sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.19__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 +107 -5
  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 +1 -2
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  13. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  15. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  17. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  18. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  19. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  20. sequenzo/multidomain/cat.py +0 -53
  21. sequenzo/multidomain/idcd.py +0 -1
  22. sequenzo/openmp_setup.py +233 -0
  23. sequenzo/visualization/plot_transition_matrix.py +21 -22
  24. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  25. sequenzo-0.1.19.dist-info/RECORD +272 -0
  26. sequenzo/dissimilarity_measures/setup.py +0 -35
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  169. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  171. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  172. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  173. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  174. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  175. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  176. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  177. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  178. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  179. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  180. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  181. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  182. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  183. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  184. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  185. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  186. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  187. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  188. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  189. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  190. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  191. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  192. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  197. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  198. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  199. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  200. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  201. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  202. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  203. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  206. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  207. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  208. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  209. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  210. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  211. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  212. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
  213. sequenzo/dissimilarity_measures/src/eigen/test/gpu_common.h +0 -176
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  395. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
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@@ -1,622 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2008 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 2010,2012 Jitse Niesen <jitse@maths.leeds.ac.uk>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_EIGENSOLVER_H
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- #define EIGEN_EIGENSOLVER_H
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-
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- #include "./RealSchur.h"
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-
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- namespace Eigen {
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-
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- /** \eigenvalues_module \ingroup Eigenvalues_Module
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- *
20
- *
21
- * \class EigenSolver
22
- *
23
- * \brief Computes eigenvalues and eigenvectors of general matrices
24
- *
25
- * \tparam _MatrixType the type of the matrix of which we are computing the
26
- * eigendecomposition; this is expected to be an instantiation of the Matrix
27
- * class template. Currently, only real matrices are supported.
28
- *
29
- * The eigenvalues and eigenvectors of a matrix \f$ A \f$ are scalars
30
- * \f$ \lambda \f$ and vectors \f$ v \f$ such that \f$ Av = \lambda v \f$. If
31
- * \f$ D \f$ is a diagonal matrix with the eigenvalues on the diagonal, and
32
- * \f$ V \f$ is a matrix with the eigenvectors as its columns, then \f$ A V =
33
- * V D \f$. The matrix \f$ V \f$ is almost always invertible, in which case we
34
- * have \f$ A = V D V^{-1} \f$. This is called the eigendecomposition.
35
- *
36
- * The eigenvalues and eigenvectors of a matrix may be complex, even when the
37
- * matrix is real. However, we can choose real matrices \f$ V \f$ and \f$ D
38
- * \f$ satisfying \f$ A V = V D \f$, just like the eigendecomposition, if the
39
- * matrix \f$ D \f$ is not required to be diagonal, but if it is allowed to
40
- * have blocks of the form
41
- * \f[ \begin{bmatrix} u & v \\ -v & u \end{bmatrix} \f]
42
- * (where \f$ u \f$ and \f$ v \f$ are real numbers) on the diagonal. These
43
- * blocks correspond to complex eigenvalue pairs \f$ u \pm iv \f$. We call
44
- * this variant of the eigendecomposition the pseudo-eigendecomposition.
45
- *
46
- * Call the function compute() to compute the eigenvalues and eigenvectors of
47
- * a given matrix. Alternatively, you can use the
48
- * EigenSolver(const MatrixType&, bool) constructor which computes the
49
- * eigenvalues and eigenvectors at construction time. Once the eigenvalue and
50
- * eigenvectors are computed, they can be retrieved with the eigenvalues() and
51
- * eigenvectors() functions. The pseudoEigenvalueMatrix() and
52
- * pseudoEigenvectors() methods allow the construction of the
53
- * pseudo-eigendecomposition.
54
- *
55
- * The documentation for EigenSolver(const MatrixType&, bool) contains an
56
- * example of the typical use of this class.
57
- *
58
- * \note The implementation is adapted from
59
- * <a href="http://math.nist.gov/javanumerics/jama/">JAMA</a> (public domain).
60
- * Their code is based on EISPACK.
