sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.20__cp310-cp310-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp310-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,657 +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) 2012 Alexey Korepanov <kaikaikai@yandex.ru>
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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_REAL_QZ_H
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- #define EIGEN_REAL_QZ_H
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-
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- namespace Eigen {
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-
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- /** \eigenvalues_module \ingroup Eigenvalues_Module
16
- *
17
- *
18
- * \class RealQZ
19
- *
20
- * \brief Performs a real QZ decomposition of a pair of square matrices
21
- *
22
- * \tparam _MatrixType the type of the matrix of which we are computing the
23
- * real QZ decomposition; this is expected to be an instantiation of the
24
- * Matrix class template.
25
- *
26
- * Given a real square matrices A and B, this class computes the real QZ
27
- * decomposition: \f$ A = Q S Z \f$, \f$ B = Q T Z \f$ where Q and Z are
28
- * real orthogonal matrixes, T is upper-triangular matrix, and S is upper
29
- * quasi-triangular matrix. An orthogonal matrix is a matrix whose
30
- * inverse is equal to its transpose, \f$ U^{-1} = U^T \f$. A quasi-triangular
31
- * matrix is a block-triangular matrix whose diagonal consists of 1-by-1
32
- * blocks and 2-by-2 blocks where further reduction is impossible due to
33
- * complex eigenvalues.
34
- *
35
- * The eigenvalues of the pencil \f$ A - z B \f$ can be obtained from
36
- * 1x1 and 2x2 blocks on the diagonals of S and T.
37
- *
38
- * Call the function compute() to compute the real QZ decomposition of a
39
- * given pair of matrices. Alternatively, you can use the
40
- * RealQZ(const MatrixType& B, const MatrixType& B, bool computeQZ)
41
- * constructor which computes the real QZ decomposition at construction
42
- * time. Once the decomposition is computed, you can use the matrixS(),
43
- * matrixT(), matrixQ() and matrixZ() functions to retrieve the matrices
44
- * S, T, Q and Z in the decomposition. If computeQZ==false, some time
45
- * is saved by not computing matrices Q and Z.
46
- *
47
- * Example: \include RealQZ_compute.cpp
48
- * Output: \include RealQZ_compute.out
49
- *
50
- * \note The implementation is based on the algorithm in "Matrix Computations"
51
- * by Gene H. Golub and Charles F. Van Loan, and a paper "An algorithm for
52
- * generalized eigenvalue problems" by C.B.Moler and G.W.Stewart.
53
- *
54
- * \sa class RealSchur, class ComplexSchur, class EigenSolver, class ComplexEigenSolver
55
- */
56
-
57
- template<typename _MatrixType> class RealQZ
58
- {
59
- public:
60
- typedef _MatrixType MatrixType;
61
- enum {
62
- RowsAtCompileTime = MatrixType::RowsAtCompileTime,
63
- ColsAtCompileTime = MatrixType::ColsAtCompileTime,
64
- Options = MatrixType::Options,
65
- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
66
- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
67
- };
68
- typedef typename MatrixType::Scalar Scalar;
69
- typedef std::complex<typename NumTraits<Scalar>::Real> ComplexScalar;
70
- typedef Eigen::Index Index; ///< \deprecated since Eigen 3.3
71
-
72
- typedef Matrix<ComplexScalar, ColsAtCompileTime, 1, Options & ~RowMajor, MaxColsAtCompileTime, 1> EigenvalueType;
73
- typedef Matrix<Scalar, ColsAtCompileTime, 1, Options & ~RowMajor, MaxColsAtCompileTime, 1> ColumnVectorType;
74
-
75
- /** \brief Default constructor.
76
- *
77
- * \param [in] size Positive integer, size of the matrix whose QZ decomposition will be computed.
78
- *
79
- * The default constructor is useful in cases in which the user intends to
80
- * perform decompositions via compute(). The \p size parameter is only
81
- * used as a hint. It is not an error to give a wrong \p size, but it may
82
- * impair performance.
