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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@@ -1,713 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 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_FULLPIVOTINGHOUSEHOLDERQR_H
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- #define EIGEN_FULLPIVOTINGHOUSEHOLDERQR_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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-
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- template<typename _MatrixType> struct traits<FullPivHouseholderQR<_MatrixType> >
19
- : traits<_MatrixType>
20
- {
21
- typedef MatrixXpr XprKind;
22
- typedef SolverStorage StorageKind;
23
- typedef int StorageIndex;
24
- enum { Flags = 0 };
25
- };
26
-
27
- template<typename MatrixType> struct FullPivHouseholderQRMatrixQReturnType;
28
-
29
- template<typename MatrixType>
30
- struct traits<FullPivHouseholderQRMatrixQReturnType<MatrixType> >
31
- {
32
- typedef typename MatrixType::PlainObject ReturnType;
33
- };
34
-
35
- } // end namespace internal
36
-
37
- /** \ingroup QR_Module
38
- *
39
- * \class FullPivHouseholderQR
40
- *
41
- * \brief Householder rank-revealing QR decomposition of a matrix with full pivoting
42
- *
43
- * \tparam _MatrixType the type of the matrix of which we are computing the QR decomposition
44
- *
45
- * This class performs a rank-revealing QR decomposition of a matrix \b A into matrices \b P, \b P', \b Q and \b R
46
- * such that
47
- * \f[
48
- * \mathbf{P} \, \mathbf{A} \, \mathbf{P}' = \mathbf{Q} \, \mathbf{R}
49
- * \f]
50
- * by using Householder transformations. Here, \b P and \b P' are permutation matrices, \b Q a unitary matrix
51
- * and \b R an upper triangular matrix.
52
- *
53
- * This decomposition performs a very prudent full pivoting in order to be rank-revealing and achieve optimal
54
- * numerical stability. The trade-off is that it is slower than HouseholderQR and ColPivHouseholderQR.
55
- *
56
- * This class supports the \link InplaceDecomposition inplace decomposition \endlink mechanism.
57
- *
58
- * \sa MatrixBase::fullPivHouseholderQr()
59
- */
60
- template<typename _MatrixType> class FullPivHouseholderQR
61
- : public SolverBase<FullPivHouseholderQR<_MatrixType> >
62
- {
63
- public:
64
-
65
- typedef _MatrixType MatrixType;
66
- typedef SolverBase<FullPivHouseholderQR> Base;
67
- friend class SolverBase<FullPivHouseholderQR>;
68
-
69
- EIGEN_GENERIC_PUBLIC_INTERFACE(FullPivHouseholderQR)
70
- enum {
71
- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
72
- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
73
- };
74
- typedef internal::FullPivHouseholderQRMatrixQReturnType<MatrixType> MatrixQReturnType;
75
- typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
76
- typedef Matrix<StorageIndex, 1,
77
- EIGEN_SIZE_MIN_PREFER_DYNAMIC(ColsAtCompileTime,RowsAtCompileTime), RowMajor, 1,
78
- EIGEN_SIZE_MIN_PREFER_FIXED(MaxColsAtCompileTime,MaxRowsAtCompileTime)> IntDiagSizeVectorType;
79
- typedef PermutationMatrix<ColsAtCompileTime, MaxColsAtCompileTime> PermutationType;
80
- typedef typename internal::plain_row_type<MatrixType>::type RowVectorType;
81
- typedef typename internal::plain_col_type<MatrixType>::type ColVectorType;
82
- typedef typename MatrixType::PlainObject PlainObject;
83
-
84
- /** \brief Default Constructor.
85
- *
86
- * The default constructor is useful in cases in which the user intends to
87
- * perform decompositions via FullPivHouseholderQR::compute(const MatrixType&).
88
- */
89
- FullPivHouseholderQR()
90
- : m_qr(),
91
- m_hCoeffs(),
92
- m_rows_transpositions(),
93
- m_cols_transpositions(),
94
- m_cols_permutation(),
95
- m_temp(),
96
- m_isInitialized(false),
97
- m_usePrescribedThreshold(false) {}
98
-
99
- /** \brief Default Constructor with memory preallocation
100
- *
101
- * Like the default constructor but with preallocation of the internal data
102
- * according to the specified problem \a size.
