sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-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 +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-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.cp311-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 +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-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
@@ -1,346 +0,0 @@
1
- // 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_STRIDING_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_STRIDING_H
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-
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- namespace Eigen {
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-
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- /** \class TensorStriding
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor striding class.
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- *
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- *
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- */
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- namespace internal {
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- template<typename Strides, typename XprType>
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- struct traits<TensorStridingOp<Strides, 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 Strides, typename XprType>
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- struct eval<TensorStridingOp<Strides, XprType>, Eigen::Dense>
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- {
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- typedef const TensorStridingOp<Strides, XprType>EIGEN_DEVICE_REF type;
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- };
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-
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- template<typename Strides, typename XprType>
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- struct nested<TensorStridingOp<Strides, XprType>, 1, typename eval<TensorStridingOp<Strides, XprType> >::type>
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- {
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- typedef TensorStridingOp<Strides, 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 Strides, typename XprType>
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- class TensorStridingOp : public TensorBase<TensorStridingOp<Strides, XprType> >
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- {
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- public:
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- typedef TensorBase<TensorStridingOp<Strides, XprType> > Base;
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- typedef typename Eigen::internal::traits<TensorStridingOp>::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<TensorStridingOp>::type Nested;
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- typedef typename Eigen::internal::traits<TensorStridingOp>::StorageKind StorageKind;
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- typedef typename Eigen::internal::traits<TensorStridingOp>::Index Index;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorStridingOp(const XprType& expr, const Strides& dims)
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- : m_xpr(expr), m_dims(dims) {}
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-
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- EIGEN_DEVICE_FUNC
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- const Strides& strides() const { return m_dims; }
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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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- EIGEN_TENSOR_INHERIT_ASSIGNMENT_OPERATORS(TensorStridingOp)
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-
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- protected:
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- typename XprType::Nested m_xpr;
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- const Strides m_dims;
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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 Strides, typename ArgType, typename Device>
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- struct TensorEvaluator<const TensorStridingOp<Strides, ArgType>, Device>
86
- {
87
- typedef TensorStridingOp<Strides, ArgType> XprType;
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- typedef typename XprType::Index Index;
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- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::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 {
99
- IsAligned = /*TensorEvaluator<ArgType, Device>::IsAligned*/false,
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- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
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- BlockAccess = false,
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- PreferBlockAccess = TensorEvaluator<ArgType, Device>::PreferBlockAccess,
103
- Layout = TensorEvaluator<ArgType, Device>::Layout,
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- CoordAccess = false, // to be implemented