83
- *
84
- * \sa compute() for an example.
85
- */
86
- explicit RealQZ(Index size = RowsAtCompileTime==Dynamic ? 1 : RowsAtCompileTime) :
87
- m_S(size, size),
88
- m_T(size, size),
89
- m_Q(size, size),
90
- m_Z(size, size),
91
- m_workspace(size*2),
92
- m_maxIters(400),
93
- m_isInitialized(false),
94
- m_computeQZ(true)
95
- {}
96
-
97
- /** \brief Constructor; computes real QZ decomposition of given matrices
98
- *
99
- * \param[in] A Matrix A.
100
- * \param[in] B Matrix B.
101
- * \param[in] computeQZ If false, A and Z are not computed.
102
- *
103
- * This constructor calls compute() to compute the QZ decomposition.
104
- */
105
- RealQZ(const MatrixType& A, const MatrixType& B, bool computeQZ = true) :
106
- m_S(A.rows(),A.cols()),
107
- m_T(A.rows(),A.cols()),
108
- m_Q(A.rows(),A.cols()),
109
- m_Z(A.rows(),A.cols()),
110
- m_workspace(A.rows()*2),
111
- m_maxIters(400),
112
- m_isInitialized(false),
113
- m_computeQZ(true)
114
- {
115
- compute(A, B, computeQZ);
116
- }
117
-
118
- /** \brief Returns matrix Q in the QZ decomposition.
119
- *
120
- * \returns A const reference to the matrix Q.
121
- */
122
- const MatrixType& matrixQ() const {
123
- eigen_assert(m_isInitialized && "RealQZ is not initialized.");
124
- eigen_assert(m_computeQZ && "The matrices Q and Z have not been computed during the QZ decomposition.");
125
- return m_Q;
126
- }
127
-
128
- /** \brief Returns matrix Z in the QZ decomposition.
129
- *
130
- * \returns A const reference to the matrix Z.
131
- */
132
- const MatrixType& matrixZ() const {
133
- eigen_assert(m_isInitialized && "RealQZ is not initialized.");
134
- eigen_assert(m_computeQZ && "The matrices Q and Z have not been computed during the QZ decomposition.");
135
- return m_Z;
136
- }
137
-
138
- /** \brief Returns matrix S in the QZ decomposition.
139
- *
140
- * \returns A const reference to the matrix S.
141
- */
142
- const MatrixType& matrixS() const {
143
- eigen_assert(m_isInitialized && "RealQZ is not initialized.");
144
- return m_S;
145
- }
146
-
147
- /** \brief Returns matrix S in the QZ decomposition.
148
- *
149
- * \returns A const reference to the matrix S.
150
- */
151
- const MatrixType& matrixT() const {
152
- eigen_assert(m_isInitialized && "RealQZ is not initialized.");
153
- return m_T;
154
- }
155
-
156
- /** \brief Computes QZ decomposition of given matrix.
157
- *
158
- * \param[in] A Matrix A.
159
- * \param[in] B Matrix B.
160
- * \param[in] computeQZ If false, A and Z are not computed.
161
- * \returns Reference to \c *this
162
- */
163
- RealQZ& compute(const MatrixType& A, const MatrixType& B, bool computeQZ = true);
164
-
165
- /** \brief Reports whether previous computation was successful.
166
- *
167
- * \returns \c Success if computation was successful, \c NoConvergence otherwise.
168
- */
169
- ComputationInfo info() const
170
- {
171
- eigen_assert(m_isInitialized && "RealQZ is not initialized.");
172
- return m_info;
173
- }
174
-
175
- /** \brief Returns number of performed QR-like iterations.
176
- */
177
- Index iterations() const
178
- {
179
- eigen_assert(m_isInitialized && "RealQZ is not initialized.");
180
- return m_global_iter;
181
- }
182
-
183
- /** Sets the maximal number of iterations allowed to converge to one eigenvalue
184
- * or decouple the problem.