103
- * \sa FullPivHouseholderQR()
104
- */
105
- FullPivHouseholderQR(Index rows, Index cols)
106
- : m_qr(rows, cols),
107
- m_hCoeffs((std::min)(rows,cols)),
108
- m_rows_transpositions((std::min)(rows,cols)),
109
- m_cols_transpositions((std::min)(rows,cols)),
110
- m_cols_permutation(cols),
111
- m_temp(cols),
112
- m_isInitialized(false),
113
- m_usePrescribedThreshold(false) {}
114
-
115
- /** \brief Constructs a QR factorization from a given matrix
116
- *
117
- * This constructor computes the QR factorization of the matrix \a matrix by calling
118
- * the method compute(). It is a short cut for:
119
- *
120
- * \code
121
- * FullPivHouseholderQR<MatrixType> qr(matrix.rows(), matrix.cols());
122
- * qr.compute(matrix);
123
- * \endcode
124
- *
125
- * \sa compute()
126
- */
127
- template<typename InputType>
128
- explicit FullPivHouseholderQR(const EigenBase<InputType>& matrix)
129
- : m_qr(matrix.rows(), matrix.cols()),
130
- m_hCoeffs((std::min)(matrix.rows(), matrix.cols())),
131
- m_rows_transpositions((std::min)(matrix.rows(), matrix.cols())),
132
- m_cols_transpositions((std::min)(matrix.rows(), matrix.cols())),
133
- m_cols_permutation(matrix.cols()),
134
- m_temp(matrix.cols()),
135
- m_isInitialized(false),
136
- m_usePrescribedThreshold(false)
137
- {
138
- compute(matrix.derived());
139
- }
140
-
141
- /** \brief Constructs a QR factorization from a given matrix
142
- *
143
- * This overloaded constructor is provided for \link InplaceDecomposition inplace decomposition \endlink when \c MatrixType is a Eigen::Ref.
144
- *
145
- * \sa FullPivHouseholderQR(const EigenBase&)
146
- */
147
- template<typename InputType>
148
- explicit FullPivHouseholderQR(EigenBase<InputType>& matrix)
149
- : m_qr(matrix.derived()),
150
- m_hCoeffs((std::min)(matrix.rows(), matrix.cols())),
151
- m_rows_transpositions((std::min)(matrix.rows(), matrix.cols())),
152
- m_cols_transpositions((std::min)(matrix.rows(), matrix.cols())),
153
- m_cols_permutation(matrix.cols()),
154
- m_temp(matrix.cols()),
155
- m_isInitialized(false),
156
- m_usePrescribedThreshold(false)
157
- {
158
- computeInPlace();
159
- }
160
-
161
- #ifdef EIGEN_PARSED_BY_DOXYGEN
162
- /** This method finds a solution x to the equation Ax=b, where A is the matrix of which
163
- * \c *this is the QR decomposition.
164
- *
165
- * \param b the right-hand-side of the equation to solve.
166
- *
167
- * \returns the exact or least-square solution if the rank is greater or equal to the number of columns of A,
168
- * and an arbitrary solution otherwise.
169
- *
170
- * \note_about_checking_solutions
171
- *
172
- * \note_about_arbitrary_choice_of_solution
173
- *
174
- * Example: \include FullPivHouseholderQR_solve.cpp
175
- * Output: \verbinclude FullPivHouseholderQR_solve.out
176
- */
177
- template<typename Rhs>
178
- inline const Solve<FullPivHouseholderQR, Rhs>
179
- solve(const MatrixBase<Rhs>& b) const;
180
- #endif
181
-
182
- /** \returns Expression object representing the matrix Q
183
- */
184
- MatrixQReturnType matrixQ(void) const;
185
-
186
- /** \returns a reference to the matrix where the Householder QR decomposition is stored
187
- */
188
- const MatrixType& matrixQR() const
189
- {
190
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
191
- return m_qr;
192
- }
193
-
194
- template<typename InputType>
195
- FullPivHouseholderQR& compute(const EigenBase<InputType>& matrix);
196
-
197
- /** \returns a const reference to the column permutation matrix */
198
- const PermutationType& colsPermutation() const
199
- {
200
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
201
- return m_cols_permutation;
202
- }
203
-
204
- /** \returns a const reference to the vector of indices representing the rows transpositions */
205
- const IntDiagSizeVectorType& rowsTranspositions() const
206
- {
207
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
208
- return m_rows_transpositions;
209
- }
210
-
211
- /** \returns the absolute value of the determinant of the matrix of which
212
- * *this is the QR decomposition. It has only linear complexity
213
- * (that is, O(n) where n is the dimension of the square matrix)
214
- * as the QR decomposition has already been computed.
