sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.19__cp39-cp39-win_amd64.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +156 -156
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp39-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp39-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +156 -156
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp39-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,708 +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_PADDING_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_PADDING_H
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-
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- namespace Eigen {
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-
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- /** \class TensorPadding
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor padding class.
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- * At the moment only padding with a constant value is supported.
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- *
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- */
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- namespace internal {
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- template<typename PaddingDimensions, typename XprType>
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- struct traits<TensorPaddingOp<PaddingDimensions, XprType> > : public traits<XprType>
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- {
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- typedef typename XprType::Scalar Scalar;
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- typedef traits<XprType> XprTraits;
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- typedef typename XprTraits::StorageKind StorageKind;
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- typedef typename XprTraits::Index Index;
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- typedef typename XprType::Nested Nested;
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- typedef typename remove_reference<Nested>::type _Nested;
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- static const int NumDimensions = XprTraits::NumDimensions;
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- static const int Layout = XprTraits::Layout;
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- typedef typename XprTraits::PointerType PointerType;
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- };
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-
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- template<typename PaddingDimensions, typename XprType>
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- struct eval<TensorPaddingOp<PaddingDimensions, XprType>, Eigen::Dense>
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- {
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- typedef const TensorPaddingOp<PaddingDimensions, XprType>& type;
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- };
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-
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- template<typename PaddingDimensions, typename XprType>
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- struct nested<TensorPaddingOp<PaddingDimensions, XprType>, 1, typename eval<TensorPaddingOp<PaddingDimensions, XprType> >::type>
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- {
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- typedef TensorPaddingOp<PaddingDimensions, XprType> type;
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- };
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-
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- } // end namespace internal
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-
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-
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-
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- template<typename PaddingDimensions, typename XprType>
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- class TensorPaddingOp : public TensorBase<TensorPaddingOp<PaddingDimensions, XprType>, ReadOnlyAccessors>
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- {
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- public:
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- typedef typename Eigen::internal::traits<TensorPaddingOp>::Scalar Scalar;
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- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
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- typedef typename XprType::CoeffReturnType CoeffReturnType;
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- typedef typename Eigen::internal::nested<TensorPaddingOp>::type Nested;
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- typedef typename Eigen::internal::traits<TensorPaddingOp>::StorageKind StorageKind;
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- typedef typename Eigen::internal::traits<TensorPaddingOp>::Index Index;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorPaddingOp(const XprType& expr, const PaddingDimensions& padding_dims, const Scalar padding_value)
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- : m_xpr(expr), m_padding_dims(padding_dims), m_padding_value(padding_value) {}
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-
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- EIGEN_DEVICE_FUNC
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- const PaddingDimensions& padding() const { return m_padding_dims; }
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- EIGEN_DEVICE_FUNC
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- Scalar padding_value() const { return m_padding_value; }
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-
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- EIGEN_DEVICE_FUNC
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- const typename internal::remove_all<typename XprType::Nested>::type&
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- expression() const { return m_xpr; }
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-
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- protected:
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- typename XprType::Nested m_xpr;
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- const PaddingDimensions m_padding_dims;
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- const Scalar m_padding_value;
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- };
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-
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-
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- // Eval as rvalue
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- template<typename PaddingDimensions, typename ArgType, typename Device>
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- struct TensorEvaluator<const TensorPaddingOp<PaddingDimensions, ArgType>, Device>
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- {
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- typedef TensorPaddingOp<PaddingDimensions, ArgType> XprType;
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- typedef typename XprType::Index Index;
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- static const int NumDims = internal::array_size<PaddingDimensions>::value;
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- typedef DSizes<Index, NumDims> Dimensions;
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- typedef typename XprType::Scalar Scalar;
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- typedef typename XprType::CoeffReturnType CoeffReturnType;
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- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
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- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
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- typedef StorageMemory<CoeffReturnType, Device> Storage;
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- typedef typename Storage::Type EvaluatorPointerType;
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-
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- enum {
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- IsAligned = true,
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- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
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- BlockAccess = TensorEvaluator<ArgType, Device>::RawAccess,
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- PreferBlockAccess = true,
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- Layout = TensorEvaluator<ArgType, Device>::Layout,
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- CoordAccess = true,
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- RawAccess = false
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- };
107
-
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- typedef typename internal::remove_const<Scalar>::type ScalarNoConst;
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-
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- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
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- typedef internal::TensorBlockDescriptor<NumDims, Index> TensorBlockDesc;
112
- typedef internal::TensorBlockScratchAllocator<Device> TensorBlockScratch;
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-
114
- typedef typename internal::TensorMaterializedBlock<ScalarNoConst, NumDims,
115
- Layout, Index>
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- TensorBlock;
117
- //===--------------------------------------------------------------------===//
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-
119
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
120
- : m_impl(op.expression(), device), m_padding(op.padding()), m_paddingValue(op.padding_value()), m_device(device)
121
- {
122
- // The padding op doesn't change the rank of the tensor. Directly padding a scalar would lead
123
- // to a vector, which doesn't make sense. Instead one should reshape the scalar into a vector
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- // of 1 element first and then pad.
