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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@@ -1,877 +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) 2006-2009 Benoit Jacob <jacob.benoit.1@gmail.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_LU_H
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- #define EIGEN_LU_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> struct traits<FullPivLU<_MatrixType> >
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- : traits<_MatrixType>
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- {
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- typedef MatrixXpr XprKind;
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- typedef SolverStorage StorageKind;
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- typedef int StorageIndex;
22
- enum { Flags = 0 };
23
- };
24
-
25
- } // end namespace internal
26
-
27
- /** \ingroup LU_Module
28
- *
29
- * \class FullPivLU
30
- *
31
- * \brief LU decomposition of a matrix with complete pivoting, and related features
32
- *
33
- * \tparam _MatrixType the type of the matrix of which we are computing the LU decomposition
34
- *
35
- * This class represents a LU decomposition of any matrix, with complete pivoting: the matrix A is
36
- * decomposed as \f$ A = P^{-1} L U Q^{-1} \f$ where L is unit-lower-triangular, U is
37
- * upper-triangular, and P and Q are permutation matrices. This is a rank-revealing LU
38
- * decomposition. The eigenvalues (diagonal coefficients) of U are sorted in such a way that any
39
- * zeros are at the end.
40
- *
41
- * This decomposition provides the generic approach to solving systems of linear equations, computing
42
- * the rank, invertibility, inverse, kernel, and determinant.
43
- *
44
- * This LU decomposition is very stable and well tested with large matrices. However there are use cases where the SVD
45
- * decomposition is inherently more stable and/or flexible. For example, when computing the kernel of a matrix,
46
- * working with the SVD allows to select the smallest singular values of the matrix, something that
47
- * the LU decomposition doesn't see.
48
- *
49
- * The data of the LU decomposition can be directly accessed through the methods matrixLU(),
50
- * permutationP(), permutationQ().
51
- *
52
- * As an example, here is how the original matrix can be retrieved:
53
- * \include class_FullPivLU.cpp
54
- * Output: \verbinclude class_FullPivLU.out
55
- *
56
- * This class supports the \link InplaceDecomposition inplace decomposition \endlink mechanism.
57
- *
58
- * \sa MatrixBase::fullPivLu(), MatrixBase::determinant(), MatrixBase::inverse()
59
- */
60
- template<typename _MatrixType> class FullPivLU
61
- : public SolverBase<FullPivLU<_MatrixType> >
62
- {
63
- public:
64
- typedef _MatrixType MatrixType;
65
- typedef SolverBase<FullPivLU> Base;
66
- friend class SolverBase<FullPivLU>;
67
-
68
- EIGEN_GENERIC_PUBLIC_INTERFACE(FullPivLU)
69
- enum {
70
- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
71
- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
72
- };
73
- typedef typename internal::plain_row_type<MatrixType, StorageIndex>::type IntRowVectorType;
74
- typedef typename internal::plain_col_type<MatrixType, StorageIndex>::type IntColVectorType;
75
- typedef PermutationMatrix<ColsAtCompileTime, MaxColsAtCompileTime> PermutationQType;
76
- typedef PermutationMatrix<RowsAtCompileTime, MaxRowsAtCompileTime> PermutationPType;
77
- typedef typename MatrixType::PlainObject PlainObject;
78
-
79
- /**
80
- * \brief Default Constructor.
81
- *
82
- * The default constructor is useful in cases in which the user intends to
83
- * perform decompositions via LU::compute(const MatrixType&).
84
- */
85
- FullPivLU();
86
-
87
- /** \brief Default Constructor with memory preallocation
88
- *
89
- * Like the default constructor but with preallocation of the internal data
90
- * according to the specified problem \a size.
91
- * \sa FullPivLU()
92
- */
93
- FullPivLU(Index rows, Index cols);
94
-
95
- /** Constructor.
96
- *
97
- * \param matrix the matrix of which to compute the LU decomposition.
98
- * It is required to be nonzero.
99
- */
100
- template<typename InputType>
101
- explicit FullPivLU(const EigenBase<InputType>& matrix);
102
-
103
- /** \brief Constructs a LU factorization from a given matrix
104
- *
105
- * This overloaded constructor is provided for \link InplaceDecomposition inplace decomposition \endlink when \c MatrixType is a Eigen::Ref.
106
- *
107
- * \sa FullPivLU(const EigenBase&)
108
- */
109
- template<typename InputType>
110
- explicit FullPivLU(EigenBase<InputType>& matrix);
111
-
112
- /** Computes the LU decomposition of the given matrix.
113
- *
114
- * \param matrix the matrix of which to compute the LU decomposition.
115
- * It is required to be nonzero.