215
- *
216
- * \note This is only for square matrices.
217
- *
218
- * \warning a determinant can be very big or small, so for matrices
219
- * of large enough dimension, there is a risk of overflow/underflow.
220
- * One way to work around that is to use logAbsDeterminant() instead.
221
- *
222
- * \sa logAbsDeterminant(), MatrixBase::determinant()
223
- */
224
- typename MatrixType::RealScalar absDeterminant() const;
225
-
226
- /** \returns the natural log of the absolute value of the determinant of the matrix of which
227
- * *this is the QR decomposition. It has only linear complexity
228
- * (that is, O(n) where n is the dimension of the square matrix)
229
- * as the QR decomposition has already been computed.
230
- *
231
- * \note This is only for square matrices.
232
- *
233
- * \note This method is useful to work around the risk of overflow/underflow that's inherent
234
- * to determinant computation.
235
- *
236
- * \sa absDeterminant(), MatrixBase::determinant()
237
- */
238
- typename MatrixType::RealScalar logAbsDeterminant() const;
239
-
240
- /** \returns the rank of the matrix of which *this is the QR decomposition.
241
- *
242
- * \note This method has to determine which pivots should be considered nonzero.
243
- * For that, it uses the threshold value that you can control by calling
244
- * setThreshold(const RealScalar&).
245
- */
246
- inline Index rank() const
247
- {
248
- using std::abs;
249
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
250
- RealScalar premultiplied_threshold = abs(m_maxpivot) * threshold();
251
- Index result = 0;
252
- for(Index i = 0; i < m_nonzero_pivots; ++i)
253
- result += (abs(m_qr.coeff(i,i)) > premultiplied_threshold);
254
- return result;
255
- }
256
-
257
- /** \returns the dimension of the kernel of the matrix of which *this is the QR decomposition.
258
- *
259
- * \note This method has to determine which pivots should be considered nonzero.
260
- * For that, it uses the threshold value that you can control by calling
261
- * setThreshold(const RealScalar&).
262
- */
263
- inline Index dimensionOfKernel() const
264
- {
265
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
266
- return cols() - rank();
267
- }
268
-
269
- /** \returns true if the matrix of which *this is the QR decomposition represents an injective
270
- * linear map, i.e. has trivial kernel; false otherwise.
271
- *
272
- * \note This method has to determine which pivots should be considered nonzero.
273
- * For that, it uses the threshold value that you can control by calling
274
- * setThreshold(const RealScalar&).
275
- */
276
- inline bool isInjective() const
277
- {
278
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
279
- return rank() == cols();
280
- }
281
-
282
- /** \returns true if the matrix of which *this is the QR decomposition represents a surjective
283
- * linear map; false otherwise.
284
- *
285
- * \note This method has to determine which pivots should be considered nonzero.
286
- * For that, it uses the threshold value that you can control by calling
287
- * setThreshold(const RealScalar&).
288
- */
289
- inline bool isSurjective() const
290
- {
291
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
292
- return rank() == rows();
293
- }
294
-
295
- /** \returns true if the matrix of which *this is the QR decomposition is invertible.
296
- *
297
- * \note This method has to determine which pivots should be considered nonzero.
298
- * For that, it uses the threshold value that you can control by calling
299
- * setThreshold(const RealScalar&).
300
- */
301
- inline bool isInvertible() const
302
- {
303
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
304
- return isInjective() && isSurjective();
305
- }
306
-
307
- /** \returns the inverse of the matrix of which *this is the QR decomposition.
308
- *
309
- * \note If this matrix is not invertible, the returned matrix has undefined coefficients.
310
- * Use isInvertible() to first determine whether this matrix is invertible.
311
- */
312
- inline const Inverse<FullPivHouseholderQR> inverse() const
313
- {
314
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
315
- return Inverse<FullPivHouseholderQR>(*this);
316
- }
317
-
318
- inline Index rows() const { return m_qr.rows(); }
319
- inline Index cols() const { return m_qr.cols(); }
320
-
321
- /** \returns a const reference to the vector of Householder coefficients used to represent the factor \c Q.
322
- *
323
- * For advanced uses only.