185
- */
186
- RealQZ& setMaxIterations(Index maxIters)
187
- {
188
- m_maxIters = maxIters;
189
- return *this;
190
- }
191
-
192
- private:
193
-
194
- MatrixType m_S, m_T, m_Q, m_Z;
195
- Matrix<Scalar,Dynamic,1> m_workspace;
196
- ComputationInfo m_info;
197
- Index m_maxIters;
198
- bool m_isInitialized;
199
- bool m_computeQZ;
200
- Scalar m_normOfT, m_normOfS;
201
- Index m_global_iter;
202
-
203
- typedef Matrix<Scalar,3,1> Vector3s;
204
- typedef Matrix<Scalar,2,1> Vector2s;
205
- typedef Matrix<Scalar,2,2> Matrix2s;
206
- typedef JacobiRotation<Scalar> JRs;
207
-
208
- void hessenbergTriangular();
209
- void computeNorms();
210
- Index findSmallSubdiagEntry(Index iu);
211
- Index findSmallDiagEntry(Index f, Index l);
212
- void splitOffTwoRows(Index i);
213
- void pushDownZero(Index z, Index f, Index l);
214
- void step(Index f, Index l, Index iter);
215
-
216
- }; // RealQZ
217
-
218
- /** \internal Reduces S and T to upper Hessenberg - triangular form */
219
- template<typename MatrixType>
220
- void RealQZ<MatrixType>::hessenbergTriangular()
221
- {
222
-
223
- const Index dim = m_S.cols();
224
-
225
- // perform QR decomposition of T, overwrite T with R, save Q
226
- HouseholderQR<MatrixType> qrT(m_T);
227
- m_T = qrT.matrixQR();
228
- m_T.template triangularView<StrictlyLower>().setZero();
229
- m_Q = qrT.householderQ();
230
- // overwrite S with Q* S
231
- m_S.applyOnTheLeft(m_Q.adjoint());
232
- // init Z as Identity
233
- if (m_computeQZ)
234
- m_Z = MatrixType::Identity(dim,dim);
235
- // reduce S to upper Hessenberg with Givens rotations
236
- for (Index j=0; j<=dim-3; j++) {
237
- for (Index i=dim-1; i>=j+2; i--) {
238
- JRs G;
239
- // kill S(i,j)
240
- if(m_S.coeff(i,j) != 0)
241
- {
242
- G.makeGivens(m_S.coeff(i-1,j), m_S.coeff(i,j), &m_S.coeffRef(i-1, j));
243
- m_S.coeffRef(i,j) = Scalar(0.0);
244
- m_S.rightCols(dim-j-1).applyOnTheLeft(i-1,i,G.adjoint());
245
- m_T.rightCols(dim-i+1).applyOnTheLeft(i-1,i,G.adjoint());
246
- // update Q
247
- if (m_computeQZ)
248
- m_Q.applyOnTheRight(i-1,i,G);
249
- }
250
- // kill T(i,i-1)
251
- if(m_T.coeff(i,i-1)!=Scalar(0))
252
- {
253
- G.makeGivens(m_T.coeff(i,i), m_T.coeff(i,i-1), &m_T.coeffRef(i,i));
254
- m_T.coeffRef(i,i-1) = Scalar(0.0);
255
- m_S.applyOnTheRight(i,i-1,G);
256
- m_T.topRows(i).applyOnTheRight(i,i-1,G);
257
- // update Z
258
- if (m_computeQZ)
259
- m_Z.applyOnTheLeft(i,i-1,G.adjoint());
260
- }
261
- }
262
- }
263
- }
264
-
265
- /** \internal Computes vector L1 norms of S and T when in Hessenberg-Triangular form already */
266
- template<typename MatrixType>
267
- inline void RealQZ<MatrixType>::computeNorms()