116
- *
117
- * \returns a reference to *this
118
- */
119
- template<typename InputType>
120
- FullPivLU& compute(const EigenBase<InputType>& matrix) {
121
- m_lu = matrix.derived();
122
- computeInPlace();
123
- return *this;
124
- }
125
-
126
- /** \returns the LU decomposition matrix: the upper-triangular part is U, the
127
- * unit-lower-triangular part is L (at least for square matrices; in the non-square
128
- * case, special care is needed, see the documentation of class FullPivLU).
129
- *
130
- * \sa matrixL(), matrixU()
131
- */
132
- inline const MatrixType& matrixLU() const
133
- {
134
- eigen_assert(m_isInitialized && "LU is not initialized.");
135
- return m_lu;
136
- }
137
-
138
- /** \returns the number of nonzero pivots in the LU decomposition.
139
- * Here nonzero is meant in the exact sense, not in a fuzzy sense.
140
- * So that notion isn't really intrinsically interesting, but it is
141
- * still useful when implementing algorithms.
142
- *
143
- * \sa rank()
144
- */
145
- inline Index nonzeroPivots() const
146
- {
147
- eigen_assert(m_isInitialized && "LU is not initialized.");
148
- return m_nonzero_pivots;
149
- }
150
-
151
- /** \returns the absolute value of the biggest pivot, i.e. the biggest
152
- * diagonal coefficient of U.
153
- */
154
- RealScalar maxPivot() const { return m_maxpivot; }
155
-
156
- /** \returns the permutation matrix P
157
- *
158
- * \sa permutationQ()
159
- */
160
- EIGEN_DEVICE_FUNC inline const PermutationPType& permutationP() const
161
- {
162
- eigen_assert(m_isInitialized && "LU is not initialized.");
163
- return m_p;
164
- }
165
-
166
- /** \returns the permutation matrix Q
167
- *
168
- * \sa permutationP()
169
- */
170
- inline const PermutationQType& permutationQ() const
171
- {
172
- eigen_assert(m_isInitialized && "LU is not initialized.");
173
- return m_q;
174
- }
175
-
176
- /** \returns the kernel of the matrix, also called its null-space. The columns of the returned matrix
177
- * will form a basis of the kernel.
178
- *
179
- * \note If the kernel has dimension zero, then the returned matrix is a column-vector filled with zeros.
180
- *
181
- * \note This method has to determine which pivots should be considered nonzero.
182
- * For that, it uses the threshold value that you can control by calling
183
- * setThreshold(const RealScalar&).
184
- *
185
- * Example: \include FullPivLU_kernel.cpp
186
- * Output: \verbinclude FullPivLU_kernel.out
187
- *
188
- * \sa image()
189
- */
190
- inline const internal::kernel_retval<FullPivLU> kernel() const
191
- {
192
- eigen_assert(m_isInitialized && "LU is not initialized.");
193
- return internal::kernel_retval<FullPivLU>(*this);
194
- }
195
-
196
- /** \returns the image of the matrix, also called its column-space. The columns of the returned matrix
197
- * will form a basis of the image (column-space).
198
- *
199
- * \param originalMatrix the original matrix, of which *this is the LU decomposition.
200
- * The reason why it is needed to pass it here, is that this allows
201
- * a large optimization, as otherwise this method would need to reconstruct it
202
- * from the LU decomposition.
203
- *
204
- * \note If the image has dimension zero, then the returned matrix is a column-vector filled with zeros.
205
- *
206
- * \note This method has to determine which pivots should be considered nonzero.
207
- * For that, it uses the threshold value that you can control by calling
208
- * setThreshold(const RealScalar&).
209
- *
210
- * Example: \include FullPivLU_image.cpp
211
- * Output: \verbinclude FullPivLU_image.out
212
- *
213
- * \sa kernel()
214
- */
215
- inline const internal::image_retval<FullPivLU>
216
- image(const MatrixType& originalMatrix) const
217
- {
218
- eigen_assert(m_isInitialized && "LU is not initialized.");
219
- return internal::image_retval<FullPivLU>(*this, originalMatrix);
220
- }
221
-
222
- #ifdef EIGEN_PARSED_BY_DOXYGEN
223
- /** \return a solution x to the equation Ax=b, where A is the matrix of which
224
- * *this is the LU decomposition.
225
- *
226
- * \param b the right-hand-side of the equation to solve. Can be a vector or a matrix,
227
- * the only requirement in order for the equation to make sense is that
228
- * b.rows()==A.rows(), where A is the matrix of which *this is the LU decomposition.
229
- *
230
- * \returns a solution.
