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
@@ -1,247 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2015 Ke Yang <yangke@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_INFLATION_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_INFLATION_H
12
-
13
- namespace Eigen {
14
-
15
- /** \class TensorInflation
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor inflation class.
19
- *
20
- *
21
- */
22
- namespace internal {
23
- template<typename Strides, typename XprType>
24
- struct traits<TensorInflationOp<Strides, XprType> > : public traits<XprType>
25
- {
26
- typedef typename XprType::Scalar Scalar;
27
- typedef traits<XprType> XprTraits;
28
- typedef typename XprTraits::StorageKind StorageKind;
29
- typedef typename XprTraits::Index Index;
30
- typedef typename XprType::Nested Nested;
31
- typedef typename remove_reference<Nested>::type _Nested;
32
- static const int NumDimensions = XprTraits::NumDimensions;
33
- static const int Layout = XprTraits::Layout;
34
- typedef typename XprTraits::PointerType PointerType;
35
- };
36
-
37
- template<typename Strides, typename XprType>
38
- struct eval<TensorInflationOp<Strides, XprType>, Eigen::Dense>
39
- {
40
- typedef const TensorInflationOp<Strides, XprType>& type;
41
- };
42
-
43
- template<typename Strides, typename XprType>
44
- struct nested<TensorInflationOp<Strides, XprType>, 1, typename eval<TensorInflationOp<Strides, XprType> >::type>
45
- {
46
- typedef TensorInflationOp<Strides, XprType> type;
47
- };
48
-
49
- } // end namespace internal
50
-
51
- template<typename Strides, typename XprType>
52
- class TensorInflationOp : public TensorBase<TensorInflationOp<Strides, XprType>, ReadOnlyAccessors>
53
- {
54
- public:
55
- typedef typename Eigen::internal::traits<TensorInflationOp>::Scalar Scalar;
56
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
57
- typedef typename XprType::CoeffReturnType CoeffReturnType;
58
- typedef typename Eigen::internal::nested<TensorInflationOp>::type Nested;
59
- typedef typename Eigen::internal::traits<TensorInflationOp>::StorageKind StorageKind;
60
- typedef typename Eigen::internal::traits<TensorInflationOp>::Index Index;
61
-
62
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorInflationOp(const XprType& expr, const Strides& strides)
63
- : m_xpr(expr), m_strides(strides) {}
64
-
65
- EIGEN_DEVICE_FUNC
66
- const Strides& strides() const { return m_strides; }
67
-
68
- EIGEN_DEVICE_FUNC
69
- const typename internal::remove_all<typename XprType::Nested>::type&
70
- expression() const { return m_xpr; }
71
-
72
- protected:
73
- typename XprType::Nested m_xpr;
74
- const Strides m_strides;
75
- };
76
-
77
- // Eval as rvalue
78
- template<typename Strides, typename ArgType, typename Device>
79
- struct TensorEvaluator<const TensorInflationOp<Strides, ArgType>, Device>
80
- {
81
- typedef TensorInflationOp<Strides, ArgType> XprType;
82
- typedef typename XprType::Index Index;
83
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
84
- typedef DSizes<Index, NumDims> Dimensions;
85
- typedef typename XprType::Scalar Scalar;
86
- typedef typename XprType::CoeffReturnType CoeffReturnType;
87
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
88
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
89
- typedef StorageMemory<CoeffReturnType, Device> Storage;
90
- typedef typename Storage::Type EvaluatorPointerType;
91
-
92
- enum {
93
- IsAligned = /*TensorEvaluator<ArgType, Device>::IsAligned*/ false,
94
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
95
- BlockAccess = false,
96
- PreferBlockAccess = false,
97
- Layout = TensorEvaluator<ArgType, Device>::Layout,
98
- CoordAccess = false, // to be implemented
99
- RawAccess = false
100
- };
101
-
102
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
103
- typedef internal::TensorBlockNotImplemented TensorBlock;
104
- //===--------------------------------------------------------------------===//
105
-
106
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
107
- : m_impl(op.expression(), device), m_strides(op.strides())
108
- {
109
- m_dimensions = m_impl.dimensions();
110
- // Expand each dimension to the inflated dimension.
111
- for (int i = 0; i < NumDims; ++i) {
112
- m_dimensions[i] = (m_dimensions[i] - 1) * op.strides()[i] + 1;
113
- }
114
-
115
- // Remember the strides for fast division.
