sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.20__cp39-cp39-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/hierarchical_clustering.py +108 -6
  6. sequenzo/define_sequence_data.py +10 -1
  7. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  8. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  9. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  11. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  12. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  14. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  16. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  18. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  19. sequenzo/multidomain/cat.py +0 -53
  20. sequenzo/multidomain/dat.py +11 -3
  21. sequenzo/multidomain/idcd.py +0 -3
  22. sequenzo/multidomain/linked_polyad.py +0 -1
  23. sequenzo/openmp_setup.py +233 -0
  24. sequenzo/visualization/plot_transition_matrix.py +21 -22
  25. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  26. sequenzo-0.1.20.dist-info/RECORD +215 -0
  27. sequenzo/dissimilarity_measures/setup.py +0 -35
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  171. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  172. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  173. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  174. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  175. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  176. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  177. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  178. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  179. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  180. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  181. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  182. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  183. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  184. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  185. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  186. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  187. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  188. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  189. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  190. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  191. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  192. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  193. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  194. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  195. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  196. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  197. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  198. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  199. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  200. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  201. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  202. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  203. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  204. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  205. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  206. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  207. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  208. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  209. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
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  359. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,635 +0,0 @@
1
- // 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) 2016 Rasmus Munk Larsen <rmlarsen@google.com>
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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_COMPLETEORTHOGONALDECOMPOSITION_H
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- #define EIGEN_COMPLETEORTHOGONALDECOMPOSITION_H
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-
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- namespace Eigen {
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-
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- namespace internal {
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- template <typename _MatrixType>
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- struct traits<CompleteOrthogonalDecomposition<_MatrixType> >
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- : traits<_MatrixType> {
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- typedef MatrixXpr XprKind;
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- typedef SolverStorage StorageKind;
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- typedef int StorageIndex;
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- enum { Flags = 0 };
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- };
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-
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- } // end namespace internal
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-
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- /** \ingroup QR_Module
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- *
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- * \class CompleteOrthogonalDecomposition
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- *
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- * \brief Complete orthogonal decomposition (COD) of a matrix.
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- *
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- * \param MatrixType the type of the matrix of which we are computing the COD.
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- *
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- * This class performs a rank-revealing complete orthogonal decomposition of a
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- * matrix \b A into matrices \b P, \b Q, \b T, and \b Z such that
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- * \f[
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- * \mathbf{A} \, \mathbf{P} = \mathbf{Q} \,
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- * \begin{bmatrix} \mathbf{T} & \mathbf{0} \\
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- * \mathbf{0} & \mathbf{0} \end{bmatrix} \, \mathbf{Z}
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- * \f]
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- * by using Householder transformations. Here, \b P is a permutation matrix,
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- * \b Q and \b Z are unitary matrices and \b T an upper triangular matrix of
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- * size rank-by-rank. \b A may be rank deficient.
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- *
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- * This class supports the \link InplaceDecomposition inplace decomposition \endlink mechanism.
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- *
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- * \sa MatrixBase::completeOrthogonalDecomposition()
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- */
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- template <typename _MatrixType> class CompleteOrthogonalDecomposition
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- : public SolverBase<CompleteOrthogonalDecomposition<_MatrixType> >
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- {
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- public:
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- typedef _MatrixType MatrixType;
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- typedef SolverBase<CompleteOrthogonalDecomposition> Base;
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-
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- template<typename Derived>
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- friend struct internal::solve_assertion;
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-
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- EIGEN_GENERIC_PUBLIC_INTERFACE(CompleteOrthogonalDecomposition)
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- enum {
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- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
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- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
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- };
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- typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
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- typedef PermutationMatrix<ColsAtCompileTime, MaxColsAtCompileTime>
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- PermutationType;
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- typedef typename internal::plain_row_type<MatrixType, Index>::type
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- IntRowVectorType;
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- typedef typename internal::plain_row_type<MatrixType>::type RowVectorType;
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- typedef typename internal::plain_row_type<MatrixType, RealScalar>::type
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- RealRowVectorType;
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- typedef HouseholderSequence<
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- MatrixType, typename internal::remove_all<
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- typename HCoeffsType::ConjugateReturnType>::type>
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- HouseholderSequenceType;
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- typedef typename MatrixType::PlainObject PlainObject;
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-
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- private:
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- typedef typename PermutationType::Index PermIndexType;
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-
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- public:
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- /**
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- * \brief Default Constructor.