268
- {
269
- const Index size = m_S.cols();
270
- m_normOfS = Scalar(0.0);
271
- m_normOfT = Scalar(0.0);
272
- for (Index j = 0; j < size; ++j)
273
- {
274
- m_normOfS += m_S.col(j).segment(0, (std::min)(size,j+2)).cwiseAbs().sum();
275
- m_normOfT += m_T.row(j).segment(j, size - j).cwiseAbs().sum();
276
- }
277
- }
278
-
279
-
280
- /** \internal Look for single small sub-diagonal element S(res, res-1) and return res (or 0) */
281
- template<typename MatrixType>
282
- inline Index RealQZ<MatrixType>::findSmallSubdiagEntry(Index iu)
283
- {
284
- using std::abs;
285
- Index res = iu;
286
- while (res > 0)
287
- {
288
- Scalar s = abs(m_S.coeff(res-1,res-1)) + abs(m_S.coeff(res,res));
289
- if (s == Scalar(0.0))
290
- s = m_normOfS;
291
- if (abs(m_S.coeff(res,res-1)) < NumTraits<Scalar>::epsilon() * s)
292
- break;
293
- res--;
294
- }
295
- return res;
296
- }
297
-
298
- /** \internal Look for single small diagonal element T(res, res) for res between f and l, and return res (or f-1) */
299
- template<typename MatrixType>
300
- inline Index RealQZ<MatrixType>::findSmallDiagEntry(Index f, Index l)
301
- {
302
- using std::abs;
303
- Index res = l;
304
- while (res >= f) {
305
- if (abs(m_T.coeff(res,res)) <= NumTraits<Scalar>::epsilon() * m_normOfT)
306
- break;
307
- res--;
308
- }
309
- return res;
310
- }
311
-
312
- /** \internal decouple 2x2 diagonal block in rows i, i+1 if eigenvalues are real */
313
- template<typename MatrixType>
314
- inline void RealQZ<MatrixType>::splitOffTwoRows(Index i)
315
- {
316
- using std::abs;
317
- using std::sqrt;
318
- const Index dim=m_S.cols();
319
- if (abs(m_S.coeff(i+1,i))==Scalar(0))
320
- return;
321
- Index j = findSmallDiagEntry(i,i+1);
322
- if (j==i-1)
323
- {
324
- // block of (S T^{-1})
325
- Matrix2s STi = m_T.template block<2,2>(i,i).template triangularView<Upper>().
326
- template solve<OnTheRight>(m_S.template block<2,2>(i,i));
327
- Scalar p = Scalar(0.5)*(STi(0,0)-STi(1,1));
328
- Scalar q = p*p + STi(1,0)*STi(0,1);
329
- if (q>=0) {
330
- Scalar z = sqrt(q);
331
- // one QR-like iteration for ABi - lambda I
332
- // is enough - when we know exact eigenvalue in advance,
333
- // convergence is immediate
334
- JRs G;
335
- if (p>=0)
336
- G.makeGivens(p + z, STi(1,0));
337
- else
338
- G.makeGivens(p - z, STi(1,0));
339
- m_S.rightCols(dim-i).applyOnTheLeft(i,i+1,G.adjoint());
340
- m_T.rightCols(dim-i).applyOnTheLeft(i,i+1,G.adjoint());
341
- // update Q
342
- if (m_computeQZ)
343
- m_Q.applyOnTheRight(i,i+1,G);
344
-
345
- G.makeGivens(m_T.coeff(i+1,i+1), m_T.coeff(i+1,i));
346
- m_S.topRows(i+2).applyOnTheRight(i+1,i,G);
347