231
- *
232
- * \note_about_checking_solutions
233
- *
234
- * \note_about_arbitrary_choice_of_solution
235
- * \note_about_using_kernel_to_study_multiple_solutions
236
- *
237
- * Example: \include FullPivLU_solve.cpp
238
- * Output: \verbinclude FullPivLU_solve.out
239
- *
240
- * \sa TriangularView::solve(), kernel(), inverse()
241
- */
242
- template<typename Rhs>
243
- inline const Solve<FullPivLU, Rhs>
244
- solve(const MatrixBase<Rhs>& b) const;
245
- #endif
246
-
247
- /** \returns an estimate of the reciprocal condition number of the matrix of which \c *this is
248
- the LU decomposition.
249
- */
250
- inline RealScalar rcond() const
251
- {
252
- eigen_assert(m_isInitialized && "PartialPivLU is not initialized.");
253
- return internal::rcond_estimate_helper(m_l1_norm, *this);
254
- }
255
-
256
- /** \returns the determinant of the matrix of which
257
- * *this is the LU decomposition. It has only linear complexity
258
- * (that is, O(n) where n is the dimension of the square matrix)
259
- * as the LU decomposition has already been computed.
260
- *
261
- * \note This is only for square matrices.
262
- *
263
- * \note For fixed-size matrices of size up to 4, MatrixBase::determinant() offers
264
- * optimized paths.
265
- *
266
- * \warning a determinant can be very big or small, so for matrices
267
- * of large enough dimension, there is a risk of overflow/underflow.
268
- *
269
- * \sa MatrixBase::determinant()
270
- */
271
- typename internal::traits<MatrixType>::Scalar determinant() const;
272
-
273
- /** Allows to prescribe a threshold to be used by certain methods, such as rank(),
274
- * who need to determine when pivots are to be considered nonzero. This is not used for the
275
- * LU decomposition itself.
276
- *
277
- * When it needs to get the threshold value, Eigen calls threshold(). By default, this
278
- * uses a formula to automatically determine a reasonable threshold.
279
- * Once you have called the present method setThreshold(const RealScalar&),
280
- * your value is used instead.
281
- *
282
- * \param threshold The new value to use as the threshold.
283
- *
284
- * A pivot will be considered nonzero if its absolute value is strictly greater than
285
- * \f$ \vert pivot \vert \leqslant threshold \times \vert maxpivot \vert \f$
286
- * where maxpivot is the biggest pivot.
287
- *
288
- * If you want to come back to the default behavior, call setThreshold(Default_t)
289
- */
290
- FullPivLU& setThreshold(const RealScalar& threshold)
291
- {
292
- m_usePrescribedThreshold = true;
293
- m_prescribedThreshold = threshold;
294
- return *this;
295
- }
296
-
297
- /** Allows to come back to the default behavior, letting Eigen use its default formula for
298
- * determining the threshold.
299
- *
300
- * You should pass the special object Eigen::Default as parameter here.
301
- * \code lu.setThreshold(Eigen::Default); \endcode
302
- *
303
- * See the documentation of setThreshold(const RealScalar&).
304
- */
305
- FullPivLU& setThreshold(Default_t)
306
- {
307
- m_usePrescribedThreshold = false;
308
- return *this;
309
- }
310
-
311
- /** Returns the threshold that will be used by certain methods such as rank().
312
- *
313
- * See the documentation of setThreshold(const RealScalar&).
314
- */
315
- RealScalar threshold() const
316
- {
317
- eigen_assert(m_isInitialized || m_usePrescribedThreshold);
318
- return m_usePrescribedThreshold ? m_prescribedThreshold
319
- // this formula comes from experimenting (see "LU precision tuning" thread on the list)
320
- // and turns out to be identical to Higham's formula used already in LDLt.
321
- : NumTraits<Scalar>::epsilon() * RealScalar(m_lu.diagonalSize());
322
- }
323
-
324
- /** \returns the rank of the matrix of which *this is the LU decomposition.
325
- *
326
- * \note This method has to determine which pivots should be considered nonzero.
327
- * For that, it uses the threshold value that you can control by calling
328
- * setThreshold(const RealScalar&).
329
- */
330
- inline Index rank() const
331
- {
332
- using std::abs;
333
- eigen_assert(m_isInitialized && "LU is not initialized.");
334
- RealScalar premultiplied_threshold = abs(m_maxpivot) * threshold();
335
- Index result = 0;
336
- for(Index i = 0; i < m_nonzero_pivots; ++i)
337
- result += (abs(m_lu.coeff(i,i)) > premultiplied_threshold);
338
- return result;
339
- }
340
-
341
- /** \returns the dimension of the kernel of the matrix of which *this is the LU decomposition.
342
- *
343
- * \note This method has to determine which pivots should be considered nonzero.
344
- * For that, it uses the threshold value that you can control by calling
345
- * setThreshold(const RealScalar&).
346
- */
347
- inline Index dimensionOfKernel() const
348
- {
349
- eigen_assert(m_isInitialized && "LU is not initialized.");
350
- return cols() - rank();
351
- }
352
-
353
- /** \returns true if the matrix of which *this is the LU decomposition represents an injective
354
- * linear map, i.e. has trivial kernel; false otherwise.