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- *
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- * The default constructor is useful in cases in which the user intends to
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- * perform decompositions via
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- * \c CompleteOrthogonalDecomposition::compute(const* MatrixType&).
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- */
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- CompleteOrthogonalDecomposition() : m_cpqr(), m_zCoeffs(), m_temp() {}
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-
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- /** \brief Default Constructor with memory preallocation
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- *
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- * Like the default constructor but with preallocation of the internal data
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- * according to the specified problem \a size.
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- * \sa CompleteOrthogonalDecomposition()
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- */
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- CompleteOrthogonalDecomposition(Index rows, Index cols)
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- : m_cpqr(rows, cols), m_zCoeffs((std::min)(rows, cols)), m_temp(cols) {}
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-
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- /** \brief Constructs a complete orthogonal decomposition from a given
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- * matrix.
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- *
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- * This constructor computes the complete orthogonal decomposition of the
105
- * matrix \a matrix by calling the method compute(). The default
106
- * threshold for rank determination will be used. It is a short cut for:
107
- *
108
- * \code
109
- * CompleteOrthogonalDecomposition<MatrixType> cod(matrix.rows(),
110
- * matrix.cols());
111
- * cod.setThreshold(Default);
112
- * cod.compute(matrix);
113
- * \endcode
114
- *
115
- * \sa compute()
116
- */
117
- template <typename InputType>
118
- explicit CompleteOrthogonalDecomposition(const EigenBase<InputType>& matrix)
119
- : m_cpqr(matrix.rows(), matrix.cols()),
120
- m_zCoeffs((std::min)(matrix.rows(), matrix.cols())),
121
- m_temp(matrix.cols())
122
- {
123
- compute(matrix.derived());
124
- }
125
-
126
- /** \brief Constructs a complete orthogonal decomposition from a given matrix
127
- *
128
- * This overloaded constructor is provided for \link InplaceDecomposition inplace decomposition \endlink when \c MatrixType is a Eigen::Ref.
129
- *
130
- * \sa CompleteOrthogonalDecomposition(const EigenBase&)
131
- */
132
- template<typename InputType>
133
- explicit CompleteOrthogonalDecomposition(EigenBase<InputType>& matrix)
134
- : m_cpqr(matrix.derived()),
135
- m_zCoeffs((std::min)(matrix.rows(), matrix.cols())),
136
- m_temp(matrix.cols())
137
- {
138
- computeInPlace();
139
- }
140
-
141
- #ifdef EIGEN_PARSED_BY_DOXYGEN
142
- /** This method computes the minimum-norm solution X to a least squares
143
- * problem \f[\mathrm{minimize} \|A X - B\|, \f] where \b A is the matrix of
144
- * which \c *this is the complete orthogonal decomposition.
145
- *
146
- * \param b the right-hand sides of the problem to solve.
147
- *
148
- * \returns a solution.
149
- *
150
- */
151
- template <typename Rhs>
152
- inline const Solve<CompleteOrthogonalDecomposition, Rhs> solve(
153
- const MatrixBase<Rhs>& b) const;
154
- #endif
155
-
156
- HouseholderSequenceType householderQ(void) const;
157
- HouseholderSequenceType matrixQ(void) const { return m_cpqr.householderQ(); }
158
-
159
- /** \returns the matrix \b Z.
160
- */
161
- MatrixType matrixZ() const {
162
- MatrixType Z = MatrixType::Identity(m_cpqr.cols(), m_cpqr.cols());
163
- applyZOnTheLeftInPlace<false>(Z);
164
- return Z;
165
- }
166
-
167
- /** \returns a reference to the matrix where the complete orthogonal
168
- * decomposition is stored
169
- */
170
- const MatrixType& matrixQTZ() const { return m_cpqr.matrixQR(); }
171
-
172
- /** \returns a reference to the matrix where the complete orthogonal
173
- * decomposition is stored.
174
- * \warning The strict lower part and \code cols() - rank() \endcode right
175
- * columns of this matrix contains internal values.