- m_T.topRows(i+2).applyOnTheRight(i+1,i,G);
348
- // update Z
349
- if (m_computeQZ)
350
- m_Z.applyOnTheLeft(i+1,i,G.adjoint());
351
-
352
- m_S.coeffRef(i+1,i) = Scalar(0.0);
353
- m_T.coeffRef(i+1,i) = Scalar(0.0);
354
- }
355
- }
356
- else
357
- {
358
- pushDownZero(j,i,i+1);
359
- }
360
- }
361
-
362
- /** \internal use zero in T(z,z) to zero S(l,l-1), working in block f..l */
363
- template<typename MatrixType>
364
- inline void RealQZ<MatrixType>::pushDownZero(Index z, Index f, Index l)
365
- {
366
- JRs G;
367
- const Index dim = m_S.cols();
368
- for (Index zz=z; zz<l; zz++)
369
- {
370
- // push 0 down
371
- Index firstColS = zz>f ? (zz-1) : zz;
372
- G.makeGivens(m_T.coeff(zz, zz+1), m_T.coeff(zz+1, zz+1));
373
- m_S.rightCols(dim-firstColS).applyOnTheLeft(zz,zz+1,G.adjoint());
374
- m_T.rightCols(dim-zz).applyOnTheLeft(zz,zz+1,G.adjoint());
375
- m_T.coeffRef(zz+1,zz+1) = Scalar(0.0);
376
- // update Q
377
- if (m_computeQZ)
378
- m_Q.applyOnTheRight(zz,zz+1,G);
379
- // kill S(zz+1, zz-1)
380
- if (zz>f)
381
- {
382
- G.makeGivens(m_S.coeff(zz+1, zz), m_S.coeff(zz+1,zz-1));
383
- m_S.topRows(zz+2).applyOnTheRight(zz, zz-1,G);
384
- m_T.topRows(zz+1).applyOnTheRight(zz, zz-1,G);
385
- m_S.coeffRef(zz+1,zz-1) = Scalar(0.0);
386
- // update Z
387
- if (m_computeQZ)
388
- m_Z.applyOnTheLeft(zz,zz-1,G.adjoint());
389
- }
390
- }
391
- // finally kill S(l,l-1)
392
- G.makeGivens(m_S.coeff(l,l), m_S.coeff(l,l-1));
393
- m_S.applyOnTheRight(l,l-1,G);
394
- m_T.applyOnTheRight(l,l-1,G);
395
- m_S.coeffRef(l,l-1)=Scalar(0.0);
396
- // update Z
397
- if (m_computeQZ)
398
- m_Z.applyOnTheLeft(l,l-1,G.adjoint());
399
- }
400
-
401
- /** \internal QR-like iterative step for block f..l */
402
- template<typename MatrixType>
403
- inline void RealQZ<MatrixType>::step(Index f, Index l, Index iter)
404
- {
405
- using std::abs;
406
- const Index dim = m_S.cols();
407
-
408
- // x, y, z
409
- Scalar x, y, z;
410
- if (iter==10)
411
- {
412
- // Wilkinson ad hoc shift
413
- const Scalar
414
- a11=m_S.coeff(f+0,f+0), a12=m_S.coeff(f+0,f+1),
415
- a21=m_S.coeff(f+1,f+0), a22=m_S.coeff(f+1,f+1), a32=m_S.coeff(f+2,f+1),
416
- b12=m_T.coeff(f+0,f+1),
417
- b11i=Scalar(1.0)/m_T.coeff(f+0,f+0),
418
- b22i=Scalar(1.0)/m_T.coeff(f+1,f+1),
419
- a87=m_S.coeff(l-1,l-2),
420
- a98=m_S.coeff(l-0,l-1),
421
- b77i=Scalar(1.0)/m_T.coeff(l-2,l-2),
422
- b88i=Scalar(1.0)/m_T.coeff(l-1,l-1);
423
- Scalar ss = abs(a87*b77i) + abs(a98*b88i),
424
- lpl = Scalar(1.5)*ss,
425
- ll = ss*ss;
426
- x = ll + a11*a11*b11i*b11i - lpl*a11*b11i + a12*a21*b11i*b22i
427
- - a11*a21*b12*b11i*b11i*b22i;
428
- y = a11*a21*b11i*b11i - lpl*a21*b11i + a21*a22*b11i*b22i