61
- *
62
- * \sa MatrixBase::eigenvalues(), class ComplexEigenSolver, class SelfAdjointEigenSolver
63
- */
64
- template<typename _MatrixType> class EigenSolver
65
- {
66
- public:
67
-
68
- /** \brief Synonym for the template parameter \p _MatrixType. */
69
- typedef _MatrixType MatrixType;
70
-
71
- enum {
72
- RowsAtCompileTime = MatrixType::RowsAtCompileTime,
73
- ColsAtCompileTime = MatrixType::ColsAtCompileTime,
74
- Options = MatrixType::Options,
75
- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
76
- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
77
- };
78
-
79
- /** \brief Scalar type for matrices of type #MatrixType. */
80
- typedef typename MatrixType::Scalar Scalar;
81
- typedef typename NumTraits<Scalar>::Real RealScalar;
82
- typedef Eigen::Index Index; ///< \deprecated since Eigen 3.3
83
-
84
- /** \brief Complex scalar type for #MatrixType.
85
- *
86
- * This is \c std::complex<Scalar> if #Scalar is real (e.g.,
87
- * \c float or \c double) and just \c Scalar if #Scalar is
88
- * complex.
89
- */
90
- typedef std::complex<RealScalar> ComplexScalar;
91
-
92
- /** \brief Type for vector of eigenvalues as returned by eigenvalues().
93
- *
94
- * This is a column vector with entries of type #ComplexScalar.
95
- * The length of the vector is the size of #MatrixType.
96
- */
97
- typedef Matrix<ComplexScalar, ColsAtCompileTime, 1, Options & ~RowMajor, MaxColsAtCompileTime, 1> EigenvalueType;
98
-
99
- /** \brief Type for matrix of eigenvectors as returned by eigenvectors().
100
- *
101
- * This is a square matrix with entries of type #ComplexScalar.
102
- * The size is the same as the size of #MatrixType.
103
- */
104
- typedef Matrix<ComplexScalar, RowsAtCompileTime, ColsAtCompileTime, Options, MaxRowsAtCompileTime, MaxColsAtCompileTime> EigenvectorsType;
105
-
106
- /** \brief Default constructor.
107
- *
108
- * The default constructor is useful in cases in which the user intends to
109
- * perform decompositions via EigenSolver::compute(const MatrixType&, bool).
110
- *
111
- * \sa compute() for an example.
112
- */
113
- EigenSolver() : m_eivec(), m_eivalues(), m_isInitialized(false), m_eigenvectorsOk(false), m_realSchur(), m_matT(), m_tmp() {}
114
-
115
- /** \brief Default constructor with memory preallocation
116
- *
117
- * Like the default constructor but with preallocation of the internal data
118
- * according to the specified problem \a size.
119
- * \sa EigenSolver()
120
- */
121
- explicit EigenSolver(Index size)
122
- : m_eivec(size, size),
123
- m_eivalues(size),
124
- m_isInitialized(false),
125
- m_eigenvectorsOk(false),
126
- m_realSchur(size),
127
- m_matT(size, size),
128
- m_tmp(size)
129
- {}
130
-
131
- /** \brief Constructor; computes eigendecomposition of given matrix.
132
- *
133
- * \param[in] matrix Square matrix whose eigendecomposition is to be computed.
134
- * \param[in] computeEigenvectors If true, both the eigenvectors and the
135
- * eigenvalues are computed; if false, only the eigenvalues are
136
- * computed.
137
- *
138
- * This constructor calls compute() to compute the eigenvalues
139
- * and eigenvectors.
140
- *
141
- * Example: \include EigenSolver_EigenSolver_MatrixType.cpp
142
- * Output: \verbinclude EigenSolver_EigenSolver_MatrixType.out
143
- *
144
- * \sa compute()
145
- */
146
- template<typename InputType>
147
- explicit EigenSolver(const EigenBase<InputType>& matrix, bool computeEigenvectors = true)
148
- : m_eivec(matrix.rows(), matrix.cols()),
149
- m_eivalues(matrix.cols()),
150
- m_isInitialized(false),
151
- m_eigenvectorsOk(false),
152
- m_realSchur(matrix.cols()),
153
- m_matT(matrix.rows(), matrix.cols()),
154
- m_tmp(matrix.cols())
155
- {
156
- compute(matrix.derived(), computeEigenvectors);
157
- }
158
-
159
- /** \brief Returns the eigenvectors of given matrix.