324
- */
325
- const HCoeffsType& hCoeffs() const { return m_hCoeffs; }
326
-
327
- /** Allows to prescribe a threshold to be used by certain methods, such as rank(),
328
- * who need to determine when pivots are to be considered nonzero. This is not used for the
329
- * QR decomposition itself.
330
- *
331
- * When it needs to get the threshold value, Eigen calls threshold(). By default, this
332
- * uses a formula to automatically determine a reasonable threshold.
333
- * Once you have called the present method setThreshold(const RealScalar&),
334
- * your value is used instead.
335
- *
336
- * \param threshold The new value to use as the threshold.
337
- *
338
- * A pivot will be considered nonzero if its absolute value is strictly greater than
339
- * \f$ \vert pivot \vert \leqslant threshold \times \vert maxpivot \vert \f$
340
- * where maxpivot is the biggest pivot.
341
- *
342
- * If you want to come back to the default behavior, call setThreshold(Default_t)
343
- */
344
- FullPivHouseholderQR& setThreshold(const RealScalar& threshold)
345
- {
346
- m_usePrescribedThreshold = true;
347
- m_prescribedThreshold = threshold;
348
- return *this;
349
- }
350
-
351
- /** Allows to come back to the default behavior, letting Eigen use its default formula for
352
- * determining the threshold.
353
- *
354
- * You should pass the special object Eigen::Default as parameter here.
355
- * \code qr.setThreshold(Eigen::Default); \endcode
356
- *
357
- * See the documentation of setThreshold(const RealScalar&).
358
- */
359
- FullPivHouseholderQR& setThreshold(Default_t)
360
- {
361
- m_usePrescribedThreshold = false;
362
- return *this;
363
- }
364
-
365
- /** Returns the threshold that will be used by certain methods such as rank().
366
- *
367
- * See the documentation of setThreshold(const RealScalar&).
368
- */
369
- RealScalar threshold() const
370
- {
371
- eigen_assert(m_isInitialized || m_usePrescribedThreshold);
372
- return m_usePrescribedThreshold ? m_prescribedThreshold
373
- // this formula comes from experimenting (see "LU precision tuning" thread on the list)
374
- // and turns out to be identical to Higham's formula used already in LDLt.
375
- : NumTraits<Scalar>::epsilon() * RealScalar(m_qr.diagonalSize());
376
- }
377
-
378
- /** \returns the number of nonzero pivots in the QR decomposition.
379
- * Here nonzero is meant in the exact sense, not in a fuzzy sense.
380
- * So that notion isn't really intrinsically interesting, but it is
381
- * still useful when implementing algorithms.
382
- *
383
- * \sa rank()
384
- */
385
- inline Index nonzeroPivots() const
386
- {
387
- eigen_assert(m_isInitialized && "LU is not initialized.");
388
- return m_nonzero_pivots;
389
- }
390
-
391
- /** \returns the absolute value of the biggest pivot, i.e. the biggest
392
- * diagonal coefficient of U.
393
- */
394
- RealScalar maxPivot() const { return m_maxpivot; }
395
-
396
- #ifndef EIGEN_PARSED_BY_DOXYGEN
397
- template<typename RhsType, typename DstType>
398
- void _solve_impl(const RhsType &rhs, DstType &dst) const;
399
-
400
- template<bool Conjugate, typename RhsType, typename DstType>
401
- void _solve_impl_transposed(const RhsType &rhs, DstType &dst) const;
402
- #endif
403
-
404
- protected:
405
-
406
- static void check_template_parameters()
407
- {
408
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
409
- }
410
-
411
- void computeInPlace();
412
-
413
- MatrixType m_qr;
414
- HCoeffsType m_hCoeffs;
415
- IntDiagSizeVectorType m_rows_transpositions;
416
- IntDiagSizeVectorType m_cols_transpositions;
417
- PermutationType m_cols_permutation;
418
- RowVectorType m_temp;
419
- bool m_isInitialized, m_usePrescribedThreshold;
420
- RealScalar m_prescribedThreshold, m_maxpivot;
421
- Index m_nonzero_pivots;
422
- RealScalar m_precision;
423
- Index m_det_pq;
424
- };
425
-
426
- template<typename MatrixType>
427
- typename MatrixType::RealScalar FullPivHouseholderQR<MatrixType>::absDeterminant() const
428
- {
429
- using std::abs;
430
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
431
- eigen_assert(m_qr.rows() == m_qr.cols() && "You can't take the determinant of a non-square matrix!");
432
- return abs(m_qr.diagonal().prod());
433
- }
434
-
435
- template<typename MatrixType>
436
- typename MatrixType::RealScalar FullPivHouseholderQR<MatrixType>::logAbsDeterminant() const
437
- {
438
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
439
- eigen_assert(m_qr.rows() == m_qr.cols() && "You can't take the determinant of a non-square matrix!");
440
- return m_qr.diagonal().cwiseAbs().array().log().sum();
441
- }
442
-
443
- /** Performs the QR factorization of the given matrix \a matrix. The result of
444
- * the factorization is stored into \c *this, and a reference to \c *this
445
- * is returned.