176
- * Only the upper triangular part should be referenced. To get it, use
177
- * \code matrixT().template triangularView<Upper>() \endcode
178
- * For rank-deficient matrices, use
179
- * \code
180
- * matrixR().topLeftCorner(rank(), rank()).template triangularView<Upper>()
181
- * \endcode
182
- */
183
- const MatrixType& matrixT() const { return m_cpqr.matrixQR(); }
184
-
185
- template <typename InputType>
186
- CompleteOrthogonalDecomposition& compute(const EigenBase<InputType>& matrix) {
187
- // Compute the column pivoted QR factorization A P = Q R.
188
- m_cpqr.compute(matrix);
189
- computeInPlace();
190
- return *this;
191
- }
192
-
193
- /** \returns a const reference to the column permutation matrix */
194
- const PermutationType& colsPermutation() const {
195
- return m_cpqr.colsPermutation();
196
- }
197
-
198
- /** \returns the absolute value of the determinant of the matrix of which
199
- * *this is the complete orthogonal decomposition. It has only linear
200
- * complexity (that is, O(n) where n is the dimension of the square matrix)
201
- * as the complete orthogonal decomposition has already been computed.
202
- *
203
- * \note This is only for square matrices.
204
- *
205
- * \warning a determinant can be very big or small, so for matrices
206
- * of large enough dimension, there is a risk of overflow/underflow.
207
- * One way to work around that is to use logAbsDeterminant() instead.
208
- *
209
- * \sa logAbsDeterminant(), MatrixBase::determinant()
210
- */
211
- typename MatrixType::RealScalar absDeterminant() const;
212
-
213
- /** \returns the natural log of the absolute value of the determinant of the
214
- * matrix of which *this is the complete orthogonal decomposition. It has
215
- * only linear complexity (that is, O(n) where n is the dimension of the
216
- * square matrix) as the complete orthogonal decomposition has already been
217
- * computed.
218
- *
219
- * \note This is only for square matrices.
220
- *
221
- * \note This method is useful to work around the risk of overflow/underflow
222
- * that's inherent to determinant computation.
223
- *
224
- * \sa absDeterminant(), MatrixBase::determinant()
225
- */
226
- typename MatrixType::RealScalar logAbsDeterminant() const;
227
-
228
- /** \returns the rank of the matrix of which *this is the complete orthogonal
229
- * decomposition.
230
- *
231
- * \note This method has to determine which pivots should be considered
232
- * nonzero. For that, it uses the threshold value that you can control by
233
- * calling setThreshold(const RealScalar&).
234
- */
235
- inline Index rank() const { return m_cpqr.rank(); }
236
-
237
- /** \returns the dimension of the kernel of the matrix of which *this is the
238
- * complete orthogonal decomposition.
239
- *
240
- * \note This method has to determine which pivots should be considered
241
- * nonzero. For that, it uses the threshold value that you can control by
242
- * calling setThreshold(const RealScalar&).
243
- */
244
- inline Index dimensionOfKernel() const { return m_cpqr.dimensionOfKernel(); }
245
-
246
- /** \returns true if the matrix of which *this is the decomposition represents
247
- * an injective linear map, i.e. has trivial kernel; false otherwise.
248
- *
249
- * \note This method has to determine which pivots should be considered
250
- * nonzero. For that, it uses the threshold value that you can control by
251
- * calling setThreshold(const RealScalar&).
252
- */
253
- inline bool isInjective() const { return m_cpqr.isInjective(); }
254
-
255
- /** \returns true if the matrix of which *this is the decomposition represents
256
- * a surjective linear map; false otherwise.
257
- *
258
- * \note This method has to determine which pivots should be considered
259
- * nonzero. For that, it uses the threshold value that you can control by
260
- * calling setThreshold(const RealScalar&).
261
- */
262
- inline bool isSurjective() const { return m_cpqr.isSurjective(); }
263
-
264
- /** \returns true if the matrix of which *this is the complete orthogonal
265
- * decomposition is invertible.
266
- *
267
- * \note This method has to determine which pivots should be considered
268
- * nonzero. For that, it uses the threshold value that you can control by
269
- * calling setThreshold(const RealScalar&).
270
- */
271
- inline bool isInvertible() const { return m_cpqr.isInvertible(); }
272
-
273
- /** \returns the pseudo-inverse of the matrix of which *this is the complete
274
- * orthogonal decomposition.
