sequenzo 0.1.17__cp311-cp311-macosx_10_9_universal2.whl → 0.1.19__cp311-cp311-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-311-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-311-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-311-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-311-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-311-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-311-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-311-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
@@ -1,117 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2014 Gael Guennebaud <gael.guennebaud@inria.fr>
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_SOLVEWITHGUESS_H
11
- #define EIGEN_SOLVEWITHGUESS_H
12
-
13
- namespace Eigen {
14
-
15
- template<typename Decomposition, typename RhsType, typename GuessType> class SolveWithGuess;
16
-
17
- /** \class SolveWithGuess
18
- * \ingroup IterativeLinearSolvers_Module
19
- *
20
- * \brief Pseudo expression representing a solving operation
21
- *
22
- * \tparam Decomposition the type of the matrix or decomposion object
23
- * \tparam Rhstype the type of the right-hand side
24
- *
25
- * This class represents an expression of A.solve(B)
26
- * and most of the time this is the only way it is used.
27
- *
28
- */
29
- namespace internal {
30
-
31
-
32
- template<typename Decomposition, typename RhsType, typename GuessType>
33
- struct traits<SolveWithGuess<Decomposition, RhsType, GuessType> >
34
- : traits<Solve<Decomposition,RhsType> >
35
- {};
36
-
37
- }
38
-
39
-
40
- template<typename Decomposition, typename RhsType, typename GuessType>
41
- class SolveWithGuess : public internal::generic_xpr_base<SolveWithGuess<Decomposition,RhsType,GuessType>, MatrixXpr, typename internal::traits<RhsType>::StorageKind>::type
42
- {
43
- public:
44
- typedef typename internal::traits<SolveWithGuess>::Scalar Scalar;
45
- typedef typename internal::traits<SolveWithGuess>::PlainObject PlainObject;
46
- typedef typename internal::generic_xpr_base<SolveWithGuess<Decomposition,RhsType,GuessType>, MatrixXpr, typename internal::traits<RhsType>::StorageKind>::type Base;
47
- typedef typename internal::ref_selector<SolveWithGuess>::type Nested;
48
-
49
- SolveWithGuess(const Decomposition &dec, const RhsType &rhs, const GuessType &guess)
50
- : m_dec(dec), m_rhs(rhs), m_guess(guess)
51
- {}
52
-
53
- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
54
- Index rows() const EIGEN_NOEXCEPT { return m_dec.cols(); }
55
- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
56
- Index cols() const EIGEN_NOEXCEPT { return m_rhs.cols(); }
57
-
58
- EIGEN_DEVICE_FUNC const Decomposition& dec() const { return m_dec; }
59
- EIGEN_DEVICE_FUNC const RhsType& rhs() const { return m_rhs; }
60
- EIGEN_DEVICE_FUNC const GuessType& guess() const { return m_guess; }
61
-
62
- protected:
63
- const Decomposition &m_dec;
64
- const RhsType &m_rhs;
65
- const GuessType &m_guess;
66
-
67
- private:
68
- Scalar coeff(Index row, Index col) const;
69
- Scalar coeff(Index i) const;
70
- };
71
-
72
- namespace internal {
73
-
74
- // Evaluator of SolveWithGuess -> eval into a temporary
75
- template<typename Decomposition, typename RhsType, typename GuessType>
76
- struct evaluator<SolveWithGuess<Decomposition,RhsType, GuessType> >
77
- : public evaluator<typename SolveWithGuess<Decomposition,RhsType,GuessType>::PlainObject>
78
- {
79
- typedef SolveWithGuess<Decomposition,RhsType,GuessType> SolveType;
80