446
- *
447
- * \sa class FullPivHouseholderQR, FullPivHouseholderQR(const MatrixType&)
448
- */
449
- template<typename MatrixType>
450
- template<typename InputType>
451
- FullPivHouseholderQR<MatrixType>& FullPivHouseholderQR<MatrixType>::compute(const EigenBase<InputType>& matrix)
452
- {
453
- m_qr = matrix.derived();
454
- computeInPlace();
455
- return *this;
456
- }
457
-
458
- template<typename MatrixType>
459
- void FullPivHouseholderQR<MatrixType>::computeInPlace()
460
- {
461
- check_template_parameters();
462
-
463
- using std::abs;
464
- Index rows = m_qr.rows();
465
- Index cols = m_qr.cols();
466
- Index size = (std::min)(rows,cols);
467
-
468
-
469
- m_hCoeffs.resize(size);
470
-
471
- m_temp.resize(cols);
472
-
473
- m_precision = NumTraits<Scalar>::epsilon() * RealScalar(size);
474
-
475
- m_rows_transpositions.resize(size);
476
- m_cols_transpositions.resize(size);
477
- Index number_of_transpositions = 0;
478
-
479
- RealScalar biggest(0);
480
-
481
- m_nonzero_pivots = size; // the generic case is that in which all pivots are nonzero (invertible case)
482
- m_maxpivot = RealScalar(0);
483
-
484
- for (Index k = 0; k < size; ++k)
485
- {
486
- Index row_of_biggest_in_corner, col_of_biggest_in_corner;
487
- typedef internal::scalar_score_coeff_op<Scalar> Scoring;
488
- typedef typename Scoring::result_type Score;
489
-
490
- Score score = m_qr.bottomRightCorner(rows-k, cols-k)
491
- .unaryExpr(Scoring())
492
- .maxCoeff(&row_of_biggest_in_corner, &col_of_biggest_in_corner);
493
- row_of_biggest_in_corner += k;
494
- col_of_biggest_in_corner += k;
495
- RealScalar biggest_in_corner = internal::abs_knowing_score<Scalar>()(m_qr(row_of_biggest_in_corner, col_of_biggest_in_corner), score);
496
- if(k==0) biggest = biggest_in_corner;
497
-
498
- // if the corner is negligible, then we have less than full rank, and we can finish early
499
- if(internal::isMuchSmallerThan(biggest_in_corner, biggest, m_precision))
500
- {
501
- m_nonzero_pivots = k;
502
- for(Index i = k; i < size; i++)
503
- {
504
- m_rows_transpositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
505
- m_cols_transpositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
506
- m_hCoeffs.coeffRef(i) = Scalar(0);
507
- }
508
- break;
509
- }
510
-
511
- m_rows_transpositions.coeffRef(k) = internal::convert_index<StorageIndex>(row_of_biggest_in_corner);
512
- m_cols_transpositions.coeffRef(k) = internal::convert_index<StorageIndex>(col_of_biggest_in_corner);
513
- if(k != row_of_biggest_in_corner) {
514
- m_qr.row(k).tail(cols-k).swap(m_qr.row(row_of_biggest_in_corner).tail(cols-k));
515
- ++number_of_transpositions;
516
- }
517
- if(k != col_of_biggest_in_corner) {
518
- m_qr.col(k).swap(m_qr.col(col_of_biggest_in_corner));
519
- ++number_of_transpositions;
520
- }
521
-
522
- RealScalar beta;
523
- m_qr.col(k).tail(rows-k).makeHouseholderInPlace(m_hCoeffs.coeffRef(k), beta);
524
- m_qr.coeffRef(k,k) = beta;
525
-
526
- // remember the maximum absolute value of diagonal coefficients
527
- if(abs(beta) > m_maxpivot) m_maxpivot = abs(beta);
528
-
529
- m_qr.bottomRightCorner(rows-k, cols-k-1)
530
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(rows-k-1), m_hCoeffs.coeffRef(k), &m_temp.coeffRef(k+1));
531
- }
532
-
533
- m_cols_permutation.setIdentity(cols);
534
- for(Index k = 0; k < size; ++k)
535
- m_cols_permutation.applyTranspositionOnTheRight(k, m_cols_transpositions.coeff(k));
536
-
537
- m_det_pq = (number_of_transpositions%2) ? -1 : 1;
538
- m_isInitialized = true;
539
- }
540
-
541
- #ifndef EIGEN_PARSED_BY_DOXYGEN
542
- template<typename _MatrixType>
543
- template<typename RhsType, typename DstType>
544
- void FullPivHouseholderQR<_MatrixType>::_solve_impl(const RhsType &rhs, DstType &dst) const
545
- {
546
- const Index l_rank = rank();
547
-
548
- // FIXME introduce nonzeroPivots() and use it here. and more generally,
549
- // make the same improvements in this dec as in FullPivLU.
