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
@@ -1,462 +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) 2009 Claire Maurice
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- // Copyright (C) 2009 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_COMPLEX_SCHUR_H
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- #define EIGEN_COMPLEX_SCHUR_H
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-
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- #include "./HessenbergDecomposition.h"
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-
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- namespace Eigen {
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-
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- namespace internal {
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- template<typename MatrixType, bool IsComplex> struct complex_schur_reduce_to_hessenberg;
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- }
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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 ComplexSchur
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- *
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- * \brief Performs a complex Schur decomposition of a real or complex square matrix
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- *
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- * \tparam _MatrixType the type of the matrix of which we are
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- * computing the Schur decomposition; this is expected to be an
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- * instantiation of the Matrix class template.
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- *
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- * Given a real or complex square matrix A, this class computes the
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- * Schur decomposition: \f$ A = U T U^*\f$ where U is a unitary
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- * complex matrix, and T is a complex upper triangular matrix. The
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- * diagonal of the matrix T corresponds to the eigenvalues of the
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- * matrix A.
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- *
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- * Call the function compute() to compute the Schur decomposition of
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- * a given matrix. Alternatively, you can use the
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- * ComplexSchur(const MatrixType&, bool) constructor which computes
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- * the Schur decomposition at construction time. Once the
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- * decomposition is computed, you can use the matrixU() and matrixT()
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- * functions to retrieve the matrices U and V in the decomposition.
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- *
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- * \note This code is inspired from Jampack
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- *
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- * \sa class RealSchur, class EigenSolver, class ComplexEigenSolver
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- */
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- template<typename _MatrixType> class ComplexSchur
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- {
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- public:
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- typedef _MatrixType MatrixType;
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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 \p _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 \p _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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- */
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- typedef std::complex<RealScalar> ComplexScalar;
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-
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- /** \brief Type for the matrices in the Schur decomposition.
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- *
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- * This is a square matrix with entries of type #ComplexScalar.
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- * The size is the same as the size of \p _MatrixType.
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- */
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- typedef Matrix<ComplexScalar, RowsAtCompileTime, ColsAtCompileTime, Options, MaxRowsAtCompileTime, MaxColsAtCompileTime> ComplexMatrixType;
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-
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- /** \brief Default constructor.
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- *
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- * \param [in] size Positive integer, size of the matrix whose Schur decomposition will be computed.
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- *
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- * The default constructor is useful in cases in which the user
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- * intends to perform decompositions via compute(). The \p size
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- * parameter is only used as a hint. It is not an error to give a
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- * wrong \p size, but it may impair performance.
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- *
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- * \sa compute() for an example.
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- */
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- explicit ComplexSchur(Index size = RowsAtCompileTime==Dynamic ? 1 : RowsAtCompileTime)
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- : m_matT(size,size),
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- m_matU(size,size),
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- m_hess(size),
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- m_isInitialized(false),
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- m_matUisUptodate(false),
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- m_maxIters(-1)
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- {}
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-
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- /** \brief Constructor; computes Schur decomposition of given matrix.
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- *
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- * \param[in] matrix Square matrix whose Schur decomposition is to be computed.
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- * \param[in] computeU If true, both T and U are computed; if false, only T is computed.
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- *
108
- * This constructor calls compute() to compute the Schur decomposition.
109
- *
110
- * \sa matrixT() and matrixU() for examples.
111
- */
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- template<typename InputType>
113
- explicit ComplexSchur(const EigenBase<InputType>& matrix, bool computeU = true)
114
- : m_matT(matrix.rows(),matrix.cols()),
115
- m_matU(matrix.rows(),matrix.cols()),
116
- m_hess(matrix.rows()),
117
- m_isInitialized(false),
118
- m_matUisUptodate(false),
119
- m_maxIters(-1)
120
- {
121
- compute(matrix.derived(), computeU);
122
- }
123
-
124
- /** \brief Returns the unitary matrix in the Schur decomposition.
125
- *
126
- * \returns A const reference to the matrix U.
