sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.19__cp39-cp39-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 +156 -156
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp39-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.cp39-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 +156 -156
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp39-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
@@ -1,622 +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) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 2010,2012 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_EIGENSOLVER_H
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- #define EIGEN_EIGENSOLVER_H
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-
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- #include "./RealSchur.h"
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-
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- namespace Eigen {
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-
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- /** \eigenvalues_module \ingroup Eigenvalues_Module
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- *
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- *
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- * \class EigenSolver
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- *
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- * \brief Computes eigenvalues and eigenvectors of general matrices
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- *
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- * \tparam _MatrixType the type of the matrix of which we are computing the
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- * eigendecomposition; this is expected to be an instantiation of the Matrix
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- * class template. Currently, only real matrices are supported.
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- *
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- * The eigenvalues and eigenvectors of a matrix \f$ A \f$ are scalars
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- * \f$ \lambda \f$ and vectors \f$ v \f$ such that \f$ Av = \lambda v \f$. If
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- * \f$ D \f$ is a diagonal matrix with the eigenvalues on the diagonal, and
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- * \f$ V \f$ is a matrix with the eigenvectors as its columns, then \f$ A V =
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- * V D \f$. The matrix \f$ V \f$ is almost always invertible, in which case we
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- * have \f$ A = V D V^{-1} \f$. This is called the eigendecomposition.
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- *
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- * The eigenvalues and eigenvectors of a matrix may be complex, even when the
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- * matrix is real. However, we can choose real matrices \f$ V \f$ and \f$ D
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- * \f$ satisfying \f$ A V = V D \f$, just like the eigendecomposition, if the
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- * matrix \f$ D \f$ is not required to be diagonal, but if it is allowed to
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- * have blocks of the form
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- * \f[ \begin{bmatrix} u & v \\ -v & u \end{bmatrix} \f]
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- * (where \f$ u \f$ and \f$ v \f$ are real numbers) on the diagonal. These
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- * blocks correspond to complex eigenvalue pairs \f$ u \pm iv \f$. We call
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- * this variant of the eigendecomposition the pseudo-eigendecomposition.
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- *
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- * Call the function compute() to compute the eigenvalues and eigenvectors of
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- * a given matrix. Alternatively, you can use the
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- * EigenSolver(const MatrixType&, bool) constructor which computes the
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- * eigenvalues and eigenvectors at construction time. Once the eigenvalue and
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- * eigenvectors are computed, they can be retrieved with the eigenvalues() and
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- * eigenvectors() functions. The pseudoEigenvalueMatrix() and
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- * pseudoEigenvectors() methods allow the construction of the
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- * pseudo-eigendecomposition.
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- *
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- * The documentation for EigenSolver(const MatrixType&, bool) contains an
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- * example of the typical use of this class.
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- *
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- * \note The implementation is adapted from
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- * <a href="http://math.nist.gov/javanumerics/jama/">JAMA</a> (public domain).
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- * Their code is based on EISPACK.
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- *
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- * \sa MatrixBase::eigenvalues(), class ComplexEigenSolver, class SelfAdjointEigenSolver
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- */
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- template<typename _MatrixType> class EigenSolver
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- {
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- public:
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-
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- /** \brief Synonym for the template parameter \p _MatrixType. */
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- typedef _MatrixType MatrixType;
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-
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- enum {
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- RowsAtCompileTime = MatrixType::RowsAtCompileTime,
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- ColsAtCompileTime = MatrixType::ColsAtCompileTime,
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- Options = MatrixType::Options,
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- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
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- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
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- };
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-
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- /** \brief Scalar type for matrices of type #MatrixType. */
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- typedef typename MatrixType::Scalar Scalar;
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- typedef typename NumTraits<Scalar>::Real RealScalar;
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- typedef Eigen::Index Index; ///< \deprecated since Eigen 3.3
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-
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- /** \brief Complex scalar type for #MatrixType.
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- *
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- * This is \c std::complex<Scalar> if #Scalar is real (e.g.,
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- * \c float or \c double) and just \c Scalar if #Scalar is
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- * complex.