- typedef typename SolveType::PlainObject PlainObject;
81
- typedef evaluator<PlainObject> Base;
82
-
83
- evaluator(const SolveType& solve)
84
- : m_result(solve.rows(), solve.cols())
85
- {
86
- ::new (static_cast<Base*>(this)) Base(m_result);
87
- m_result = solve.guess();
88
- solve.dec()._solve_with_guess_impl(solve.rhs(), m_result);
89
- }
90
-
91
- protected:
92
- PlainObject m_result;
93
- };
94
-
95
- // Specialization for "dst = dec.solveWithGuess(rhs)"
96
- // NOTE we need to specialize it for Dense2Dense to avoid ambiguous specialization error and a Sparse2Sparse specialization must exist somewhere
97
- template<typename DstXprType, typename DecType, typename RhsType, typename GuessType, typename Scalar>
98
- struct Assignment<DstXprType, SolveWithGuess<DecType,RhsType,GuessType>, internal::assign_op<Scalar,Scalar>, Dense2Dense>
99
- {
100
- typedef SolveWithGuess<DecType,RhsType,GuessType> SrcXprType;
101
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<Scalar,Scalar> &)
102
- {
103
- Index dstRows = src.rows();
104
- Index dstCols = src.cols();
105
- if((dst.rows()!=dstRows) || (dst.cols()!=dstCols))
106
- dst.resize(dstRows, dstCols);
107
-
108
- dst = src.guess();
109
- src.dec()._solve_with_guess_impl(src.rhs(), dst/*, src.guess()*/);
110
- }
111
- };
112
-
113
- } // end namespace internal
114
-
115
- } // end namespace Eigen
116
-
117
- #endif // EIGEN_SOLVEWITHGUESS_H
@@ -1,483 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
5
- // Copyright (C) 2009 Gael Guennebaud <gael.guennebaud@inria.fr>
6
- //
7
- // This Source Code Form is subject to the terms of the Mozilla
8
- // Public License v. 2.0. If a copy of the MPL was not distributed
9
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
-
11
- #ifndef EIGEN_JACOBI_H
12
- #define EIGEN_JACOBI_H
13
-
14
- namespace Eigen {
15
-
16
- /** \ingroup Jacobi_Module
17
- * \jacobi_module
18
- * \class JacobiRotation
19
- * \brief Rotation given by a cosine-sine pair.
20
- *
21
- * This class represents a Jacobi or Givens rotation.
22
- * This is a 2D rotation in the plane \c J of angle \f$ \theta \f$ defined by
23
- * its cosine \c c and sine \c s as follow:
24
- * \f$ J = \left ( \begin{array}{cc} c & \overline s \\ -s & \overline c \end{array} \right ) \f$
25
- *
26
- * You can apply the respective counter-clockwise rotation to a column vector \c v by
27
- * applying its adjoint on the left: \f$ v = J^* v \f$ that translates to the following Eigen code:
28
- * \code
29
- * v.applyOnTheLeft(J.adjoint());
30
- * \endcode
31
- *
32
- * \sa MatrixBase::applyOnTheLeft(), MatrixBase::applyOnTheRight()
33
- */
34
- template<typename Scalar> class JacobiRotation
35
- {
36
- public:
37
- typedef typename NumTraits<Scalar>::Real RealScalar;
38
-
39
- /** Default constructor without any initialization. */
40
- EIGEN_DEVICE_FUNC
41
- JacobiRotation() {}
42
-
43
- /** Construct a planar rotation from a cosine-sine pair (\a c, \c s). */
44
- EIGEN_DEVICE_FUNC
45
- JacobiRotation(const Scalar& c, const Scalar& s) : m_c(c), m_s(s) {}
46
-
47
- EIGEN_DEVICE_FUNC Scalar& c() { return m_c; }
48
- EIGEN_DEVICE_FUNC Scalar c() const { return m_c; }
49
- EIGEN_DEVICE_FUNC Scalar& s() { return m_s; }
50
- EIGEN_DEVICE_FUNC Scalar s() const { return m_s; }
51
-
52
- /** Concatenates two planar rotation */
53
- EIGEN_DEVICE_FUNC
54
- JacobiRotation operator*(const JacobiRotation& other)
55
- {
56
- using numext::conj;
57
- return JacobiRotation(m_c * other.m_c - conj(m_s) * other.m_s,
58
- conj(m_c * conj(other.m_s) + conj(m_s) * conj(other.m_c)));