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- EIGEN_STATIC_ASSERT((NumDims > 0), YOU_MADE_A_PROGRAMMING_MISTAKE);
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-
127
- // Compute dimensions
128
- m_dimensions = m_impl.dimensions();
129
- for (int i = 0; i < NumDims; ++i) {
130
- m_dimensions[i] += m_padding[i].first + m_padding[i].second;
131
- }
132
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
133
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
134
- m_inputStrides[0] = 1;
135
- m_outputStrides[0] = 1;
136
- for (int i = 1; i < NumDims; ++i) {
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- m_inputStrides[i] = m_inputStrides[i-1] * input_dims[i-1];
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- m_outputStrides[i] = m_outputStrides[i-1] * m_dimensions[i-1];
139
- }
140
- m_outputStrides[NumDims] = m_outputStrides[NumDims-1] * m_dimensions[NumDims-1];
141
- } else {
142
- m_inputStrides[NumDims - 1] = 1;
143
- m_outputStrides[NumDims] = 1;
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- for (int i = NumDims - 2; i >= 0; --i) {
145
- m_inputStrides[i] = m_inputStrides[i+1] * input_dims[i+1];
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- m_outputStrides[i+1] = m_outputStrides[i+2] * m_dimensions[i+1];
147
- }
148
- m_outputStrides[0] = m_outputStrides[1] * m_dimensions[0];
149
- }
150
- }
151
-
152
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
153
-
154
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType) {
155
- m_impl.evalSubExprsIfNeeded(NULL);
156
- return true;
157
- }
158
-
159
- #ifdef EIGEN_USE_THREADS
160
- template <typename EvalSubExprsCallback>
161
- EIGEN_STRONG_INLINE void evalSubExprsIfNeededAsync(
162
- EvaluatorPointerType, EvalSubExprsCallback done) {
163
- m_impl.evalSubExprsIfNeededAsync(nullptr, [done](bool) { done(true); });
164
- }
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- #endif // EIGEN_USE_THREADS
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-
167
- EIGEN_STRONG_INLINE void cleanup() {
168
- m_impl.cleanup();
169
- }
170
-
171
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
172
- {
173
- eigen_assert(index < dimensions().TotalSize());
174
- Index inputIndex = 0;
175
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
176
- EIGEN_UNROLL_LOOP
177
- for (int i = NumDims - 1; i > 0; --i) {
178
- const Index idx = index / m_outputStrides[i];
179
- if (isPaddingAtIndexForDim(idx, i)) {
180
- return m_paddingValue;
181
- }
182
- inputIndex += (idx - m_padding[i].first) * m_inputStrides[i];
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- index -= idx * m_outputStrides[i];
184
- }
185
- if (isPaddingAtIndexForDim(index, 0)) {
186
- return m_paddingValue;
187
- }
188
- inputIndex += (index - m_padding[0].first);
189
- } else {
190
- EIGEN_UNROLL_LOOP
191
- for (int i = 0; i < NumDims - 1; ++i) {
192
- const Index idx = index / m_outputStrides[i+1];
193
- if (isPaddingAtIndexForDim(idx, i)) {
194
- return m_paddingValue;
195
- }
196
- inputIndex += (idx - m_padding[i].first) * m_inputStrides[i];
197
- index -= idx * m_outputStrides[i+1];
198
- }
199
- if (isPaddingAtIndexForDim(index, NumDims-1)) {
200
- return m_paddingValue;
201
- }
202