105
- RawAccess = false
106
- };
107
-
108
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
109
- typedef internal::TensorBlockNotImplemented TensorBlock;
110
- //===--------------------------------------------------------------------===//
111
-
112
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
113
- : m_impl(op.expression(), device)
114
- {
115
- m_dimensions = m_impl.dimensions();
116
- for (int i = 0; i < NumDims; ++i) {
117
- m_dimensions[i] =Eigen::numext::ceil(static_cast<float>(m_dimensions[i]) / op.strides()[i]);
118
- }
119
-
120
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
121
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
122
- m_outputStrides[0] = 1;
123
- m_inputStrides[0] = 1;
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- for (int i = 1; i < NumDims; ++i) {
125
- m_outputStrides[i] = m_outputStrides[i-1] * m_dimensions[i-1];
126
- m_inputStrides[i] = m_inputStrides[i-1] * input_dims[i-1];
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- m_inputStrides[i-1] *= op.strides()[i-1];
128
- }
129
- m_inputStrides[NumDims-1] *= op.strides()[NumDims-1];
130
- } else { // RowMajor
131
- m_outputStrides[NumDims-1] = 1;
132
- m_inputStrides[NumDims-1] = 1;
133
- for (int i = NumDims - 2; i >= 0; --i) {
134
- m_outputStrides[i] = m_outputStrides[i+1] * m_dimensions[i+1];
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- m_inputStrides[i] = m_inputStrides[i+1] * input_dims[i+1];
136
- m_inputStrides[i+1] *= op.strides()[i+1];
137
- }
138
- m_inputStrides[0] *= op.strides()[0];
139
- }
140
- }
141
-
142
-
143
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
144
-
145
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType/*data*/) {
146
- m_impl.evalSubExprsIfNeeded(NULL);
147
- return true;
148
- }
149
- EIGEN_STRONG_INLINE void cleanup() {
150
- m_impl.cleanup();
151
- }
152
-
153
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
154
- {
155
- return m_impl.coeff(srcCoeff(index));
156
- }
157
-
158
- template<int LoadMode>
159
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
160
- {
161
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
162
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
163
-
164
- Index inputIndices[] = {0, 0};
165
- Index indices[] = {index, index + PacketSize - 1};
166
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
167
- EIGEN_UNROLL_LOOP
168
- for (int i = NumDims - 1; i > 0; --i) {
169
- const Index idx0 = indices[0] / m_outputStrides[i];
170
- const Index idx1 = indices[1] / m_outputStrides[i];
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- inputIndices[0] += idx0 * m_inputStrides[i];
172
- inputIndices[1] += idx1 * m_inputStrides[i];
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- indices[0] -= idx0 * m_outputStrides[i];
174
- indices[1] -= idx1 * m_outputStrides[i];
175
- }
176
- inputIndices[0] += indices[0] * m_inputStrides[0];
177
- inputIndices[1] += indices[1] * m_inputStrides[0];
178
- } else { // RowMajor
179
- EIGEN_UNROLL_LOOP
180
- for (int i = 0; i < NumDims - 1; ++i) {
181
- const Index idx0 = indices[0] / m_outputStrides[i];
182
- const Index idx1 = indices[1] / m_outputStrides[i];
183
- inputIndices[0] += idx0 * m_inputStrides[i];
184
- inputIndices[1] += idx1 * m_inputStrides[i];
185
- indices[0] -= idx0 * m_outputStrides[i];
186
- indices[1] -= idx1 * m_outputStrides[i];
187
- }
188
- inputIndices[0] += indices[0] * m_inputStrides[NumDims-1];
189
- inputIndices[1] += indices[1] * m_inputStrides[NumDims-1];
190
- }
191
- if (inputIndices[1] - inputIndices[0] == PacketSize - 1) {
192
- PacketReturnType rslt = m_impl.template packet<Unaligned>(inputIndices[0]);
193
- return rslt;
194
- }
195
- else {
196
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
197
- values[0] = m_impl.coeff(inputIndices[0]);
198
- values[PacketSize-1] = m_impl.coeff(inputIndices[1]);
199
- EIGEN_UNROLL_LOOP
200
- for (int i = 1; i < PacketSize-1; ++i) {
201
- values[i] = coeff(index+i);
202
- }
203
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
204
- return rslt;
205
- }
206
- }
207
-
208
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
209
- double compute_cost = (NumDims - 1) * (TensorOpCost::AddCost<Index>() +
210
- TensorOpCost::MulCost<Index>() +
211
- TensorOpCost::DivCost<Index>()) +
212
- TensorOpCost::MulCost<Index>();
213
- if (vectorized) {
214
- compute_cost *= 2; // packet() computes two indices
215
- }
216
- const int innerDim = (static_cast<int>(Layout) == static_cast<int>(ColMajor)) ? 0 : (NumDims - 1);
217
- return m_impl.costPerCoeff(vectorized && m_inputStrides[innerDim] == 1) +
218
- // Computation is not vectorized per se, but it is done once per packet.
219
- TensorOpCost(0, 0, compute_cost, vectorized, PacketSize);
220
- }
221
-
222
- EIGEN_DEVICE_FUNC typename Storage::Type data() const { return NULL; }
223
-
224
- #ifdef EIGEN_USE_SYCL
225
- // binding placeholder accessors to a command group handler for SYCL
226
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
227
- m_impl.bind(cgh);
228
- }
229
- #endif
230
- protected:
231
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index srcCoeff(Index index) const
232
- {
233
- Index inputIndex = 0;
