sequenzo 0.1.17__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-macosx_10_9_universal2.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 +155 -155
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-310-darwin.so +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-310-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-310-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-310-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-310-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-310-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-310-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
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  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,377 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_CXX11_TENSOR_TENSOR_CONCATENATION_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_CONCATENATION_H
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-
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- namespace Eigen {
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-
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- /** \class TensorConcatenationOp
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Tensor concatenation 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 Axis, typename LhsXprType, typename RhsXprType>
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- struct traits<TensorConcatenationOp<Axis, LhsXprType, RhsXprType> >
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- {
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- // Type promotion to handle the case where the types of the lhs and the rhs are different.
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- typedef typename promote_storage_type<typename LhsXprType::Scalar,
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- typename RhsXprType::Scalar>::ret Scalar;
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- typedef typename promote_storage_type<typename traits<LhsXprType>::StorageKind,
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- typename traits<RhsXprType>::StorageKind>::ret StorageKind;
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- typedef typename promote_index_type<typename traits<LhsXprType>::Index,
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- typename traits<RhsXprType>::Index>::type Index;
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- typedef typename LhsXprType::Nested LhsNested;
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- typedef typename RhsXprType::Nested RhsNested;
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- typedef typename remove_reference<LhsNested>::type _LhsNested;
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- typedef typename remove_reference<RhsNested>::type _RhsNested;
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- static const int NumDimensions = traits<LhsXprType>::NumDimensions;
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- static const int Layout = traits<LhsXprType>::Layout;
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- enum { Flags = 0 };
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- typedef typename conditional<Pointer_type_promotion<typename LhsXprType::Scalar, Scalar>::val,
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- typename traits<LhsXprType>::PointerType, typename traits<RhsXprType>::PointerType>::type PointerType;
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- };
43
-
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- template<typename Axis, typename LhsXprType, typename RhsXprType>
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- struct eval<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, Eigen::Dense>
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- {
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- typedef const TensorConcatenationOp<Axis, LhsXprType, RhsXprType>& type;
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- };
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-
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- template<typename Axis, typename LhsXprType, typename RhsXprType>
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- struct nested<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, 1, typename eval<TensorConcatenationOp<Axis, LhsXprType, RhsXprType> >::type>
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- {
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- typedef TensorConcatenationOp<Axis, LhsXprType, RhsXprType> 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 Axis, typename LhsXprType, typename RhsXprType>
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- class TensorConcatenationOp : public TensorBase<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, WriteAccessors>
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- {
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- public:
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- typedef TensorBase<TensorConcatenationOp<Axis, LhsXprType, RhsXprType>, WriteAccessors> Base;
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- typedef typename internal::traits<TensorConcatenationOp>::Scalar Scalar;
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- typedef typename internal::traits<TensorConcatenationOp>::StorageKind StorageKind;
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- typedef typename internal::traits<TensorConcatenationOp>::Index Index;
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- typedef typename internal::nested<TensorConcatenationOp>::type Nested;
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- typedef typename internal::promote_storage_type<typename LhsXprType::CoeffReturnType,
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- typename RhsXprType::CoeffReturnType>::ret CoeffReturnType;
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- typedef typename NumTraits<Scalar>::Real RealScalar;
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorConcatenationOp(const LhsXprType& lhs, const RhsXprType& rhs, Axis axis)
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- : m_lhs_xpr(lhs), m_rhs_xpr(rhs), m_axis(axis) {}
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-
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- EIGEN_DEVICE_FUNC
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- const typename internal::remove_all<typename LhsXprType::Nested>::type&
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- lhsExpression() const { return m_lhs_xpr; }
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-
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- EIGEN_DEVICE_FUNC
