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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@@ -1,462 +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 {
20
- template<typename MatrixType, bool IsComplex> struct complex_schur_reduce_to_hessenberg;
21
- }
22
-
23
- /** \eigenvalues_module \ingroup Eigenvalues_Module
24
- *
25
- *
26
- * \class ComplexSchur
27
- *
28
- * \brief Performs a complex Schur decomposition of a real or complex square matrix
29
- *
30
- * \tparam _MatrixType the type of the matrix of which we are
31
- * computing the Schur decomposition; this is expected to be an
32
- * instantiation of the Matrix class template.
33
- *
34
- * Given a real or complex square matrix A, this class computes the
35
- * Schur decomposition: \f$ A = U T U^*\f$ where U is a unitary
36
- * complex matrix, and T is a complex upper triangular matrix. The
37
- * diagonal of the matrix T corresponds to the eigenvalues of the
38
- * matrix A.
39
- *
40
- * Call the function compute() to compute the Schur decomposition of
41
- * a given matrix. Alternatively, you can use the
42
- * ComplexSchur(const MatrixType&, bool) constructor which computes
43
- * the Schur decomposition at construction time. Once the
44
- * decomposition is computed, you can use the matrixU() and matrixT()
45
- * functions to retrieve the matrices U and V in the decomposition.
46
- *
47
- * \note This code is inspired from Jampack
48
- *
49
- * \sa class RealSchur, class EigenSolver, class ComplexEigenSolver
50
- */
51
- template<typename _MatrixType> class ComplexSchur
52
- {
53
- public:
54
- typedef _MatrixType MatrixType;
55
- enum {
56
- RowsAtCompileTime = MatrixType::RowsAtCompileTime,
57
- ColsAtCompileTime = MatrixType::ColsAtCompileTime,
58
- Options = MatrixType::Options,
59
- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
60
- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
61
- };
62
-
63
- /** \brief Scalar type for matrices of type \p _MatrixType. */
64
- typedef typename MatrixType::Scalar Scalar;
65
- typedef typename NumTraits<Scalar>::Real RealScalar;
66
- typedef Eigen::Index Index; ///< \deprecated since Eigen 3.3
67
-
68
- /** \brief Complex scalar type for \p _MatrixType.
69
- *
70
- * This is \c std::complex<Scalar> if #Scalar is real (e.g.,
71
- * \c float or \c double) and just \c Scalar if #Scalar is
72
- * complex.
73
- */
74
- typedef std::complex<RealScalar> ComplexScalar;
75
-
76
- /** \brief Type for the matrices in the Schur decomposition.
77
- *
78
- * This is a square matrix with entries of type #ComplexScalar.
79
- * The size is the same as the size of \p _MatrixType.
80
- */
81
- typedef Matrix<ComplexScalar, RowsAtCompileTime, ColsAtCompileTime, Options, MaxRowsAtCompileTime, MaxColsAtCompileTime> ComplexMatrixType;
82
-
83
- /** \brief Default constructor.
84
- *
85
- * \param [in] size Positive integer, size of the matrix whose Schur decomposition will be computed.
86
- *
87
- * The default constructor is useful in cases in which the user
88
- * intends to perform decompositions via compute(). The \p size
89
- * parameter is only used as a hint. It is not an error to give a
90
- * wrong \p size, but it may impair performance.
91
- *
92
- * \sa compute() for an example.
93
- */
94
- explicit ComplexSchur(Index size = RowsAtCompileTime==Dynamic ? 1 : RowsAtCompileTime)
95
- : m_matT(size,size),
96
- m_matU(size,size),
97
- m_hess(size),
98
- m_isInitialized(false),
99
- m_matUisUptodate(false),
100
- m_maxIters(-1)
101
- {}
102
-
103
- /** \brief Constructor; computes Schur decomposition of given matrix.
104
- *
105
- * \param[in] matrix Square matrix whose Schur decomposition is to be computed.
106
- * \param[in] computeU If true, both T and U are computed; if false, only T is computed.
107
- *
108
- * This constructor calls compute() to compute the Schur decomposition.
109
- *
110
- * \sa matrixT() and matrixU() for examples.
111
- */
112
- 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)
131
- * has been called before to compute the Schur decomposition of a
132
- * matrix, and that \p computeU was set to true (the default
133
- * 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.");
141
- eigen_assert(m_matUisUptodate && "The matrix U has not been computed during the ComplexSchur decomposition.");
142
- return m_matU;
143
- }
144
-
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
151
- * member function compute(const MatrixType& matrix, bool computeU)
152
- * has been called before to compute the Schur decomposition of a
153
- * matrix.
154
- *
155
- * Note that this function returns a plain square matrix. If you want to reference
156
- * only the upper triangular part, use:
157
- * \code schur.matrixT().triangularView<Upper>() \endcode
158
- *
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
- *
170
- * \param[in] matrix Square matrix whose Schur decomposition is to be computed.
171
- * \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
- *
175
- * The Schur decomposition is computed by first reducing the
176
- * matrix to Hessenberg form using the class
177
- * HessenbergDecomposition. The Hessenberg matrix is then reduced
178
- * to triangular form by performing QR iterations with a single
179
- * shift. The cost of computing the Schur decomposition depends
180
- * on the number of iterations; as a rough guide, it may be taken
181
- * on the number of iterations; as a rough guide, it may be taken
182
- * to be \f$25n^3\f$ complex flops, or \f$10n^3\f$ complex flops
183
- * if \a computeU is false.
