sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.19__cp310-cp310-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of sequenzo might be problematic. Click here for more details.

Files changed (396) hide show
  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
  214. sequenzo/dissimilarity_measures/src/eigen/test/main.h +0 -857
  215. sequenzo/dissimilarity_measures/src/eigen/test/packetmath_test_shared.h +0 -275
  216. sequenzo/dissimilarity_measures/src/eigen/test/product.h +0 -259
  217. sequenzo/dissimilarity_measures/src/eigen/test/random_without_cast_overflow.h +0 -152
  218. sequenzo/dissimilarity_measures/src/eigen/test/solverbase.h +0 -36
  219. sequenzo/dissimilarity_measures/src/eigen/test/sparse.h +0 -204
  220. sequenzo/dissimilarity_measures/src/eigen/test/sparse_solver.h +0 -699
  221. sequenzo/dissimilarity_measures/src/eigen/test/split_test_helper.h +0 -5994
  222. sequenzo/dissimilarity_measures/src/eigen/test/svd_common.h +0 -521
  223. sequenzo/dissimilarity_measures/src/eigen/test/svd_fill.h +0 -118
  224. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  225. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  226. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  227. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  228. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  229. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  230. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  231. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  232. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  233. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  234. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  235. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  236. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  237. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  238. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  239. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  240. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  241. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  242. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  243. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  244. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  245. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
  246. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h +0 -104
  247. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h +0 -389
  248. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h +0 -1048
  249. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h +0 -409
  250. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h +0 -236
  251. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h +0 -490
  252. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h +0 -236
  253. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h +0 -983
  254. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h +0 -703
  255. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h +0 -388
  256. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h +0 -669
  257. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h +0 -379
  258. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h +0 -237
  259. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h +0 -191
  260. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h +0 -488
  261. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h +0 -302
  262. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGlobalFunctions.h +0 -33
  263. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h +0 -99
  264. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h +0 -44
  265. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIO.h +0 -79
  266. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h +0 -603
  267. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h +0 -738
  268. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h +0 -247
  269. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h +0 -82
  270. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h +0 -263
  271. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h +0 -216
  272. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h +0 -98
  273. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h +0 -327
  274. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h +0 -311
  275. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h +0 -1102
  276. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h +0 -708
  277. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h +0 -291
  278. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h +0 -322
  279. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h +0 -998
  280. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h +0 -6
  281. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h +0 -966
  282. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h +0 -582
  283. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h +0 -454
  284. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h +0 -465
  285. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h +0 -528
  286. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScanSycl.h +0 -513
  287. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h +0 -471
  288. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h +0 -161
  289. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStriding.h +0 -346
  290. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTrace.h +0 -303
  291. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h +0 -264
  292. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h +0 -249
  293. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h +0 -629
  294. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/DynamicSymmetry.h +0 -293
  295. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/StaticSymmetry.h +0 -236
  296. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/Symmetry.h +0 -338
  297. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h +0 -669
  298. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/Barrier.h +0 -67
  299. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h +0 -249
  300. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h +0 -486
  301. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h +0 -236
  302. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadCancel.h +0 -23
  303. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h +0 -40
  304. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h +0 -301
  305. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h +0 -48
  306. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h +0 -20
  307. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Meta.h +0 -537
  308. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h +0 -88
  309. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/EmulateArray.h +0 -261
  310. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h +0 -158
  311. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h +0 -108
  312. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h +0 -730
  313. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffVector.h +0 -220
  314. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/BVAlgorithms.h +0 -293
  315. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/KdBVH.h +0 -223
  316. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h +0 -790
  317. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerAngles.h +0 -355