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- */
90
- typedef std::complex<RealScalar> ComplexScalar;
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-
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- /** \brief Type for vector of eigenvalues as returned by eigenvalues().
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- *
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- * This is a column vector with entries of type #ComplexScalar.
95
- * The length of the vector is the size of #MatrixType.
96
- */
97
- typedef Matrix<ComplexScalar, ColsAtCompileTime, 1, Options & ~RowMajor, MaxColsAtCompileTime, 1> EigenvalueType;
98
-
99
- /** \brief Type for matrix of eigenvectors as returned by eigenvectors().
100
- *
101
- * This is a square matrix with entries of type #ComplexScalar.
102
- * The size is the same as the size of #MatrixType.
103
- */
104
- typedef Matrix<ComplexScalar, RowsAtCompileTime, ColsAtCompileTime, Options, MaxRowsAtCompileTime, MaxColsAtCompileTime> EigenvectorsType;
105
-
106
- /** \brief Default constructor.
107
- *
108
- * The default constructor is useful in cases in which the user intends to
109
- * perform decompositions via EigenSolver::compute(const MatrixType&, bool).
110
- *
111
- * \sa compute() for an example.
112
- */
113
- EigenSolver() : m_eivec(), m_eivalues(), m_isInitialized(false), m_eigenvectorsOk(false), m_realSchur(), m_matT(), m_tmp() {}
114
-
115
- /** \brief Default constructor with memory preallocation
116
- *
117
- * Like the default constructor but with preallocation of the internal data
118
- * according to the specified problem \a size.
119
- * \sa EigenSolver()
120
- */
121
- explicit EigenSolver(Index size)
122
- : m_eivec(size, size),
123
- m_eivalues(size),
124
- m_isInitialized(false),
125
- m_eigenvectorsOk(false),
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- m_realSchur(size),
127
- m_matT(size, size),
128
- m_tmp(size)
129
- {}
130
-
131
- /** \brief Constructor; computes eigendecomposition of given matrix.
132
- *
133
- * \param[in] matrix Square matrix whose eigendecomposition is to be computed.
134
- * \param[in] computeEigenvectors If true, both the eigenvectors and the
135
- * eigenvalues are computed; if false, only the eigenvalues are
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- * computed.
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- *
138
- * This constructor calls compute() to compute the eigenvalues
139
- * and eigenvectors.
140
- *
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- * Example: \include EigenSolver_EigenSolver_MatrixType.cpp
142
- * Output: \verbinclude EigenSolver_EigenSolver_MatrixType.out
143
- *
144
- * \sa compute()
145
- */
146
- template<typename InputType>
147
- explicit EigenSolver(const EigenBase<InputType>& matrix, bool computeEigenvectors = true)
148
- : m_eivec(matrix.rows(), matrix.cols()),
149
- m_eivalues(matrix.cols()),
150
- m_isInitialized(false),
151
- m_eigenvectorsOk(false),
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- m_realSchur(matrix.cols()),
153
- m_matT(matrix.rows(), matrix.cols()),
154
- m_tmp(matrix.cols())
155
- {
156
- compute(matrix.derived(), computeEigenvectors);
157
- }
158
-
159
- /** \brief Returns the eigenvectors of given matrix.
160
- *
161
- * \returns %Matrix whose columns are the (possibly complex) eigenvectors.
162
- *
163
- * \pre Either the constructor
164
- * EigenSolver(const MatrixType&,bool) or the member function
165
- * compute(const MatrixType&, bool) has been called before, and
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- * \p computeEigenvectors was set to true (the default).
167
- *
168
- * Column \f$ k \f$ of the returned matrix is an eigenvector corresponding
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- * to eigenvalue number \f$ k \f$ as returned by eigenvalues(). The
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- * eigenvectors are normalized to have (Euclidean) norm equal to one. The
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- * matrix returned by this function is the matrix \f$ V \f$ in the
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- * eigendecomposition \f$ A = V D V^{-1} \f$, if it exists.