184
- *
185
- * Example: \include ComplexSchur_compute.cpp
186
- * Output: \verbinclude ComplexSchur_compute.out
187
- *
188
- * \sa compute(const MatrixType&, bool, Index)
189
- */
190
- template<typename InputType>
191
- ComplexSchur& compute(const EigenBase<InputType>& matrix, bool computeU = true);
192
-
193
- /** \brief Compute Schur decomposition from a given Hessenberg matrix
194
- * \param[in] matrixH Matrix in Hessenberg form H
195
- * \param[in] matrixQ orthogonal matrix Q that transform a matrix A to H : A = Q H Q^T
196
- * \param computeU Computes the matriX U of the Schur vectors
197
- * \return Reference to \c *this
198
- *
199
- * This routine assumes that the matrix is already reduced in Hessenberg form matrixH
200
- * using either the class HessenbergDecomposition or another mean.
201
- * It computes the upper quasi-triangular matrix T of the Schur decomposition of H
202
- * When computeU is true, this routine computes the matrix U such that
203
- * A = U T U^T = (QZ) T (QZ)^T = Q H Q^T where A is the initial matrix
204
- *
205
- * NOTE Q is referenced if computeU is true; so, if the initial orthogonal matrix
206
- * is not available, the user should give an identity matrix (Q.setIdentity())
207
- *
208
- * \sa compute(const MatrixType&, bool)
209
- */
210
- 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.
214
- *
215
- * \returns \c Success if computation was successful, \c NoConvergence otherwise.
216
- */
217
- ComputationInfo info() const
218
- {
219
- eigen_assert(m_isInitialized && "ComplexSchur is not initialized.");
220
- return m_info;
221
- }
222
-
223
- /** \brief Sets the maximum number of iterations allowed.
224
- *
225
- * If not specified by the user, the maximum number of iterations is m_maxIterationsPerRow times the size
226
- * of the matrix.
227
- */
228
- ComplexSchur& setMaxIterations(Index maxIters)
229
- {
230
- m_maxIters = maxIters;
231
- 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;
254
-
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>
344
- ComplexSchur<MatrixType>& ComplexSchur<MatrixType>::computeFromHessenberg(const HessMatrixType& matrixH, const OrthMatrixType& matrixQ, bool computeU)
345
- {
346
- m_matT = matrixH;
347
- if(computeU)
348
- m_matU = matrixQ;
349
- reduceToTriangularForm(computeU);
350
- return *this;
351
- }
352
- namespace internal {
353
-
354
- /* Reduce given matrix to Hessenberg form */
355
- template<typename MatrixType, bool IsComplex>
356
- struct complex_schur_reduce_to_hessenberg
357
- {
358
- // this is the implementation for the case IsComplex = true
359
- static void run(ComplexSchur<MatrixType>& _this, const MatrixType& matrix, bool computeU)
360
- {
361
- _this.m_hess.compute(matrix);
362
- _this.m_matT = _this.m_hess.matrixH();
363
- if(computeU) _this.m_matU = _this.m_hess.matrixQ();
364
- }
365
- };
366
-
367
- template<typename MatrixType>
368
- struct complex_schur_reduce_to_hessenberg<MatrixType, false>
369
- {
370
- static void run(ComplexSchur<MatrixType>& _this, const MatrixType& matrix, bool computeU)
371
- {
372
- typedef typename ComplexSchur<MatrixType>::ComplexScalar ComplexScalar;
373
-
374
- // Note: m_hess is over RealScalar; m_matT and m_matU is over ComplexScalar
375
- _this.m_hess.compute(matrix);
376
- _this.m_matT = _this.m_hess.matrixH().template cast<ComplexScalar>();
377
- if(computeU)
378
- {
379
- // This may cause an allocation which seems to be avoidable
380
- MatrixType Q = _this.m_hess.matrixQ();
381
- _this.m_matU = Q.template cast<ComplexScalar>();
382
- }
383
- }
384
- };
385
-
386
- } // end namespace internal
387
-
388
- // Reduce the Hessenberg matrix m_matT to triangular form by QR iteration.
389
- template<typename MatrixType>
390
- void ComplexSchur<MatrixType>::reduceToTriangularForm(bool computeU)
391
- {
392
- Index maxIters = m_maxIters;
393
- if (maxIters == -1)
394
- maxIters = m_maxIterationsPerRow * m_matT.rows();
395
-
396
- // The matrix m_matT is divided in three parts.
397
- // Rows 0,...,il-1 are decoupled from the rest because m_matT(il,il-1) is zero.
398
- // Rows il,...,iu is the part we are working on (the active submatrix).
399
- // Rows iu+1,...,end are already brought in triangular form.
400
- Index iu = m_matT.cols() - 1;
401
- Index il;
402
- Index iter = 0; // number of iterations we are working on the (iu,iu) element
403
- Index totalIter = 0; // number of iterations for whole matrix
404
-
405
- while(true)
406
- {
407
- // 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
- }
414
-
415
- // if iu is zero then we are done; the whole matrix is triangularized
416
- if(iu==0) break;
417
-
418
- // 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