355
- *
356
- * \note This method has to determine which pivots should be considered nonzero.
357
- * For that, it uses the threshold value that you can control by calling
358
- * setThreshold(const RealScalar&).
359
- */
360
- inline bool isInjective() const
361
- {
362
- eigen_assert(m_isInitialized && "LU is not initialized.");
363
- return rank() == cols();
364
- }
365
-
366
- /** \returns true if the matrix of which *this is the LU decomposition represents a surjective
367
- * linear map; false otherwise.
368
- *
369
- * \note This method has to determine which pivots should be considered nonzero.
370
- * For that, it uses the threshold value that you can control by calling
371
- * setThreshold(const RealScalar&).
372
- */
373
- inline bool isSurjective() const
374
- {
375
- eigen_assert(m_isInitialized && "LU is not initialized.");
376
- return rank() == rows();
377
- }
378
-
379
- /** \returns true if the matrix of which *this is the LU decomposition is invertible.
380
- *
381
- * \note This method has to determine which pivots should be considered nonzero.
382
- * For that, it uses the threshold value that you can control by calling
383
- * setThreshold(const RealScalar&).
384
- */
385
- inline bool isInvertible() const
386
- {
387
- eigen_assert(m_isInitialized && "LU is not initialized.");
388
- return isInjective() && (m_lu.rows() == m_lu.cols());
389
- }
390
-
391
- /** \returns the inverse of the matrix of which *this is the LU decomposition.
392
- *
393
- * \note If this matrix is not invertible, the returned matrix has undefined coefficients.
394
- * Use isInvertible() to first determine whether this matrix is invertible.
395
- *
396
- * \sa MatrixBase::inverse()
397
- */
398
- inline const Inverse<FullPivLU> inverse() const
399
- {
400
- eigen_assert(m_isInitialized && "LU is not initialized.");
401
- eigen_assert(m_lu.rows() == m_lu.cols() && "You can't take the inverse of a non-square matrix!");
402
- return Inverse<FullPivLU>(*this);
403
- }
404
-
405
- MatrixType reconstructedMatrix() const;
406
-
407
- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
408
- inline Index rows() const EIGEN_NOEXCEPT { return m_lu.rows(); }
409
- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
410
- inline Index cols() const EIGEN_NOEXCEPT { return m_lu.cols(); }
411
-
412
- #ifndef EIGEN_PARSED_BY_DOXYGEN
413
- template<typename RhsType, typename DstType>
414
- void _solve_impl(const RhsType &rhs, DstType &dst) const;
415
-
416
- template<bool Conjugate, typename RhsType, typename DstType>
417
- void _solve_impl_transposed(const RhsType &rhs, DstType &dst) const;
418
- #endif
419
-
420
- protected:
421
-
422
- static void check_template_parameters()
423
- {
424
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
425
- }
426
-
427
- void computeInPlace();
428
-
429
- MatrixType m_lu;
430
- PermutationPType m_p;
431
- PermutationQType m_q;
432
- IntColVectorType m_rowsTranspositions;
433
- IntRowVectorType m_colsTranspositions;
434
- Index m_nonzero_pivots;
435
- RealScalar m_l1_norm;
436
- RealScalar m_maxpivot, m_prescribedThreshold;
437
- signed char m_det_pq;
438
- bool m_isInitialized, m_usePrescribedThreshold;
439
- };
440
-
441
- template<typename MatrixType>
442
- FullPivLU<MatrixType>::FullPivLU()
443
- : m_isInitialized(false), m_usePrescribedThreshold(false)
444
- {
445
- }
446
-
447
- template<typename MatrixType>
448
- FullPivLU<MatrixType>::FullPivLU(Index rows, Index cols)
449
- : m_lu(rows, cols),
450
- m_p(rows),
451
- m_q(cols),
452
- m_rowsTranspositions(rows),
453
- m_colsTranspositions(cols),
454
- m_isInitialized(false),
455
- m_usePrescribedThreshold(false)
456
- {
457
- }
458
-
459
- template<typename MatrixType>
460
- template<typename InputType>
461
- FullPivLU<MatrixType>::FullPivLU(const EigenBase<InputType>& matrix)
462
- : m_lu(matrix.rows(), matrix.cols()),
463
- m_p(matrix.rows()),
464
- m_q(matrix.cols()),
465
- m_rowsTranspositions(matrix.rows()),
466
- m_colsTranspositions(matrix.cols()),
467
- m_isInitialized(false),
468
- m_usePrescribedThreshold(false)
469
- {
470
- compute(matrix.derived());
471
- }
472
-
473
- template<typename MatrixType>
474
- template<typename InputType>
475
- FullPivLU<MatrixType>::FullPivLU(EigenBase<InputType>& matrix)
476
- : m_lu(matrix.derived()),
477
- m_p(matrix.rows()),
478
- m_q(matrix.cols()),
479
- m_rowsTranspositions(matrix.rows()),
480
- m_colsTranspositions(matrix.cols()),
481
- m_isInitialized(false),
482
- m_usePrescribedThreshold(false)
483
- {
484
- computeInPlace();
485
- }
486
-
487
- template<typename MatrixType>
488
- void FullPivLU<MatrixType>::computeInPlace()
489
- {
490
- check_template_parameters();
491
-
492
- // the permutations are stored as int indices, so just to be sure:
493
- eigen_assert(m_lu.rows()<=NumTraits<int>::highest() && m_lu.cols()<=NumTraits<int>::highest());
494
-
495
- m_l1_norm = m_lu.cwiseAbs().colwise().sum().maxCoeff();
496
-
497
- const Index size = m_lu.diagonalSize();
498
- const Index rows = m_lu.rows();
499
- const Index cols = m_lu.cols();
500
-
501
- // will store the transpositions, before we accumulate them at the end.