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- *
174
- * Example: \include EigenSolver_eigenvectors.cpp
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- * Output: \verbinclude EigenSolver_eigenvectors.out
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- *
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- * \sa eigenvalues(), pseudoEigenvectors()
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- */
179
- EigenvectorsType eigenvectors() const;
180
-
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- /** \brief Returns the pseudo-eigenvectors of given matrix.
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- *
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- * \returns Const reference to matrix whose columns are the pseudo-eigenvectors.
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- *
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- * \pre Either the constructor
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- * EigenSolver(const MatrixType&,bool) or the member function
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- * compute(const MatrixType&, bool) has been called before, and
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- * \p computeEigenvectors was set to true (the default).
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- *
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- * The real matrix \f$ V \f$ returned by this function and the
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- * block-diagonal matrix \f$ D \f$ returned by pseudoEigenvalueMatrix()
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- * satisfy \f$ AV = VD \f$.
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- *
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- * Example: \include EigenSolver_pseudoEigenvectors.cpp
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- * Output: \verbinclude EigenSolver_pseudoEigenvectors.out
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- *
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- * \sa pseudoEigenvalueMatrix(), eigenvectors()
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- */
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- const MatrixType& pseudoEigenvectors() const
200
- {
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- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
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- eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
203
- return m_eivec;
204
- }
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-
206
- /** \brief Returns the block-diagonal matrix in the pseudo-eigendecomposition.
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- *
208
- * \returns A block-diagonal matrix.
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- *
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- * \pre Either the constructor
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- * EigenSolver(const MatrixType&,bool) or the member function
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- * compute(const MatrixType&, bool) has been called before.
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- *
214
- * The matrix \f$ D \f$ returned by this function is real and
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- * block-diagonal. The blocks on the diagonal are either 1-by-1 or 2-by-2
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- * blocks of the form
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- * \f$ \begin{bmatrix} u & v \\ -v & u \end{bmatrix} \f$.
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- * These blocks are not sorted in any particular order.
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- * The matrix \f$ D \f$ and the matrix \f$ V \f$ returned by
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- * pseudoEigenvectors() satisfy \f$ AV = VD \f$.
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- *
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- * \sa pseudoEigenvectors() for an example, eigenvalues()
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- */
224
- MatrixType pseudoEigenvalueMatrix() const;
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-
226
- /** \brief Returns the eigenvalues of given matrix.
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- *
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- * \returns A const reference to the column vector containing the eigenvalues.
229
- *
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- * \pre Either the constructor
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- * EigenSolver(const MatrixType&,bool) or the member function
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- * compute(const MatrixType&, bool) has been called before.
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- *
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- * The eigenvalues are repeated according to their algebraic multiplicity,
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- * so there are as many eigenvalues as rows in the matrix. The eigenvalues
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- * are not sorted in any particular order.
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- *
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- * Example: \include EigenSolver_eigenvalues.cpp
239
- * Output: \verbinclude EigenSolver_eigenvalues.out
240
- *
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- * \sa eigenvectors(), pseudoEigenvalueMatrix(),
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- * MatrixBase::eigenvalues()
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- */
244
- const EigenvalueType& eigenvalues() const
245
- {
246
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
247
- return m_eivalues;
248
- }
249
-
250
- /** \brief Computes eigendecomposition of given matrix.
251
- *
252
- * \param[in] matrix Square matrix whose eigendecomposition is to be computed.
253
- * \param[in] computeEigenvectors If true, both the eigenvectors and the
254
- * eigenvalues are computed; if false, only the eigenvalues are
255
- * computed.
256
- * \returns Reference to \c *this
257
- *
258
- * This function computes the eigenvalues of the real matrix \p matrix.
259
- * The eigenvalues() function can be used to retrieve them. If
260
- * \p computeEigenvectors is true, then the eigenvectors are also computed
261
- * and can be retrieved by calling eigenvectors().
262
- *
263
- * The matrix is first reduced to real Schur form using the RealSchur
264
- * class. The Schur decomposition is then used to compute the eigenvalues
265
- * and eigenvectors.