160
- *
161
- * \returns %Matrix whose columns are the (possibly complex) eigenvectors.
162
- *
163
- * \pre Either the constructor
164
- * EigenSolver(const MatrixType&,bool) or the member function
165
- * compute(const MatrixType&, bool) has been called before, and
166
- * \p computeEigenvectors was set to true (the default).
167
- *
168
- * Column \f$ k \f$ of the returned matrix is an eigenvector corresponding
169
- * to eigenvalue number \f$ k \f$ as returned by eigenvalues(). The
170
- * eigenvectors are normalized to have (Euclidean) norm equal to one. The
171
- * matrix returned by this function is the matrix \f$ V \f$ in the
172
- * eigendecomposition \f$ A = V D V^{-1} \f$, if it exists.
173
- *
174
- * Example: \include EigenSolver_eigenvectors.cpp
175
- * Output: \verbinclude EigenSolver_eigenvectors.out
176
- *
177
- * \sa eigenvalues(), pseudoEigenvectors()
178
- */
179
- EigenvectorsType eigenvectors() const;
180
-
181
- /** \brief Returns the pseudo-eigenvectors of given matrix.
182
- *
183
- * \returns Const reference to matrix whose columns are the pseudo-eigenvectors.
184
- *
185
- * \pre Either the constructor
186
- * EigenSolver(const MatrixType&,bool) or the member function
187
- * compute(const MatrixType&, bool) has been called before, and
188
- * \p computeEigenvectors was set to true (the default).
189
- *
190
- * The real matrix \f$ V \f$ returned by this function and the
191
- * block-diagonal matrix \f$ D \f$ returned by pseudoEigenvalueMatrix()
192
- * satisfy \f$ AV = VD \f$.
193
- *
194
- * Example: \include EigenSolver_pseudoEigenvectors.cpp
195
- * Output: \verbinclude EigenSolver_pseudoEigenvectors.out
196
- *
197
- * \sa pseudoEigenvalueMatrix(), eigenvectors()
198
- */
199
- const MatrixType& pseudoEigenvectors() const
200
- {
201
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
202
- eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
203
- return m_eivec;
204
- }
205
-
206
- /** \brief Returns the block-diagonal matrix in the pseudo-eigendecomposition.
207
- *
208
- * \returns A block-diagonal matrix.
209
- *
210
- * \pre Either the constructor
211
- * EigenSolver(const MatrixType&,bool) or the member function
212
- * compute(const MatrixType&, bool) has been called before.
213
- *
214
- * The matrix \f$ D \f$ returned by this function is real and
215
- * block-diagonal. The blocks on the diagonal are either 1-by-1 or 2-by-2
216
- * blocks of the form
217
- * \f$ \begin{bmatrix} u & v \\ -v & u \end{bmatrix} \f$.
218
- * These blocks are not sorted in any particular order.
219
- * The matrix \f$ D \f$ and the matrix \f$ V \f$ returned by
220
- * pseudoEigenvectors() satisfy \f$ AV = VD \f$.
221
- *
222
- * \sa pseudoEigenvectors() for an example, eigenvalues()
223
- */
224
- MatrixType pseudoEigenvalueMatrix() const;
225
-
226
- /** \brief Returns the eigenvalues of given matrix.
227
- *
228
- * \returns A const reference to the column vector containing the eigenvalues.
229
- *
230
- * \pre Either the constructor
231
- * EigenSolver(const MatrixType&,bool) or the member function
232
- * compute(const MatrixType&, bool) has been called before.
233
- *
234
- * The eigenvalues are repeated according to their algebraic multiplicity,
235
- * so there are as many eigenvalues as rows in the matrix. The eigenvalues
236
- * are not sorted in any particular order.
237
- *
238
- * Example: \include EigenSolver_eigenvalues.cpp
239
- * Output: \verbinclude EigenSolver_eigenvalues.out
240
- *
241
- * \sa eigenvectors(), pseudoEigenvalueMatrix(),
242
- * MatrixBase::eigenvalues()
243
- */
244
- const EigenvalueType& eigenvalues() const
245
- {
246
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
247
- return m_eivalues;
248
- }
249
-
250
- /** \brief Computes eigendecomposition of given matrix.