502
- // can't accumulate on-the-fly because that will be done in reverse order for the rows.
503
- m_rowsTranspositions.resize(m_lu.rows());
504
- m_colsTranspositions.resize(m_lu.cols());
505
- Index number_of_transpositions = 0; // number of NONTRIVIAL transpositions, i.e. m_rowsTranspositions[i]!=i
506
-
507
- m_nonzero_pivots = size; // the generic case is that in which all pivots are nonzero (invertible case)
508
- m_maxpivot = RealScalar(0);
509
-
510
- for(Index k = 0; k < size; ++k)
511
- {
512
- // First, we need to find the pivot.
513
-
514
- // biggest coefficient in the remaining bottom-right corner (starting at row k, col k)
515
- Index row_of_biggest_in_corner, col_of_biggest_in_corner;
516
- typedef internal::scalar_score_coeff_op<Scalar> Scoring;
517
- typedef typename Scoring::result_type Score;
518
- Score biggest_in_corner;
519
- biggest_in_corner = m_lu.bottomRightCorner(rows-k, cols-k)
520
- .unaryExpr(Scoring())
521
- .maxCoeff(&row_of_biggest_in_corner, &col_of_biggest_in_corner);
522
- row_of_biggest_in_corner += k; // correct the values! since they were computed in the corner,
523
- col_of_biggest_in_corner += k; // need to add k to them.
524
-
525
- if(biggest_in_corner==Score(0))
526
- {
527
- // before exiting, make sure to initialize the still uninitialized transpositions
528
- // in a sane state without destroying what we already have.
529
- m_nonzero_pivots = k;
530
- for(Index i = k; i < size; ++i)
531
- {
532
- m_rowsTranspositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
533
- m_colsTranspositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
534
- }
535
- break;
536
- }
537
-
538
- RealScalar abs_pivot = internal::abs_knowing_score<Scalar>()(m_lu(row_of_biggest_in_corner, col_of_biggest_in_corner), biggest_in_corner);
539
- if(abs_pivot > m_maxpivot) m_maxpivot = abs_pivot;
540
-
541
- // Now that we've found the pivot, we need to apply the row/col swaps to
542
- // bring it to the location (k,k).
543
-
544
- m_rowsTranspositions.coeffRef(k) = internal::convert_index<StorageIndex>(row_of_biggest_in_corner);
545
- m_colsTranspositions.coeffRef(k) = internal::convert_index<StorageIndex>(col_of_biggest_in_corner);
546
- if(k != row_of_biggest_in_corner) {
547
- m_lu.row(k).swap(m_lu.row(row_of_biggest_in_corner));
548
- ++number_of_transpositions;
549
- }
550
- if(k != col_of_biggest_in_corner) {
551
- m_lu.col(k).swap(m_lu.col(col_of_biggest_in_corner));
552
- ++number_of_transpositions;
553
- }
554
-
555
- // Now that the pivot is at the right location, we update the remaining
556
- // bottom-right corner by Gaussian elimination.
