sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-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 +157 -157
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-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-39-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 +157 -157
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-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
@@ -1,454 +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_REF_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_REF_H
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-
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- namespace Eigen {
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-
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- namespace internal {
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-
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- template <typename Dimensions, typename Scalar>
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- class TensorLazyBaseEvaluator {
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- public:
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- TensorLazyBaseEvaluator() : m_refcount(0) { }
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- virtual ~TensorLazyBaseEvaluator() { }
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-
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- EIGEN_DEVICE_FUNC virtual const Dimensions& dimensions() const = 0;
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- EIGEN_DEVICE_FUNC virtual const Scalar* data() const = 0;
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-
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- EIGEN_DEVICE_FUNC virtual const Scalar coeff(DenseIndex index) const = 0;
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- EIGEN_DEVICE_FUNC virtual Scalar& coeffRef(DenseIndex index) = 0;
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-
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- void incrRefCount() { ++m_refcount; }
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- void decrRefCount() { --m_refcount; }
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- int refCount() const { return m_refcount; }
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-
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- private:
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- // No copy, no assignment;
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- TensorLazyBaseEvaluator(const TensorLazyBaseEvaluator& other);
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- TensorLazyBaseEvaluator& operator = (const TensorLazyBaseEvaluator& other);
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-
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- int m_refcount;
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- };
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-
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-
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- template <typename Dimensions, typename Expr, typename Device>
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- class TensorLazyEvaluatorReadOnly : public TensorLazyBaseEvaluator<Dimensions, typename TensorEvaluator<Expr, Device>::Scalar> {
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- public:
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- // typedef typename TensorEvaluator<Expr, Device>::Dimensions Dimensions;
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- typedef typename TensorEvaluator<Expr, Device>::Scalar Scalar;
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- typedef StorageMemory<Scalar, Device> Storage;
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- typedef typename Storage::Type EvaluatorPointerType;
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- typedef TensorEvaluator<Expr, Device> EvalType;
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-
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- TensorLazyEvaluatorReadOnly(const Expr& expr, const Device& device) : m_impl(expr, device), m_dummy(Scalar(0)) {
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- m_dims = m_impl.dimensions();
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- m_impl.evalSubExprsIfNeeded(NULL);
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- }
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- virtual ~TensorLazyEvaluatorReadOnly() {
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- m_impl.cleanup();
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- }
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-
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- EIGEN_DEVICE_FUNC virtual const Dimensions& dimensions() const {
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- return m_dims;
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- }
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- EIGEN_DEVICE_FUNC virtual const Scalar* data() const {
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- return m_impl.data();
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- }
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-
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- EIGEN_DEVICE_FUNC virtual const Scalar coeff(DenseIndex index) const {
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- return m_impl.coeff(index);
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- }
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- EIGEN_DEVICE_FUNC virtual Scalar& coeffRef(DenseIndex /*index*/) {
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- eigen_assert(false && "can't reference the coefficient of a rvalue");
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- return m_dummy;
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- };
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-
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- protected:
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- TensorEvaluator<Expr, Device> m_impl;
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- Dimensions m_dims;
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- Scalar m_dummy;
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- };
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-
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- template <typename Dimensions, typename Expr, typename Device>
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- class TensorLazyEvaluatorWritable : public TensorLazyEvaluatorReadOnly<Dimensions, Expr, Device> {
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- public:
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- typedef TensorLazyEvaluatorReadOnly<Dimensions, Expr, Device> Base;
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- typedef typename Base::Scalar Scalar;
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- typedef StorageMemory<Scalar, Device> Storage;
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- typedef typename Storage::Type EvaluatorPointerType;
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-
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- TensorLazyEvaluatorWritable(const Expr& expr, const Device& device) : Base(expr, device) {
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- }
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- virtual ~TensorLazyEvaluatorWritable() {
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- }
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-
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- EIGEN_DEVICE_FUNC virtual Scalar& coeffRef(DenseIndex index) {
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- return this->m_impl.coeffRef(index);
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- }
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- };
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-
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- template <typename Dimensions, typename Expr, typename Device>
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- class TensorLazyEvaluator : public internal::conditional<bool(internal::is_lvalue<Expr>::value),
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- TensorLazyEvaluatorWritable<Dimensions, Expr, Device>,
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- TensorLazyEvaluatorReadOnly<Dimensions, const Expr, Device> >::type {
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- public:
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- typedef typename internal::conditional<bool(internal::is_lvalue<Expr>::value),
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- TensorLazyEvaluatorWritable<Dimensions, Expr, Device>,
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- TensorLazyEvaluatorReadOnly<Dimensions, const Expr, Device> >::type Base;
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- typedef typename Base::Scalar Scalar;
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-
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- TensorLazyEvaluator(const Expr& expr, const Device& device) : Base(expr, device) {
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- }
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- virtual ~TensorLazyEvaluator() {
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- }
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- };
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-
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- } // namespace internal
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-
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-
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- /** \class TensorRef
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief A reference to a tensor expression
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- * The expression will be evaluated lazily (as much as possible).