266
- *
267
- * The cost of the computation is dominated by the cost of the
268
- * Schur decomposition, which is very approximately \f$ 25n^3 \f$
269
- * (where \f$ n \f$ is the size of the matrix) if \p computeEigenvectors
270
- * is true, and \f$ 10n^3 \f$ if \p computeEigenvectors is false.
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- *
272
- * This method reuses of the allocated data in the EigenSolver object.
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- *
274
- * Example: \include EigenSolver_compute.cpp
275
- * Output: \verbinclude EigenSolver_compute.out
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- */
277
- template<typename InputType>
278
- EigenSolver& compute(const EigenBase<InputType>& matrix, bool computeEigenvectors = true);
279
-
280
- /** \returns NumericalIssue if the input contains INF or NaN values or overflow occurred. Returns Success otherwise. */
281
- ComputationInfo info() const
282
- {
283
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
284
- return m_info;
285
- }
286
-
287
- /** \brief Sets the maximum number of iterations allowed. */
288
- EigenSolver& setMaxIterations(Index maxIters)
289
- {
290
- m_realSchur.setMaxIterations(maxIters);
291
- return *this;
292
- }
293
-
294
- /** \brief Returns the maximum number of iterations. */
295
- Index getMaxIterations()
296
- {
297
- return m_realSchur.getMaxIterations();
298
- }
299
-
300
- private:
301
- void doComputeEigenvectors();
302
-
303
- protected:
304
-
305
- static void check_template_parameters()
306
- {
307
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
308
- EIGEN_STATIC_ASSERT(!NumTraits<Scalar>::IsComplex, NUMERIC_TYPE_MUST_BE_REAL);
309
- }
310
-
311
- MatrixType m_eivec;
312
- EigenvalueType m_eivalues;
313
- bool m_isInitialized;
314
- bool m_eigenvectorsOk;
315
- ComputationInfo m_info;
316
- RealSchur<MatrixType> m_realSchur;
317
- MatrixType m_matT;
318
-
319
- typedef Matrix<Scalar, ColsAtCompileTime, 1, Options & ~RowMajor, MaxColsAtCompileTime, 1> ColumnVectorType;
320
- ColumnVectorType m_tmp;
321
- };
322
-
323
- template<typename MatrixType>
324
- MatrixType EigenSolver<MatrixType>::pseudoEigenvalueMatrix() const
325
- {
326
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
327
- const RealScalar precision = RealScalar(2)*NumTraits<RealScalar>::epsilon();
328
- Index n = m_eivalues.rows();
329
- MatrixType matD = MatrixType::Zero(n,n);
330
- for (Index i=0; i<n; ++i)
331
- {
332
- if (internal::isMuchSmallerThan(numext::imag(m_eivalues.coeff(i)), numext::real(m_eivalues.coeff(i)), precision))
333
- matD.coeffRef(i,i) = numext::real(m_eivalues.coeff(i));
334
- else
335
- {
336
- matD.template block<2,2>(i,i) << numext::real(m_eivalues.coeff(i)), numext::imag(m_eivalues.coeff(i)),
337
- -numext::imag(m_eivalues.coeff(i)), numext::real(m_eivalues.coeff(i));
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- ++i;
339
- }
340
- }
341
- return matD;
342
- }
343
-
344
- template<typename MatrixType>
345
- typename EigenSolver<MatrixType>::EigenvectorsType EigenSolver<MatrixType>::eigenvectors() const
346
- {
347
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
348
- eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
349
- const RealScalar precision = RealScalar(2)*NumTraits<RealScalar>::epsilon();
350
- Index n = m_eivec.cols();
351
- EigenvectorsType matV(n,n);
352
- for (Index j=0; j<n; ++j)
353
- {
354
- if (internal::isMuchSmallerThan(numext::imag(m_eivalues.coeff(j)), numext::real(m_eivalues.coeff(j)), precision) || j+1==n)
355
- {
356
- // we have a real eigen value
357
- matV.col(j) = m_eivec.col(j).template cast<ComplexScalar>();
358
- matV.col(j).normalize();
359
- }
360
- else
361
- {
362
- // we have a pair of complex eigen values
363
- for (Index i=0; i<n; ++i)
364
- {
365
- matV.coeffRef(i,j) = ComplexScalar(m_eivec.coeff(i,j), m_eivec.coeff(i,j+1));
366
- matV.coeffRef(i,j+1) = ComplexScalar(m_eivec.coeff(i,j), -m_eivec.coeff(i,j+1));
367
- }
368
- matV.col(j).normalize();
369
- matV.col(j+1).normalize();
370
- ++j;
371
- }
372
- }
373
- return matV;
374
- }
375
-
376
- template<typename MatrixType>
377
- template<typename InputType>
378
- EigenSolver<MatrixType>&
379
- EigenSolver<MatrixType>::compute(const EigenBase<InputType>& matrix, bool computeEigenvectors)
380
- {
381
- check_template_parameters();
382
-
383
- using std::sqrt;
384
- using std::abs;
385
- using numext::isfinite;
386
- eigen_assert(matrix.cols() == matrix.rows());
387
-
388
- // Reduce to real Schur form.