429
- - a21*a21*b12*b11i*b11i*b22i;
430
- z = a21*a32*b11i*b22i;
431
- }
432
- else if (iter==16)
433
- {
434
- // another exceptional shift
435
- x = m_S.coeff(f,f)/m_T.coeff(f,f)-m_S.coeff(l,l)/m_T.coeff(l,l) + m_S.coeff(l,l-1)*m_T.coeff(l-1,l) /
436
- (m_T.coeff(l-1,l-1)*m_T.coeff(l,l));
437
- y = m_S.coeff(f+1,f)/m_T.coeff(f,f);
438
- z = 0;
439
- }
440
- else if (iter>23 && !(iter%8))
441
- {
442
- // extremely exceptional shift
443
- x = internal::random<Scalar>(-1.0,1.0);
444
- y = internal::random<Scalar>(-1.0,1.0);
445
- z = internal::random<Scalar>(-1.0,1.0);
446
- }
447
- else
448
- {
449
- // Compute the shifts: (x,y,z,0...) = (AB^-1 - l1 I) (AB^-1 - l2 I) e1
450
- // where l1 and l2 are the eigenvalues of the 2x2 matrix C = U V^-1 where
451
- // U and V are 2x2 bottom right sub matrices of A and B. Thus:
452
- // = AB^-1AB^-1 + l1 l2 I - (l1+l2)(AB^-1)
453
- // = AB^-1AB^-1 + det(M) - tr(M)(AB^-1)
454
- // Since we are only interested in having x, y, z with a correct ratio, we have:
455
- const Scalar
456
- a11 = m_S.coeff(f,f), a12 = m_S.coeff(f,f+1),
457
- a21 = m_S.coeff(f+1,f), a22 = m_S.coeff(f+1,f+1),
458
- a32 = m_S.coeff(f+2,f+1),
459
-
460
- a88 = m_S.coeff(l-1,l-1), a89 = m_S.coeff(l-1,l),
461
- a98 = m_S.coeff(l,l-1), a99 = m_S.coeff(l,l),
462
-
463
- b11 = m_T.coeff(f,f), b12 = m_T.coeff(f,f+1),
464
- b22 = m_T.coeff(f+1,f+1),
465
-
466
- b88 = m_T.coeff(l-1,l-1), b89 = m_T.coeff(l-1,l),
467
- b99 = m_T.coeff(l,l);
468
-
469
- x = ( (a88/b88 - a11/b11)*(a99/b99 - a11/b11) - (a89/b99)*(a98/b88) + (a98/b88)*(b89/b99)*(a11/b11) ) * (b11/a21)
470
- + a12/b22 - (a11/b11)*(b12/b22);
471
- y = (a22/b22-a11/b11) - (a21/b11)*(b12/b22) - (a88/b88-a11/b11) - (a99/b99-a11/b11) + (a98/b88)*(b89/b99);
472
- z = a32/b22;
473
- }
474
-
475
- JRs G;
476
-
477
- for (Index k=f; k<=l-2; k++)
478
- {
479
- // variables for Householder reflections
480
- Vector2s essential2;
481
- Scalar tau, beta;
482
-
483
- Vector3s hr(x,y,z);
484
-
485
- // Q_k to annihilate S(k+1,k-1) and S(k+2,k-1)
486
- hr.makeHouseholderInPlace(tau, beta);
487
- essential2 = hr.template bottomRows<2>();
488
- Index fc=(std::max)(k-1,Index(0)); // first col to update
489
- m_S.template middleRows<3>(k).rightCols(dim-fc).applyHouseholderOnTheLeft(essential2, tau, m_workspace.data());
490
- m_T.template middleRows<3>(k).rightCols(dim-fc).applyHouseholderOnTheLeft(essential2, tau, m_workspace.data());
491
- if (m_computeQZ)
492
- m_Q.template middleCols<3>(k).applyHouseholderOnTheRight(essential2, tau, m_workspace.data());
493
- if (k>f)
494
- m_S.coeffRef(k+2,k-1) = m_S.coeffRef(k+1,k-1) = Scalar(0.0);