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- *
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- */
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- template<typename PlainObjectType> class TensorRef : public TensorBase<TensorRef<PlainObjectType> >
125
- {
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- public:
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- typedef TensorRef<PlainObjectType> Self;
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- typedef typename PlainObjectType::Base Base;
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- typedef typename Eigen::internal::nested<Self>::type Nested;
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- typedef typename internal::traits<PlainObjectType>::StorageKind StorageKind;
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- typedef typename internal::traits<PlainObjectType>::Index Index;
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- typedef typename internal::traits<PlainObjectType>::Scalar Scalar;
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- typedef typename NumTraits<Scalar>::Real RealScalar;
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- typedef typename Base::CoeffReturnType CoeffReturnType;
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- typedef Scalar* PointerType;
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- typedef PointerType PointerArgType;
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-
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- static const Index NumIndices = PlainObjectType::NumIndices;
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- typedef typename PlainObjectType::Dimensions Dimensions;
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-
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- enum {
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- IsAligned = false,
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- PacketAccess = false,
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- BlockAccess = false,
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- PreferBlockAccess = false,
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- Layout = PlainObjectType::Layout,
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- CoordAccess = false, // to be implemented
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- RawAccess = false
149
- };
150
-
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- //===- Tensor block evaluation strategy (see TensorBlock.h) -----------===//
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- typedef internal::TensorBlockNotImplemented TensorBlock;
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- //===------------------------------------------------------------------===//
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-
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- EIGEN_STRONG_INLINE TensorRef() : m_evaluator(NULL) {
156
- }
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-
158
- template <typename Expression>
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- EIGEN_STRONG_INLINE TensorRef(const Expression& expr) : m_evaluator(new internal::TensorLazyEvaluator<Dimensions, Expression, DefaultDevice>(expr, DefaultDevice())) {
160
- m_evaluator->incrRefCount();
161
- }
162
-
163
- template <typename Expression>
164
- EIGEN_STRONG_INLINE TensorRef& operator = (const Expression& expr) {
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- unrefEvaluator();
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- m_evaluator = new internal::TensorLazyEvaluator<Dimensions, Expression, DefaultDevice>(expr, DefaultDevice());
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- m_evaluator->incrRefCount();
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- return *this;
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- }
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-
171
- ~TensorRef() {
172
- unrefEvaluator();
173
- }
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-
175
- TensorRef(const TensorRef& other) : m_evaluator(other.m_evaluator) {
176
- eigen_assert(m_evaluator->refCount() > 0);
177
- m_evaluator->incrRefCount();
178
- }
179
-
180
- TensorRef& operator = (const TensorRef& other) {
181
- if (this != &other) {
182
- unrefEvaluator();
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- m_evaluator = other.m_evaluator;
184
- eigen_assert(m_evaluator->refCount() > 0);
185
- m_evaluator->incrRefCount();
186
- }
187
- return *this;
188
- }
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-
190
- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE Index rank() const { return m_evaluator->dimensions().size(); }
192
- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE Index dimension(Index n) const { return m_evaluator->dimensions()[n]; }
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_evaluator->dimensions(); }
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE Index size() const { return m_evaluator->dimensions().TotalSize(); }