275
- * \warning: Do not compute \c this->pseudoInverse()*rhs to solve a linear systems.
276
- * It is more efficient and numerically stable to call \c this->solve(rhs).
277
- */
278
- inline const Inverse<CompleteOrthogonalDecomposition> pseudoInverse() const
279
- {
280
- eigen_assert(m_cpqr.m_isInitialized && "CompleteOrthogonalDecomposition is not initialized.");
281
- return Inverse<CompleteOrthogonalDecomposition>(*this);
282
- }
283
-
284
- inline Index rows() const { return m_cpqr.rows(); }
285
- inline Index cols() const { return m_cpqr.cols(); }
286
-
287
- /** \returns a const reference to the vector of Householder coefficients used
288
- * to represent the factor \c Q.
289
- *
290
- * For advanced uses only.
291
- */
292
- inline const HCoeffsType& hCoeffs() const { return m_cpqr.hCoeffs(); }
293
-
294
- /** \returns a const reference to the vector of Householder coefficients
295
- * used to represent the factor \c Z.
296
- *
297
- * For advanced uses only.
298
- */
299
- const HCoeffsType& zCoeffs() const { return m_zCoeffs; }
300
-
301
- /** Allows to prescribe a threshold to be used by certain methods, such as
302
- * rank(), who need to determine when pivots are to be considered nonzero.
303
- * Most be called before calling compute().
304
- *
305
- * When it needs to get the threshold value, Eigen calls threshold(). By
306
- * default, this uses a formula to automatically determine a reasonable
307
- * threshold. Once you have called the present method
308
- * setThreshold(const RealScalar&), your value is used instead.
309
- *
310
- * \param threshold The new value to use as the threshold.
311
- *
312
- * A pivot will be considered nonzero if its absolute value is strictly
313
- * greater than
314
- * \f$ \vert pivot \vert \leqslant threshold \times \vert maxpivot \vert \f$
315
- * where maxpivot is the biggest pivot.
316
- *
317
- * If you want to come back to the default behavior, call
318
- * setThreshold(Default_t)
319
- */
320
- CompleteOrthogonalDecomposition& setThreshold(const RealScalar& threshold) {
321
- m_cpqr.setThreshold(threshold);
322
- return *this;
323
- }
324
-
325
- /** Allows to come back to the default behavior, letting Eigen use its default
326
- * formula for determining the threshold.
327
- *
328
- * You should pass the special object Eigen::Default as parameter here.
329
- * \code qr.setThreshold(Eigen::Default); \endcode
330
- *
331
- * See the documentation of setThreshold(const RealScalar&).
332
- */
333
- CompleteOrthogonalDecomposition& setThreshold(Default_t) {
334
- m_cpqr.setThreshold(Default);
335
- return *this;
336
- }
337
-
338
- /** Returns the threshold that will be used by certain methods such as rank().
339
- *
340
- * See the documentation of setThreshold(const RealScalar&).
341
- */
342
- RealScalar threshold() const { return m_cpqr.threshold(); }
343
-
344
- /** \returns the number of nonzero pivots in the complete orthogonal
345
- * decomposition. Here nonzero is meant in the exact sense, not in a
346
- * fuzzy sense. So that notion isn't really intrinsically interesting,
347
- * but it is still useful when implementing algorithms.
348
- *
349
- * \sa rank()
350
- */
351
- inline Index nonzeroPivots() const { return m_cpqr.nonzeroPivots(); }
352
-
353
- /** \returns the absolute value of the biggest pivot, i.e. the biggest
354
- * diagonal coefficient of R.
355
- */
356
- inline RealScalar maxPivot() const { return m_cpqr.maxPivot(); }
357
-
358
- /** \brief Reports whether the complete orthogonal decomposition was
359
- * successful.
360
- *
361
- * \note This function always returns \c Success. It is provided for
362
- * compatibility
363
- * with other factorization routines.