59
- }
60
-
61
- /** Returns the transposed transformation */
62
- EIGEN_DEVICE_FUNC
63
- JacobiRotation transpose() const { using numext::conj; return JacobiRotation(m_c, -conj(m_s)); }
64
-
65
- /** Returns the adjoint transformation */
66
- EIGEN_DEVICE_FUNC
67
- JacobiRotation adjoint() const { using numext::conj; return JacobiRotation(conj(m_c), -m_s); }
68
-
69
- template<typename Derived>
70
- EIGEN_DEVICE_FUNC
71
- bool makeJacobi(const MatrixBase<Derived>&, Index p, Index q);
72
- EIGEN_DEVICE_FUNC
73
- bool makeJacobi(const RealScalar& x, const Scalar& y, const RealScalar& z);
74
-
75
- EIGEN_DEVICE_FUNC
76
- void makeGivens(const Scalar& p, const Scalar& q, Scalar* r=0);
77
-
78
- protected:
79
- EIGEN_DEVICE_FUNC
80
- void makeGivens(const Scalar& p, const Scalar& q, Scalar* r, internal::true_type);
81
- EIGEN_DEVICE_FUNC
82
- void makeGivens(const Scalar& p, const Scalar& q, Scalar* r, internal::false_type);
83
-
84
- Scalar m_c, m_s;
85
- };
86
-
87
- /** Makes \c *this as a Jacobi rotation \a J such that applying \a J on both the right and left sides of the selfadjoint 2x2 matrix
88
- * \f$ B = \left ( \begin{array}{cc} x & y \\ \overline y & z \end{array} \right )\f$ yields a diagonal matrix \f$ A = J^* B J \f$
89
- *
90
- * \sa MatrixBase::makeJacobi(const MatrixBase<Derived>&, Index, Index), MatrixBase::applyOnTheLeft(), MatrixBase::applyOnTheRight()
91
- */
92
- template<typename Scalar>
93
- EIGEN_DEVICE_FUNC
94
- bool JacobiRotation<Scalar>::makeJacobi(const RealScalar& x, const Scalar& y, const RealScalar& z)
95
- {
96
- using std::sqrt;
97
- using std::abs;
98
-
99
- RealScalar deno = RealScalar(2)*abs(y);
100
- if(deno < (std::numeric_limits<RealScalar>::min)())
101
- {
102
- m_c = Scalar(1);
103
- m_s = Scalar(0);
104
- return false;
105
- }
106
- else
107
- {
108
- RealScalar tau = (x-z)/deno;
109
- RealScalar w = sqrt(numext::abs2(tau) + RealScalar(1));
110
- RealScalar t;
111
- if(tau>RealScalar(0))
112
- {
113
- t = RealScalar(1) / (tau + w);
114
- }
115
- else
116
- {
117
- t = RealScalar(1) / (tau - w);
118
- }
119
- RealScalar sign_t = t > RealScalar(0) ? RealScalar(1) : RealScalar(-1);
120
- RealScalar n = RealScalar(1) / sqrt(numext::abs2(t)+RealScalar(1));
121
- m_s = - sign_t * (numext::conj(y) / abs(y)) * abs(t) * n;
122
- m_c = n;
123
- return true;
124
- }
125
- }
126
-
127
- /** Makes \c *this as a Jacobi rotation \c J such that applying \a J on both the right and left sides of the 2x2 selfadjoint matrix
128
- * \f$ B = \left ( \begin{array}{cc} \text{this}_{pp} & \text{this}_{pq} \\ (\text{this}_{pq})^* & \text{this}_{qq} \end{array} \right )\f$ yields
129
- * a diagonal matrix \f$ A = J^* B J \f$
130
- *
131
- * Example: \include Jacobi_makeJacobi.cpp
132
- * Output: \verbinclude Jacobi_makeJacobi.out
133
- *
134
- * \sa JacobiRotation::makeJacobi(RealScalar, Scalar, RealScalar), MatrixBase::applyOnTheLeft(), MatrixBase::applyOnTheRight()
135
- */
136
- template<typename Scalar>
137
- template<typename Derived>
138
- EIGEN_DEVICE_FUNC
139
- inline bool JacobiRotation<Scalar>::makeJacobi(const MatrixBase<Derived>& m, Index p, Index q)
140
- {
141
- return makeJacobi(numext::real(m.coeff(p,p)), m.coeff(p,q), numext::real(m.coeff(q,q)));
142
- }
143
-
144
- /** Makes \c *this as a Givens rotation \c G such that applying \f$ G^* \f$ to the left of the vector
145
- * \f$ V = \left ( \begin{array}{c} p \\ q \end{array} \right )\f$ yields:
146
- * \f$ G^* V = \left ( \begin{array}{c} r \\ 0 \end{array} \right )\f$.