- inputIndex += (index - m_padding[NumDims-1].first);
203
- }
204
- return m_impl.coeff(inputIndex);
205
- }
206
-
207
- template<int LoadMode>
208
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
209
- {
210
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
211
- return packetColMajor(index);
212
- }
213
- return packetRowMajor(index);
214
- }
215
-
216
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
217
- TensorOpCost cost = m_impl.costPerCoeff(vectorized);
218
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
219
- EIGEN_UNROLL_LOOP
220
- for (int i = 0; i < NumDims; ++i)
221
- updateCostPerDimension(cost, i, i == 0);
222
- } else {
223
- EIGEN_UNROLL_LOOP
224
- for (int i = NumDims - 1; i >= 0; --i)
225
- updateCostPerDimension(cost, i, i == NumDims - 1);
226
- }
227
- return cost;
228
- }
229
-
230
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
231
- internal::TensorBlockResourceRequirements getResourceRequirements() const {
232
- const size_t target_size = m_device.lastLevelCacheSize();
233
- return internal::TensorBlockResourceRequirements::merge(
234
- internal::TensorBlockResourceRequirements::skewed<Scalar>(target_size),
235
- m_impl.getResourceRequirements());
236
- }
237
-
238
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorBlock
239
- block(TensorBlockDesc& desc, TensorBlockScratch& scratch,
240
- bool /*root_of_expr_ast*/ = false) const {
241
- // If one of the dimensions is zero, return empty block view.
242
- if (desc.size() == 0) {
243
- return TensorBlock(internal::TensorBlockKind::kView, NULL,
244
- desc.dimensions());
245
- }
246
-
247
- static const bool IsColMajor = Layout == static_cast<int>(ColMajor);
248
- const int inner_dim_idx = IsColMajor ? 0 : NumDims - 1;
249
-
250
- Index offset = desc.offset();
251
-
252
- // Compute offsets in the output tensor corresponding to the desc.offset().
253
- DSizes<Index, NumDims> output_offsets;
254
- for (int i = NumDims - 1; i > 0; --i) {
255
- const int dim = IsColMajor ? i : NumDims - i - 1;
256
- const int stride_dim = IsColMajor ? dim : dim + 1;
257
- output_offsets[dim] = offset / m_outputStrides[stride_dim];
258
- offset -= output_offsets[dim] * m_outputStrides[stride_dim];
259
- }
260
- output_offsets[inner_dim_idx] = offset;
261
-
262
- // Offsets in the input corresponding to output offsets.
263
- DSizes<Index, NumDims> input_offsets = output_offsets;
264
- for (int i = 0; i < NumDims; ++i) {
265
- const int dim = IsColMajor ? i : NumDims - i - 1;
266
- input_offsets[dim] = input_offsets[dim] - m_padding[dim].first;
267
- }
268
-
269
- // Compute offset in the input buffer (at this point it might be illegal and
270
- // point outside of the input buffer, because we don't check for negative
271
- // offsets, it will be autocorrected in the block iteration loop below).
272
- Index input_offset = 0;
273
- for (int i = 0; i < NumDims; ++i) {
274
- const int dim = IsColMajor ? i : NumDims - i - 1;
275
- input_offset += input_offsets[dim] * m_inputStrides[dim];
276
- }
277
-
278
- // Destination buffer and scratch buffer both indexed from 0 and have the
279
- // same dimensions as the requested block (for destination buffer this
280
- // property is guaranteed by `desc.destination()`).