127
- *
128
- * It is assumed that either the constructor
129
- * ComplexSchur(const MatrixType& matrix, bool computeU) or the
130
- * member function compute(const MatrixType& matrix, bool computeU)
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- * has been called before to compute the Schur decomposition of a
132
- * matrix, and that \p computeU was set to true (the default
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- * value).
134
- *
135
- * Example: \include ComplexSchur_matrixU.cpp
136
- * Output: \verbinclude ComplexSchur_matrixU.out
137
- */
138
- const ComplexMatrixType& matrixU() const
139
- {
140
- eigen_assert(m_isInitialized && "ComplexSchur is not initialized.");
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- eigen_assert(m_matUisUptodate && "The matrix U has not been computed during the ComplexSchur decomposition.");
142
- return m_matU;
143
- }
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-
145
- /** \brief Returns the triangular matrix in the Schur decomposition.
146
- *
147
- * \returns A const reference to the matrix T.
148
- *
149
- * It is assumed that either the constructor
150
- * ComplexSchur(const MatrixType& matrix, bool computeU) or the
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- * member function compute(const MatrixType& matrix, bool computeU)
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- * has been called before to compute the Schur decomposition of a
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- * matrix.
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- *
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- * Note that this function returns a plain square matrix. If you want to reference
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- * only the upper triangular part, use:
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- * \code schur.matrixT().triangularView<Upper>() \endcode
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- *
159
- * Example: \include ComplexSchur_matrixT.cpp
160
- * Output: \verbinclude ComplexSchur_matrixT.out
161
- */
162
- const ComplexMatrixType& matrixT() const
163
- {
164
- eigen_assert(m_isInitialized && "ComplexSchur is not initialized.");
165
- return m_matT;
166
- }
167
-
168
- /** \brief Computes Schur decomposition of given matrix.
169
- *
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- * \param[in] matrix Square matrix whose Schur decomposition is to be computed.
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- * \param[in] computeU If true, both T and U are computed; if false, only T is computed.
172
-
173
- * \returns Reference to \c *this
174
- *
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- * The Schur decomposition is computed by first reducing the
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- * matrix to Hessenberg form using the class
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- * HessenbergDecomposition. The Hessenberg matrix is then reduced
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- * to triangular form by performing QR iterations with a single
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- * shift. The cost of computing the Schur decomposition depends
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- * on the number of iterations; as a rough guide, it may be taken
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- * on the number of iterations; as a rough guide, it may be taken
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- * to be \f$25n^3\f$ complex flops, or \f$10n^3\f$ complex flops
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- * if \a computeU is false.
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- *
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- * Example: \include ComplexSchur_compute.cpp
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- * Output: \verbinclude ComplexSchur_compute.out
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- *
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- * \sa compute(const MatrixType&, bool, Index)
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- */
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- template<typename InputType>
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- ComplexSchur& compute(const EigenBase<InputType>& matrix, bool computeU = true);
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-
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- /** \brief Compute Schur decomposition from a given Hessenberg matrix
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- * \param[in] matrixH Matrix in Hessenberg form H
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- * \param[in] matrixQ orthogonal matrix Q that transform a matrix A to H : A = Q H Q^T
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- * \param computeU Computes the matriX U of the Schur vectors
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- * \return Reference to \c *this
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- *
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- * This routine assumes that the matrix is already reduced in Hessenberg form matrixH
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- * using either the class HessenbergDecomposition or another mean.
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- * It computes the upper quasi-triangular matrix T of the Schur decomposition of H
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- * When computeU is true, this routine computes the matrix U such that
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- * A = U T U^T = (QZ) T (QZ)^T = Q H Q^T where A is the initial matrix
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- *
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- * NOTE Q is referenced if computeU is true; so, if the initial orthogonal matrix
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- * is not available, the user should give an identity matrix (Q.setIdentity())
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- *
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- * \sa compute(const MatrixType&, bool)
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- */
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- template<typename HessMatrixType, typename OrthMatrixType>
211
- ComplexSchur& computeFromHessenberg(const HessMatrixType& matrixH, const OrthMatrixType& matrixQ, bool computeU=true);
212
-
213
- /** \brief Reports whether previous computation was successful.