251
- *
252
- * \param[in] matrix Square matrix whose eigendecomposition is to be computed.
253
- * \param[in] computeEigenvectors If true, both the eigenvectors and the
254
- * eigenvalues are computed; if false, only the eigenvalues are
255
- * computed.
256
- * \returns Reference to \c *this
257
- *
258
- * This function computes the eigenvalues of the real matrix \p matrix.
259
- * The eigenvalues() function can be used to retrieve them. If
260
- * \p computeEigenvectors is true, then the eigenvectors are also computed
261
- * and can be retrieved by calling eigenvectors().
262
- *
263
- * The matrix is first reduced to real Schur form using the RealSchur
264
- * class. The Schur decomposition is then used to compute the eigenvalues
265
- * and eigenvectors.
266
- *
267
- * The cost of the computation is dominated by the cost of the
268
- * Schur decomposition, which is very approximately \f$ 25n^3 \f$
269
- * (where \f$ n \f$ is the size of the matrix) if \p computeEigenvectors
270
- * is true, and \f$ 10n^3 \f$ if \p computeEigenvectors is false.
271
- *
272
- * This method reuses of the allocated data in the EigenSolver object.
273
- *
274
- * Example: \include EigenSolver_compute.cpp
275
- * Output: \verbinclude EigenSolver_compute.out
276
- */
277
- template<typename InputType>
278
- EigenSolver& compute(const EigenBase<InputType>& matrix, bool computeEigenvectors = true);
279
-
280
- /** \returns NumericalIssue if the input contains INF or NaN values or overflow occurred. Returns Success otherwise. */
281
- ComputationInfo info() const
282
- {
283
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
284
- return m_info;
285
- }
286
-
287
- /** \brief Sets the maximum number of iterations allowed. */
288
- EigenSolver& setMaxIterations(Index maxIters)
289
- {
290
- m_realSchur.setMaxIterations(maxIters);
291
- return *this;
292
- }
293
-
294
- /** \brief Returns the maximum number of iterations. */
295
- Index getMaxIterations()
296
- {
297
- return m_realSchur.getMaxIterations();
298
- }
299
-
300
- private:
301
- void doComputeEigenvectors();
302
-
303
- protected:
304
-
305
- static void check_template_parameters()
306
- {
307
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
308
- EIGEN_STATIC_ASSERT(!NumTraits<Scalar>::IsComplex, NUMERIC_TYPE_MUST_BE_REAL);
309
- }
310
-
311
- MatrixType m_eivec;
312
- EigenvalueType m_eivalues;
313
- bool m_isInitialized;
314
- bool m_eigenvectorsOk;
315
- ComputationInfo m_info;
316
- RealSchur<MatrixType> m_realSchur;
317
- MatrixType m_matT;
318
-
319
- typedef Matrix<Scalar, ColsAtCompileTime, 1, Options & ~RowMajor, MaxColsAtCompileTime, 1> ColumnVectorType;
320
- ColumnVectorType m_tmp;
321
- };
322
-
323
- template<typename MatrixType>
324
- MatrixType EigenSolver<MatrixType>::pseudoEigenvalueMatrix() const
325
- {
326
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
327
- const RealScalar precision = RealScalar(2)*NumTraits<RealScalar>::epsilon();
328
- Index n = m_eivalues.rows();
329
- MatrixType matD = MatrixType::Zero(n,n);
330
- for (Index i=0; i<n; ++i)
331
- {
332
- if (internal::isMuchSmallerThan(numext::imag(m_eivalues.coeff(i)), numext::real(m_eivalues.coeff(i)), precision))
333
- matD.coeffRef(i,i) = numext::real(m_eivalues.coeff(i));
334
- else
335
- {
336
- matD.template block<2,2>(i,i) << numext::real(m_eivalues.coeff(i)), numext::imag(m_eivalues.coeff(i)),
337