116
- for (int i = 0; i < NumDims; ++i) {
117
- m_fastStrides[i] = internal::TensorIntDivisor<Index>(m_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;
124
- 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];
127
- }
128
- } else { // RowMajor
129
- m_outputStrides[NumDims-1] = 1;
130
- m_inputStrides[NumDims-1] = 1;
131
- for (int i = NumDims - 2; i >= 0; --i) {
132
- m_outputStrides[i] = m_outputStrides[i+1] * m_dimensions[i+1];
133
- m_inputStrides[i] = m_inputStrides[i+1] * input_dims[i+1];
134
- }
135
- }
136
- }
137
-
138
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
139
-
140
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType /*data*/) {
141
- m_impl.evalSubExprsIfNeeded(NULL);
142
- return true;
143
- }
144
- EIGEN_STRONG_INLINE void cleanup() {
145
- m_impl.cleanup();
146
- }
147
-
148
- // Computes the input index given the output index. Returns true if the output
149
- // index doesn't fall into a hole.
150
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE bool getInputIndex(Index index, Index* inputIndex) const
151
- {
152
- eigen_assert(index < dimensions().TotalSize());
153
- *inputIndex = 0;
154
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
155
- EIGEN_UNROLL_LOOP
156
- for (int i = NumDims - 1; i > 0; --i) {
157
- const Index idx = index / m_outputStrides[i];
158
- if (idx != idx / m_fastStrides[i] * m_strides[i]) {
159
- return false;
160
- }
161
- *inputIndex += idx / m_strides[i] * m_inputStrides[i];
162
- index -= idx * m_outputStrides[i];
163
- }
164
- if (index != index / m_fastStrides[0] * m_strides[0]) {
165
- return false;
166
- }
167
- *inputIndex += index / m_strides[0];
168
- return true;
169
- } else {
170
- EIGEN_UNROLL_LOOP
171
- for (int i = 0; i < NumDims - 1; ++i) {
172
- const Index idx = index / m_outputStrides[i];
173
- if (idx != idx / m_fastStrides[i] * m_strides[i]) {
174
- return false;
175
- }
176
- *inputIndex += idx / m_strides[i] * m_inputStrides[i];
177
- index -= idx * m_outputStrides[i];
178
- }
179
- if (index != index / m_fastStrides[NumDims-1] * m_strides[NumDims-1]) {
180
- return false;
181
- }
182
- *inputIndex += index / m_strides[NumDims - 1];
183
- }
184
- return true;
185
- }
186
-
187
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
188
- {
189
- Index inputIndex = 0;
190
- if (getInputIndex(index, &inputIndex)) {
191
- return m_impl.coeff(inputIndex);
192
- } else {
193
- return Scalar(0);
194
- }
195
- }
196
-
197
- // TODO(yangke): optimize this function so that we can detect and produce
198
- // all-zero packets
199
- template<int LoadMode>
200
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
201
- {
202
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
203
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
204
-
205
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
206
- EIGEN_UNROLL_LOOP
207
- for (int i = 0; i < PacketSize; ++i) {
208
- values[i] = coeff(index+i);
209
- }
210
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
211
- return rslt;
212
- }
213
-
214
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost costPerCoeff(bool vectorized) const {
215
- const double compute_cost = NumDims * (3 * TensorOpCost::DivCost<Index>() +
216
- 3 * TensorOpCost::MulCost<Index>() +
217
- 2 * TensorOpCost::AddCost<Index>());
218
- const double input_size = m_impl.dimensions().TotalSize();
219
- const double output_size = m_dimensions.TotalSize();
220
- if (output_size == 0)
221
- return TensorOpCost();
222
- return m_impl.costPerCoeff(vectorized) +
223
- TensorOpCost(sizeof(CoeffReturnType) * input_size / output_size, 0,
224
- compute_cost, vectorized, PacketSize);
225
- }
226
-
227
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return NULL; }
228
-
229
- #ifdef EIGEN_USE_SYCL
230
- // binding placeholder accessors to a command group handler for SYCL
231
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
232
- m_impl.bind(cgh);
233
- }
234
- #endif
235
-
236
- protected:
237
- Dimensions m_dimensions;
238
- array<Index, NumDims> m_outputStrides;
239
- array<Index, NumDims> m_inputStrides;
240
- TensorEvaluator<ArgType, Device> m_impl;
241
- const Strides m_strides;
242
- array<internal::TensorIntDivisor<Index>, NumDims> m_fastStrides;
243
- };
244
-
245
- } // end namespace Eigen
246
-
247
- #endif // EIGEN_CXX11_TENSOR_TENSOR_INFLATION_H
@@ -1,82 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_INITIALIZER_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_INITIALIZER_H
12
-
13
- #if EIGEN_HAS_VARIADIC_TEMPLATES
14
-
15
- #include <initializer_list>
16
-
17
- namespace Eigen {
18
-
19
- /** \class TensorInitializer
20
- * \ingroup CXX11_Tensor_Module
21
- *
22
- * \brief Helper template to initialize Tensors from std::initializer_lists.
