sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,368 +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) 2011, 2013 Jitse Niesen <jitse@maths.leeds.ac.uk>
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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_MATRIX_SQUARE_ROOT
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- #define EIGEN_MATRIX_SQUARE_ROOT
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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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- // pre: T.block(i,i,2,2) has complex conjugate eigenvalues
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- // post: sqrtT.block(i,i,2,2) is square root of T.block(i,i,2,2)
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- template <typename MatrixType, typename ResultType>
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- void matrix_sqrt_quasi_triangular_2x2_diagonal_block(const MatrixType& T, Index i, ResultType& sqrtT)
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- {
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- // TODO: This case (2-by-2 blocks with complex conjugate eigenvalues) is probably hidden somewhere
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- // in EigenSolver. If we expose it, we could call it directly from here.
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- typedef typename traits<MatrixType>::Scalar Scalar;
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- Matrix<Scalar,2,2> block = T.template block<2,2>(i,i);
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- EigenSolver<Matrix<Scalar,2,2> > es(block);
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- sqrtT.template block<2,2>(i,i)
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- = (es.eigenvectors() * es.eigenvalues().cwiseSqrt().asDiagonal() * es.eigenvectors().inverse()).real();
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- }
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-
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- // pre: block structure of T is such that (i,j) is a 1x1 block,
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- // all blocks of sqrtT to left of and below (i,j) are correct
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- // post: sqrtT(i,j) has the correct value
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- template <typename MatrixType, typename ResultType>
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- void matrix_sqrt_quasi_triangular_1x1_off_diagonal_block(const MatrixType& T, Index i, Index j, ResultType& sqrtT)
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- {
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- typedef typename traits<MatrixType>::Scalar Scalar;
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- Scalar tmp = (sqrtT.row(i).segment(i+1,j-i-1) * sqrtT.col(j).segment(i+1,j-i-1)).value();
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- sqrtT.coeffRef(i,j) = (T.coeff(i,j) - tmp) / (sqrtT.coeff(i,i) + sqrtT.coeff(j,j));
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- }
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-
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- // similar to compute1x1offDiagonalBlock()
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- template <typename MatrixType, typename ResultType>
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- void matrix_sqrt_quasi_triangular_1x2_off_diagonal_block(const MatrixType& T, Index i, Index j, ResultType& sqrtT)
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- {
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- typedef typename traits<MatrixType>::Scalar Scalar;
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- Matrix<Scalar,1,2> rhs = T.template block<1,2>(i,j);
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- if (j-i > 1)
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- rhs -= sqrtT.block(i, i+1, 1, j-i-1) * sqrtT.block(i+1, j, j-i-1, 2);
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- Matrix<Scalar,2,2> A = sqrtT.coeff(i,i) * Matrix<Scalar,2,2>::Identity();
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- A += sqrtT.template block<2,2>(j,j).transpose();
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- sqrtT.template block<1,2>(i,j).transpose() = A.fullPivLu().solve(rhs.transpose());
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- }
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-