281
- Index output_offset = 0;
282
- const DSizes<Index, NumDims> output_strides =
283
- internal::strides<Layout>(desc.dimensions());
284
-
285
- // NOTE(ezhulenev): We initialize bock iteration state for `NumDims - 1`
286
- // dimensions, skipping innermost dimension. In theory it should be possible
287
- // to squeeze matching innermost dimensions, however in practice that did
288
- // not show any improvements in benchmarks. Also in practice first outer
289
- // dimension usually has padding, and will prevent squeezing.
290
-
291
- // Initialize output block iterator state. Dimension in this array are
292
- // always in inner_most -> outer_most order (col major layout).
293
- array<BlockIteratorState, NumDims - 1> it;
294
- for (int i = 0; i < NumDims - 1; ++i) {
295
- const int dim = IsColMajor ? i + 1 : NumDims - i - 2;
296
- it[i].count = 0;
297
- it[i].size = desc.dimension(dim);
298
-
299
- it[i].input_stride = m_inputStrides[dim];
300
- it[i].input_span = it[i].input_stride * (it[i].size - 1);
301
-
302
- it[i].output_stride = output_strides[dim];
303
- it[i].output_span = it[i].output_stride * (it[i].size - 1);
304
- }
305
-
306
- const Index input_inner_dim_size =
307
- static_cast<Index>(m_impl.dimensions()[inner_dim_idx]);
308
-
309
- // Total output size.
310
- const Index output_size = desc.size();
311
-
312
- // We will fill inner dimension of this size in the output. It might be
313
- // larger than the inner dimension in the input, so we might have to pad
314
- // before/after we copy values from the input inner dimension.
315
- const Index output_inner_dim_size = desc.dimension(inner_dim_idx);
316
-
317
- // How many values to fill with padding BEFORE reading from the input inner
318
- // dimension.
319
- const Index output_inner_pad_before_size =
320
- input_offsets[inner_dim_idx] < 0
321
- ? numext::mini(numext::abs(input_offsets[inner_dim_idx]),
322
- output_inner_dim_size)
323
- : 0;
324
-
325
- // How many values we can actually copy from the input inner dimension.
326
- const Index output_inner_copy_size = numext::mini(
327
- // Want to copy from input.
328
- (output_inner_dim_size - output_inner_pad_before_size),
329
- // Can copy from input.
330
- numext::maxi(input_inner_dim_size - (input_offsets[inner_dim_idx] +
331
- output_inner_pad_before_size),
332
- Index(0)));
333
-
334
- eigen_assert(output_inner_copy_size >= 0);
335
-
336
- // How many values to fill with padding AFTER reading from the input inner
337
- // dimension.
338
- const Index output_inner_pad_after_size =
339
- (output_inner_dim_size - output_inner_copy_size -
340
- output_inner_pad_before_size);
341
-
342
- // Sanity check, sum of all sizes must be equal to the output size.
343
- eigen_assert(output_inner_dim_size ==
344
- (output_inner_pad_before_size + output_inner_copy_size +
345
- output_inner_pad_after_size));
346
-
347
- // Keep track of current coordinates and padding in the output.
348
- DSizes<Index, NumDims> output_coord = output_offsets;
349
- DSizes<Index, NumDims> output_padded;
350
- for (int i = 0; i < NumDims; ++i) {
351
- const int dim = IsColMajor ? i : NumDims - i - 1;
352
- output_padded[dim] = isPaddingAtIndexForDim(output_coord[dim], dim);
353
- }
354
-
355
- typedef internal::StridedLinearBufferCopy<ScalarNoConst, Index> LinCopy;
356
-
357
- // Prepare storage for the materialized padding result.
358
- const typename TensorBlock::Storage block_storage =
359
- TensorBlock::prepareStorage(desc, scratch);
360
-
361
- // TODO(ezhulenev): Squeeze multiple non-padded inner dimensions into a
362
- // single logical inner dimension.