234
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
235
- EIGEN_UNROLL_LOOP
236
- for (int i = NumDims - 1; i > 0; --i) {
237
- const Index idx = index / m_outputStrides[i];
238
- inputIndex += idx * m_inputStrides[i];
239
- index -= idx * m_outputStrides[i];
240
- }
241
- inputIndex += index * m_inputStrides[0];
242
- } else { // RowMajor
243
- EIGEN_UNROLL_LOOP
244
- for (int i = 0; i < NumDims - 1; ++i) {
245
- const Index idx = index / m_outputStrides[i];
246
- inputIndex += idx * m_inputStrides[i];
247
- index -= idx * m_outputStrides[i];
248
- }
249
- inputIndex += index * m_inputStrides[NumDims-1];
250
- }
251
- return inputIndex;
252
- }
253
-
254
- Dimensions m_dimensions;
255
- array<Index, NumDims> m_outputStrides;
256
- array<Index, NumDims> m_inputStrides;
257
- TensorEvaluator<ArgType, Device> m_impl;
258
- };
259
-
260
- // Eval as lvalue
261
- template<typename Strides, typename ArgType, typename Device>
262
- struct TensorEvaluator<TensorStridingOp<Strides, ArgType>, Device>
263
- : public TensorEvaluator<const TensorStridingOp<Strides, ArgType>, Device>
264
- {
265
- typedef TensorStridingOp<Strides, ArgType> XprType;
266
- typedef TensorEvaluator<const XprType, Device> Base;
267
- // typedef typename XprType::Index Index;
268
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
269
- // typedef DSizes<Index, NumDims> Dimensions;
270
-
271
- enum {
272
- IsAligned = /*TensorEvaluator<ArgType, Device>::IsAligned*/false,
273
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
274
- PreferBlockAccess = false,
275
- Layout = TensorEvaluator<ArgType, Device>::Layout,
276
- CoordAccess = false, // to be implemented
277
- RawAccess = false
278
- };
279
-
280
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
281
- : Base(op, device) { }
282
-
283
- typedef typename XprType::Index Index;
284
- typedef typename XprType::Scalar Scalar;
285
- typedef typename XprType::CoeffReturnType CoeffReturnType;
286
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
287
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
288
-
289
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& coeffRef(Index index)
290
- {
291
- return this->m_impl.coeffRef(this->srcCoeff(index));
292
- }
293
-
294
- template <int StoreMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
295
- void writePacket(Index index, const PacketReturnType& x)
296
- {
297
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
298
- eigen_assert(index+PacketSize-1 < this->dimensions().TotalSize());
299
-
300
- Index inputIndices[] = {0, 0};
301
- Index indices[] = {index, index + PacketSize - 1};
302
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
303
- EIGEN_UNROLL_LOOP
304
- for (int i = NumDims - 1; i > 0; --i) {
305
- const Index idx0 = indices[0] / this->m_outputStrides[i];
306
- const Index idx1 = indices[1] / this->m_outputStrides[i];
307
- inputIndices[0] += idx0 * this->m_inputStrides[i];
308
- inputIndices[1] += idx1 * this->m_inputStrides[i];
309
- indices[0] -= idx0 * this->m_outputStrides[i];
310
- indices[1] -= idx1 * this->m_outputStrides[i];
311
- }
312
- inputIndices[0] += indices[0] * this->m_inputStrides[0];
313
- inputIndices[1] += indices[1] * this->m_inputStrides[0];
314
- } else { // RowMajor
315
- EIGEN_UNROLL_LOOP
316
- for (int i = 0; i < NumDims - 1; ++i) {
317
- const Index idx0 = indices[0] / this->m_outputStrides[i];
318
- const Index idx1 = indices[1] / this->m_outputStrides[i];
319
- inputIndices[0] += idx0 * this->m_inputStrides[i];
320
- inputIndices[1] += idx1 * this->m_inputStrides[i];
321
- indices[0] -= idx0 * this->m_outputStrides[i];
322
- indices[1] -= idx1 * this->m_outputStrides[i];
323
- }
324
- inputIndices[0] += indices[0] * this->m_inputStrides[NumDims-1];
325
- inputIndices[1] += indices[1] * this->m_inputStrides[NumDims-1];
326
- }
327
- if (inputIndices[1] - inputIndices[0] == PacketSize - 1) {
328
- this->m_impl.template writePacket<Unaligned>(inputIndices[0], x);
329
- }
330
- else {
331
- EIGEN_ALIGN_MAX Scalar values[PacketSize];
332
- internal::pstore<Scalar, PacketReturnType>(values, x);
333
- this->m_impl.coeffRef(inputIndices[0]) = values[0];
334
- this->m_impl.coeffRef(inputIndices[1]) = values[PacketSize-1];
335
- EIGEN_UNROLL_LOOP
336
- for (int i = 1; i < PacketSize-1; ++i) {
337
- this->coeffRef(index+i) = values[i];
338
- }
339
- }
340
- }
341
- };
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-
343
-
344
- } // end namespace Eigen
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-
346
- #endif // EIGEN_CXX11_TENSOR_TENSOR_STRIDING_H
@@ -1,303 +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) 2017 Gagan Goel <gagan.nith@gmail.com>
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- // Copyright (C) 2017 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_TRACE_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_TRACE_H
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-
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- namespace Eigen {
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-
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- /** \class TensorTrace
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor Trace class.
