizeBoth(const T saccum, const Packet& vaccum) const {
222
- scalar_max_op<T, T, NaNPropagation> op;
223
- return op(saccum, op.predux(vaccum));
224
- }
225
- };
226
-
227
- template <typename T, typename Device, int NaNPropagation>
228
- struct reducer_traits<MaxReducer<T, NaNPropagation>, Device> {
229
- enum {
230
- Cost = NumTraits<T>::AddCost,
231
- PacketAccess = PacketType<T, Device>::HasMax,
232
- IsStateful = false,
233
- IsExactlyAssociative = (NaNPropagation!=PropagateFast)
234
- };
235
- };
236
-
237
- template <typename T, int NaNPropagation=PropagateFast> struct MinReducer
238
- {
239
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(const T t, T* accum) const {
240
- scalar_min_op<T, T, NaNPropagation> op;
241
- *accum = op(t, *accum);
242
- }
243
- template <typename Packet>
244
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reducePacket(const Packet& p, Packet* accum) const {
245
- scalar_min_op<T, T, NaNPropagation> op;
246
- (*accum) = op.packetOp(*accum, p);
247
- }
248
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T initialize() const {
249
- return MinMaxBottomValue<T, /*IsMax=*/false, Eigen::NumTraits<T>::IsInteger>::bottom_value();
250
- }
251
- template <typename Packet>
252
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet initializePacket() const {
253
- return pset1<Packet>(initialize());
254
- }
255
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalize(const T accum) const {
256
- return accum;
257
- }
258
- template <typename Packet>
259
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet finalizePacket(const Packet& vaccum) const {
260
- return vaccum;
261
- }
262
- template <typename Packet>
263
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalizeBoth(const T saccum, const Packet& vaccum) const {
264
- scalar_min_op<T, T, NaNPropagation> op;
265
- return op(saccum, op.predux(vaccum));
266
- }
267
- };
268
-
269
- template <typename T, typename Device, int NaNPropagation>
270
- struct reducer_traits<MinReducer<T, NaNPropagation>, Device> {
271
- enum {
272
- Cost = NumTraits<T>::AddCost,
273
- PacketAccess = PacketType<T, Device>::HasMin,
274
- IsStateful = false,
275
- IsExactlyAssociative = (NaNPropagation!=PropagateFast)
276
- };
277
- };
278
-
279
- template <typename T> struct ProdReducer
280
- {
281
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(const T t, T* accum) const {
282
- internal::scalar_product_op<T> prod_op;
283
- (*accum) = prod_op(*accum, t);
284
- }
285
- template <typename Packet>
286
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reducePacket(const Packet& p, Packet* accum) const {
287
- (*accum) = pmul<Packet>(*accum, p);
288
- }
289
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T initialize() const {
290
- internal::scalar_cast_op<int, T> conv;
291
- return conv(1);
292
- }
293
- template <typename Packet>
294
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet initializePacket() const {
295
- return pset1<Packet>(initialize());
296
- }
297
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalize(const T accum) const {
298
- return accum;
299
- }
300
- template <typename Packet>
301
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Packet finalizePacket(const Packet& vaccum) const {
302
- return vaccum;
303
- }
304
- template <typename Packet>
305
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalizeBoth(const T saccum, const Packet& vaccum) const {
306
- internal::scalar_product_op<T> prod_op;
307
- return prod_op(saccum, predux_mul(vaccum));
308
- }
309
- };
310
-
311
- template <typename T, typename Device>
312
- struct reducer_traits<ProdReducer<T>, Device> {
313
- enum {
314
- Cost = NumTraits<T>::MulCost,
315
- PacketAccess = PacketType<T, Device>::HasMul,
316
- IsStateful = false,
317
- IsExactlyAssociative = true
318
- };
319
- };
320
-
321
-
322
- struct AndReducer
323
- {
324
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(bool t, bool* accum) const {
325
- *accum = *accum && t;
326
- }
327
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool initialize() const {
328
- return true;
329
- }
330
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool finalize(bool accum) const {
331
- return accum;
332
- }
333
- };
334
-
335
- template <typename Device>
336
- struct reducer_traits<AndReducer, Device> {
337
- enum {
338
- Cost = 1,
339
- PacketAccess = false,
340
- IsStateful = false,
341
- IsExactlyAssociative = true
342
- };
343
- };
344
-
345
-
346
- struct OrReducer {
347
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(bool t, bool* accum) const {
348
- *accum = *accum || t;
349
- }
350
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool initialize() const {
351
- return false;
352
- }
353
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool finalize(bool accum) const {
354
- return accum;
355
- }
356
- };
357
-
358
- template <typename Device>
359
- struct reducer_traits<OrReducer, Device> {
360
- enum {
361
- Cost = 1,
362
- PacketAccess = false,
363
- IsStateful = false,
364
- IsExactlyAssociative = true
365
- };
366
- };
367
-
368
- // Argmin/Argmax reducers. Returns the first occurrence if multiple locations
369
- // contain the same min/max value.