363
-
364
- // When possible we squeeze writes for the innermost (only if non-padded)
365
- // dimension with the first padded dimension. This allows to reduce the
366
- // number of calls to LinCopy and better utilize vector instructions.
367
- const bool squeeze_writes =
368
- NumDims > 1 &&
369
- // inner dimension is not padded
370
- (input_inner_dim_size == m_dimensions[inner_dim_idx]) &&
371
- // and equal to the block inner dimension
372
- (input_inner_dim_size == output_inner_dim_size);
373
-
374
- const int squeeze_dim = IsColMajor ? inner_dim_idx + 1 : inner_dim_idx - 1;
375
-
376
- // Maximum coordinate on a squeeze dimension that we can write to.
377
- const Index squeeze_max_coord =
378
- squeeze_writes ? numext::mini(
379
- // max non-padded element in the input
380
- static_cast<Index>(m_dimensions[squeeze_dim] -
381
- m_padding[squeeze_dim].second),
382
- // max element in the output buffer
383
- static_cast<Index>(output_offsets[squeeze_dim] +
384
- desc.dimension(squeeze_dim)))
385
- : static_cast<Index>(0);
386
-
387
- // Iterate copying data from `m_impl.data()` to the output buffer.
388
- for (Index size = 0; size < output_size;) {
389
- // Detect if we are in the padded region (exclude innermost dimension).
390
- bool is_padded = false;
391
- for (int j = 1; j < NumDims; ++j) {
392
- const int dim = IsColMajor ? j : NumDims - j - 1;
393
- is_padded = output_padded[dim];
394
- if (is_padded) break;
395
- }
396
-
397
- if (is_padded) {
398
- // Fill single innermost dimension with padding value.
399
- size += output_inner_dim_size;
400
-
401
- LinCopy::template Run<LinCopy::Kind::FillLinear>(
402
- typename LinCopy::Dst(output_offset, 1, block_storage.data()),
403
- typename LinCopy::Src(0, 0, &m_paddingValue),
404
- output_inner_dim_size);
405
-
406
-
407
- } else if (squeeze_writes) {
408
- // Squeeze multiple reads from innermost dimensions.
409
- const Index squeeze_num = squeeze_max_coord - output_coord[squeeze_dim];
410
- size += output_inner_dim_size * squeeze_num;
411
-
412
- // Copy `squeeze_num` inner dimensions from input to output.
413
- LinCopy::template Run<LinCopy::Kind::Linear>(
414
- typename LinCopy::Dst(output_offset, 1, block_storage.data()),
415
- typename LinCopy::Src(input_offset, 1, m_impl.data()),
416
- output_inner_dim_size * squeeze_num);
417
-
418
- // Update iteration state for only `squeeze_num - 1` processed inner
419
- // dimensions, because we have another iteration state update at the end
420
- // of the loop that will update iteration state for the last inner
421
- // processed dimension.
422
- it[0].count += (squeeze_num - 1);
423
- input_offset += it[0].input_stride * (squeeze_num - 1);
424
- output_offset += it[0].output_stride * (squeeze_num - 1);
425
- output_coord[squeeze_dim] += (squeeze_num - 1);
426
-
427
- } else {
428
- // Single read from innermost dimension.
429
- size += output_inner_dim_size;
430
-
431
- { // Fill with padding before copying from input inner dimension.
432
- const Index out = output_offset;
433
-
434
- LinCopy::template Run<LinCopy::Kind::FillLinear>(
435
- typename LinCopy::Dst(out, 1, block_storage.data()),
436
- typename LinCopy::Src(0, 0, &m_paddingValue),
437
- output_inner_pad_before_size);
438
- }
439
-
440
- { // Copy data from input inner dimension.
441
- const Index out = output_offset + output_inner_pad_before_size;
442
- const Index in = input_offset + output_inner_pad_before_size;
443
-
444
- eigen_assert(output_inner_copy_size == 0 || m_impl.data() != NULL);
445
-
446
- LinCopy::template Run<LinCopy::Kind::Linear>(
447
- typename LinCopy::Dst(out, 1, block_storage.data()),
448
- typename LinCopy::Src(in, 1, m_impl.data()),
449
- output_inner_copy_size);
450
- }
451
-
452
- { // Fill with padding after copying from input inner dimension.