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- *
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- *
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- */
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-
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- namespace internal {
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- template<typename Dims, typename XprType>
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- struct traits<TensorTraceOp<Dims, 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 - array_size<Dims>::value;
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- static const int Layout = XprTraits::Layout;
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- };
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-
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- template<typename Dims, typename XprType>
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- struct eval<TensorTraceOp<Dims, XprType>, Eigen::Dense>
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- {
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- typedef const TensorTraceOp<Dims, XprType>& type;
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- };
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-
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- template<typename Dims, typename XprType>
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- struct nested<TensorTraceOp<Dims, XprType>, 1, typename eval<TensorTraceOp<Dims, XprType> >::type>
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- {
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- typedef TensorTraceOp<Dims, 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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- template<typename Dims, typename XprType>
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- class TensorTraceOp : public TensorBase<TensorTraceOp<Dims, XprType> >
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- {
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- public:
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- typedef typename Eigen::internal::traits<TensorTraceOp>::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<TensorTraceOp>::type Nested;
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- typedef typename Eigen::internal::traits<TensorTraceOp>::StorageKind StorageKind;
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- typedef typename Eigen::internal::traits<TensorTraceOp>::Index Index;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorTraceOp(const XprType& expr, const Dims& dims)
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- : m_xpr(expr), m_dims(dims) {
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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- const Dims& dims() const { return m_dims; }
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
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- const typename internal::remove_all<typename XprType::Nested>::type& 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 Dims m_dims;
77
- };
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-
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-
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- // Eval as rvalue
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- template<typename Dims, typename ArgType, typename Device>
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- struct TensorEvaluator<const TensorTraceOp<Dims, ArgType>, Device>
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- {
84
- typedef TensorTraceOp<Dims, ArgType> XprType;
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- static const int NumInputDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
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- static const int NumReducedDims = internal::array_size<Dims>::value;
87
- static const int NumOutputDims = NumInputDims - NumReducedDims;
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- typedef typename XprType::Index Index;
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- typedef DSizes<Index, NumOutputDims> 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 = internal::unpacket_traits<PacketReturnType>::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 = false,
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- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
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- BlockAccess = false,
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- PreferBlockAccess = TensorEvaluator<ArgType, Device>::PreferBlockAccess,
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- Layout = TensorEvaluator<ArgType, Device>::Layout,
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- CoordAccess = false,
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- RawAccess = false
105
- };
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-
107
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
108
- typedef internal::TensorBlockNotImplemented TensorBlock;
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- //===--------------------------------------------------------------------===//
110
-
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- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
112
- : m_impl(op.expression(), device), m_traceDim(1), m_device(device)
113
- {
114
-
115
- EIGEN_STATIC_ASSERT((NumOutputDims >= 0), YOU_MADE_A_PROGRAMMING_MISTAKE);
116
- EIGEN_STATIC_ASSERT((NumReducedDims >= 2) || ((NumReducedDims == 0) && (NumInputDims == 0)), YOU_MADE_A_PROGRAMMING_MISTAKE);
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-
118
- for (int i = 0; i < NumInputDims; ++i) {
119
- m_reduced[i] = false;
120
- }
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-
122
- const Dims& op_dims = op.dims();
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- for (int i = 0; i < NumReducedDims; ++i) {
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- eigen_assert(op_dims[i] >= 0);
125
- eigen_assert(op_dims[i] < NumInputDims);
126
- m_reduced[op_dims[i]] = true;
127
- }
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-
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- // All the dimensions should be distinct to compute the trace
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- int num_distinct_reduce_dims = 0;
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- for (int i = 0; i < NumInputDims; ++i) {
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- if (m_reduced[i]) {
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- ++num_distinct_reduce_dims;
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- }
135
- }
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-
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- eigen_assert(num_distinct_reduce_dims == NumReducedDims);
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-
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- // Compute the dimensions of the result.