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- // similar to compute1x1offDiagonalBlock()
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- template <typename MatrixType, typename ResultType>
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- void matrix_sqrt_quasi_triangular_2x1_off_diagonal_block(const MatrixType& T, Index i, Index j, ResultType& sqrtT)
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- {
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- typedef typename traits<MatrixType>::Scalar Scalar;
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- Matrix<Scalar,2,1> rhs = T.template block<2,1>(i,j);
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- if (j-i > 2)
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- rhs -= sqrtT.block(i, i+2, 2, j-i-2) * sqrtT.block(i+2, j, j-i-2, 1);
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- Matrix<Scalar,2,2> A = sqrtT.coeff(j,j) * Matrix<Scalar,2,2>::Identity();
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- A += sqrtT.template block<2,2>(i,i);
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- sqrtT.template block<2,1>(i,j) = A.fullPivLu().solve(rhs);
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- }
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-
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- // solves the equation A X + X B = C where all matrices are 2-by-2
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- template <typename MatrixType>
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- void matrix_sqrt_quasi_triangular_solve_auxiliary_equation(MatrixType& X, const MatrixType& A, const MatrixType& B, const MatrixType& C)
71
- {
72
- typedef typename traits<MatrixType>::Scalar Scalar;
73
- Matrix<Scalar,4,4> coeffMatrix = Matrix<Scalar,4,4>::Zero();
74
- coeffMatrix.coeffRef(0,0) = A.coeff(0,0) + B.coeff(0,0);
75
- coeffMatrix.coeffRef(1,1) = A.coeff(0,0) + B.coeff(1,1);
76
- coeffMatrix.coeffRef(2,2) = A.coeff(1,1) + B.coeff(0,0);
77
- coeffMatrix.coeffRef(3,3) = A.coeff(1,1) + B.coeff(1,1);
78
- coeffMatrix.coeffRef(0,1) = B.coeff(1,0);
79
- coeffMatrix.coeffRef(0,2) = A.coeff(0,1);
80
- coeffMatrix.coeffRef(1,0) = B.coeff(0,1);
81
- coeffMatrix.coeffRef(1,3) = A.coeff(0,1);
82
- coeffMatrix.coeffRef(2,0) = A.coeff(1,0);
83
- coeffMatrix.coeffRef(2,3) = B.coeff(1,0);
84
- coeffMatrix.coeffRef(3,1) = A.coeff(1,0);
85
- coeffMatrix.coeffRef(3,2) = B.coeff(0,1);
86
-
87
- Matrix<Scalar,4,1> rhs;
88
- rhs.coeffRef(0) = C.coeff(0,0);
89
- rhs.coeffRef(1) = C.coeff(0,1);
90
- rhs.coeffRef(2) = C.coeff(1,0);
91
- rhs.coeffRef(3) = C.coeff(1,1);
92
-
93
- Matrix<Scalar,4,1> result;
94
- result = coeffMatrix.fullPivLu().solve(rhs);
95
-
96
- X.coeffRef(0,0) = result.coeff(0);
97
- X.coeffRef(0,1) = result.coeff(1);
98
- X.coeffRef(1,0) = result.coeff(2);
99
- X.coeffRef(1,1) = result.coeff(3);
100
- }
101
-
102
- // similar to compute1x1offDiagonalBlock()
103
- template <typename MatrixType, typename ResultType>
104
- void matrix_sqrt_quasi_triangular_2x2_off_diagonal_block(const MatrixType& T, Index i, Index j, ResultType& sqrtT)
105
- {
106
- typedef typename traits<MatrixType>::Scalar Scalar;
107
- Matrix<Scalar,2,2> A = sqrtT.template block<2,2>(i,i);
108
- Matrix<Scalar,2,2> B = sqrtT.template block<2,2>(j,j);
109
- Matrix<Scalar,2,2> C = T.template block<2,2>(i,j);
110
- if (j-i > 2)
111
- C -= sqrtT.block(i, i+2, 2, j-i-2) * sqrtT.block(i+2, j, j-i-2, 2);
112
- Matrix<Scalar,2,2> X;
113
- matrix_sqrt_quasi_triangular_solve_auxiliary_equation(X, A, B, C);
114
- sqrtT.template block<2,2>(i,j) = X;
115
- }
116
-
117
- // pre: T is quasi-upper-triangular and sqrtT is a zero matrix of the same size
118
- // post: the diagonal blocks of sqrtT are the square roots of the diagonal blocks of T
119
- template <typename MatrixType, typename ResultType>
120
- void matrix_sqrt_quasi_triangular_diagonal(const MatrixType& T, ResultType& sqrtT)
121
- {
122
- using std::sqrt;
123
- const Index size = T.rows();
124
- for (Index i = 0; i < size; i++) {
125
- if (i == size - 1 || T.coeff(i+1, i) == 0) {
126
- eigen_assert(T(i,i) >= 0);
127
- sqrtT.coeffRef(i,i) = sqrt(T.coeff(i,i));
128
- }
129
- else {
130
- matrix_sqrt_quasi_triangular_2x2_diagonal_block(T, i, sqrtT);
131
- ++i;
132
- }
133
- }
134
- }
135
-
136
- // pre: T is quasi-upper-triangular and diagonal blocks of sqrtT are square root of diagonal blocks of T.
137
- // post: sqrtT is the square root of T.