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- const typename internal::remove_all<typename RhsXprType::Nested>::type&
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- rhsExpression() const { return m_rhs_xpr; }
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-
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- EIGEN_DEVICE_FUNC const Axis& axis() const { return m_axis; }
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-
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- EIGEN_TENSOR_INHERIT_ASSIGNMENT_OPERATORS(TensorConcatenationOp)
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- protected:
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- typename LhsXprType::Nested m_lhs_xpr;
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- typename RhsXprType::Nested m_rhs_xpr;
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- const Axis m_axis;
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- };
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-
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-
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- // Eval as rvalue
94
- template<typename Axis, typename LeftArgType, typename RightArgType, typename Device>
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- struct TensorEvaluator<const TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device>
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- {
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- typedef TensorConcatenationOp<Axis, LeftArgType, RightArgType> XprType;
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- typedef typename XprType::Index Index;
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- static const int NumDims = internal::array_size<typename TensorEvaluator<LeftArgType, Device>::Dimensions>::value;
100
- static const int RightNumDims = internal::array_size<typename TensorEvaluator<RightArgType, Device>::Dimensions>::value;
101
- typedef DSizes<Index, NumDims> Dimensions;
102
- 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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- typedef StorageMemory<CoeffReturnType, Device> Storage;
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- typedef typename Storage::Type EvaluatorPointerType;
107
- enum {
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- IsAligned = false,
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- PacketAccess = TensorEvaluator<LeftArgType, Device>::PacketAccess &&
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- TensorEvaluator<RightArgType, Device>::PacketAccess,
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- BlockAccess = false,
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- PreferBlockAccess = TensorEvaluator<LeftArgType, Device>::PreferBlockAccess ||
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- TensorEvaluator<RightArgType, Device>::PreferBlockAccess,
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- Layout = TensorEvaluator<LeftArgType, Device>::Layout,
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- RawAccess = false
116
- };
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-
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- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
119
- typedef internal::TensorBlockNotImplemented TensorBlock;
120
- //===--------------------------------------------------------------------===//
121
-
122
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device)
123
- : m_leftImpl(op.lhsExpression(), device), m_rightImpl(op.rhsExpression(), device), m_axis(op.axis())
124
- {
125
- EIGEN_STATIC_ASSERT((static_cast<int>(TensorEvaluator<LeftArgType, Device>::Layout) == static_cast<int>(TensorEvaluator<RightArgType, Device>::Layout) || NumDims == 1), YOU_MADE_A_PROGRAMMING_MISTAKE);
126
- EIGEN_STATIC_ASSERT((NumDims == RightNumDims), YOU_MADE_A_PROGRAMMING_MISTAKE);
127
- EIGEN_STATIC_ASSERT((NumDims > 0), YOU_MADE_A_PROGRAMMING_MISTAKE);
128
-
129
- eigen_assert(0 <= m_axis && m_axis < NumDims);
130
- const Dimensions& lhs_dims = m_leftImpl.dimensions();
131
- const Dimensions& rhs_dims = m_rightImpl.dimensions();
132
- {
133
- int i = 0;
134
- for (; i < m_axis; ++i) {
135
- eigen_assert(lhs_dims[i] > 0);
136
- eigen_assert(lhs_dims[i] == rhs_dims[i]);
137
- m_dimensions[i] = lhs_dims[i];
138
- }
139
- eigen_assert(lhs_dims[i] > 0); // Now i == m_axis.
140
- eigen_assert(rhs_dims[i] > 0);
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- m_dimensions[i] = lhs_dims[i] + rhs_dims[i];
142
- for (++i; i < NumDims; ++i) {
143
- eigen_assert(lhs_dims[i] > 0);
144
- eigen_assert(lhs_dims[i] == rhs_dims[i]);
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- m_dimensions[i] = lhs_dims[i];
146
- }
147
- }
148
-
149
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
150
- m_leftStrides[0] = 1;
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- m_rightStrides[0] = 1;
152
- m_outputStrides[0] = 1;
153
-
154
- for (int j = 1; j < NumDims; ++j) {
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- m_leftStrides[j] = m_leftStrides[j-1] * lhs_dims[j-1];
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- m_rightStrides[j] = m_rightStrides[j-1] * rhs_dims[j-1];
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- m_outputStrides[j] = m_outputStrides[j-1] * m_dimensions[j-1];
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- }
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- } else {
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- m_leftStrides[NumDims - 1] = 1;
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- m_rightStrides[NumDims - 1] = 1;
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- m_outputStrides[NumDims - 1] = 1;
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-
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- for (int j = NumDims - 2; j >= 0; --j) {
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- m_leftStrides[j] = m_leftStrides[j+1] * lhs_dims[j+1];
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- m_rightStrides[j] = m_rightStrides[j+1] * rhs_dims[j+1];
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- m_outputStrides[j] = m_outputStrides[j+1] * m_dimensions[j+1];
168
- }
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- }
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- }
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-
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- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
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-
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- // TODO(phli): Add short-circuit memcpy evaluation if underlying data are linear?