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- *
215
- * \returns \c Success if computation was successful, \c NoConvergence otherwise.
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- */
217
- ComputationInfo info() const
218
- {
219
- eigen_assert(m_isInitialized && "ComplexSchur is not initialized.");
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- return m_info;
221
- }
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-
223
- /** \brief Sets the maximum number of iterations allowed.
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- *
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- * If not specified by the user, the maximum number of iterations is m_maxIterationsPerRow times the size
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- * of the matrix.
227
- */
228
- ComplexSchur& setMaxIterations(Index maxIters)
229
- {
230
- m_maxIters = maxIters;
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- return *this;
232
- }
233
-
234
- /** \brief Returns the maximum number of iterations. */
235
- Index getMaxIterations()
236
- {
237
- return m_maxIters;
238
- }
239
-
240
- /** \brief Maximum number of iterations per row.
241
- *
242
- * If not otherwise specified, the maximum number of iterations is this number times the size of the
243
- * matrix. It is currently set to 30.
244
- */
245
- static const int m_maxIterationsPerRow = 30;
246
-
247
- protected:
248
- ComplexMatrixType m_matT, m_matU;
249
- HessenbergDecomposition<MatrixType> m_hess;
250
- ComputationInfo m_info;
251
- bool m_isInitialized;
252
- bool m_matUisUptodate;
253
- Index m_maxIters;
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-
255
- private:
256
- bool subdiagonalEntryIsNeglegible(Index i);
257
- ComplexScalar computeShift(Index iu, Index iter);
258
- void reduceToTriangularForm(bool computeU);
259
- friend struct internal::complex_schur_reduce_to_hessenberg<MatrixType, NumTraits<Scalar>::IsComplex>;
260
- };
261
-
262
- /** If m_matT(i+1,i) is neglegible in floating point arithmetic
263
- * compared to m_matT(i,i) and m_matT(j,j), then set it to zero and
264
- * return true, else return false. */
265
- template<typename MatrixType>
266
- inline bool ComplexSchur<MatrixType>::subdiagonalEntryIsNeglegible(Index i)
267
- {
268
- RealScalar d = numext::norm1(m_matT.coeff(i,i)) + numext::norm1(m_matT.coeff(i+1,i+1));
269
- RealScalar sd = numext::norm1(m_matT.coeff(i+1,i));
270
- if (internal::isMuchSmallerThan(sd, d, NumTraits<RealScalar>::epsilon()))
271
- {
272
- m_matT.coeffRef(i+1,i) = ComplexScalar(0);
273
- return true;
274
- }
275
- return false;
276
- }
277
-
278
-
279
- /** Compute the shift in the current QR iteration. */
280
- template<typename MatrixType>
281
- typename ComplexSchur<MatrixType>::ComplexScalar ComplexSchur<MatrixType>::computeShift(Index iu, Index iter)
282
- {
283
- using std::abs;
284
- if (iter == 10 || iter == 20)
285
- {
286
- // exceptional shift, taken from http://www.netlib.org/eispack/comqr.f
287
- return abs(numext::real(m_matT.coeff(iu,iu-1))) + abs(numext::real(m_matT.coeff(iu-1,iu-2)));
288
- }
289
-
290
- // compute the shift as one of the eigenvalues of t, the 2x2
291
- // diagonal block on the bottom of the active submatrix
292
- Matrix<ComplexScalar,2,2> t = m_matT.template block<2,2>(iu-1,iu-1);
293
- RealScalar normt = t.cwiseAbs().sum();
294
- t /= normt; // the normalization by sf is to avoid under/overflow
295
-
296
- ComplexScalar b = t.coeff(0,1) * t.coeff(1,0);
297
- ComplexScalar c = t.coeff(0,0) - t.coeff(1,1);
298
- ComplexScalar disc = sqrt(c*c + RealScalar(4)*b);
299
- ComplexScalar det = t.coeff(0,0) * t.coeff(1,1) - b;
300
- ComplexScalar trace = t.coeff(0,0) + t.coeff(1,1);
301
- ComplexScalar eival1 = (trace + disc) / RealScalar(2);
302
- ComplexScalar eival2 = (trace - disc) / RealScalar(2);
303
- RealScalar eival1_norm = numext::norm1(eival1);
304
- RealScalar eival2_norm = numext::norm1(eival2);
305
- // A division by zero can only occur if eival1==eival2==0.