557
-
558
- if(k<rows-1)
559
- m_lu.col(k).tail(rows-k-1) /= m_lu.coeff(k,k);
560
- if(k<size-1)
561
- m_lu.block(k+1,k+1,rows-k-1,cols-k-1).noalias() -= m_lu.col(k).tail(rows-k-1) * m_lu.row(k).tail(cols-k-1);
562
- }
563
-
564
- // the main loop is over, we still have to accumulate the transpositions to find the
565
- // permutations P and Q
566
-
567
- m_p.setIdentity(rows);
568
- for(Index k = size-1; k >= 0; --k)
569
- m_p.applyTranspositionOnTheRight(k, m_rowsTranspositions.coeff(k));
570
-
571
- m_q.setIdentity(cols);
572
- for(Index k = 0; k < size; ++k)
573
- m_q.applyTranspositionOnTheRight(k, m_colsTranspositions.coeff(k));
574
-
575
- m_det_pq = (number_of_transpositions%2) ? -1 : 1;
576
-
577
- m_isInitialized = true;
578
- }
579
-
580
- template<typename MatrixType>
581
- typename internal::traits<MatrixType>::Scalar FullPivLU<MatrixType>::determinant() const
582
- {
583
- eigen_assert(m_isInitialized && "LU is not initialized.");
584
- eigen_assert(m_lu.rows() == m_lu.cols() && "You can't take the determinant of a non-square matrix!");
585
- return Scalar(m_det_pq) * Scalar(m_lu.diagonal().prod());
586
- }
587
-
588
- /** \returns the matrix represented by the decomposition,
589
- * i.e., it returns the product: \f$ P^{-1} L U Q^{-1} \f$.
590
- * This function is provided for debug purposes. */
591
- template<typename MatrixType>
592
- MatrixType FullPivLU<MatrixType>::reconstructedMatrix() const
593
- {
594
- eigen_assert(m_isInitialized && "LU is not initialized.");
595
- const Index smalldim = (std::min)(m_lu.rows(), m_lu.cols());
596
- // LU
597
- MatrixType res(m_lu.rows(),m_lu.cols());
598
- // FIXME the .toDenseMatrix() should not be needed...
599
- res = m_lu.leftCols(smalldim)
600
- .template triangularView<UnitLower>().toDenseMatrix()
601
- * m_lu.topRows(smalldim)
602
- .template triangularView<Upper>().toDenseMatrix();
603
-
604
- // P^{-1}(LU)
605
- res = m_p.inverse() * res;
606
-
607
- // (P^{-1}LU)Q^{-1}
608
- res = res * m_q.inverse();
609
-
610
- return res;
611
- }
612
-
613
- /********* Implementation of kernel() **************************************************/
614
-
615
- namespace internal {
616
- template<typename _MatrixType>
617
- struct kernel_retval<FullPivLU<_MatrixType> >
618
- : kernel_retval_base<FullPivLU<_MatrixType> >
619
- {
620
- EIGEN_MAKE_KERNEL_HELPERS(FullPivLU<_MatrixType>)
621
-
622
- enum { MaxSmallDimAtCompileTime = EIGEN_SIZE_MIN_PREFER_FIXED(
623
- MatrixType::MaxColsAtCompileTime,
624
- MatrixType::MaxRowsAtCompileTime)
625
- };
626
-
627
- template<typename Dest> void evalTo(Dest& dst) const
628
- {
629
- using std::abs;
630
- const Index cols = dec().matrixLU().cols(), dimker = cols - rank();
631
- if(dimker == 0)
632
- {
633
- // The Kernel is just {0}, so it doesn't have a basis properly speaking, but let's
634
- // avoid crashing/asserting as that depends on floating point calculations. Let's
635
- // just return a single column vector filled with zeros.
636
- dst.setZero();
637
- return;
638
- }
639
-
640
- /* Let us use the following lemma:
641
- *
642
- * Lemma: If the matrix A has the LU decomposition PAQ = LU,
643
- * then Ker A = Q(Ker U).
644
- *
645
- * Proof: trivial: just keep in mind that P, Q, L are invertible.
646
- */
647
-
648
- /* Thus, all we need to do is to compute Ker U, and then apply Q.
649
- *
650
- * U is upper triangular, with eigenvalues sorted so that any zeros appear at the end.
651
- * Thus, the diagonal of U ends with exactly
652
- * dimKer zero's. Let us use that to construct dimKer linearly
653
- * independent vectors in Ker U.
654
- */
655
-
656
- Matrix<Index, Dynamic, 1, 0, MaxSmallDimAtCompileTime, 1> pivots(rank());
657
- RealScalar premultiplied_threshold = dec().maxPivot() * dec().threshold();
658
- Index p = 0;
659
- for(Index i = 0; i < dec().nonzeroPivots(); ++i)
660
- if(abs(dec().matrixLU().coeff(i,i)) > premultiplied_threshold)
661
- pivots.coeffRef(p++) = i;
662
- eigen_internal_assert(p == rank());
663
-
664
- // we construct a temporaty trapezoid matrix m, by taking the U matrix and
665
- // permuting the rows and cols to bring the nonnegligible pivots to the top of
666
- // the main diagonal. We need that to be able to apply our triangular solvers.