- -numext::imag(m_eivalues.coeff(i)), numext::real(m_eivalues.coeff(i));
338
- ++i;
339
- }
340
- }
341
- return matD;
342
- }
343
-
344
- template<typename MatrixType>
345
- typename EigenSolver<MatrixType>::EigenvectorsType EigenSolver<MatrixType>::eigenvectors() const
346
- {
347
- eigen_assert(m_isInitialized && "EigenSolver is not initialized.");
348
- eigen_assert(m_eigenvectorsOk && "The eigenvectors have not been computed together with the eigenvalues.");
349
- const RealScalar precision = RealScalar(2)*NumTraits<RealScalar>::epsilon();
350
- Index n = m_eivec.cols();
351
- EigenvectorsType matV(n,n);
352
- for (Index j=0; j<n; ++j)
353
- {
354
- if (internal::isMuchSmallerThan(numext::imag(m_eivalues.coeff(j)), numext::real(m_eivalues.coeff(j)), precision) || j+1==n)
355
- {
356
- // we have a real eigen value
357
- matV.col(j) = m_eivec.col(j).template cast<ComplexScalar>();
358
- matV.col(j).normalize();
359
- }
360
- else
361
- {
362
- // we have a pair of complex eigen values
363
- for (Index i=0; i<n; ++i)
364
- {
365
- matV.coeffRef(i,j) = ComplexScalar(m_eivec.coeff(i,j), m_eivec.coeff(i,j+1));
366
- matV.coeffRef(i,j+1) = ComplexScalar(m_eivec.coeff(i,j), -m_eivec.coeff(i,j+1));
367
- }
368
- matV.col(j).normalize();
369
- matV.col(j+1).normalize();
370
- ++j;
371
- }
372
- }
373
- return matV;
374
- }
375
-
376
- template<typename MatrixType>
377
- template<typename InputType>
378
- EigenSolver<MatrixType>&
379
- EigenSolver<MatrixType>::compute(const EigenBase<InputType>& matrix, bool computeEigenvectors)
380
- {
381
- check_template_parameters();
382
-
383
- using std::sqrt;
384
- using std::abs;
385
- using numext::isfinite;
386
- eigen_assert(matrix.cols() == matrix.rows());
387
-
388
- // Reduce to real Schur form.
389
- m_realSchur.compute(matrix.derived(), computeEigenvectors);
390
-
391
- m_info = m_realSchur.info();
392
-
393
- if (m_info == Success)
394
- {
395
- m_matT = m_realSchur.matrixT();
396
- if (computeEigenvectors)
397
- m_eivec = m_realSchur.matrixU();
398
-
399
- // Compute eigenvalues from matT
400
- m_eivalues.resize(matrix.cols());
401
- Index i = 0;
402
- while (i < matrix.cols())
403
- {
404
- if (i == matrix.cols() - 1 || m_matT.coeff(i+1, i) == Scalar(0))
405
- {
406
- m_eivalues.coeffRef(i) = m_matT.coeff(i, i);
407
- if(!(isfinite)(m_eivalues.coeffRef(i)))
408
- {
409
- m_isInitialized = true;
410
- m_eigenvectorsOk = false;
411
- m_info = NumericalIssue;
412
- return *this;
413
- }
414
- ++i;
415
- }
416
- else
417
- {
418
- Scalar p = Scalar(0.5) * (m_matT.coeff(i, i) - m_matT.coeff(i+1, i+1));
419
- Scalar z;
420
- // Compute z = sqrt(abs(p * p + m_matT.coeff(i+1, i) * m_matT.coeff(i, i+1)));
421
- // without overflow
422
- {
423
- Scalar t0 = m_matT.coeff(i+1, i);
424
- Scalar t1 = m_matT.coeff(i, i+1);
425
- Scalar maxval = numext::maxi<Scalar>(abs(p),numext::maxi<Scalar>(abs(t0),abs(t1)));
426
- t0 /= maxval;
427
- t1 /= maxval;
428
- Scalar p0 = p/maxval;
429
- z = maxval * sqrt(abs(p0 * p0 + t0 * t1));
430
- }
431
-
432
- m_eivalues.coeffRef(i) = ComplexScalar(m_matT.coeff(i+1, i+1) + p, z);
433
- m_eivalues.coeffRef(i+1) = ComplexScalar(m_matT.coeff(i+1, i+1) + p, -z);
434
- if(!((isfinite)(m_eivalues.coeffRef(i)) && (isfinite)(m_eivalues.coeffRef(i+1))))
435
- {
436
- m_isInitialized = true;
437
- m_eigenvectorsOk = false;
438
- m_info = NumericalIssue;
439
- return *this;
440
- }
441
- i += 2;
442
- }
443
- }
444
-
445
- // Compute eigenvectors.