453
- const Index out = output_offset + output_inner_pad_before_size +
454
- output_inner_copy_size;
455
-
456
- LinCopy::template Run<LinCopy::Kind::FillLinear>(
457
- typename LinCopy::Dst(out, 1, block_storage.data()),
458
- typename LinCopy::Src(0, 0, &m_paddingValue),
459
- output_inner_pad_after_size);
460
- }
461
- }
462
-
463
- for (int j = 0; j < NumDims - 1; ++j) {
464
- const int dim = IsColMajor ? j + 1 : NumDims - j - 2;
465
-
466
- if (++it[j].count < it[j].size) {
467
- input_offset += it[j].input_stride;
468
- output_offset += it[j].output_stride;
469
- output_coord[dim] += 1;
470
- output_padded[dim] = isPaddingAtIndexForDim(output_coord[dim], dim);
471
- break;
472
- }
473
- it[j].count = 0;
474
- input_offset -= it[j].input_span;
475
- output_offset -= it[j].output_span;
476
- output_coord[dim] -= it[j].size - 1;
477
- output_padded[dim] = isPaddingAtIndexForDim(output_coord[dim], dim);
478
- }
479
- }
480
-
481
- return block_storage.AsTensorMaterializedBlock();
482
- }
483
-
484
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE EvaluatorPointerType data() const { return NULL; }
485
-
486
- #ifdef EIGEN_USE_SYCL
487
- // binding placeholder accessors to a command group handler for SYCL
488
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
489
- m_impl.bind(cgh);
490
- }
491
- #endif
492
-
493
- private:
494
- struct BlockIteratorState {
495
- BlockIteratorState()
496
- : count(0),
497
- size(0),
498
- input_stride(0),
499
- input_span(0),
500
- output_stride(0),
501
- output_span(0) {}
502
-
503
- Index count;
504
- Index size;
505
- Index input_stride;
506
- Index input_span;
507
- Index output_stride;
508
- Index output_span;
509
- };
510
-
511
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool isPaddingAtIndexForDim(
512
- Index index, int dim_index) const {
513
- #if defined(EIGEN_HAS_INDEX_LIST)
514
- return (!internal::index_pair_first_statically_eq<PaddingDimensions>(dim_index, 0) &&
515
- index < m_padding[dim_index].first) ||
516
- (!internal::index_pair_second_statically_eq<PaddingDimensions>(dim_index, 0) &&
517
- index >= m_dimensions[dim_index] - m_padding[dim_index].second);
518
- #else
519
- return (index < m_padding[dim_index].first) ||
520
- (index >= m_dimensions[dim_index] - m_padding[dim_index].second);
521
- #endif
522
- }
523
-
524
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool isLeftPaddingCompileTimeZero(
525
- int dim_index) const {
526
- #if defined(EIGEN_HAS_INDEX_LIST)
527
- return internal::index_pair_first_statically_eq<PaddingDimensions>(dim_index, 0);
528
- #else
529
- EIGEN_UNUSED_VARIABLE(dim_index);
530
- return false;
531
- #endif
532
- }
533
-
534
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE bool isRightPaddingCompileTimeZero(
535
- int dim_index) const {
536
- #if defined(EIGEN_HAS_INDEX_LIST)
537
- return internal::index_pair_second_statically_eq<PaddingDimensions>(dim_index, 0);
538
- #else
539
- EIGEN_UNUSED_VARIABLE(dim_index);
540
- return false;
541
- #endif
542
- }
543
-
544
-
545
- void updateCostPerDimension(TensorOpCost& cost, int i, bool first) const {
546
- const double in = static_cast<double>(m_impl.dimensions()[i]);