667
- // FIXME when we get triangularView-for-rectangular-matrices, this can be simplified
668
- Matrix<typename MatrixType::Scalar, Dynamic, Dynamic, MatrixType::Options,
669
- MaxSmallDimAtCompileTime, MatrixType::MaxColsAtCompileTime>
670
- m(dec().matrixLU().block(0, 0, rank(), cols));
671
- for(Index i = 0; i < rank(); ++i)
672
- {
673
- if(i) m.row(i).head(i).setZero();
674
- m.row(i).tail(cols-i) = dec().matrixLU().row(pivots.coeff(i)).tail(cols-i);
675
- }
676
- m.block(0, 0, rank(), rank());
677
- m.block(0, 0, rank(), rank()).template triangularView<StrictlyLower>().setZero();
678
- for(Index i = 0; i < rank(); ++i)
679
- m.col(i).swap(m.col(pivots.coeff(i)));
680
-
681
- // ok, we have our trapezoid matrix, we can apply the triangular solver.
682
- // notice that the math behind this suggests that we should apply this to the
683
- // negative of the RHS, but for performance we just put the negative sign elsewhere, see below.
684
- m.topLeftCorner(rank(), rank())
685
- .template triangularView<Upper>().solveInPlace(
686
- m.topRightCorner(rank(), dimker)
687
- );
688
-
689
- // now we must undo the column permutation that we had applied!
690
- for(Index i = rank()-1; i >= 0; --i)
691
- m.col(i).swap(m.col(pivots.coeff(i)));
692
-
693
- // see the negative sign in the next line, that's what we were talking about above.
694
- for(Index i = 0; i < rank(); ++i) dst.row(dec().permutationQ().indices().coeff(i)) = -m.row(i).tail(dimker);
695
- for(Index i = rank(); i < cols; ++i) dst.row(dec().permutationQ().indices().coeff(i)).setZero();
696
- for(Index k = 0; k < dimker; ++k) dst.coeffRef(dec().permutationQ().indices().coeff(rank()+k), k) = Scalar(1);
697
- }
698
- };
699
-
700
- /***** Implementation of image() *****************************************************/
701
-
702
- template<typename _MatrixType>
703
- struct image_retval<FullPivLU<_MatrixType> >
704
- : image_retval_base<FullPivLU<_MatrixType> >
705
- {
706
- EIGEN_MAKE_IMAGE_HELPERS(FullPivLU<_MatrixType>)
707
-
708
- enum { MaxSmallDimAtCompileTime = EIGEN_SIZE_MIN_PREFER_FIXED(
709
- MatrixType::MaxColsAtCompileTime,
710
- MatrixType::MaxRowsAtCompileTime)
711
- };
712
-
713
- template<typename Dest> void evalTo(Dest& dst) const
714
- {
715
- using std::abs;
716
- if(rank() == 0)
717
- {
718
- // The Image is just {0}, so it doesn't have a basis properly speaking, but let's
719
- // avoid crashing/asserting as that depends on floating point calculations. Let's
720
- // just return a single column vector filled with zeros.
721
- dst.setZero();
722
- return;
723
- }
724
-
725
- Matrix<Index, Dynamic, 1, 0, MaxSmallDimAtCompileTime, 1> pivots(rank());
726
- RealScalar premultiplied_threshold = dec().maxPivot() * dec().threshold();
727
- Index p = 0;
728
- for(Index i = 0; i < dec().nonzeroPivots(); ++i)
729
- if(abs(dec().matrixLU().coeff(i,i)) > premultiplied_threshold)
730
- pivots.coeffRef(p++) = i;
731
- eigen_internal_assert(p == rank());
732
-
733
- for(Index i = 0; i < rank(); ++i)
734
- dst.col(i) = originalMatrix().col(dec().permutationQ().indices().coeff(pivots.coeff(i)));
735
- }
736
- };
737
-
738
- /***** Implementation of solve() *****************************************************/
739
-
740
- } // end namespace internal
741
-
742
- #ifndef EIGEN_PARSED_BY_DOXYGEN
743
- template<typename _MatrixType>
744
- template<typename RhsType, typename DstType>
745
- void FullPivLU<_MatrixType>::_solve_impl(const RhsType &rhs, DstType &dst) const
746
- {
747
- /* The decomposition PAQ = LU can be rewritten as A = P^{-1} L U Q^{-1}.
748
- * So we proceed as follows:
749
- * Step 1: compute c = P * rhs.
750
- * Step 2: replace c by the solution x to Lx = c. Exists because L is invertible.
751
- * Step 3: replace c by the solution x to Ux = c. May or may not exist.