446
- if (computeEigenvectors)
447
- doComputeEigenvectors();
448
- }
449
-
450
- m_isInitialized = true;
451
- m_eigenvectorsOk = computeEigenvectors;
452
-
453
- return *this;
454
- }
455
-
456
-
457
- template<typename MatrixType>
458
- void EigenSolver<MatrixType>::doComputeEigenvectors()
459
- {
460
- using std::abs;
461
- const Index size = m_eivec.cols();
462
- const Scalar eps = NumTraits<Scalar>::epsilon();
463
-
464
- // inefficient! this is already computed in RealSchur
465
- Scalar norm(0);
466
- for (Index j = 0; j < size; ++j)
467
- {
468
- norm += m_matT.row(j).segment((std::max)(j-1,Index(0)), size-(std::max)(j-1,Index(0))).cwiseAbs().sum();
469
- }
470
-
471
- // Backsubstitute to find vectors of upper triangular form
472
- if (norm == Scalar(0))
473
- {
474
- return;
475
- }
476
-
477
- for (Index n = size-1; n >= 0; n--)
478
- {
479
- Scalar p = m_eivalues.coeff(n).real();
480
- Scalar q = m_eivalues.coeff(n).imag();
481
-
482
- // Scalar vector
483
- if (q == Scalar(0))
484
- {
485
- Scalar lastr(0), lastw(0);
486
- Index l = n;
487
-
488
- m_matT.coeffRef(n,n) = Scalar(1);
489
- for (Index i = n-1; i >= 0; i--)
490
- {
491
- Scalar w = m_matT.coeff(i,i) - p;
492
- Scalar r = m_matT.row(i).segment(l,n-l+1).dot(m_matT.col(n).segment(l, n-l+1));
493
-
494
- if (m_eivalues.coeff(i).imag() < Scalar(0))
495
- {
496
- lastw = w;
497
- lastr = r;
498
- }
499
- else
500
- {
501
- l = i;
502
- if (m_eivalues.coeff(i).imag() == Scalar(0))
503
- {
504
- if (w != Scalar(0))
505
- m_matT.coeffRef(i,n) = -r / w;
506
- else
507
- m_matT.coeffRef(i,n) = -r / (eps * norm);
508
- }
509
- else // Solve real equations
510
- {
511
- Scalar x = m_matT.coeff(i,i+1);
512
- Scalar y = m_matT.coeff(i+1,i);
513
- Scalar denom = (m_eivalues.coeff(i).real() - p) * (m_eivalues.coeff(i).real() - p) + m_eivalues.coeff(i).imag() * m_eivalues.coeff(i).imag();
514
- Scalar t = (x * lastr - lastw * r) / denom;
515
- m_matT.coeffRef(i,n) = t;
516
- if (abs(x) > abs(lastw))
517
- m_matT.coeffRef(i+1,n) = (-r - w * t) / x;
518
- else
519
- m_matT.coeffRef(i+1,n) = (-lastr - y * t) / lastw;
520
- }
521
-
522
- // Overflow control
523
- Scalar t = abs(m_matT.coeff(i,n));
524
- if ((eps * t) * t > Scalar(1))
525
- m_matT.col(n).tail(size-i) /= t;
526
- }
527
- }
528
- }
529
- else if (q < Scalar(0) && n > 0) // Complex vector
530
- {
531
- Scalar lastra(0), lastsa(0), lastw(0);
532
- Index l = n-1;
533
-
534
- // Last vector component imaginary so matrix is triangular
535
- if (abs(m_matT.coeff(n,n-1)) > abs(m_matT.coeff(n-1,n)))
536
- {
537
- m_matT.coeffRef(n-1,n-1) = q / m_matT.coeff(n,n-1);
538
- m_matT.coeffRef(n-1,n) = -(m_matT.coeff(n,n) - p) / m_matT.coeff(n,n-1);
539
- }
540
- else
541
- {
542
- ComplexScalar cc = ComplexScalar(Scalar(0),-m_matT.coeff(n-1,n)) / ComplexScalar(m_matT.coeff(n-1,n-1)-p,q);