364
- * \returns \c Success
365
- */
366
- ComputationInfo info() const {
367
- eigen_assert(m_cpqr.m_isInitialized && "Decomposition is not initialized.");
368
- return Success;
369
- }
370
-
371
- #ifndef EIGEN_PARSED_BY_DOXYGEN
372
- template <typename RhsType, typename DstType>
373
- void _solve_impl(const RhsType& rhs, DstType& dst) const;
374
-
375
- template<bool Conjugate, typename RhsType, typename DstType>
376
- void _solve_impl_transposed(const RhsType &rhs, DstType &dst) const;
377
- #endif
378
-
379
- protected:
380
- static void check_template_parameters() {
381
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
382
- }
383
-
384
- template<bool Transpose_, typename Rhs>
385
- void _check_solve_assertion(const Rhs& b) const {
386
- EIGEN_ONLY_USED_FOR_DEBUG(b);
387
- eigen_assert(m_cpqr.m_isInitialized && "CompleteOrthogonalDecomposition is not initialized.");
388
- eigen_assert((Transpose_?derived().cols():derived().rows())==b.rows() && "CompleteOrthogonalDecomposition::solve(): invalid number of rows of the right hand side matrix b");
389
- }
390
-
391
- void computeInPlace();
392
-
393
- /** Overwrites \b rhs with \f$ \mathbf{Z} * \mathbf{rhs} \f$ or
394
- * \f$ \mathbf{\overline Z} * \mathbf{rhs} \f$ if \c Conjugate
395
- * is set to \c true.
396
- */
397
- template <bool Conjugate, typename Rhs>
398
- void applyZOnTheLeftInPlace(Rhs& rhs) const;
399
-
400
- /** Overwrites \b rhs with \f$ \mathbf{Z}^* * \mathbf{rhs} \f$.
401
- */
402
- template <typename Rhs>
403
- void applyZAdjointOnTheLeftInPlace(Rhs& rhs) const;
404
-
405
- ColPivHouseholderQR<MatrixType> m_cpqr;
406
- HCoeffsType m_zCoeffs;
407
- RowVectorType m_temp;
408
- };
409
-
410
- template <typename MatrixType>
411
- typename MatrixType::RealScalar
412
- CompleteOrthogonalDecomposition<MatrixType>::absDeterminant() const {
413
- return m_cpqr.absDeterminant();
414
- }
415
-
416
- template <typename MatrixType>
417
- typename MatrixType::RealScalar
418
- CompleteOrthogonalDecomposition<MatrixType>::logAbsDeterminant() const {
419
- return m_cpqr.logAbsDeterminant();
420
- }
421
-
422
- /** Performs the complete orthogonal decomposition of the given matrix \a
423
- * matrix. The result of the factorization is stored into \c *this, and a
424
- * reference to \c *this is returned.
425
- *
426
- * \sa class CompleteOrthogonalDecomposition,
427
- * CompleteOrthogonalDecomposition(const MatrixType&)
428
- */
429
- template <typename MatrixType>
430
- void CompleteOrthogonalDecomposition<MatrixType>::computeInPlace()
431
- {
432
- check_template_parameters();
433
-
434
- // the column permutation is stored as int indices, so just to be sure:
435
- eigen_assert(m_cpqr.cols() <= NumTraits<int>::highest());
436
-
437
- const Index rank = m_cpqr.rank();
438
- const Index cols = m_cpqr.cols();
439
- const Index rows = m_cpqr.rows();
440
- m_zCoeffs.resize((std::min)(rows, cols));
441
- m_temp.resize(cols);
442
-
443
- if (rank < cols) {
444
- // We have reduced the (permuted) matrix to the form
445
- // [R11 R12]
446
- // [ 0 R22]
447
- // where R11 is r-by-r (r = rank) upper triangular, R12 is
448
- // r-by-(n-r), and R22 is empty or the norm of R22 is negligible.
449
- // We now compute the complete orthogonal decomposition by applying
450
- // Householder transformations from the right to the upper trapezoidal
451
- // matrix X = [R11 R12] to zero out R12 and obtain the factorization
452
- // [R11 R12] = [T11 0] * Z, where T11 is r-by-r upper triangular and
453
- // Z = Z(0) * Z(1) ... Z(r-1) is an n-by-n orthogonal matrix.
454
- // We store the data representing Z in R12 and m_zCoeffs.