547
- const double out = in + m_padding[i].first + m_padding[i].second;
548
- if (out == 0)
549
- return;
550
- const double reduction = in / out;
551
- cost *= reduction;
552
- if (first) {
553
- cost += TensorOpCost(0, 0, 2 * TensorOpCost::AddCost<Index>() +
554
- reduction * (1 * TensorOpCost::AddCost<Index>()));
555
- } else {
556
- cost += TensorOpCost(0, 0, 2 * TensorOpCost::AddCost<Index>() +
557
- 2 * TensorOpCost::MulCost<Index>() +
558
- reduction * (2 * TensorOpCost::MulCost<Index>() +
559
- 1 * TensorOpCost::DivCost<Index>()));
560
- }
561
- }
562
-
563
- protected:
564
-
565
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packetColMajor(Index index) const
566
- {
567
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
568
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
569
-
570
- const Index initialIndex = index;
571
- Index inputIndex = 0;
572
- EIGEN_UNROLL_LOOP
573
- for (int i = NumDims - 1; i > 0; --i) {
574
- const Index firstIdx = index;
575
- const Index lastIdx = index + PacketSize - 1;
576
- const Index lastPaddedLeft = m_padding[i].first * m_outputStrides[i];
577
- const Index firstPaddedRight = (m_dimensions[i] - m_padding[i].second) * m_outputStrides[i];
578
- const Index lastPaddedRight = m_outputStrides[i+1];
579
-
580
- if (!isLeftPaddingCompileTimeZero(i) && lastIdx < lastPaddedLeft) {
581
- // all the coefficient are in the padding zone.
582
- return internal::pset1<PacketReturnType>(m_paddingValue);
583
- }
584
- else if (!isRightPaddingCompileTimeZero(i) && firstIdx >= firstPaddedRight && lastIdx < lastPaddedRight) {
585
- // all the coefficient are in the padding zone.
586
- return internal::pset1<PacketReturnType>(m_paddingValue);
587
- }
588
- else if ((isLeftPaddingCompileTimeZero(i) && isRightPaddingCompileTimeZero(i)) || (firstIdx >= lastPaddedLeft && lastIdx < firstPaddedRight)) {
589
- // all the coefficient are between the 2 padding zones.
590
- const Index idx = index / m_outputStrides[i];
591
- inputIndex += (idx - m_padding[i].first) * m_inputStrides[i];
592
- index -= idx * m_outputStrides[i];
593
- }
594
- else {
595
- // Every other case
596
- return packetWithPossibleZero(initialIndex);
597
- }
598
- }
599
-
600
- const Index lastIdx = index + PacketSize - 1;
601
- const Index firstIdx = index;
602
- const Index lastPaddedLeft = m_padding[0].first;
603
- const Index firstPaddedRight = (m_dimensions[0] - m_padding[0].second);
604
- const Index lastPaddedRight = m_outputStrides[1];
605
-
606
- if (!isLeftPaddingCompileTimeZero(0) && lastIdx < lastPaddedLeft) {
607
- // all the coefficient are in the padding zone.
608
- return internal::pset1<PacketReturnType>(m_paddingValue);
609
- }
610
- else if (!isRightPaddingCompileTimeZero(0) && firstIdx >= firstPaddedRight && lastIdx < lastPaddedRight) {
611
- // all the coefficient are in the padding zone.
612
- return internal::pset1<PacketReturnType>(m_paddingValue);
613
- }
614
- else if ((isLeftPaddingCompileTimeZero(0) && isRightPaddingCompileTimeZero(0)) || (firstIdx >= lastPaddedLeft && lastIdx < firstPaddedRight)) {
615
- // all the coefficient are between the 2 padding zones.