495
-
496
- // Z_{k1} to annihilate T(k+2,k+1) and T(k+2,k)
497
- hr << m_T.coeff(k+2,k+2),m_T.coeff(k+2,k),m_T.coeff(k+2,k+1);
498
- hr.makeHouseholderInPlace(tau, beta);
499
- essential2 = hr.template bottomRows<2>();
500
- {
501
- Index lr = (std::min)(k+4,dim); // last row to update
502
- Map<Matrix<Scalar,Dynamic,1> > tmp(m_workspace.data(),lr);
503
- // S
504
- tmp = m_S.template middleCols<2>(k).topRows(lr) * essential2;
505
- tmp += m_S.col(k+2).head(lr);
506
- m_S.col(k+2).head(lr) -= tau*tmp;
507
- m_S.template middleCols<2>(k).topRows(lr) -= (tau*tmp) * essential2.adjoint();
508
- // T
509
- tmp = m_T.template middleCols<2>(k).topRows(lr) * essential2;
510
- tmp += m_T.col(k+2).head(lr);
511
- m_T.col(k+2).head(lr) -= tau*tmp;
512
- m_T.template middleCols<2>(k).topRows(lr) -= (tau*tmp) * essential2.adjoint();
513
- }
514
- if (m_computeQZ)
515
- {
516
- // Z
517
- Map<Matrix<Scalar,1,Dynamic> > tmp(m_workspace.data(),dim);
518
- tmp = essential2.adjoint()*(m_Z.template middleRows<2>(k));
519
- tmp += m_Z.row(k+2);
520
- m_Z.row(k+2) -= tau*tmp;
521
- m_Z.template middleRows<2>(k) -= essential2 * (tau*tmp);
522
- }
523
- m_T.coeffRef(k+2,k) = m_T.coeffRef(k+2,k+1) = Scalar(0.0);
524
-
525
- // Z_{k2} to annihilate T(k+1,k)
526
- G.makeGivens(m_T.coeff(k+1,k+1), m_T.coeff(k+1,k));
527
- m_S.applyOnTheRight(k+1,k,G);
528
- m_T.applyOnTheRight(k+1,k,G);
529
- // update Z
530
- if (m_computeQZ)
531
- m_Z.applyOnTheLeft(k+1,k,G.adjoint());
532
- m_T.coeffRef(k+1,k) = Scalar(0.0);
533
-
534
- // update x,y,z
535
- x = m_S.coeff(k+1,k);
536
- y = m_S.coeff(k+2,k);
537
- if (k < l-2)
538
- z = m_S.coeff(k+3,k);
539
- } // loop over k
540
-
541
- // Q_{n-1} to annihilate y = S(l,l-2)
542
- G.makeGivens(x,y);
543
- m_S.applyOnTheLeft(l-1,l,G.adjoint());
544
- m_T.applyOnTheLeft(l-1,l,G.adjoint());
545
- if (m_computeQZ)
546
- m_Q.applyOnTheRight(l-1,l,G);
547
- m_S.coeffRef(l,l-2) = Scalar(0.0);
548
-
549
- // Z_{n-1} to annihilate T(l,l-1)
550
- G.makeGivens(m_T.coeff(l,l),m_T.coeff(l,l-1));
551
- m_S.applyOnTheRight(l,l-1,G);
552
- m_T.applyOnTheRight(l,l-1,G);
553
- if (m_computeQZ)
554
- m_Z.applyOnTheLeft(l,l-1,G.adjoint());
555
- m_T.coeffRef(l,l-1) = Scalar(0.0);
556
- }
557
-
558
- template<typename MatrixType>
559
- RealQZ<MatrixType>& RealQZ<MatrixType>::compute(const MatrixType& A_in, const MatrixType& B_in, bool computeQZ)
560
- {
561
-
562
- const Index dim = A_in.cols();
563
-
564
- eigen_assert (A_in.rows()==dim && A_in.cols()==dim
565
- && B_in.rows()==dim && B_in.cols()==dim
566
- && "Need square matrices of the same dimension");
567
-
568
- m_isInitialized = true;
569