138
- template <typename MatrixType, typename ResultType>
139
- void matrix_sqrt_quasi_triangular_off_diagonal(const MatrixType& T, ResultType& sqrtT)
140
- {
141
- const Index size = T.rows();
142
- for (Index j = 1; j < size; j++) {
143
- if (T.coeff(j, j-1) != 0) // if T(j-1:j, j-1:j) is a 2-by-2 block
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- continue;
145
- for (Index i = j-1; i >= 0; i--) {
146
- if (i > 0 && T.coeff(i, i-1) != 0) // if T(i-1:i, i-1:i) is a 2-by-2 block
147
- continue;
148
- bool iBlockIs2x2 = (i < size - 1) && (T.coeff(i+1, i) != 0);
149
- bool jBlockIs2x2 = (j < size - 1) && (T.coeff(j+1, j) != 0);
150
- if (iBlockIs2x2 && jBlockIs2x2)
151
- matrix_sqrt_quasi_triangular_2x2_off_diagonal_block(T, i, j, sqrtT);
152
- else if (iBlockIs2x2 && !jBlockIs2x2)
153
- matrix_sqrt_quasi_triangular_2x1_off_diagonal_block(T, i, j, sqrtT);
154
- else if (!iBlockIs2x2 && jBlockIs2x2)
155
- matrix_sqrt_quasi_triangular_1x2_off_diagonal_block(T, i, j, sqrtT);
156
- else if (!iBlockIs2x2 && !jBlockIs2x2)
157
- matrix_sqrt_quasi_triangular_1x1_off_diagonal_block(T, i, j, sqrtT);
158
- }
159
- }
160
- }
161
-
162
- } // end of namespace internal
163
-
164
- /** \ingroup MatrixFunctions_Module
165
- * \brief Compute matrix square root of quasi-triangular matrix.
166
- *
167
- * \tparam MatrixType type of \p arg, the argument of matrix square root,
168
- * expected to be an instantiation of the Matrix class template.
169
- * \tparam ResultType type of \p result, where result is to be stored.
170
- * \param[in] arg argument of matrix square root.
171
- * \param[out] result matrix square root of upper Hessenberg part of \p arg.
172
- *
173
- * This function computes the square root of the upper quasi-triangular matrix stored in the upper
174
- * Hessenberg part of \p arg. Only the upper Hessenberg part of \p result is updated, the rest is
175
- * not touched. See MatrixBase::sqrt() for details on how this computation is implemented.
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- *
177
- * \sa MatrixSquareRoot, MatrixSquareRootQuasiTriangular
178
- */
179
- template <typename MatrixType, typename ResultType>
180
- void matrix_sqrt_quasi_triangular(const MatrixType &arg, ResultType &result)
181
- {
182
- eigen_assert(arg.rows() == arg.cols());
183
- result.resize(arg.rows(), arg.cols());
184
- internal::matrix_sqrt_quasi_triangular_diagonal(arg, result);
185
- internal::matrix_sqrt_quasi_triangular_off_diagonal(arg, result);
186
- }
187
-
188
-
189
- /** \ingroup MatrixFunctions_Module
190
- * \brief Compute matrix square root of triangular matrix.
191
- *
192
- * \tparam MatrixType type of \p arg, the argument of matrix square root,
193
- * expected to be an instantiation of the Matrix class template.
194
- * \tparam ResultType type of \p result, where result is to be stored.
195
- * \param[in] arg argument of matrix square root.
196
- * \param[out] result matrix square root of upper triangular part of \p arg.
197
- *
198
- * Only the upper triangular part (including the diagonal) of \p result is updated, the rest is not
199
- * touched. See MatrixBase::sqrt() for details on how this computation is implemented.
200
- *
201
- * \sa MatrixSquareRoot, MatrixSquareRootQuasiTriangular
202
- */
203
- template <typename MatrixType, typename ResultType>
204
- void matrix_sqrt_triangular(const MatrixType &arg, ResultType &result)
205
- {
206
- using std::sqrt;
207
- typedef typename MatrixType::Scalar Scalar;
208
-
209
- eigen_assert(arg.rows() == arg.cols());
210
-
211
- // Compute square root of arg and store it in upper triangular part of result
212
- // This uses that the square root of triangular matrices can be computed directly.