616
- inputIndex += (index - m_padding[0].first);
617
- return m_impl.template packet<Unaligned>(inputIndex);
618
- }
619
- // Every other case
620
- return packetWithPossibleZero(initialIndex);
621
- }
622
-
623
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packetRowMajor(Index index) const
624
- {
625
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
626
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
627
-
628
- const Index initialIndex = index;
629
- Index inputIndex = 0;
630
- EIGEN_UNROLL_LOOP
631
- for (int i = 0; i < NumDims - 1; ++i) {
632
- const Index firstIdx = index;
633
- const Index lastIdx = index + PacketSize - 1;
634
- const Index lastPaddedLeft = m_padding[i].first * m_outputStrides[i+1];
635
- const Index firstPaddedRight = (m_dimensions[i] - m_padding[i].second) * m_outputStrides[i+1];
636
- const Index lastPaddedRight = m_outputStrides[i];
637
-
638
- if (!isLeftPaddingCompileTimeZero(i) && lastIdx < lastPaddedLeft) {
639
- // all the coefficient are in the padding zone.
640
- return internal::pset1<PacketReturnType>(m_paddingValue);
641
- }
642
- else if (!isRightPaddingCompileTimeZero(i) && firstIdx >= firstPaddedRight && lastIdx < lastPaddedRight) {
643
- // all the coefficient are in the padding zone.
644
- return internal::pset1<PacketReturnType>(m_paddingValue);
645
- }
646
- else if ((isLeftPaddingCompileTimeZero(i) && isRightPaddingCompileTimeZero(i)) || (firstIdx >= lastPaddedLeft && lastIdx < firstPaddedRight)) {
647
- // all the coefficient are between the 2 padding zones.
648
- const Index idx = index / m_outputStrides[i+1];
649
- inputIndex += (idx - m_padding[i].first) * m_inputStrides[i];
650
- index -= idx * m_outputStrides[i+1];
651
- }
652
- else {
653
- // Every other case
654
- return packetWithPossibleZero(initialIndex);
655
- }
656
- }
657
-
658
- const Index lastIdx = index + PacketSize - 1;
659
- const Index firstIdx = index;
660
- const Index lastPaddedLeft = m_padding[NumDims-1].first;
661
- const Index firstPaddedRight = (m_dimensions[NumDims-1] - m_padding[NumDims-1].second);
662
- const Index lastPaddedRight = m_outputStrides[NumDims-1];
663
-
664
- if (!isLeftPaddingCompileTimeZero(NumDims-1) && lastIdx < lastPaddedLeft) {
665
- // all the coefficient are in the padding zone.
666
- return internal::pset1<PacketReturnType>(m_paddingValue);
667
- }
668
- else if (!isRightPaddingCompileTimeZero(NumDims-1) && firstIdx >= firstPaddedRight && lastIdx < lastPaddedRight) {
669
- // all the coefficient are in the padding zone.
670
- return internal::pset1<PacketReturnType>(m_paddingValue);
671
- }
672
- else if ((isLeftPaddingCompileTimeZero(NumDims-1) && isRightPaddingCompileTimeZero(NumDims-1)) || (firstIdx >= lastPaddedLeft && lastIdx < firstPaddedRight)) {
673
- // all the coefficient are between the 2 padding zones.
674
- inputIndex += (index - m_padding[NumDims-1].first);
675
- return m_impl.template packet<Unaligned>(inputIndex);
676
- }
677
- // Every other case
678
- return packetWithPossibleZero(initialIndex);
679
- }
680
-
681
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packetWithPossibleZero(Index index) const
682
- {
683
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
684
- EIGEN_UNROLL_LOOP
685
- for (int i = 0; i < PacketSize; ++i) {
686
- values[i] = coeff(index+i);
687
- }
688
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
689
- return rslt;
690
- }
691
-
692
- Dimensions m_dimensions;
693
- array<Index, NumDims+1> m_outputStrides;
694
- array<Index, NumDims> m_inputStrides;
695
- TensorEvaluator<ArgType, Device> m_impl;
696
- PaddingDimensions m_padding;
697
-
698
- Scalar m_paddingValue;
699
-
700
- const Device EIGEN_DEVICE_REF m_device;
701
- };
702
-
703
-
704
-
705
-
706
- } // end namespace Eigen
707
-
708
- #endif // EIGEN_CXX11_TENSOR_TENSOR_PADDING_H