550
- if(l_rank==0)
551
- {
552
- dst.setZero();
553
- return;
554
- }
555
-
556
- typename RhsType::PlainObject c(rhs);
557
-
558
- Matrix<typename RhsType::Scalar,1,RhsType::ColsAtCompileTime> temp(rhs.cols());
559
- for (Index k = 0; k < l_rank; ++k)
560
- {
561
- Index remainingSize = rows()-k;
562
- c.row(k).swap(c.row(m_rows_transpositions.coeff(k)));
563
- c.bottomRightCorner(remainingSize, rhs.cols())
564
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(remainingSize-1),
565
- m_hCoeffs.coeff(k), &temp.coeffRef(0));
566
- }
567
-
568
- m_qr.topLeftCorner(l_rank, l_rank)
569
- .template triangularView<Upper>()
570
- .solveInPlace(c.topRows(l_rank));
571
-
572
- for(Index i = 0; i < l_rank; ++i) dst.row(m_cols_permutation.indices().coeff(i)) = c.row(i);
573
- for(Index i = l_rank; i < cols(); ++i) dst.row(m_cols_permutation.indices().coeff(i)).setZero();
574
- }
575
-
576
- template<typename _MatrixType>
577
- template<bool Conjugate, typename RhsType, typename DstType>
578
- void FullPivHouseholderQR<_MatrixType>::_solve_impl_transposed(const RhsType &rhs, DstType &dst) const
579
- {
580
- const Index l_rank = rank();
581
-
582
- if(l_rank == 0)
583
- {
584
- dst.setZero();
585
- return;
586
- }
587
-
588
- typename RhsType::PlainObject c(m_cols_permutation.transpose()*rhs);
589
-
590
- m_qr.topLeftCorner(l_rank, l_rank)
591
- .template triangularView<Upper>()
592
- .transpose().template conjugateIf<Conjugate>()
593
- .solveInPlace(c.topRows(l_rank));
594
-
595
- dst.topRows(l_rank) = c.topRows(l_rank);
596
- dst.bottomRows(rows()-l_rank).setZero();
597
-
598
- Matrix<Scalar, 1, DstType::ColsAtCompileTime> temp(dst.cols());
599
- const Index size = (std::min)(rows(), cols());
600
- for (Index k = size-1; k >= 0; --k)
601
- {
602
- Index remainingSize = rows()-k;
603
-
604
- dst.bottomRightCorner(remainingSize, dst.cols())
605
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(remainingSize-1).template conjugateIf<!Conjugate>(),
606
- m_hCoeffs.template conjugateIf<Conjugate>().coeff(k), &temp.coeffRef(0));
607
-
608
- dst.row(k).swap(dst.row(m_rows_transpositions.coeff(k)));
609
- }
610
- }
611
- #endif
612
-
613
- namespace internal {
614
-
615
- template<typename DstXprType, typename MatrixType>
616
- struct Assignment<DstXprType, Inverse<FullPivHouseholderQR<MatrixType> >, internal::assign_op<typename DstXprType::Scalar,typename FullPivHouseholderQR<MatrixType>::Scalar>, Dense2Dense>
617
- {
618
- typedef FullPivHouseholderQR<MatrixType> QrType;
619
- typedef Inverse<QrType> SrcXprType;
620
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename QrType::Scalar> &)
621
- {
622
- dst = src.nestedExpression().solve(MatrixType::Identity(src.rows(), src.cols()));
623
- }
624
- };
625
-
626
- /** \ingroup QR_Module
627
- *
628
- * \brief Expression type for return value of FullPivHouseholderQR::matrixQ()
629
- *
630
- * \tparam MatrixType type of underlying dense matrix
631
- */
632
- template<typename MatrixType> struct FullPivHouseholderQRMatrixQReturnType
633