389
- m_realSchur.compute(matrix.derived(), computeEigenvectors);
390
-
391
- m_info = m_realSchur.info();
392
-
393
- if (m_info == Success)
394
- {
395
- m_matT = m_realSchur.matrixT();
396
- if (computeEigenvectors)
397
- m_eivec = m_realSchur.matrixU();
398
-
399
- // Compute eigenvalues from matT
400
- m_eivalues.resize(matrix.cols());
401
- Index i = 0;
402
- while (i < matrix.cols())
403
- {
404
- if (i == matrix.cols() - 1 || m_matT.coeff(i+1, i) == Scalar(0))
405
- {
406
- m_eivalues.coeffRef(i) = m_matT.coeff(i, i);
407
- if(!(isfinite)(m_eivalues.coeffRef(i)))
408
- {
409
- m_isInitialized = true;
410
- m_eigenvectorsOk = false;
411
- m_info = NumericalIssue;
412
- return *this;
413
- }
414
- ++i;
415
- }
416
- else
417
- {
418
- Scalar p = Scalar(0.5) * (m_matT.coeff(i, i) - m_matT.coeff(i+1, i+1));
419
- Scalar z;
420
- // Compute z = sqrt(abs(p * p + m_matT.coeff(i+1, i) * m_matT.coeff(i, i+1)));
421
- // without overflow
422
- {
423
- Scalar t0 = m_matT.coeff(i+1, i);
424
- Scalar t1 = m_matT.coeff(i, i+1);
425
- Scalar maxval = numext::maxi<Scalar>(abs(p),numext::maxi<Scalar>(abs(t0),abs(t1)));
426
- t0 /= maxval;
427
- t1 /= maxval;
428
- Scalar p0 = p/maxval;
429
- z = maxval * sqrt(abs(p0 * p0 + t0 * t1));
430
- }
431
-
432
- m_eivalues.coeffRef(i) = ComplexScalar(m_matT.coeff(i+1, i+1) + p, z);
433
- m_eivalues.coeffRef(i+1) = ComplexScalar(m_matT.coeff(i+1, i+1) + p, -z);
434
- if(!((isfinite)(m_eivalues.coeffRef(i)) && (isfinite)(m_eivalues.coeffRef(i+1))))
435
- {
436
- m_isInitialized = true;
437
- m_eigenvectorsOk = false;
438
- m_info = NumericalIssue;
439
- return *this;
440
- }
441
- i += 2;
442
- }
443
- }
444
-
445
- // Compute eigenvectors.