306
- // In this case, det==0, and all we have to do is checking that eival2_norm!=0
307
- if(eival1_norm > eival2_norm)
308
- eival2 = det / eival1;
309
- else if(eival2_norm!=RealScalar(0))
310
- eival1 = det / eival2;
311
-
312
- // choose the eigenvalue closest to the bottom entry of the diagonal
313
- if(numext::norm1(eival1-t.coeff(1,1)) < numext::norm1(eival2-t.coeff(1,1)))
314
- return normt * eival1;
315
- else
316
- return normt * eival2;
317
- }
318
-
319
-
320
- template<typename MatrixType>
321
- template<typename InputType>
322
- ComplexSchur<MatrixType>& ComplexSchur<MatrixType>::compute(const EigenBase<InputType>& matrix, bool computeU)
323
- {
324
- m_matUisUptodate = false;
325
- eigen_assert(matrix.cols() == matrix.rows());
326
-
327
- if(matrix.cols() == 1)
328
- {
329
- m_matT = matrix.derived().template cast<ComplexScalar>();
330
- if(computeU) m_matU = ComplexMatrixType::Identity(1,1);
331
- m_info = Success;
332
- m_isInitialized = true;
333
- m_matUisUptodate = computeU;
334
- return *this;
335
- }
336
-
337
- internal::complex_schur_reduce_to_hessenberg<MatrixType, NumTraits<Scalar>::IsComplex>::run(*this, matrix.derived(), computeU);
338
- computeFromHessenberg(m_matT, m_matU, computeU);
339
- return *this;
340
- }
341
-
342
- template<typename MatrixType>
343
- template<typename HessMatrixType, typename OrthMatrixType>
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- ComplexSchur<MatrixType>& ComplexSchur<MatrixType>::computeFromHessenberg(const HessMatrixType& matrixH, const OrthMatrixType& matrixQ, bool computeU)
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- {
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- m_matT = matrixH;
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- if(computeU)
348
- m_matU = matrixQ;
349
- reduceToTriangularForm(computeU);
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- return *this;
351
- }
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- namespace internal {
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-
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- /* Reduce given matrix to Hessenberg form */
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- template<typename MatrixType, bool IsComplex>
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- struct complex_schur_reduce_to_hessenberg
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- {
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- // this is the implementation for the case IsComplex = true
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- static void run(ComplexSchur<MatrixType>& _this, const MatrixType& matrix, bool computeU)
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- {
361
- _this.m_hess.compute(matrix);
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- _this.m_matT = _this.m_hess.matrixH();
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- if(computeU) _this.m_matU = _this.m_hess.matrixQ();
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- }
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- };
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-
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- template<typename MatrixType>
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- struct complex_schur_reduce_to_hessenberg<MatrixType, false>
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- {
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- static void run(ComplexSchur<MatrixType>& _this, const MatrixType& matrix, bool computeU)
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- {
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- typedef typename ComplexSchur<MatrixType>::ComplexScalar ComplexScalar;
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-
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- // Note: m_hess is over RealScalar; m_matT and m_matU is over ComplexScalar
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- _this.m_hess.compute(matrix);
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- _this.m_matT = _this.m_hess.matrixH().template cast<ComplexScalar>();
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- if(computeU)
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- {
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- // This may cause an allocation which seems to be avoidable
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- MatrixType Q = _this.m_hess.matrixQ();
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- _this.m_matU = Q.template cast<ComplexScalar>();
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- }
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- }
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- };
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-
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- } // end namespace internal
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-
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- // Reduce the Hessenberg matrix m_matT to triangular form by QR iteration.