455
- for (Index k = rank - 1; k >= 0; --k) {
456
- if (k != rank - 1) {
457
- // Given the API for Householder reflectors, it is more convenient if
458
- // we swap the leading parts of columns k and r-1 (zero-based) to form
459
- // the matrix X_k = [X(0:k, k), X(0:k, r:n)]
460
- m_cpqr.m_qr.col(k).head(k + 1).swap(
461
- m_cpqr.m_qr.col(rank - 1).head(k + 1));
462
- }
463
- // Construct Householder reflector Z(k) to zero out the last row of X_k,
464
- // i.e. choose Z(k) such that
465
- // [X(k, k), X(k, r:n)] * Z(k) = [beta, 0, .., 0].
466
- RealScalar beta;
467
- m_cpqr.m_qr.row(k)
468
- .tail(cols - rank + 1)
469
- .makeHouseholderInPlace(m_zCoeffs(k), beta);
470
- m_cpqr.m_qr(k, rank - 1) = beta;
471
- if (k > 0) {
472
- // Apply Z(k) to the first k rows of X_k
473
- m_cpqr.m_qr.topRightCorner(k, cols - rank + 1)
474
- .applyHouseholderOnTheRight(
475
- m_cpqr.m_qr.row(k).tail(cols - rank).adjoint(), m_zCoeffs(k),
476
- &m_temp(0));
477
- }
478
- if (k != rank - 1) {
479
- // Swap X(0:k,k) back to its proper location.
480
- m_cpqr.m_qr.col(k).head(k + 1).swap(
481
- m_cpqr.m_qr.col(rank - 1).head(k + 1));
482
- }
483
- }
484
- }
485
- }
486
-
487
- template <typename MatrixType>
488
- template <bool Conjugate, typename Rhs>
489
- void CompleteOrthogonalDecomposition<MatrixType>::applyZOnTheLeftInPlace(
490
- Rhs& rhs) const {
491
- const Index cols = this->cols();
492
- const Index nrhs = rhs.cols();
493
- const Index rank = this->rank();
494
- Matrix<typename Rhs::Scalar, Dynamic, 1> temp((std::max)(cols, nrhs));
495
- for (Index k = rank-1; k >= 0; --k) {
496
- if (k != rank - 1) {
497
- rhs.row(k).swap(rhs.row(rank - 1));
498
- }
499
- rhs.middleRows(rank - 1, cols - rank + 1)
500
- .applyHouseholderOnTheLeft(
501
- matrixQTZ().row(k).tail(cols - rank).transpose().template conjugateIf<!Conjugate>(), zCoeffs().template conjugateIf<Conjugate>()(k),
502
- &temp(0));
503
- if (k != rank - 1) {
504
- rhs.row(k).swap(rhs.row(rank - 1));
505
- }
506
- }
507
- }
508
-
509
- template <typename MatrixType>
510
- template <typename Rhs>
511
- void CompleteOrthogonalDecomposition<MatrixType>::applyZAdjointOnTheLeftInPlace(
512
- Rhs& rhs) const {
513
- const Index cols = this->cols();
514
- const Index nrhs = rhs.cols();
515
- const Index rank = this->rank();
516
- Matrix<typename Rhs::Scalar, Dynamic, 1> temp((std::max)(cols, nrhs));
517
- for (Index k = 0; k < rank; ++k) {
518
- if (k != rank - 1) {
519
- rhs.row(k).swap(rhs.row(rank - 1));
520
- }
521
- rhs.middleRows(rank - 1, cols - rank + 1)
522
- .applyHouseholderOnTheLeft(
523
- matrixQTZ().row(k).tail(cols - rank).adjoint(), zCoeffs()(k),
524
- &temp(0));
525
- if (k != rank - 1) {
526
- rhs.row(k).swap(rhs.row(rank - 1));
527
- }
528
- }
529
- }
530
-
531
- #ifndef EIGEN_PARSED_BY_DOXYGEN
532
- template <typename _MatrixType>
533
- template <typename RhsType, typename DstType>
534
- void CompleteOrthogonalDecomposition<_MatrixType>::_solve_impl(
535
- const RhsType& rhs, DstType& dst) const {
536
- const Index rank = this->rank();
537
- if (rank == 0) {
538
- dst.setZero();
539
- return;
540
- }
541
-
542
- // Compute c = Q^* * rhs
543
- typename RhsType::PlainObject c(rhs);
544
- c.applyOnTheLeft(matrixQ().setLength(rank).adjoint());
545
-
546
- // Solve T z = c(1:rank, :)
547
- dst.topRows(rank) = matrixT()
548
- .topLeftCorner(rank, rank)
549
- .template triangularView<Upper>()
550
- .solve(c.topRows(rank));
551
-
552
- const Index cols = this->cols();
553
- if (rank < cols) {
554
- // Compute y = Z^* * [ z ]
555
- // [ 0 ]
556
- dst.bottomRows(cols - rank).setZero();
557
- applyZAdjointOnTheLeftInPlace(dst);
558
- }
559
-
560
- // Undo permutation to get x = P^{-1} * y.