147
- *
148
- * The value of \a r is returned if \a r is not null (the default is null).
149
- * Also note that G is built such that the cosine is always real.
150
- *
151
- * Example: \include Jacobi_makeGivens.cpp
152
- * Output: \verbinclude Jacobi_makeGivens.out
153
- *
154
- * This function implements the continuous Givens rotation generation algorithm
155
- * found in Anderson (2000), Discontinuous Plane Rotations and the Symmetric Eigenvalue Problem.
156
- * LAPACK Working Note 150, University of Tennessee, UT-CS-00-454, December 4, 2000.
157
- *
158
- * \sa MatrixBase::applyOnTheLeft(), MatrixBase::applyOnTheRight()
159
- */
160
- template<typename Scalar>
161
- EIGEN_DEVICE_FUNC
162
- void JacobiRotation<Scalar>::makeGivens(const Scalar& p, const Scalar& q, Scalar* r)
163
- {
164
- makeGivens(p, q, r, typename internal::conditional<NumTraits<Scalar>::IsComplex, internal::true_type, internal::false_type>::type());
165
- }
166
-
167
-
168
- // specialization for complexes
169
- template<typename Scalar>
170
- EIGEN_DEVICE_FUNC
171
- void JacobiRotation<Scalar>::makeGivens(const Scalar& p, const Scalar& q, Scalar* r, internal::true_type)
172
- {
173
- using std::sqrt;
174
- using std::abs;
175
- using numext::conj;
176
-
177
- if(q==Scalar(0))
178
- {
179
- m_c = numext::real(p)<0 ? Scalar(-1) : Scalar(1);
180
- m_s = 0;
181
- if(r) *r = m_c * p;
182
- }
183
- else if(p==Scalar(0))
184
- {
185
- m_c = 0;
186
- m_s = -q/abs(q);
187
- if(r) *r = abs(q);
188
- }
189
- else
190
- {
191
- RealScalar p1 = numext::norm1(p);
192
- RealScalar q1 = numext::norm1(q);
193
- if(p1>=q1)
194
- {
195
- Scalar ps = p / p1;
196
- RealScalar p2 = numext::abs2(ps);
197
- Scalar qs = q / p1;
198
- RealScalar q2 = numext::abs2(qs);
199
-
200
- RealScalar u = sqrt(RealScalar(1) + q2/p2);
201
- if(numext::real(p)<RealScalar(0))
202
- u = -u;
203
-
204
- m_c = Scalar(1)/u;
205
- m_s = -qs*conj(ps)*(m_c/p2);
206
- if(r) *r = p * u;
207
- }
208
- else
209
- {
210
- Scalar ps = p / q1;
211
- RealScalar p2 = numext::abs2(ps);
212
- Scalar qs = q / q1;
213
- RealScalar q2 = numext::abs2(qs);
214
-
215
- RealScalar u = q1 * sqrt(p2 + q2);
216
- if(numext::real(p)<RealScalar(0))
217
- u = -u;
218
-
219
- p1 = abs(p);
220
- ps = p/p1;
221
- m_c = p1/u;
222
- m_s = -conj(ps) * (q/u);
223
- if(r) *r = ps * u;
224
- }
225
- }
226
- }
227
-
228
- // specialization for reals
229
- template<typename Scalar>
230
- EIGEN_DEVICE_FUNC
231
- void JacobiRotation<Scalar>::makeGivens(const Scalar& p, const Scalar& q, Scalar* r, internal::false_type)
232
- {
233
- using std::sqrt;
234