752
- * Step 4: result = Q * c;
753
- */
754
-
755
- const Index rows = this->rows(),
756
- cols = this->cols(),
757
- nonzero_pivots = this->rank();
758
- const Index smalldim = (std::min)(rows, cols);
759
-
760
- if(nonzero_pivots == 0)
761
- {
762
- dst.setZero();
763
- return;
764
- }
765
-
766
- typename RhsType::PlainObject c(rhs.rows(), rhs.cols());
767
-
768
- // Step 1
769
- c = permutationP() * rhs;
770
-
771
- // Step 2
772
- m_lu.topLeftCorner(smalldim,smalldim)
773
- .template triangularView<UnitLower>()
774
- .solveInPlace(c.topRows(smalldim));
775
- if(rows>cols)
776
- c.bottomRows(rows-cols) -= m_lu.bottomRows(rows-cols) * c.topRows(cols);
777
-
778
- // Step 3
779
- m_lu.topLeftCorner(nonzero_pivots, nonzero_pivots)
780
- .template triangularView<Upper>()
781
- .solveInPlace(c.topRows(nonzero_pivots));
782
-
783
- // Step 4
784
- for(Index i = 0; i < nonzero_pivots; ++i)
785
- dst.row(permutationQ().indices().coeff(i)) = c.row(i);
786
- for(Index i = nonzero_pivots; i < m_lu.cols(); ++i)
787
- dst.row(permutationQ().indices().coeff(i)).setZero();
788
- }
789
-
790
- template<typename _MatrixType>
791
- template<bool Conjugate, typename RhsType, typename DstType>
792
- void FullPivLU<_MatrixType>::_solve_impl_transposed(const RhsType &rhs, DstType &dst) const
793
- {
794
- /* The decomposition PAQ = LU can be rewritten as A = P^{-1} L U Q^{-1},
795
- * and since permutations are real and unitary, we can write this
796
- * as A^T = Q U^T L^T P,
797
- * So we proceed as follows:
798
- * Step 1: compute c = Q^T rhs.
799
- * Step 2: replace c by the solution x to U^T x = c. May or may not exist.
800
- * Step 3: replace c by the solution x to L^T x = c.
801
- * Step 4: result = P^T c.
802
- * If Conjugate is true, replace "^T" by "^*" above.
803
- */
804
-
805
- const Index rows = this->rows(), cols = this->cols(),
806
- nonzero_pivots = this->rank();
807
- const Index smalldim = (std::min)(rows, cols);
808
-
809
- if(nonzero_pivots == 0)
810
- {
811
- dst.setZero();
812
- return;
813
- }
814
-
815
- typename RhsType::PlainObject c(rhs.rows(), rhs.cols());
816
-
817
- // Step 1
818
- c = permutationQ().inverse() * rhs;
819
-
820
- // Step 2
821
- m_lu.topLeftCorner(nonzero_pivots, nonzero_pivots)
822
- .template triangularView<Upper>()
823
- .transpose()
824
- .template conjugateIf<Conjugate>()
825
- .solveInPlace(c.topRows(nonzero_pivots));
826
-
827
- // Step 3
828
- m_lu.topLeftCorner(smalldim, smalldim)
829
- .template triangularView<UnitLower>()
830
- .transpose()
831
- .template conjugateIf<Conjugate>()
832
- .solveInPlace(c.topRows(smalldim));
833
-
834
- // Step 4
835
- PermutationPType invp = permutationP().inverse().eval();
836
- for(Index i = 0; i < smalldim; ++i)
837
- dst.row(invp.indices().coeff(i)) = c.row(i);
838
- for(Index i = smalldim; i < rows; ++i)
839
- dst.row(invp.indices().coeff(i)).setZero();
840
- }
841
-
842
- #endif
843
-
844
- namespace internal {
845
-
846
-
847
- /***** Implementation of inverse() *****************************************************/
848
- template<typename DstXprType, typename MatrixType>
849
- struct Assignment<DstXprType, Inverse<FullPivLU<MatrixType> >, internal::assign_op<typename DstXprType::Scalar,typename FullPivLU<MatrixType>::Scalar>, Dense2Dense>
850
- {
851
- typedef FullPivLU<MatrixType> LuType;
852
- typedef Inverse<LuType> SrcXprType;
853
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename MatrixType::Scalar> &)
854
- {
855
- dst = src.nestedExpression().solve(MatrixType::Identity(src.rows(), src.cols()));
856
- }
857
- };
858
- } // end namespace internal
859
-
860
- /******* MatrixBase methods *****************************************************************/
861
-
862
- /** \lu_module
863
- *
864
- * \return the full-pivoting LU decomposition of \c *this.
865
- *
866
- * \sa class FullPivLU
867
- */
868
- template<typename Derived>
869
- inline const FullPivLU<typename MatrixBase<Derived>::PlainObject>
870
- MatrixBase<Derived>::fullPivLu() const
871
- {
872
- return FullPivLU<PlainObject>(eval());
873
- }
874
-
875
- } // end namespace Eigen
876
-
877
- #endif // EIGEN_LU_H