175
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType)
176
- {
177
- m_leftImpl.evalSubExprsIfNeeded(NULL);
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- m_rightImpl.evalSubExprsIfNeeded(NULL);
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- return true;
180
- }
181
-
182
- EIGEN_STRONG_INLINE void cleanup()
183
- {
184
- m_leftImpl.cleanup();
185
- m_rightImpl.cleanup();
186
- }
187
-
188
- // TODO(phli): attempt to speed this up. The integer divisions and modulo are slow.
189
- // See CL/76180724 comments for more ideas.
190
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
191
- {
192
- // Collect dimension-wise indices (subs).
193
- array<Index, NumDims> subs;
194
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
195
- for (int i = NumDims - 1; i > 0; --i) {
196
- subs[i] = index / m_outputStrides[i];
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- index -= subs[i] * m_outputStrides[i];
198
- }
199
- subs[0] = index;
200
- } else {
201
- for (int i = 0; i < NumDims - 1; ++i) {
202
- subs[i] = index / m_outputStrides[i];
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- index -= subs[i] * m_outputStrides[i];
204
- }
205
- subs[NumDims - 1] = index;
206
- }
207
-
208
- const Dimensions& left_dims = m_leftImpl.dimensions();
209
- if (subs[m_axis] < left_dims[m_axis]) {
210
- Index left_index;
211
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
212
- left_index = subs[0];
213
- EIGEN_UNROLL_LOOP
214
- for (int i = 1; i < NumDims; ++i) {
215
- left_index += (subs[i] % left_dims[i]) * m_leftStrides[i];
216
- }
217
- } else {
218
- left_index = subs[NumDims - 1];
219
- EIGEN_UNROLL_LOOP
220
- for (int i = NumDims - 2; i >= 0; --i) {
221
- left_index += (subs[i] % left_dims[i]) * m_leftStrides[i];
222
- }
223
- }
224
- return m_leftImpl.coeff(left_index);
225
- } else {
226
- subs[m_axis] -= left_dims[m_axis];
227
- const Dimensions& right_dims = m_rightImpl.dimensions();
228
- Index right_index;
229
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
230
- right_index = subs[0];
231
- EIGEN_UNROLL_LOOP
232
- for (int i = 1; i < NumDims; ++i) {
233
- right_index += (subs[i] % right_dims[i]) * m_rightStrides[i];
234
- }
235
- } else {
236
- right_index = subs[NumDims - 1];
237
- EIGEN_UNROLL_LOOP
238
- for (int i = NumDims - 2; i >= 0; --i) {
239
- right_index += (subs[i] % right_dims[i]) * m_rightStrides[i];
240
- }
241
- }
242
- return m_rightImpl.coeff(right_index);
243
- }
244
- }
245
-
246
- // TODO(phli): Add a real vectorization.
247
- template<int LoadMode>
248
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
249
- {
250
- const int packetSize = PacketType<CoeffReturnType, Device>::size;
251
- EIGEN_STATIC_ASSERT((packetSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
252
- eigen_assert(index + packetSize - 1 < dimensions().TotalSize());
253
-
254
- EIGEN_ALIGN_MAX CoeffReturnType values[packetSize];
255
- EIGEN_UNROLL_LOOP
256
- for (int i = 0; i < packetSize; ++i) {
257
- values[i] = coeff(index+i);
258
- }
259
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
260
- return rslt;
261
- }
262
-
263
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
264
- costPerCoeff(bool vectorized) const {
265
- const double compute_cost = NumDims * (2 * TensorOpCost::AddCost<Index>() +
266
- 2 * TensorOpCost::MulCost<Index>() +
267
- TensorOpCost::DivCost<Index>() +
268
- TensorOpCost::ModCost<Index>());
269
- const double lhs_size = m_leftImpl.dimensions().TotalSize();
270
- const double rhs_size = m_rightImpl.dimensions().TotalSize();
271
- return (lhs_size / (lhs_size + rhs_size)) *
272
- m_leftImpl.costPerCoeff(vectorized) +
273
- (rhs_size / (lhs_size + rhs_size)) *
274
- m_rightImpl.costPerCoeff(vectorized) +
275
- TensorOpCost(0, 0, compute_cost);
276
- }
277
-
278
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return NULL; }
279
-
280
- #ifdef EIGEN_USE_SYCL
281
- // binding placeholder accessors to a command group handler for SYCL