- using std::abs;
235
- if(q==Scalar(0))
236
- {
237
- m_c = p<Scalar(0) ? Scalar(-1) : Scalar(1);
238
- m_s = Scalar(0);
239
- if(r) *r = abs(p);
240
- }
241
- else if(p==Scalar(0))
242
- {
243
- m_c = Scalar(0);
244
- m_s = q<Scalar(0) ? Scalar(1) : Scalar(-1);
245
- if(r) *r = abs(q);
246
- }
247
- else if(abs(p) > abs(q))
248
- {
249
- Scalar t = q/p;
250
- Scalar u = sqrt(Scalar(1) + numext::abs2(t));
251
- if(p<Scalar(0))
252
- u = -u;
253
- m_c = Scalar(1)/u;
254
- m_s = -t * m_c;
255
- if(r) *r = p * u;
256
- }
257
- else
258
- {
259
- Scalar t = p/q;
260
- Scalar u = sqrt(Scalar(1) + numext::abs2(t));
261
- if(q<Scalar(0))
262
- u = -u;
263
- m_s = -Scalar(1)/u;
264
- m_c = -t * m_s;
265
- if(r) *r = q * u;
266
- }
267
-
268
- }
269
-
270
- /****************************************************************************************
271
- * Implementation of MatrixBase methods
272
- ****************************************************************************************/
273
-
274
- namespace internal {
275
- /** \jacobi_module
276
- * Applies the clock wise 2D rotation \a j to the set of 2D vectors of coordinates \a x and \a y:
277
- * \f$ \left ( \begin{array}{cc} x \\ y \end{array} \right ) = J \left ( \begin{array}{cc} x \\ y \end{array} \right ) \f$
278
- *
279
- * \sa MatrixBase::applyOnTheLeft(), MatrixBase::applyOnTheRight()
280
- */
281
- template<typename VectorX, typename VectorY, typename OtherScalar>
282
- EIGEN_DEVICE_FUNC
283
- void apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x, DenseBase<VectorY>& xpr_y, const JacobiRotation<OtherScalar>& j);
284
- }
285
-
286
- /** \jacobi_module
287
- * Applies the rotation in the plane \a j to the rows \a p and \a q of \c *this, i.e., it computes B = J * B,
288
- * with \f$ B = \left ( \begin{array}{cc} \text{*this.row}(p) \\ \text{*this.row}(q) \end{array} \right ) \f$.
289
- *
290
- * \sa class JacobiRotation, MatrixBase::applyOnTheRight(), internal::apply_rotation_in_the_plane()
291
- */
292
- template<typename Derived>
293
- template<typename OtherScalar>
294
- EIGEN_DEVICE_FUNC
295
- inline void MatrixBase<Derived>::applyOnTheLeft(Index p, Index q, const JacobiRotation<OtherScalar>& j)
296
- {
297
- RowXpr x(this->row(p));
298
- RowXpr y(this->row(q));
299
- internal::apply_rotation_in_the_plane(x, y, j);
300
- }
301
-
302
- /** \ingroup Jacobi_Module
303
- * Applies the rotation in the plane \a j to the columns \a p and \a q of \c *this, i.e., it computes B = B * J
304
- * with \f$ B = \left ( \begin{array}{cc} \text{*this.col}(p) & \text{*this.col}(q) \end{array} \right ) \f$.