- : public ReturnByValue<FullPivHouseholderQRMatrixQReturnType<MatrixType> >
634
- {
635
- public:
636
- typedef typename FullPivHouseholderQR<MatrixType>::IntDiagSizeVectorType IntDiagSizeVectorType;
637
- typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
638
- typedef Matrix<typename MatrixType::Scalar, 1, MatrixType::RowsAtCompileTime, RowMajor, 1,
639
- MatrixType::MaxRowsAtCompileTime> WorkVectorType;
640
-
641
- FullPivHouseholderQRMatrixQReturnType(const MatrixType& qr,
642
- const HCoeffsType& hCoeffs,
643
- const IntDiagSizeVectorType& rowsTranspositions)
644
- : m_qr(qr),
645
- m_hCoeffs(hCoeffs),
646
- m_rowsTranspositions(rowsTranspositions)
647
- {}
648
-
649
- template <typename ResultType>
650
- void evalTo(ResultType& result) const
651
- {
652
- const Index rows = m_qr.rows();
653
- WorkVectorType workspace(rows);
654
- evalTo(result, workspace);
655
- }
656
-
657
- template <typename ResultType>
658
- void evalTo(ResultType& result, WorkVectorType& workspace) const
659
- {
660
- using numext::conj;
661
- // compute the product H'_0 H'_1 ... H'_n-1,
662
- // where H_k is the k-th Householder transformation I - h_k v_k v_k'
663
- // and v_k is the k-th Householder vector [1,m_qr(k+1,k), m_qr(k+2,k), ...]
664
- const Index rows = m_qr.rows();
665
- const Index cols = m_qr.cols();
666
- const Index size = (std::min)(rows, cols);
667
- workspace.resize(rows);
668
- result.setIdentity(rows, rows);
669
- for (Index k = size-1; k >= 0; k--)
670
- {
671
- result.block(k, k, rows-k, rows-k)
672
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(rows-k-1), conj(m_hCoeffs.coeff(k)), &workspace.coeffRef(k));
673
- result.row(k).swap(result.row(m_rowsTranspositions.coeff(k)));
674
- }
675
- }
676
-
677
- Index rows() const { return m_qr.rows(); }
678
- Index cols() const { return m_qr.rows(); }
679
-
680
- protected:
681
- typename MatrixType::Nested m_qr;
682
- typename HCoeffsType::Nested m_hCoeffs;
683
- typename IntDiagSizeVectorType::Nested m_rowsTranspositions;
684
- };
685
-
686
- // template<typename MatrixType>
687
- // struct evaluator<FullPivHouseholderQRMatrixQReturnType<MatrixType> >
688
- // : public evaluator<ReturnByValue<FullPivHouseholderQRMatrixQReturnType<MatrixType> > >
689
- // {};
690
-
691
- } // end namespace internal
692
-
693
- template<typename MatrixType>
694
- inline typename FullPivHouseholderQR<MatrixType>::MatrixQReturnType FullPivHouseholderQR<MatrixType>::matrixQ() const
695
- {
696
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
697
- return MatrixQReturnType(m_qr, m_hCoeffs, m_rows_transpositions);
698
- }
699
-
700
- /** \return the full-pivoting Householder QR decomposition of \c *this.
701
- *
702
- * \sa class FullPivHouseholderQR
703
- */
704
- template<typename Derived>
705
- const FullPivHouseholderQR<typename MatrixBase<Derived>::PlainObject>
706
- MatrixBase<Derived>::fullPivHouseholderQr() const
707
- {
708
- return FullPivHouseholderQR<PlainObject>(eval());
709
- }
710
-
711
- } // end namespace Eigen
712
-
713
- #endif // EIGEN_FULLPIVOTINGHOUSEHOLDERQR_H