370
- template <typename T> struct ArgMaxTupleReducer
371
- {
372
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(const T t, T* accum) const {
373
- if (t.second < accum->second) {
374
- return;
375
- } else if (t.second > accum->second || accum->first > t.first ) {
376
- *accum = t;
377
- }
378
- }
379
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T initialize() const {
380
- return T(0, NumTraits<typename T::second_type>::lowest());
381
- }
382
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalize(const T& accum) const {
383
- return accum;
384
- }
385
- };
386
-
387
- template <typename T, typename Device>
388
- struct reducer_traits<ArgMaxTupleReducer<T>, Device> {
389
- enum {
390
- Cost = NumTraits<T>::AddCost,
391
- PacketAccess = false,
392
- IsStateful = false,
393
- IsExactlyAssociative = true
394
- };
395
- };
396
-
397
-
398
- template <typename T> struct ArgMinTupleReducer
399
- {
400
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void reduce(const T& t, T* accum) const {
401
- if (t.second > accum->second) {
402
- return;
403
- } else if (t.second < accum->second || accum->first > t.first) {
404
- *accum = t;
405
- }
406
- }
407
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T initialize() const {
408
- return T(0, NumTraits<typename T::second_type>::highest());
409
- }
410
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T finalize(const T& accum) const {
411
- return accum;
412
- }
413
- };
414
-
415
- template <typename T, typename Device>
416
- struct reducer_traits<ArgMinTupleReducer<T>, Device> {
417
- enum {
418
- Cost = NumTraits<T>::AddCost,
419
- PacketAccess = false,
420
- IsStateful = false,
421
- IsExactlyAssociative = true
422
- };
423
- };
424
-
425
-
426
- template <typename T, typename Index, size_t NumDims>
427
- class GaussianGenerator {
428
- public:
429
- static const bool PacketAccess = false;
430
-
431
- EIGEN_DEVICE_FUNC GaussianGenerator(const array<T, NumDims>& means,
432
- const array<T, NumDims>& std_devs)
433
- : m_means(means)
434
- {
435
- EIGEN_UNROLL_LOOP
436
- for (size_t i = 0; i < NumDims; ++i) {
437
- m_two_sigmas[i] = std_devs[i] * std_devs[i] * 2;
438
- }
439
- }
440
-
441
- EIGEN_DEVICE_FUNC T operator()(const array<Index, NumDims>& coordinates) const {
442
- T tmp = T(0);
443
- EIGEN_UNROLL_LOOP
444
- for (size_t i = 0; i < NumDims; ++i) {
445
- T offset = coordinates[i] - m_means[i];
446
- tmp += offset * offset / m_two_sigmas[i];
447
- }
448
- return numext::exp(-tmp);
449
- }
450
-
451
- private:
452
- array<T, NumDims> m_means;
453
- array<T, NumDims> m_two_sigmas;
454
- };
455
-
456
- template <typename T, typename Index, size_t NumDims>
457
- struct functor_traits<GaussianGenerator<T, Index, NumDims> > {
458
- enum {
459
- Cost = NumDims * (2 * NumTraits<T>::AddCost + NumTraits<T>::MulCost +
460
- functor_traits<scalar_quotient_op<T, T> >::Cost) +
461
- functor_traits<scalar_exp_op<T> >::Cost,
462
- PacketAccess = GaussianGenerator<T, Index, NumDims>::PacketAccess
463
- };
464
- };
465
-
466
- template <typename Scalar>
467
- struct scalar_clamp_op {
468
- EIGEN_DEVICE_FUNC inline scalar_clamp_op(const Scalar& _min, const Scalar& _max) : m_min(_min), m_max(_max) {}
469
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Scalar
470
- operator()(const Scalar& x) const {
471
- return numext::mini(numext::maxi(x, m_min), m_max);
472
- }
473
- template <typename Packet>
474
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Packet
475
- packetOp(const Packet& x) const {
476
- return internal::pmin(internal::pmax(x, pset1<Packet>(m_min)), pset1<Packet>(m_max));
477
- }
478
- const Scalar m_min;
479
- const Scalar m_max;
480
- };
481
- template<typename Scalar>
482
- struct functor_traits<scalar_clamp_op<Scalar> >
483
- { enum { Cost = 2 * NumTraits<Scalar>::AddCost, PacketAccess = (packet_traits<Scalar>::HasMin && packet_traits<Scalar>::HasMax)}; };
484
-
485
- } // end namespace internal
486
- } // end namespace Eigen
487
-
488
- #endif // EIGEN_CXX11_TENSOR_TENSOR_FUNCTORS_H