305
- *
306
- * \sa class JacobiRotation, MatrixBase::applyOnTheLeft(), internal::apply_rotation_in_the_plane()
307
- */
308
- template<typename Derived>
309
- template<typename OtherScalar>
310
- EIGEN_DEVICE_FUNC
311
- inline void MatrixBase<Derived>::applyOnTheRight(Index p, Index q, const JacobiRotation<OtherScalar>& j)
312
- {
313
- ColXpr x(this->col(p));
314
- ColXpr y(this->col(q));
315
- internal::apply_rotation_in_the_plane(x, y, j.transpose());
316
- }
317
-
318
- namespace internal {
319
-
320
- template<typename Scalar, typename OtherScalar,
321
- int SizeAtCompileTime, int MinAlignment, bool Vectorizable>
322
- struct apply_rotation_in_the_plane_selector
323
- {
324
- static EIGEN_DEVICE_FUNC
325
- inline void run(Scalar *x, Index incrx, Scalar *y, Index incry, Index size, OtherScalar c, OtherScalar s)
326
- {
327
- for(Index i=0; i<size; ++i)
328
- {
329
- Scalar xi = *x;
330
- Scalar yi = *y;
331
- *x = c * xi + numext::conj(s) * yi;
332
- *y = -s * xi + numext::conj(c) * yi;
333
- x += incrx;
334
- y += incry;
335
- }
336
- }
337
- };
338
-
339
- template<typename Scalar, typename OtherScalar,
340
- int SizeAtCompileTime, int MinAlignment>
341
- struct apply_rotation_in_the_plane_selector<Scalar,OtherScalar,SizeAtCompileTime,MinAlignment,true /* vectorizable */>
342
- {
343
- static inline void run(Scalar *x, Index incrx, Scalar *y, Index incry, Index size, OtherScalar c, OtherScalar s)
344
- {
345
- enum {
346
- PacketSize = packet_traits<Scalar>::size,
347
- OtherPacketSize = packet_traits<OtherScalar>::size
348
- };
349
- typedef typename packet_traits<Scalar>::type Packet;
350
- typedef typename packet_traits<OtherScalar>::type OtherPacket;
351
-
352
- /*** dynamic-size vectorized paths ***/
353
- if(SizeAtCompileTime == Dynamic && ((incrx==1 && incry==1) || PacketSize == 1))
354
- {
355
- // both vectors are sequentially stored in memory => vectorization
356
- enum { Peeling = 2 };
357
-
358
- Index alignedStart = internal::first_default_aligned(y, size);
359
- Index alignedEnd = alignedStart + ((size-alignedStart)/PacketSize)*PacketSize;
360
-
361
- const OtherPacket pc = pset1<OtherPacket>(c);
362
- const OtherPacket ps = pset1<OtherPacket>(s);
363
- conj_helper<OtherPacket,Packet,NumTraits<OtherScalar>::IsComplex,false> pcj;
364
- conj_helper<OtherPacket,Packet,false,false> pm;
365
-
366
- for(Index i=0; i<alignedStart; ++i)
367
- {
368
- Scalar xi = x[i];
369
- Scalar yi = y[i];
370
- x[i] = c * xi + numext::conj(s) * yi;
371
- y[i] = -s * xi + numext::conj(c) * yi;
372
- }
373
-
374
- Scalar* EIGEN_RESTRICT px = x + alignedStart;
375
- Scalar* EIGEN_RESTRICT py = y + alignedStart;
376
-
377
- if(internal::first_default_aligned(x, size)==alignedStart)
378
- {
379
- for(Index i=alignedStart; i<alignedEnd; i+=PacketSize)
380
- {
381
- Packet xi = pload<Packet>(px);
382
- Packet yi = pload<Packet>(py);
383
- pstore(px, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
384
- pstore(py, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
385
- px += PacketSize;
386
- py += PacketSize;
387
- }
388
- }
389
- else
390
- {
391
- Index peelingEnd = alignedStart + ((size-alignedStart)/(Peeling*PacketSize))*(Peeling*PacketSize);
392
- for(Index i=alignedStart; i<peelingEnd; i+=Peeling*PacketSize)
393
- {
394
- Packet xi = ploadu<Packet>(px);
395