23
- */
24
- namespace internal {
25
-
26
- template <typename Derived, int N>
27
- struct Initializer {
28
- typedef std::initializer_list<
29
- typename Initializer<Derived, N - 1>::InitList> InitList;
30
-
31
- static void run(TensorEvaluator<Derived, DefaultDevice>& tensor,
32
- Eigen::array<typename traits<Derived>::Index, traits<Derived>::NumDimensions>* indices,
33
- const InitList& vals) {
34
- int i = 0;
35
- for (const auto& v : vals) {
36
- (*indices)[traits<Derived>::NumDimensions - N] = i++;
37
- Initializer<Derived, N - 1>::run(tensor, indices, v);
38
- }
39
- }
40
- };
41
-
42
- template <typename Derived>
43
- struct Initializer<Derived, 1> {
44
- typedef std::initializer_list<typename traits<Derived>::Scalar> InitList;
45
-
46
- static void run(TensorEvaluator<Derived, DefaultDevice>& tensor,
47
- Eigen::array<typename traits<Derived>::Index, traits<Derived>::NumDimensions>* indices,
48
- const InitList& vals) {
49
- int i = 0;
50
- // There is likely a faster way to do that than iterating.
51
- for (const auto& v : vals) {
52
- (*indices)[traits<Derived>::NumDimensions - 1] = i++;
53
- tensor.coeffRef(*indices) = v;
54
- }
55
- }
56
- };
57
-
58
- template <typename Derived>
59
- struct Initializer<Derived, 0> {
60
- typedef typename traits<Derived>::Scalar InitList;
61
-
62
- static void run(TensorEvaluator<Derived, DefaultDevice>& tensor,
63
- Eigen::array<typename traits<Derived>::Index, traits<Derived>::NumDimensions>*,
64
- const InitList& v) {
65
- tensor.coeffRef(0) = v;
66
- }
67
- };
68
-
69
-
70
- template <typename Derived, int N>
71
- void initialize_tensor(TensorEvaluator<Derived, DefaultDevice>& tensor,
72
- const typename Initializer<Derived, traits<Derived>::NumDimensions>::InitList& vals) {
73
- Eigen::array<typename traits<Derived>::Index, traits<Derived>::NumDimensions> indices;
74
- Initializer<Derived, traits<Derived>::NumDimensions>::run(tensor, &indices, vals);
75
- }
76
-
77
- } // namespace internal
78
- } // namespace Eigen
79
-
80
- #endif // EIGEN_HAS_VARIADIC_TEMPLATES
81
-
82
- #endif // EIGEN_CXX11_TENSOR_TENSOR_INITIALIZER_H
@@ -1,263 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_INTDIV_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_INTDIV_H
12
-
13
-
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- namespace Eigen {
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-
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- /** \internal
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- *
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- * \class TensorIntDiv
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Fast integer division by a constant.
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- *
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- * See the paper from Granlund and Montgomery for explanation.
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- * (at https://doi.org/10.1145/773473.178249)
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- *
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- * \sa Tensor
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- */
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-
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- namespace internal {
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-
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- namespace {
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-
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- // Note: result is undefined if val == 0
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- template <typename T>
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
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- typename internal::enable_if<sizeof(T)==4,int>::type count_leading_zeros(const T val)
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- {
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- #ifdef EIGEN_GPU_COMPILE_PHASE
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- return __clz(val);
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- #elif defined(SYCL_DEVICE_ONLY)
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- return cl::sycl::clz(val);
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- #elif EIGEN_COMP_MSVC
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- unsigned long index;
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- _BitScanReverse(&index, val);
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- return 31 - index;
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- #else
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- EIGEN_STATIC_ASSERT(sizeof(unsigned long long) == 8, YOU_MADE_A_PROGRAMMING_MISTAKE);
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- return __builtin_clz(static_cast<uint32_t>(val));
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- #endif
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- }
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-
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- template <typename T>
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE
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- typename internal::enable_if<sizeof(T)==8,int>::type count_leading_zeros(const T val)
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- {
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- #ifdef EIGEN_GPU_COMPILE_PHASE
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- return __clzll(val);
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- #elif defined(SYCL_DEVICE_ONLY)
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- return static_cast<int>(cl::sycl::clz(val));
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- #elif EIGEN_COMP_MSVC && EIGEN_ARCH_x86_64
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- unsigned long index;
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- _BitScanReverse64(&index, val);
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- return 63 - index;
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- #elif EIGEN_COMP_MSVC
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- // MSVC's _BitScanReverse64 is not available for 32bits builds.