213
- result.resize(arg.rows(), arg.cols());
214
- for (Index i = 0; i < arg.rows(); i++) {
215
- result.coeffRef(i,i) = sqrt(arg.coeff(i,i));
216
- }
217
- for (Index j = 1; j < arg.cols(); j++) {
218
- for (Index i = j-1; i >= 0; i--) {
219
- // if i = j-1, then segment has length 0 so tmp = 0
220
- Scalar tmp = (result.row(i).segment(i+1,j-i-1) * result.col(j).segment(i+1,j-i-1)).value();
221
- // denominator may be zero if original matrix is singular
222
- result.coeffRef(i,j) = (arg.coeff(i,j) - tmp) / (result.coeff(i,i) + result.coeff(j,j));
223
- }
224
- }
225
- }
226
-
227
-
228
- namespace internal {
229
-
230
- /** \ingroup MatrixFunctions_Module
231
- * \brief Helper struct for computing matrix square roots of general matrices.
232
- * \tparam MatrixType type of the argument of the matrix square root,
233
- * expected to be an instantiation of the Matrix class template.
234
- *
235
- * \sa MatrixSquareRootTriangular, MatrixSquareRootQuasiTriangular, MatrixBase::sqrt()
236
- */
237
- template <typename MatrixType, int IsComplex = NumTraits<typename internal::traits<MatrixType>::Scalar>::IsComplex>
238
- struct matrix_sqrt_compute
239
- {
240
- /** \brief Compute the matrix square root
241
- *
242
- * \param[in] arg matrix whose square root is to be computed.
243
- * \param[out] result square root of \p arg.
244
- *
245
- * See MatrixBase::sqrt() for details on how this computation is implemented.
246
- */
247
- template <typename ResultType> static void run(const MatrixType &arg, ResultType &result);
248
- };
249
-
250
-
251
- // ********** Partial specialization for real matrices **********
252
-
253
- template <typename MatrixType>
254
- struct matrix_sqrt_compute<MatrixType, 0>
255
- {
256
- typedef typename MatrixType::PlainObject PlainType;
257
- template <typename ResultType>
258
- static void run(const MatrixType &arg, ResultType &result)
259
- {
260
- eigen_assert(arg.rows() == arg.cols());
261
-
262
- // Compute Schur decomposition of arg
263
- const RealSchur<PlainType> schurOfA(arg);
264
- const PlainType& T = schurOfA.matrixT();
265
- const PlainType& U = schurOfA.matrixU();
266
-
267
- // Compute square root of T
268
- PlainType sqrtT = PlainType::Zero(arg.rows(), arg.cols());
269
- matrix_sqrt_quasi_triangular(T, sqrtT);
270
-
271
- // Compute square root of arg
272
- result = U * sqrtT * U.adjoint();
273
- }
274
- };
275
-
276
-
277
- // ********** Partial specialization for complex matrices **********
278
-
279
- template <typename MatrixType>
280
- struct matrix_sqrt_compute<MatrixType, 1>
281
- {
282
- typedef typename MatrixType::PlainObject PlainType;
283
- template <typename ResultType>
284
- static void run(const MatrixType &arg, ResultType &result)
285
- {
286
- eigen_assert(arg.rows() == arg.cols());
287
-
288
- // Compute Schur decomposition of arg
289
- const ComplexSchur<PlainType> schurOfA(arg);
290
- const PlainType& T = schurOfA.matrixT();
291
- const PlainType& U = schurOfA.matrixU();
292
-
293
- // Compute square root of T
294
- PlainType sqrtT;
295
- matrix_sqrt_triangular(T, sqrtT);
296
-
297
- // Compute square root of arg
298
- result = U * (sqrtT.template triangularView<Upper>() * U.adjoint());
299
- }
300
- };
301
-
302
- } // end namespace internal
303
-
304
- /** \ingroup MatrixFunctions_Module
305
- *
306
- * \brief Proxy for the matrix square root of some matrix (expression).
307
- *
308
- * \tparam Derived Type of the argument to the matrix square root.
309
- *
310
- * This class holds the argument to the matrix square root until it
311
- * is assigned or evaluated for some other reason (so the argument
312
- * should not be changed in the meantime). It is the return type of
313
- * MatrixBase::sqrt() and most of the time this is the only way it is
314
- * used.
315
- */
316
- template<typename Derived> class MatrixSquareRootReturnValue
317
- : public ReturnByValue<MatrixSquareRootReturnValue<Derived> >
318
- {
319
- protected:
320
- typedef typename internal::ref_selector<Derived>::type DerivedNested;
321
-
322
- public:
323
- /** \brief Constructor.
324
- *
325
- * \param[in] src %Matrix (expression) forming the argument of the
326
- * matrix square root.
327
- */
328
- explicit MatrixSquareRootReturnValue(const Derived& src) : m_src(src) { }
329
-
330
- /** \brief Compute the matrix square root.