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- template<typename MatrixType>
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- void ComplexSchur<MatrixType>::reduceToTriangularForm(bool computeU)
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- {
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- Index maxIters = m_maxIters;
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- if (maxIters == -1)
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- maxIters = m_maxIterationsPerRow * m_matT.rows();
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-
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- // The matrix m_matT is divided in three parts.
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- // Rows 0,...,il-1 are decoupled from the rest because m_matT(il,il-1) is zero.
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- // Rows il,...,iu is the part we are working on (the active submatrix).
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- // Rows iu+1,...,end are already brought in triangular form.
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- Index iu = m_matT.cols() - 1;
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- Index il;
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- Index iter = 0; // number of iterations we are working on the (iu,iu) element
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- Index totalIter = 0; // number of iterations for whole matrix
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-
405
- while(true)
406
- {
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- // find iu, the bottom row of the active submatrix
408
- while(iu > 0)
409
- {
410
- if(!subdiagonalEntryIsNeglegible(iu-1)) break;
411
- iter = 0;
412
- --iu;
413
- }
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-
415
- // if iu is zero then we are done; the whole matrix is triangularized
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- if(iu==0) break;
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-
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- // if we spent too many iterations, we give up
419
- iter++;
420
- totalIter++;
421
- if(totalIter > maxIters) break;
422
-
423
- // find il, the top row of the active submatrix
424
- il = iu-1;
425
- while(il > 0 && !subdiagonalEntryIsNeglegible(il-1))
426
- {
427
- --il;
428
- }
429
-
430
- /* perform the QR step using Givens rotations. The first rotation
431
- creates a bulge; the (il+2,il) element becomes nonzero. This
432
- bulge is chased down to the bottom of the active submatrix. */
433
-
434
- ComplexScalar shift = computeShift(iu, iter);
435
- JacobiRotation<ComplexScalar> rot;
436
- rot.makeGivens(m_matT.coeff(il,il) - shift, m_matT.coeff(il+1,il));
437
- m_matT.rightCols(m_matT.cols()-il).applyOnTheLeft(il, il+1, rot.adjoint());
438
- m_matT.topRows((std::min)(il+2,iu)+1).applyOnTheRight(il, il+1, rot);
439
- if(computeU) m_matU.applyOnTheRight(il, il+1, rot);
440
-
441
- for(Index i=il+1 ; i<iu ; i++)
442
- {
443
- rot.makeGivens(m_matT.coeffRef(i,i-1), m_matT.coeffRef(i+1,i-1), &m_matT.coeffRef(i,i-1));
444
- m_matT.coeffRef(i+1,i-1) = ComplexScalar(0);
445
- m_matT.rightCols(m_matT.cols()-i).applyOnTheLeft(i, i+1, rot.adjoint());
446
- m_matT.topRows((std::min)(i+2,iu)+1).applyOnTheRight(i, i+1, rot);
447
- if(computeU) m_matU.applyOnTheRight(i, i+1, rot);
448
- }
449
- }
450
-
451
- if(totalIter <= maxIters)
452
- m_info = Success;
453
- else
454
- m_info = NoConvergence;
455
-
456
- m_isInitialized = true;
457
- m_matUisUptodate = computeU;
458
- }
459
-
460
- } // end namespace Eigen
461
-
462
- #endif // EIGEN_COMPLEX_SCHUR_H
@@ -1,91 +0,0 @@
1
- /*
2
- Copyright (c) 2011, Intel Corporation. All rights reserved.
3
-
4
- Redistribution and use in source and binary forms, with or without modification,
5
- are permitted provided that the following conditions are met:
6
-
7
- * Redistributions of source code must retain the above copyright notice, this
8
- list of conditions and the following disclaimer.
9
- * Redistributions in binary form must reproduce the above copyright notice,
10
- this list of conditions and the following disclaimer in the documentation
11
- and/or other materials provided with the distribution.
12
- * Neither the name of Intel Corporation nor the names of its contributors may
13
- be used to endorse or promote products derived from this software without
14
- specific prior written permission.