561
- dst = colsPermutation() * dst;
562
- }
563
-
564
- template<typename _MatrixType>
565
- template<bool Conjugate, typename RhsType, typename DstType>
566
- void CompleteOrthogonalDecomposition<_MatrixType>::_solve_impl_transposed(const RhsType &rhs, DstType &dst) const
567
- {
568
- const Index rank = this->rank();
569
-
570
- if (rank == 0) {
571
- dst.setZero();
572
- return;
573
- }
574
-
575
- typename RhsType::PlainObject c(colsPermutation().transpose()*rhs);
576
-
577
- if (rank < cols()) {
578
- applyZOnTheLeftInPlace<!Conjugate>(c);
579
- }
580
-
581
- matrixT().topLeftCorner(rank, rank)
582
- .template triangularView<Upper>()
583
- .transpose().template conjugateIf<Conjugate>()
584
- .solveInPlace(c.topRows(rank));
585
-
586
- dst.topRows(rank) = c.topRows(rank);
587
- dst.bottomRows(rows()-rank).setZero();
588
-
589
- dst.applyOnTheLeft(householderQ().setLength(rank).template conjugateIf<!Conjugate>() );
590
- }
591
- #endif
592
-
593
- namespace internal {
594
-
595
- template<typename MatrixType>
596
- struct traits<Inverse<CompleteOrthogonalDecomposition<MatrixType> > >
597
- : traits<typename Transpose<typename MatrixType::PlainObject>::PlainObject>
598
- {
599
- enum { Flags = 0 };
600
- };
601
-
602
- template<typename DstXprType, typename MatrixType>
603
- struct Assignment<DstXprType, Inverse<CompleteOrthogonalDecomposition<MatrixType> >, internal::assign_op<typename DstXprType::Scalar,typename CompleteOrthogonalDecomposition<MatrixType>::Scalar>, Dense2Dense>
604
- {
605
- typedef CompleteOrthogonalDecomposition<MatrixType> CodType;
606
- typedef Inverse<CodType> SrcXprType;
607
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename CodType::Scalar> &)
608
- {
609
- typedef Matrix<typename CodType::Scalar, CodType::RowsAtCompileTime, CodType::RowsAtCompileTime, 0, CodType::MaxRowsAtCompileTime, CodType::MaxRowsAtCompileTime> IdentityMatrixType;
610
- dst = src.nestedExpression().solve(IdentityMatrixType::Identity(src.cols(), src.cols()));
611
- }
612
- };
613
-
614
- } // end namespace internal
615
-
616
- /** \returns the matrix Q as a sequence of householder transformations */
617
- template <typename MatrixType>
618
- typename CompleteOrthogonalDecomposition<MatrixType>::HouseholderSequenceType
619
- CompleteOrthogonalDecomposition<MatrixType>::householderQ() const {
620
- return m_cpqr.householderQ();
621
- }
622
-
623
- /** \return the complete orthogonal decomposition of \c *this.
624
- *
625
- * \sa class CompleteOrthogonalDecomposition
626
- */
627
- template <typename Derived>
628
- const CompleteOrthogonalDecomposition<typename MatrixBase<Derived>::PlainObject>
629
- MatrixBase<Derived>::completeOrthogonalDecomposition() const {
630
- return CompleteOrthogonalDecomposition<PlainObject>(eval());
631
- }
632
-
633
- } // end namespace Eigen
634
-
635
- #endif // EIGEN_COMPLETEORTHOGONALDECOMPOSITION_H