446
- if (computeEigenvectors)
447
- doComputeEigenvectors();
448
- }
449
-
450
- m_isInitialized = true;
451
- m_eigenvectorsOk = computeEigenvectors;
452
-
453
- return *this;
454
- }
455
-
456
-
457
- template<typename MatrixType>
458
- void EigenSolver<MatrixType>::doComputeEigenvectors()
459
- {
460
- using std::abs;
461
- const Index size = m_eivec.cols();
462
- const Scalar eps = NumTraits<Scalar>::epsilon();
463
-
464
- // inefficient! this is already computed in RealSchur
465
- Scalar norm(0);
466
- for (Index j = 0; j < size; ++j)
467
- {
468
- norm += m_matT.row(j).segment((std::max)(j-1,Index(0)), size-(std::max)(j-1,Index(0))).cwiseAbs().sum();
469
- }
470
-
471
- // Backsubstitute to find vectors of upper triangular form
472
- if (norm == Scalar(0))
473
- {
474
- return;
475
- }
476
-
477
- for (Index n = size-1; n >= 0; n--)
478
- {
479
- Scalar p = m_eivalues.coeff(n).real();
480
- Scalar q = m_eivalues.coeff(n).imag();
481
-
482
- // Scalar vector
483
- if (q == Scalar(0))
484
- {
485
- Scalar lastr(0), lastw(0);
486
- Index l = n;
487
-
488
- m_matT.coeffRef(n,n) = Scalar(1);
489
- for (Index i = n-1; i >= 0; i--)
490
- {
491
- Scalar w = m_matT.coeff(i,i) - p;
492
- Scalar r = m_matT.row(i).segment(l,n-l+1).dot(m_matT.col(n).segment(l, n-l+1));
493
-
494
- if (m_eivalues.coeff(i).imag() < Scalar(0))
495
- {
496
- lastw = w;
497
- lastr = r;
498
- }
499
- else
500
- {
501
- l = i;
502
- if (m_eivalues.coeff(i).imag() == Scalar(0))
503
- {
504
- if (w != Scalar(0))
505
- m_matT.coeffRef(i,n) = -r / w;
506
- else
507
- m_matT.coeffRef(i,n) = -r / (eps * norm);
508
- }
509
- else // Solve real equations
510
- {
511
- Scalar x = m_matT.coeff(i,i+1);
512
- Scalar y = m_matT.coeff(i+1,i);
513
- Scalar denom = (m_eivalues.coeff(i).real() - p) * (m_eivalues.coeff(i).real() - p) + m_eivalues.coeff(i).imag() * m_eivalues.coeff(i).imag();
514
- Scalar t = (x * lastr - lastw * r) / denom;
515
- m_matT.coeffRef(i,n) = t;
516
- if (abs(x) > abs(lastw))
517
- m_matT.coeffRef(i+1,n) = (-r - w * t) / x;
518
- else
519
- m_matT.coeffRef(i+1,n) = (-lastr - y * t) / lastw;
520
- }
521
-
522
- // Overflow control
523
- Scalar t = abs(m_matT.coeff(i,n));
524
- if ((eps * t) * t > Scalar(1))
525
- m_matT.col(n).tail(size-i) /= t;
526
- }
527
- }
528
- }
529
- else if (q < Scalar(0) && n > 0) // Complex vector
530
- {
531
- Scalar lastra(0), lastsa(0), lastw(0);
532
- Index l = n-1;
533
-
534
- // Last vector component imaginary so matrix is triangular
535
- if (abs(m_matT.coeff(n,n-1)) > abs(m_matT.coeff(n-1,n)))
536
- {
537
- m_matT.coeffRef(n-1,n-1) = q / m_matT.coeff(n,n-1);
538
- m_matT.coeffRef(n-1,n) = -(m_matT.coeff(n,n) - p) / m_matT.coeff(n,n-1);
539
- }
540
- else
541
- {
542
- ComplexScalar cc = ComplexScalar(Scalar(0),-m_matT.coeff(n-1,n)) / ComplexScalar(m_matT.coeff(n-1,n-1)-p,q);