- m_computeQZ = computeQZ;
570
- m_S = A_in; m_T = B_in;
571
- m_workspace.resize(dim*2);
572
- m_global_iter = 0;
573
-
574
- // entrance point: hessenberg triangular decomposition
575
- hessenbergTriangular();
576
- // compute L1 vector norms of T, S into m_normOfS, m_normOfT
577
- computeNorms();
578
-
579
- Index l = dim-1,
580
- f,
581
- local_iter = 0;
582
-
583
- while (l>0 && local_iter<m_maxIters)
584
- {
585
- f = findSmallSubdiagEntry(l);
586
- // now rows and columns f..l (including) decouple from the rest of the problem
587
- if (f>0) m_S.coeffRef(f,f-1) = Scalar(0.0);
588
- if (f == l) // One root found
589
- {
590
- l--;
591
- local_iter = 0;
592
- }
593
- else if (f == l-1) // Two roots found
594
- {
595
- splitOffTwoRows(f);
596
- l -= 2;
597
- local_iter = 0;
598
- }
599
- else // No convergence yet
600
- {
601
- // if there's zero on diagonal of T, we can isolate an eigenvalue with Givens rotations
602
- Index z = findSmallDiagEntry(f,l);
603
- if (z>=f)
604
- {
605
- // zero found
606
- pushDownZero(z,f,l);
607
- }
608
- else
609
- {
610
- // We are sure now that S.block(f,f, l-f+1,l-f+1) is underuced upper-Hessenberg
611
- // and T.block(f,f, l-f+1,l-f+1) is invertible uper-triangular, which allows to
612
- // apply a QR-like iteration to rows and columns f..l.
613
- step(f,l, local_iter);
614
- local_iter++;
615
- m_global_iter++;
616
- }
617
- }
618
- }
619
- // check if we converged before reaching iterations limit
620
- m_info = (local_iter<m_maxIters) ? Success : NoConvergence;
621
-
622
- // For each non triangular 2x2 diagonal block of S,
623
- // reduce the respective 2x2 diagonal block of T to positive diagonal form using 2x2 SVD.
624
- // This step is not mandatory for QZ, but it does help further extraction of eigenvalues/eigenvectors,
625
- // and is in par with Lapack/Matlab QZ.
626
- if(m_info==Success)
627
- {
628
- for(Index i=0; i<dim-1; ++i)
629
- {
630
- if(m_S.coeff(i+1, i) != Scalar(0))
631
- {
632
- JacobiRotation<Scalar> j_left, j_right;
633
- internal::real_2x2_jacobi_svd(m_T, i, i+1, &j_left, &j_right);
634
-
635
- // Apply resulting Jacobi rotations
636
- m_S.applyOnTheLeft(i,i+1,j_left);
637
- m_S.applyOnTheRight(i,i+1,j_right);
638
- m_T.applyOnTheLeft(i,i+1,j_left);
639
- m_T.applyOnTheRight(i,i+1,j_right);
640
- m_T(i+1,i) = m_T(i,i+1) = Scalar(0);
641
-
642
- if(m_computeQZ) {
643
- m_Q.applyOnTheRight(i,i+1,j_left.transpose());
644
- m_Z.applyOnTheLeft(i,i+1,j_right.transpose());
645
- }
646
-
647
- i++;
648
- }
649
- }
650
- }
651
-
652
- return *this;
653
- } // end compute
654
-
655
- } // end namespace Eigen
656
-
657
- #endif //EIGEN_REAL_QZ