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- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
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-
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- int output_index = 0;
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- int reduced_index = 0;
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- for (int i = 0; i < NumInputDims; ++i) {
145
- if (m_reduced[i]) {
146
- m_reducedDims[reduced_index] = input_dims[i];
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- if (reduced_index > 0) {
148
- // All the trace dimensions must have the same size
149
- eigen_assert(m_reducedDims[0] == m_reducedDims[reduced_index]);
150
- }
151
- ++reduced_index;
152
- }
153
- else {
154
- m_dimensions[output_index] = input_dims[i];
155
- ++output_index;
156
- }
157
- }
158
-
159
- if (NumReducedDims != 0) {
160
- m_traceDim = m_reducedDims[0];
161
- }
162
-
163
- // Compute the output strides
164
- if (NumOutputDims > 0) {
165
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
166
- m_outputStrides[0] = 1;
167
- for (int i = 1; i < NumOutputDims; ++i) {
168
- m_outputStrides[i] = m_outputStrides[i - 1] * m_dimensions[i - 1];
169
- }
170
- }
171
- else {
172
- m_outputStrides.back() = 1;
173
- for (int i = NumOutputDims - 2; i >= 0; --i) {
174
- m_outputStrides[i] = m_outputStrides[i + 1] * m_dimensions[i + 1];
175
- }
176
- }
177
- }
178
-
179
- // Compute the input strides
180
- if (NumInputDims > 0) {
181
- array<Index, NumInputDims> input_strides;
182
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
183
- input_strides[0] = 1;
184
- for (int i = 1; i < NumInputDims; ++i) {
185
- input_strides[i] = input_strides[i - 1] * input_dims[i - 1];
186
- }
187
- }
188
- else {
189
- input_strides.back() = 1;
190
- for (int i = NumInputDims - 2; i >= 0; --i) {
191
- input_strides[i] = input_strides[i + 1] * input_dims[i + 1];
192
- }
193
- }
194
-
195
- output_index = 0;
196
- reduced_index = 0;
197
- for (int i = 0; i < NumInputDims; ++i) {
198
- if(m_reduced[i]) {
199
- m_reducedStrides[reduced_index] = input_strides[i];
200
- ++reduced_index;
201
- }
202
- else {
203
- m_preservedStrides[output_index] = input_strides[i];
204
- ++output_index;
205
- }
206
- }
207
- }
208
- }
209
-
210
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const {
211
- return m_dimensions;
212
- }
213
-
214
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType /*data*/) {
215
- m_impl.evalSubExprsIfNeeded(NULL);
216
- return true;
217
- }
218
-
219
- EIGEN_STRONG_INLINE void cleanup() {
220
- m_impl.cleanup();
221
- }
222
-
223
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
224
- {
225
- // Initialize the result
226
- CoeffReturnType result = internal::cast<int, CoeffReturnType>(0);
227
- Index index_stride = 0;
228
- for (int i = 0; i < NumReducedDims; ++i) {
229
- index_stride += m_reducedStrides[i];
230
- }
231
-
232
- // If trace is requested along all dimensions, starting index would be 0
233
- Index cur_index = 0;
234
- if (NumOutputDims != 0)
235
- cur_index = firstInput(index);
236
- for (Index i = 0; i < m_traceDim; ++i) {
237
- result += m_impl.coeff(cur_index);
238
- cur_index += index_stride;
239
- }
240
-
241
- return result;
242
- }
243
-
244
- template<int LoadMode>
245
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const {
246
-
247
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE);
248
- eigen_assert(index + PacketSize - 1 < dimensions().TotalSize());
249
-
250
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
251
- for (int i = 0; i < PacketSize; ++i) {
252
- values[i] = coeff(index + i);
253
- }
254
- PacketReturnType result = internal::ploadt<PacketReturnType, LoadMode>(values);
255
- return result;
256
- }
257
-
258
- #ifdef EIGEN_USE_SYCL
259
- // binding placeholder accessors to a command group handler for SYCL
260
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
261
- m_impl.bind(cgh);
262
- }
263
- #endif
264
-
265
- protected:
266
- // Given the output index, finds the first index in the input tensor used to compute the trace
267
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index firstInput(Index index) const {
268
- Index startInput = 0;
269
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
270
- for (int i = NumOutputDims - 1; i > 0; --i) {
271
- const Index idx = index / m_outputStrides[i];
272
- startInput += idx * m_preservedStrides[i];
273
- index -= idx * m_outputStrides[i];
274
- }
275
- startInput += index * m_preservedStrides[0];
276
- }
277
- else {
278
- for (int i = 0; i < NumOutputDims - 1; ++i) {
279
- const Index idx = index / m_outputStrides[i];
280
- startInput += idx * m_preservedStrides[i];
281
- index -= idx * m_outputStrides[i];
282
- }
283
- startInput += index * m_preservedStrides[NumOutputDims - 1];
284
- }
285
- return startInput;
286
- }
287
-
288
- Dimensions m_dimensions;
289
- TensorEvaluator<ArgType, Device> m_impl;
290
- // Initialize the size of the trace dimension
291
- Index m_traceDim;
292
- const Device EIGEN_DEVICE_REF m_device;
293
- array<bool, NumInputDims> m_reduced;
294
- array<Index, NumReducedDims> m_reducedDims;
295
- array<Index, NumOutputDims> m_outputStrides;
296
- array<Index, NumReducedDims> m_reducedStrides;
297
- array<Index, NumOutputDims> m_preservedStrides;
298
- };
299
-
300
-
301
- } // End namespace Eigen
302
-
303
- #endif // EIGEN_CXX11_TENSOR_TENSOR_TRACE_H