331
- *
332
- * \param[out] result the matrix square root of \p src in the
333
- * constructor.
334
- */
335
- template <typename ResultType>
336
- inline void evalTo(ResultType& result) const
337
- {
338
- typedef typename internal::nested_eval<Derived, 10>::type DerivedEvalType;
339
- typedef typename internal::remove_all<DerivedEvalType>::type DerivedEvalTypeClean;
340
- DerivedEvalType tmp(m_src);
341
- internal::matrix_sqrt_compute<DerivedEvalTypeClean>::run(tmp, result);
342
- }
343
-
344
- Index rows() const { return m_src.rows(); }
345
- Index cols() const { return m_src.cols(); }
346
-
347
- protected:
348
- const DerivedNested m_src;
349
- };
350
-
351
- namespace internal {
352
- template<typename Derived>
353
- struct traits<MatrixSquareRootReturnValue<Derived> >
354
- {
355
- typedef typename Derived::PlainObject ReturnType;
356
- };
357
- }
358
-
359
- template <typename Derived>
360
- const MatrixSquareRootReturnValue<Derived> MatrixBase<Derived>::sqrt() const
361
- {
362
- eigen_assert(rows() == cols());
363
- return MatrixSquareRootReturnValue<Derived>(derived());
364
- }
365
-
366
- } // end namespace Eigen
367
-
368
- #endif // EIGEN_MATRIX_FUNCTION
@@ -1,117 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2010, 2013 Jitse Niesen <jitse@maths.leeds.ac.uk>
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_STEM_FUNCTION
11
- #define EIGEN_STEM_FUNCTION
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
- /** \brief The exponential function (and its derivatives). */
18
- template <typename Scalar>
19
- Scalar stem_function_exp(Scalar x, int)
20
- {
21
- using std::exp;
22
- return exp(x);
23
- }
24
-
25
- /** \brief Cosine (and its derivatives). */
26
- template <typename Scalar>
27
- Scalar stem_function_cos(Scalar x, int n)
28
- {
29
- using std::cos;
30
- using std::sin;
31
- Scalar res;
32
-
33
- switch (n % 4) {
34
- case 0:
35
- res = std::cos(x);
36
- break;
37
- case 1:
38
- res = -std::sin(x);
39
- break;
40
- case 2:
41
- res = -std::cos(x);
42
- break;
43
- case 3:
44
- res = std::sin(x);
45
- break;
46
- }
47
- return res;
48
- }
49
-
50
- /** \brief Sine (and its derivatives). */
51
- template <typename Scalar>
52
- Scalar stem_function_sin(Scalar x, int n)
53
- {
54
- using std::cos;
55
- using std::sin;
56
- Scalar res;
57
-
58
- switch (n % 4) {
59
- case 0:
60
- res = std::sin(x);
61
- break;
62
- case 1:
63
- res = std::cos(x);
64
- break;
65
- case 2:
66
- res = -std::sin(x);
67
- break;
68
- case 3:
69
- res = -std::cos(x);
70
- break;
71
- }
72
- return res;
73
- }
74
-
75
- /** \brief Hyperbolic cosine (and its derivatives). */
76
- template <typename Scalar>
77
- Scalar stem_function_cosh(Scalar x, int n)
78
- {
79
- using std::cosh;
80
- using std::sinh;
81
- Scalar res;
82
-
83
- switch (n % 2) {
84
- case 0:
85
- res = std::cosh(x);
86
- break;
87
- case 1:
88
- res = std::sinh(x);
89
- break;
90
- }
91
- return res;
92
- }
93
-
94
- /** \brief Hyperbolic sine (and its derivatives). */
95
- template <typename Scalar>
96
- Scalar stem_function_sinh(Scalar x, int n)
97
- {
98
- using std::cosh;
99
- using std::sinh;
100
- Scalar res;
101
-
102
- switch (n % 2) {
103
- case 0:
104
- res = std::sinh(x);
105
- break;
106
- case 1:
107
- res = std::cosh(x);