198
- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const Scalar* data() const { return m_evaluator->data(); }
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-
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const Scalar operator()(Index index) const
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- {
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- return m_evaluator->coeff(index);
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- }
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-
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- #if EIGEN_HAS_VARIADIC_TEMPLATES
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- template<typename... IndexTypes> EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const Scalar operator()(Index firstIndex, IndexTypes... otherIndices) const
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- {
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- const std::size_t num_indices = (sizeof...(otherIndices) + 1);
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- const array<Index, num_indices> indices{{firstIndex, otherIndices...}};
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- return coeff(indices);
214
- }
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- template<typename... IndexTypes> EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE Scalar& coeffRef(Index firstIndex, IndexTypes... otherIndices)
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- {
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- const std::size_t num_indices = (sizeof...(otherIndices) + 1);
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- const array<Index, num_indices> indices{{firstIndex, otherIndices...}};
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- return coeffRef(indices);
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- }
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- #else
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-
224
- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1) const
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- {
227
- array<Index, 2> indices;
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- indices[0] = i0;
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- indices[1] = i1;
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- return coeff(indices);
231
- }
232
- EIGEN_DEVICE_FUNC
233
- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1, Index i2) const
234
- {
235
- array<Index, 3> indices;
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- indices[0] = i0;
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- indices[1] = i1;
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- indices[2] = i2;
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- return coeff(indices);
240
- }
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1, Index i2, Index i3) const
243
- {
244
- array<Index, 4> indices;
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- indices[0] = i0;
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- indices[1] = i1;
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- indices[2] = i2;
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- indices[3] = i3;
249
- return coeff(indices);
250
- }
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- EIGEN_DEVICE_FUNC
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- EIGEN_STRONG_INLINE const Scalar operator()(Index i0, Index i1, Index i2, Index i3, Index i4) const
253
- {
254
- array<Index, 5> indices;
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- indices[0] = i0;
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- indices[1] = i1;
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- indices[2] = i2;
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- indices[3] = i3;
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- indices[4] = i4;
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- return coeff(indices);
261
- }
262
- EIGEN_DEVICE_FUNC
263
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index i0, Index i1)
264
- {
265
- array<Index, 2> indices;
266
- indices[0] = i0;
267
- indices[1] = i1;
268
- return coeffRef(indices);
269
- }
270
- EIGEN_DEVICE_FUNC
271
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index i0, Index i1, Index i2)
272
- {
273
- array<Index, 3> indices;
274
- indices[0] = i0;
275
- indices[1] = i1;
276
- indices[2] = i2;
277
- return coeffRef(indices);
278
- }
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- EIGEN_DEVICE_FUNC
280
- EIGEN_STRONG_INLINE Scalar& operator()(Index i0, Index i1, Index i2, Index i3)
281
- {
282
- array<Index, 4> indices;
283
- indices[0] = i0;
284
- indices[1] = i1;
285
- indices[2] = i2;
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- indices[3] = i3;
287
- return coeffRef(indices);
288
- }
289
- EIGEN_DEVICE_FUNC
290
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index i0, Index i1, Index i2, Index i3, Index i4)
291
- {
292
- array<Index, 5> indices;
293
- indices[0] = i0;
294