543
- m_matT.coeffRef(n-1,n-1) = numext::real(cc);
544
- m_matT.coeffRef(n-1,n) = numext::imag(cc);
545
- }
546
- m_matT.coeffRef(n,n-1) = Scalar(0);
547
- m_matT.coeffRef(n,n) = Scalar(1);
548
- for (Index i = n-2; i >= 0; i--)
549
- {
550
- Scalar ra = m_matT.row(i).segment(l, n-l+1).dot(m_matT.col(n-1).segment(l, n-l+1));
551
- Scalar sa = m_matT.row(i).segment(l, n-l+1).dot(m_matT.col(n).segment(l, n-l+1));
552
- Scalar w = m_matT.coeff(i,i) - p;
553
-
554
- if (m_eivalues.coeff(i).imag() < Scalar(0))
555
- {
556
- lastw = w;
557
- lastra = ra;
558
- lastsa = sa;
559
- }
560
- else
561
- {
562
- l = i;
563
- if (m_eivalues.coeff(i).imag() == RealScalar(0))
564
- {
565
- ComplexScalar cc = ComplexScalar(-ra,-sa) / ComplexScalar(w,q);
566
- m_matT.coeffRef(i,n-1) = numext::real(cc);
567
- m_matT.coeffRef(i,n) = numext::imag(cc);
568
- }
569
- else
570
- {
571
- // Solve complex equations
572
- Scalar x = m_matT.coeff(i,i+1);
573
- Scalar y = m_matT.coeff(i+1,i);
574
- Scalar vr = (m_eivalues.coeff(i).real() - p) * (m_eivalues.coeff(i).real() - p) + m_eivalues.coeff(i).imag() * m_eivalues.coeff(i).imag() - q * q;
575
- Scalar vi = (m_eivalues.coeff(i).real() - p) * Scalar(2) * q;
576
- if ((vr == Scalar(0)) && (vi == Scalar(0)))
577
- vr = eps * norm * (abs(w) + abs(q) + abs(x) + abs(y) + abs(lastw));
578
-
579
- ComplexScalar cc = ComplexScalar(x*lastra-lastw*ra+q*sa,x*lastsa-lastw*sa-q*ra) / ComplexScalar(vr,vi);
580
- m_matT.coeffRef(i,n-1) = numext::real(cc);
581
- m_matT.coeffRef(i,n) = numext::imag(cc);
582
- if (abs(x) > (abs(lastw) + abs(q)))
583
- {
584
- m_matT.coeffRef(i+1,n-1) = (-ra - w * m_matT.coeff(i,n-1) + q * m_matT.coeff(i,n)) / x;
585
- m_matT.coeffRef(i+1,n) = (-sa - w * m_matT.coeff(i,n) - q * m_matT.coeff(i,n-1)) / x;
586
- }
587
- else
588
- {
589
- cc = ComplexScalar(-lastra-y*m_matT.coeff(i,n-1),-lastsa-y*m_matT.coeff(i,n)) / ComplexScalar(lastw,q);
590
- m_matT.coeffRef(i+1,n-1) = numext::real(cc);
591
- m_matT.coeffRef(i+1,n) = numext::imag(cc);
592
- }
593
- }
594
-
595
- // Overflow control
596
- Scalar t = numext::maxi<Scalar>(abs(m_matT.coeff(i,n-1)),abs(m_matT.coeff(i,n)));
597
- if ((eps * t) * t > Scalar(1))
598
- m_matT.block(i, n-1, size-i, 2) /= t;
599
-
600
- }
601
- }
602
-
603
- // We handled a pair of complex conjugate eigenvalues, so need to skip them both
604
- n--;
605
- }
606
- else
607
- {
608
- eigen_assert(0 && "Internal bug in EigenSolver (INF or NaN has not been detected)"); // this should not happen
609
- }
610
- }
611
-
612
- // Back transformation to get eigenvectors of original matrix
613
- for (Index j = size-1; j >= 0; j--)
614
- {
615
- m_tmp.noalias() = m_eivec.leftCols(j+1) * m_matT.col(j).segment(0, j+1);
616
- m_eivec.col(j) = m_tmp;
617
- }
618
- }
619
-
620
- } // end namespace Eigen
621
-
622
- #endif // EIGEN_EIGENSOLVER_H