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- unsigned int lo = (unsigned int)(val&0xffffffff);
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- unsigned int hi = (unsigned int)((val>>32)&0xffffffff);
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- int n;
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- if(hi==0)
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- n = 32 + count_leading_zeros<unsigned int>(lo);
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- else
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- n = count_leading_zeros<unsigned int>(hi);
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- return n;
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- #else
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- EIGEN_STATIC_ASSERT(sizeof(unsigned long long) == 8, YOU_MADE_A_PROGRAMMING_MISTAKE);
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- return __builtin_clzll(static_cast<uint64_t>(val));
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- #endif
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- }
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-
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- template <typename T>
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- struct UnsignedTraits {
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- typedef typename conditional<sizeof(T) == 8, uint64_t, uint32_t>::type type;
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- };
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-
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- template <typename T>
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- struct DividerTraits {
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- typedef typename UnsignedTraits<T>::type type;
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- static const int N = sizeof(T) * 8;
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- };
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-
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- template <typename T>
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE uint32_t muluh(const uint32_t a, const T b) {
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- #if defined(EIGEN_GPU_COMPILE_PHASE)
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- return __umulhi(a, b);
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- #elif defined(SYCL_DEVICE_ONLY)
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- return cl::sycl::mul_hi(a, static_cast<uint32_t>(b));
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- #else
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- return (static_cast<uint64_t>(a) * b) >> 32;
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- #endif
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- }
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-
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- template <typename T>
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE uint64_t muluh(const uint64_t a, const T b) {
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- #if defined(EIGEN_GPU_COMPILE_PHASE)
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- return __umul64hi(a, b);
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- #elif defined(SYCL_DEVICE_ONLY)
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- return cl::sycl::mul_hi(a, static_cast<uint64_t>(b));
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- #elif EIGEN_HAS_BUILTIN_INT128
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- __uint128_t v = static_cast<__uint128_t>(a) * static_cast<__uint128_t>(b);
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- return static_cast<uint64_t>(v >> 64);
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- #else
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- return (TensorUInt128<static_val<0>, uint64_t>(a) * TensorUInt128<static_val<0>, uint64_t>(b)).upper();
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- #endif
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- }
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-
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- template <int N, typename T>
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- struct DividerHelper {
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- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE uint32_t computeMultiplier(const int log_div, const T divider) {
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- EIGEN_STATIC_ASSERT(N == 32, YOU_MADE_A_PROGRAMMING_MISTAKE);
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- return static_cast<uint32_t>((static_cast<uint64_t>(1) << (N+log_div)) / divider - (static_cast<uint64_t>(1) << N) + 1);
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- }
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- };
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-
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- template <typename T>
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- struct DividerHelper<64, T> {
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- static EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE uint64_t computeMultiplier(const int log_div, const T divider) {
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- #if EIGEN_HAS_BUILTIN_INT128 && !defined(EIGEN_GPU_COMPILE_PHASE) && !defined(SYCL_DEVICE_ONLY)
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- return static_cast<uint64_t>((static_cast<__uint128_t>(1) << (64+log_div)) / static_cast<__uint128_t>(divider) - (static_cast<__uint128_t>(1) << 64) + 1);
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- #else
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- const uint64_t shift = 1ULL << log_div;
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- TensorUInt128<uint64_t, uint64_t> result = TensorUInt128<uint64_t, static_val<0> >(shift, 0) / TensorUInt128<static_val<0>, uint64_t>(divider)
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- - TensorUInt128<static_val<1>, static_val<0> >(1, 0)
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- + TensorUInt128<static_val<0>, static_val<1> >(1);
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- return static_cast<uint64_t>(result);
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- #endif
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- }
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- };
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- }
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-
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-
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- template <typename T, bool div_gt_one = false>
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- struct TensorIntDivisor {
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- public:
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorIntDivisor() {
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- multiplier = 0;
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- shift1 = 0;
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- shift2 = 0;
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- }
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-
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- // Must have 0 < divider < 2^31. This is relaxed to
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- // 0 < divider < 2^63 when using 64-bit indices on platforms that support
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- // the __uint128_t type.
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorIntDivisor(const T divider) {
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- const int N = DividerTraits<T>::N;
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- eigen_assert(static_cast<typename UnsignedTraits<T>::type>(divider) < NumTraits<UnsignedType>::highest()/2);
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- eigen_assert(divider > 0);
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-
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- // fast ln2
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- const int leading_zeros = count_leading_zeros(static_cast<UnsignedType>(divider));
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- int log_div = N - leading_zeros;
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- // if divider is a power of two then log_div is 1 more than it should be.