543
- m_matT.coeffRef(n-1,n-1) = numext::real(cc);
544
- m_matT.coeffRef(n-1,n) = numext::imag(cc);
545
- }
546
- m_matT.coeffRef(n,n-1) = Scalar(0);
547
- m_matT.coeffRef(n,n) = Scalar(1);
548
- for (Index i = n-2; i >= 0; i--)
549
- {
550
- Scalar ra = m_matT.row(i).segment(l, n-l+1).dot(m_matT.col(n-1).segment(l, n-l+1));
551
- Scalar sa = m_matT.row(i).segment(l, n-l+1).dot(m_matT.col(n).segment(l, n-l+1));
552
- Scalar w = m_matT.coeff(i,i) - p;
553
-
554
- if (m_eivalues.coeff(i).imag() < Scalar(0))
555
- {
556
- lastw = w;
557
- lastra = ra;
558
- lastsa = sa;
559
- }
560
- else
561
- {
562
- l = i;
563
- if (m_eivalues.coeff(i).imag() == RealScalar(0))
564
- {
565
- ComplexScalar cc = ComplexScalar(-ra,-sa) / ComplexScalar(w,q);
566
- m_matT.coeffRef(i,n-1) = numext::real(cc);
567
- m_matT.coeffRef(i,n) = numext::imag(cc);
568
- }
569
- else
570
- {
571
- // Solve complex equations
572
- Scalar x = m_matT.coeff(i,i+1);
573
- Scalar y = m_matT.coeff(i+1,i);
574
- Scalar vr = (m_eivalues.coeff(i).real() - p) * (m_eivalues.coeff(i).real() - p) + m_eivalues.coeff(i).imag() * m_eivalues.coeff(i).imag() - q * q;
575
- Scalar vi = (m_eivalues.coeff(i).real() - p) * Scalar(2) * q;
576
- if ((vr == Scalar(0)) && (vi == Scalar(0)))
577
- vr = eps * norm * (abs(w) + abs(q) + abs(x) + abs(y) + abs(lastw));
578
-
579
- ComplexScalar cc = ComplexScalar(x*lastra-lastw*ra+q*sa,x*lastsa-lastw*sa-q*ra) / ComplexScalar(vr,vi);
580
- m_matT.coeffRef(i,n-1) = numext::real(cc);
581
- m_matT.coeffRef(i,n) = numext::imag(cc);
582
- if (abs(x) > (abs(lastw) + abs(q)))
583
- {
584
- m_matT.coeffRef(i+1,n-1) = (-ra - w * m_matT.coeff(i,n-1) + q * m_matT.coeff(i,n)) / x;
585
- m_matT.coeffRef(i+1,n) = (-sa - w * m_matT.coeff(i,n) - q * m_matT.coeff(i,n-1)) / x;
586
- }
587
- else
588
- {
589
- cc = ComplexScalar(-lastra-y*m_matT.coeff(i,n-1),-lastsa-y*m_matT.coeff(i,n)) / ComplexScalar(lastw,q);
590
- m_matT.coeffRef(i+1,n-1) = numext::real(cc);
591
- m_matT.coeffRef(i+1,n) = numext::imag(cc);
592
- }
593
- }
594
-
595
- // Overflow control
596
- Scalar t = numext::maxi<Scalar>(abs(m_matT.coeff(i,n-1)),abs(m_matT.coeff(i,n)));
597
- if ((eps * t) * t > Scalar(1))
598
- m_matT.block(i, n-1, size-i, 2) /= t;
599
-
600
- }
601
- }
602
-
603
- // We handled a pair of complex conjugate eigenvalues, so need to skip them both
604
- n--;
605
- }
606
- else
607
- {
608
- eigen_assert(0 && "Internal bug in EigenSolver (INF or NaN has not been detected)"); // this should not happen
609
- }
610
- }
611
-
612
- // Back transformation to get eigenvectors of original matrix
613
- for (Index j = size-1; j >= 0; j--)
614
- {
615
- m_tmp.noalias() = m_eivec.leftCols(j+1) * m_matT.col(j).segment(0, j+1);
616
- m_eivec.col(j) = m_tmp;
617
- }
618
- }
619
-
620
- } // end namespace Eigen
621
-
622
- #endif // EIGEN_EIGENSOLVER_H