282
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
283
- m_leftImpl.bind(cgh);
284
- m_rightImpl.bind(cgh);
285
- }
286
- #endif
287
-
288
- protected:
289
- Dimensions m_dimensions;
290
- array<Index, NumDims> m_outputStrides;
291
- array<Index, NumDims> m_leftStrides;
292
- array<Index, NumDims> m_rightStrides;
293
- TensorEvaluator<LeftArgType, Device> m_leftImpl;
294
- TensorEvaluator<RightArgType, Device> m_rightImpl;
295
- const Axis m_axis;
296
- };
297
-
298
- // Eval as lvalue
299
- template<typename Axis, typename LeftArgType, typename RightArgType, typename Device>
300
- struct TensorEvaluator<TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device>
301
- : public TensorEvaluator<const TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device>
302
- {
303
- typedef TensorEvaluator<const TensorConcatenationOp<Axis, LeftArgType, RightArgType>, Device> Base;
304
- typedef TensorConcatenationOp<Axis, LeftArgType, RightArgType> XprType;
305
- typedef typename Base::Dimensions Dimensions;
306
- enum {
307
- IsAligned = false,
308
- PacketAccess = TensorEvaluator<LeftArgType, Device>::PacketAccess &&
309
- TensorEvaluator<RightArgType, Device>::PacketAccess,
310
- BlockAccess = false,
311
- PreferBlockAccess = TensorEvaluator<LeftArgType, Device>::PreferBlockAccess ||
312
- TensorEvaluator<RightArgType, Device>::PreferBlockAccess,
313
- Layout = TensorEvaluator<LeftArgType, Device>::Layout,
314
- RawAccess = false
315
- };
316
-
317
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
318
- typedef internal::TensorBlockNotImplemented TensorBlock;
319
- //===--------------------------------------------------------------------===//
320
-
321
- EIGEN_STRONG_INLINE TensorEvaluator(XprType& op, const Device& device)
322
- : Base(op, device)
323
- {
324
- EIGEN_STATIC_ASSERT((static_cast<int>(Layout) == static_cast<int>(ColMajor)), YOU_MADE_A_PROGRAMMING_MISTAKE);
325
- }
326
-
327
- typedef typename XprType::Index Index;
328
- typedef typename XprType::Scalar Scalar;
329
- typedef typename XprType::CoeffReturnType CoeffReturnType;
330
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
331
-
332
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType& coeffRef(Index index)
333
- {
334
- // Collect dimension-wise indices (subs).
335
- array<Index, Base::NumDims> subs;
336
- for (int i = Base::NumDims - 1; i > 0; --i) {
337
- subs[i] = index / this->m_outputStrides[i];
338
- index -= subs[i] * this->m_outputStrides[i];
339
- }
340
- subs[0] = index;
341
-
342
- const Dimensions& left_dims = this->m_leftImpl.dimensions();
343
- if (subs[this->m_axis] < left_dims[this->m_axis]) {
344
- Index left_index = subs[0];
345
- for (int i = 1; i < Base::NumDims; ++i) {
346
- left_index += (subs[i] % left_dims[i]) * this->m_leftStrides[i];
347
- }
348
- return this->m_leftImpl.coeffRef(left_index);
349
- } else {
350
- subs[this->m_axis] -= left_dims[this->m_axis];
351
- const Dimensions& right_dims = this->m_rightImpl.dimensions();
352
- Index right_index = subs[0];
353
- for (int i = 1; i < Base::NumDims; ++i) {
354
- right_index += (subs[i] % right_dims[i]) * this->m_rightStrides[i];
355
- }
356
- return this->m_rightImpl.coeffRef(right_index);
357
- }
358
- }
359
-
360
- template <int StoreMode> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
361
- void writePacket(Index index, const PacketReturnType& x)
362
- {
363
- const int packetSize = PacketType<CoeffReturnType, Device>::size;
364
- EIGEN_STATIC_ASSERT((packetSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
365
- eigen_assert(index + packetSize - 1 < this->dimensions().TotalSize());
366
-
367
- EIGEN_ALIGN_MAX CoeffReturnType values[packetSize];
368
- internal::pstore<CoeffReturnType, PacketReturnType>(values, x);
369
- for (int i = 0; i < packetSize; ++i) {
370
- coeffRef(index+i) = values[i];
371
- }
372
- }
373
- };
374
-
375
- } // end namespace Eigen
376
-
377
- #endif // EIGEN_CXX11_TENSOR_TENSOR_CONCATENATION_H