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- if ((static_cast<typename UnsignedTraits<T>::type>(1) << (log_div-1)) == static_cast<typename UnsignedTraits<T>::type>(divider))
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- log_div--;
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-
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- multiplier = DividerHelper<N, T>::computeMultiplier(log_div, divider);
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- shift1 = log_div > 1 ? 1 : log_div;
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- shift2 = log_div > 1 ? log_div-1 : 0;
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- }
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-
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- // Must have 0 <= numerator. On platforms that don't support the __uint128_t
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- // type numerator should also be less than 2^32-1.
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T divide(const T numerator) const {
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- eigen_assert(static_cast<typename UnsignedTraits<T>::type>(numerator) < NumTraits<UnsignedType>::highest()/2);
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- //eigen_assert(numerator >= 0); // this is implicitly asserted by the line above
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-
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- UnsignedType t1 = muluh(multiplier, numerator);
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- UnsignedType t = (static_cast<UnsignedType>(numerator) - t1) >> shift1;
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- return (t1 + t) >> shift2;
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- }
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-
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- private:
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- typedef typename DividerTraits<T>::type UnsignedType;
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- UnsignedType multiplier;
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- int32_t shift1;
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- int32_t shift2;
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- };
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-
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-
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- // Optimized version for signed 32 bit integers.
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- // Derived from Hacker's Delight.
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- // Only works for divisors strictly greater than one
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- template <>
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- class TensorIntDivisor<int32_t, true> {
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- public:
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorIntDivisor() {
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- magic = 0;
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- shift = 0;
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- }
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- // Must have 2 <= divider
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- EIGEN_DEVICE_FUNC TensorIntDivisor(int32_t divider) {
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- eigen_assert(divider >= 2);
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- calcMagic(divider);
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE int divide(const int32_t n) const {
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- #ifdef EIGEN_GPU_COMPILE_PHASE
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- return (__umulhi(magic, n) >> shift);
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- #elif defined(SYCL_DEVICE_ONLY)
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- return (cl::sycl::mul_hi(magic, static_cast<uint32_t>(n)) >> shift);
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- #else
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- uint64_t v = static_cast<uint64_t>(magic) * static_cast<uint64_t>(n);
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- return (static_cast<uint32_t>(v >> 32) >> shift);
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- #endif
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- }
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-
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- private:
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- // Compute the magic numbers. See Hacker's Delight section 10 for an in
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- // depth explanation.
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- EIGEN_DEVICE_FUNC void calcMagic(int32_t d) {
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- const unsigned two31 = 0x80000000; // 2**31.
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- unsigned ad = d;
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- unsigned t = two31 + (ad >> 31);
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- unsigned anc = t - 1 - t%ad; // Absolute value of nc.
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- int p = 31; // Init. p.
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- unsigned q1 = two31/anc; // Init. q1 = 2**p/|nc|.
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- unsigned r1 = two31 - q1*anc; // Init. r1 = rem(2**p, |nc|).
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- unsigned q2 = two31/ad; // Init. q2 = 2**p/|d|.
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- unsigned r2 = two31 - q2*ad; // Init. r2 = rem(2**p, |d|).
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- unsigned delta = 0;
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- do {
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- p = p + 1;
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- q1 = 2*q1; // Update q1 = 2**p/|nc|.
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- r1 = 2*r1; // Update r1 = rem(2**p, |nc|).
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- if (r1 >= anc) { // (Must be an unsigned
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- q1 = q1 + 1; // comparison here).
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- r1 = r1 - anc;}
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- q2 = 2*q2; // Update q2 = 2**p/|d|.
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- r2 = 2*r2; // Update r2 = rem(2**p, |d|).
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- if (r2 >= ad) { // (Must be an unsigned
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- q2 = q2 + 1; // comparison here).
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- r2 = r2 - ad;}
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- delta = ad - r2;
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- } while (q1 < delta || (q1 == delta && r1 == 0));
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-
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- magic = (unsigned)(q2 + 1);
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- shift = p - 32;
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- }
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-
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- uint32_t magic;
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- int32_t shift;
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- };
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-
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-
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- template <typename T, bool div_gt_one>
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- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE T operator / (const T& numerator, const TensorIntDivisor<T, div_gt_one>& divisor) {
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- return divisor.divide(numerator);
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- }
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-
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-
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- } // end namespace internal
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- } // end namespace Eigen
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-
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- #endif // EIGEN_CXX11_TENSOR_TENSOR_INTDIV_H