108
- break;
109
- }
110
- return res;
111
- }
112
-
113
- } // end namespace internal
114
-
115
- } // end namespace Eigen
116
-
117
- #endif // EIGEN_STEM_FUNCTION
@@ -1,95 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2009 Rohit Garg <rpg.314@gmail.com>
5
- // Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
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_MOREVECTORIZATION_MATHFUNCTIONS_H
12
- #define EIGEN_MOREVECTORIZATION_MATHFUNCTIONS_H
13
-
14
- namespace Eigen {
15
-
16
- namespace internal {
17
-
18
- /** \internal \returns the arcsin of \a a (coeff-wise) */
19
- template<typename Packet> inline static Packet pasin(Packet a) { return std::asin(a); }
20
-
21
- #ifdef EIGEN_VECTORIZE_SSE
22
-
23
- template<> EIGEN_DONT_INLINE Packet4f pasin(Packet4f x)
24
- {
25
- _EIGEN_DECLARE_CONST_Packet4f(half, 0.5);
26
- _EIGEN_DECLARE_CONST_Packet4f(minus_half, -0.5);
27
- _EIGEN_DECLARE_CONST_Packet4f(3half, 1.5);
28
-
29
- _EIGEN_DECLARE_CONST_Packet4f_FROM_INT(sign_mask, 0x80000000);
30
-
31
- _EIGEN_DECLARE_CONST_Packet4f(pi, 3.141592654);
32
- _EIGEN_DECLARE_CONST_Packet4f(pi_over_2, 3.141592654*0.5);
33
-
34
- _EIGEN_DECLARE_CONST_Packet4f(asin1, 4.2163199048E-2);
35
- _EIGEN_DECLARE_CONST_Packet4f(asin2, 2.4181311049E-2);
36
- _EIGEN_DECLARE_CONST_Packet4f(asin3, 4.5470025998E-2);
37
- _EIGEN_DECLARE_CONST_Packet4f(asin4, 7.4953002686E-2);
38
- _EIGEN_DECLARE_CONST_Packet4f(asin5, 1.6666752422E-1);
39
-
40
- Packet4f a = pabs(x);//got the absolute value
41
-
42
- Packet4f sign_bit= _mm_and_ps(x, p4f_sign_mask);//extracted the sign bit
43
-
44
- Packet4f z1,z2;//will need them during computation
45
-
46
-
47
- //will compute the two branches for asin
48
- //so first compare with half
49
-
50
- Packet4f branch_mask= _mm_cmpgt_ps(a, p4f_half);//this is to select which branch to take
51
- //both will be taken, and finally results will be merged
52
- //the branch for values >0.5
53
-
54
- {
55
- //the core series expansion
56
- z1=pmadd(p4f_minus_half,a,p4f_half);
57
- Packet4f x1=psqrt(z1);
58
- Packet4f s1=pmadd(p4f_asin1, z1, p4f_asin2);
59
- Packet4f s2=pmadd(s1, z1, p4f_asin3);
60
- Packet4f s3=pmadd(s2,z1, p4f_asin4);
61
- Packet4f s4=pmadd(s3,z1, p4f_asin5);
62
- Packet4f temp=pmul(s4,z1);//not really a madd but a mul by z so that the next term can be a madd
63
- z1=pmadd(temp,x1,x1);
64
- z1=padd(z1,z1);
65
- z1=psub(p4f_pi_over_2,z1);
66
- }
67
-
68
- {
69
- //the core series expansion
70
- Packet4f x2=a;
71
- z2=pmul(x2,x2);
72
- Packet4f s1=pmadd(p4f_asin1, z2, p4f_asin2);
73
- Packet4f s2=pmadd(s1, z2, p4f_asin3);
74
- Packet4f s3=pmadd(s2,z2, p4f_asin4);
75
- Packet4f s4=pmadd(s3,z2, p4f_asin5);
76
- Packet4f temp=pmul(s4,z2);//not really a madd but a mul by z so that the next term can be a madd
77
- z2=pmadd(temp,x2,x2);
78
- }
79
-
80
- /* select the correct result from the two branch evaluations */
81
- z1 = _mm_and_ps(branch_mask, z1);
82
- z2 = _mm_andnot_ps(branch_mask, z2);
83
- Packet4f z = _mm_or_ps(z1,z2);
84
-
85
- /* update the sign */
86
- return _mm_xor_ps(z, sign_bit);
87
- }
88
-
89
- #endif // EIGEN_VECTORIZE_SSE
90
-
91
- } // end namespace internal
92
-
93
- } // end namespace Eigen
94
-
95
- #endif // EIGEN_MOREVECTORIZATION_MATHFUNCTIONS_H