- Packet xi1 = ploadu<Packet>(px+PacketSize);
396
- Packet yi = pload <Packet>(py);
397
- Packet yi1 = pload <Packet>(py+PacketSize);
398
- pstoreu(px, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
399
- pstoreu(px+PacketSize, padd(pm.pmul(pc,xi1),pcj.pmul(ps,yi1)));
400
- pstore (py, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
401
- pstore (py+PacketSize, psub(pcj.pmul(pc,yi1),pm.pmul(ps,xi1)));
402
- px += Peeling*PacketSize;
403
- py += Peeling*PacketSize;
404
- }
405
- if(alignedEnd!=peelingEnd)
406
- {
407
- Packet xi = ploadu<Packet>(x+peelingEnd);
408
- Packet yi = pload <Packet>(y+peelingEnd);
409
- pstoreu(x+peelingEnd, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
410
- pstore (y+peelingEnd, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
411
- }
412
- }
413
-
414
- for(Index i=alignedEnd; i<size; ++i)
415
- {
416
- Scalar xi = x[i];
417
- Scalar yi = y[i];
418
- x[i] = c * xi + numext::conj(s) * yi;
419
- y[i] = -s * xi + numext::conj(c) * yi;
420
- }
421
- }
422
-
423
- /*** fixed-size vectorized path ***/
424
- else if(SizeAtCompileTime != Dynamic && MinAlignment>0) // FIXME should be compared to the required alignment
425
- {
426
- const OtherPacket pc = pset1<OtherPacket>(c);
427
- const OtherPacket ps = pset1<OtherPacket>(s);
428
- conj_helper<OtherPacket,Packet,NumTraits<OtherPacket>::IsComplex,false> pcj;
429
- conj_helper<OtherPacket,Packet,false,false> pm;
430
- Scalar* EIGEN_RESTRICT px = x;
431
- Scalar* EIGEN_RESTRICT py = y;
432
- for(Index i=0; i<size; i+=PacketSize)
433
- {
434
- Packet xi = pload<Packet>(px);
435
- Packet yi = pload<Packet>(py);
436
- pstore(px, padd(pm.pmul(pc,xi),pcj.pmul(ps,yi)));
437
- pstore(py, psub(pcj.pmul(pc,yi),pm.pmul(ps,xi)));
438
- px += PacketSize;
439
- py += PacketSize;
440
- }
441
- }
442
-
443
- /*** non-vectorized path ***/
444
- else
445
- {
446
- apply_rotation_in_the_plane_selector<Scalar,OtherScalar,SizeAtCompileTime,MinAlignment,false>::run(x,incrx,y,incry,size,c,s);
447
- }
448
- }
449
- };
450
-
451
- template<typename VectorX, typename VectorY, typename OtherScalar>
452
- EIGEN_DEVICE_FUNC
453
- void /*EIGEN_DONT_INLINE*/ apply_rotation_in_the_plane(DenseBase<VectorX>& xpr_x, DenseBase<VectorY>& xpr_y, const JacobiRotation<OtherScalar>& j)
454
- {
455
- typedef typename VectorX::Scalar Scalar;
456
- const bool Vectorizable = (int(VectorX::Flags) & int(VectorY::Flags) & PacketAccessBit)
457
- && (int(packet_traits<Scalar>::size) == int(packet_traits<OtherScalar>::size));
458
-
459
- eigen_assert(xpr_x.size() == xpr_y.size());
460
- Index size = xpr_x.size();
461
- Index incrx = xpr_x.derived().innerStride();
462
- Index incry = xpr_y.derived().innerStride();
463
-
464
- Scalar* EIGEN_RESTRICT x = &xpr_x.derived().coeffRef(0);
465
- Scalar* EIGEN_RESTRICT y = &xpr_y.derived().coeffRef(0);
466
-
467
- OtherScalar c = j.c();
468
- OtherScalar s = j.s();
469
- if (c==OtherScalar(1) && s==OtherScalar(0))
470
- return;
471
-
472
- apply_rotation_in_the_plane_selector<
473
- Scalar,OtherScalar,
474
- VectorX::SizeAtCompileTime,
475
- EIGEN_PLAIN_ENUM_MIN(evaluator<VectorX>::Alignment, evaluator<VectorY>::Alignment),
476
- Vectorizable>::run(x,incrx,y,incry,size,c,s);
477
- }
478
-
479
- } // end namespace internal
480
-
481
- } // end namespace Eigen
482
-
483
- #endif // EIGEN_JACOBI_H