- indices[1] = i1;
295
- indices[2] = i2;
296
- indices[3] = i3;
297
- indices[4] = i4;
298
- return coeffRef(indices);
299
- }
300
- #endif
301
-
302
- template <std::size_t NumIndices> EIGEN_DEVICE_FUNC
303
- EIGEN_STRONG_INLINE const Scalar coeff(const array<Index, NumIndices>& indices) const
304
- {
305
- const Dimensions& dims = this->dimensions();
306
- Index index = 0;
307
- if (PlainObjectType::Options & RowMajor) {
308
- index += indices[0];
309
- for (size_t i = 1; i < NumIndices; ++i) {
310
- index = index * dims[i] + indices[i];
311
- }
312
- } else {
313
- index += indices[NumIndices-1];
314
- for (int i = NumIndices-2; i >= 0; --i) {
315
- index = index * dims[i] + indices[i];
316
- }
317
- }
318
- return m_evaluator->coeff(index);
319
- }
320
- template <std::size_t NumIndices> EIGEN_DEVICE_FUNC
321
- EIGEN_STRONG_INLINE Scalar& coeffRef(const array<Index, NumIndices>& indices)
322
- {
323
- const Dimensions& dims = this->dimensions();
324
- Index index = 0;
325
- if (PlainObjectType::Options & RowMajor) {
326
- index += indices[0];
327
- for (size_t i = 1; i < NumIndices; ++i) {
328
- index = index * dims[i] + indices[i];
329
- }
330
- } else {
331
- index += indices[NumIndices-1];
332
- for (int i = NumIndices-2; i >= 0; --i) {
333
- index = index * dims[i] + indices[i];
334
- }
335
- }
336
- return m_evaluator->coeffRef(index);
337
- }
338
-
339
- EIGEN_DEVICE_FUNC
340
- EIGEN_STRONG_INLINE const Scalar coeff(Index index) const
341
- {
342
- return m_evaluator->coeff(index);
343
- }
344
-
345
- EIGEN_DEVICE_FUNC
346
- EIGEN_STRONG_INLINE Scalar& coeffRef(Index index)
347
- {
348
- return m_evaluator->coeffRef(index);
349
- }
350
-
351
- private:
352
- EIGEN_STRONG_INLINE void unrefEvaluator() {
353
- if (m_evaluator) {
354
- m_evaluator->decrRefCount();
355
- if (m_evaluator->refCount() == 0) {
356
- delete m_evaluator;
357
- }
358
- }
359
- }
360
-
361
- internal::TensorLazyBaseEvaluator<Dimensions, Scalar>* m_evaluator;
362
- };
363
-
364
-
365
- // evaluator for rvalues
366
- template<typename Derived, typename Device>
367
- struct TensorEvaluator<const TensorRef<Derived>, Device>
368
- {
369
- typedef typename Derived::Index Index;
370
- typedef typename Derived::Scalar Scalar;
371
- typedef typename Derived::Scalar CoeffReturnType;
372
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
373
- typedef typename Derived::Dimensions Dimensions;
374
- typedef StorageMemory<CoeffReturnType, Device> Storage;
375
- typedef typename Storage::Type EvaluatorPointerType;
376
-
377
- enum {
378
- IsAligned = false,
379
- PacketAccess = false,
380
- BlockAccess = false,
381
- PreferBlockAccess = false,
382
- Layout = TensorRef<Derived>::Layout,
383
- CoordAccess = false, // to be implemented
384
- RawAccess = false
385
- };
386
-
387
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
388
- typedef internal::TensorBlockNotImplemented TensorBlock;
389
- //===--------------------------------------------------------------------===//
390
-
391
- EIGEN_STRONG_INLINE TensorEvaluator(const TensorRef<Derived>& m, const Device&)
392
- : m_ref(m)
393
- { }
394
-
395
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_ref.dimensions(); }
396
-
397
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType) {
398
- return true;
399
- }
400
-
401
- EIGEN_STRONG_INLINE void cleanup() { }
402
-
403
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const {
404
- return m_ref.coeff(index);
405
- }
406
-
407
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& coeffRef(Index index) {
408
- return m_ref.coeffRef(index);
409
- }
410
-
411
- EIGEN_DEVICE_FUNC const Scalar* data() const { return m_ref.data(); }
412
-
413
- protected:
414
- TensorRef<Derived> m_ref;
415
- };
416
-
417
-
418
- // evaluator for lvalues
419
- template<typename Derived, typename Device>
420
- struct TensorEvaluator<TensorRef<Derived>, Device> : public TensorEvaluator<const TensorRef<Derived>, Device>
421
- {
422
- typedef typename Derived::Index Index;
423
- typedef typename Derived::Scalar Scalar;
424
- typedef typename Derived::Scalar CoeffReturnType;
425
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
426
- typedef typename Derived::Dimensions Dimensions;
427
-
428
- typedef TensorEvaluator<const TensorRef<Derived>, Device> Base;
429
-
430
- enum {
431
- IsAligned = false,
432
- PacketAccess = false,
433
- BlockAccess = false,
434
- PreferBlockAccess = false,
435
- RawAccess = false
436
- };
437
-
438
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
439
- typedef internal::TensorBlockNotImplemented TensorBlock;
440
- //===--------------------------------------------------------------------===//
441
-
442
- EIGEN_STRONG_INLINE TensorEvaluator(TensorRef<Derived>& m, const Device& d) : Base(m, d)
443
- { }
444
-
445
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Scalar& coeffRef(Index index) {
446
- return this->m_ref.coeffRef(index);
447
- }
448
- };
449
-
450
-
451
-
452
- } // end namespace Eigen
453
-
454
- #endif // EIGEN_CXX11_TENSOR_TENSOR_REF_H