15
-
16
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
17
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
18
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
19
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
20
- ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
21
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
22
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
23
- ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
24
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
25
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
26
-
27
- ********************************************************************************
28
- * Content : Eigen bindings to LAPACKe
29
- * Complex Schur needed to complex unsymmetrical eigenvalues/eigenvectors.
30
- ********************************************************************************
31
- */
32
-
33
- #ifndef EIGEN_COMPLEX_SCHUR_LAPACKE_H
34
- #define EIGEN_COMPLEX_SCHUR_LAPACKE_H
35
-
36
- namespace Eigen {
37
-
38
- /** \internal Specialization for the data types supported by LAPACKe */
39
-
40
- #define EIGEN_LAPACKE_SCHUR_COMPLEX(EIGTYPE, LAPACKE_TYPE, LAPACKE_PREFIX, LAPACKE_PREFIX_U, EIGCOLROW, LAPACKE_COLROW) \
41
- template<> template<typename InputType> inline \
42
- ComplexSchur<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> >& \
43
- ComplexSchur<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> >::compute(const EigenBase<InputType>& matrix, bool computeU) \
44
- { \
45
- typedef Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW> MatrixType; \
46
- typedef MatrixType::RealScalar RealScalar; \
47
- typedef std::complex<RealScalar> ComplexScalar; \
48
- \
49
- eigen_assert(matrix.cols() == matrix.rows()); \
50
- \
51
- m_matUisUptodate = false; \
52
- if(matrix.cols() == 1) \
53
- { \
54
- m_matT = matrix.derived().template cast<ComplexScalar>(); \
55
- if(computeU) m_matU = ComplexMatrixType::Identity(1,1); \
56
- m_info = Success; \
57
- m_isInitialized = true; \
58
- m_matUisUptodate = computeU; \
59
- return *this; \
60
- } \
61
- lapack_int n = internal::convert_index<lapack_int>(matrix.cols()), sdim, info; \
62
- lapack_int matrix_order = LAPACKE_COLROW; \
63
- char jobvs, sort='N'; \
64
- LAPACK_##LAPACKE_PREFIX_U##_SELECT1 select = 0; \
65
- jobvs = (computeU) ? 'V' : 'N'; \
66
- m_matU.resize(n, n); \
67
- lapack_int ldvs = internal::convert_index<lapack_int>(m_matU.outerStride()); \
68
- m_matT = matrix; \
69
- lapack_int lda = internal::convert_index<lapack_int>(m_matT.outerStride()); \
70
- Matrix<EIGTYPE, Dynamic, Dynamic> w; \
71
- w.resize(n, 1);\
72
- info = LAPACKE_##LAPACKE_PREFIX##gees( matrix_order, jobvs, sort, select, n, (LAPACKE_TYPE*)m_matT.data(), lda, &sdim, (LAPACKE_TYPE*)w.data(), (LAPACKE_TYPE*)m_matU.data(), ldvs ); \
73
- if(info == 0) \
74
- m_info = Success; \
75
- else \
76
- m_info = NoConvergence; \
77
- \
78
- m_isInitialized = true; \
79
- m_matUisUptodate = computeU; \
80
- return *this; \
81
- \
82
- }
83
-
84
- EIGEN_LAPACKE_SCHUR_COMPLEX(dcomplex, lapack_complex_double, z, Z, ColMajor, LAPACK_COL_MAJOR)
85
- EIGEN_LAPACKE_SCHUR_COMPLEX(scomplex, lapack_complex_float, c, C, ColMajor, LAPACK_COL_MAJOR)
86
- EIGEN_LAPACKE_SCHUR_COMPLEX(dcomplex, lapack_complex_double, z, Z, RowMajor, LAPACK_ROW_MAJOR)
87
- EIGEN_LAPACKE_SCHUR_COMPLEX(scomplex, lapack_complex_float, c, C, RowMajor, LAPACK_ROW_MAJOR)
88
-
89
- } // end namespace Eigen
90
-
91
- #endif // EIGEN_COMPLEX_SCHUR_LAPACKE_H