  318. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerSystem.h +0 -305
  319. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_fftw_impl.h +0 -261
  320. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_kissfft_impl.h +0 -449
  321. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h +0 -187
  322. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/DGMRES.h +0 -511
  323. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/GMRES.h +0 -335
  324. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IDRS.h +0 -436
  325. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h +0 -90
  326. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IterationController.h +0 -154
  327. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/MINRES.h +0 -267
  328. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/Scaling.h +0 -193
  329. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h +0 -305
  330. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h +0 -84
  331. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMonestep.h +0 -202
  332. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h +0 -160
  333. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h +0 -188
  334. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  335. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  336. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  337. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  338. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  339. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  340. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  341. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  342. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  343. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  344. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  345. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  346. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  347. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  348. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  349. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  350. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  351. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  352. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  353. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  354. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  355. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  356. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  357. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  358. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  359. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  360. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  361. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  362. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  363. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  364. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  365. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  366. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  367. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  368. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  369. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  370. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  371. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  372. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  373. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  374. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  375. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  376. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  377. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  378. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  379. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  380. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  381. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  382. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  383. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  384. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  385. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  386. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  387. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  388. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  389. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  390. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  391. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  392. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  393. sequenzo-0.1.18.dist-info/RECORD +0 -638
  394. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  395. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  396. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,635 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2016 Rasmus Munk Larsen <rmlarsen@google.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_COMPLETEORTHOGONALDECOMPOSITION_H
11
- #define EIGEN_COMPLETEORTHOGONALDECOMPOSITION_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
- template <typename _MatrixType>
17
- struct traits<CompleteOrthogonalDecomposition<_MatrixType> >
18
- : traits<_MatrixType> {
19
- typedef MatrixXpr XprKind;
20
- typedef SolverStorage StorageKind;
21
- typedef int StorageIndex;
22
- enum { Flags = 0 };
23
- };
24
-
25
- } // end namespace internal
26
-
27
- /** \ingroup QR_Module
28
- *
29
- * \class CompleteOrthogonalDecomposition
30
- *
31
- * \brief Complete orthogonal decomposition (COD) of a matrix.
32
- *
33
- * \param MatrixType the type of the matrix of which we are computing the COD.
34
- *
35
- * This class performs a rank-revealing complete orthogonal decomposition of a
36
- * matrix \b A into matrices \b P, \b Q, \b T, and \b Z such that
37
- * \f[
38
- * \mathbf{A} \, \mathbf{P} = \mathbf{Q} \,
39
- * \begin{bmatrix} \mathbf{T} & \mathbf{0} \\
40
- * \mathbf{0} & \mathbf{0} \end{bmatrix} \, \mathbf{Z}
41
- * \f]
42
- * by using Householder transformations. Here, \b P is a permutation matrix,
43
- * \b Q and \b Z are unitary matrices and \b T an upper triangular matrix of
44
- * size rank-by-rank. \b A may be rank deficient.
45
- *
46
- * This class supports the \link InplaceDecomposition inplace decomposition \endlink mechanism.
47
- *
48
- * \sa MatrixBase::completeOrthogonalDecomposition()
49
- */
50
- template <typename _MatrixType> class CompleteOrthogonalDecomposition
51
- : public SolverBase<CompleteOrthogonalDecomposition<_MatrixType> >
52
- {
53
- public:
54
- typedef _MatrixType MatrixType;
55
- typedef SolverBase<CompleteOrthogonalDecomposition> Base;
56
-
57
- template<typename Derived>
58
- friend struct internal::solve_assertion;
59
-
60
- EIGEN_GENERIC_PUBLIC_INTERFACE(CompleteOrthogonalDecomposition)
61
- enum {
62
- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
63
- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
64
- };
65
- typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
66
- typedef PermutationMatrix<ColsAtCompileTime, MaxColsAtCompileTime>
67
- PermutationType;
68
- typedef typename internal::plain_row_type<MatrixType, Index>::type
69
- IntRowVectorType;
70
- typedef typename internal::plain_row_type<MatrixType>::type RowVectorType;
71
- typedef typename internal::plain_row_type<MatrixType, RealScalar>::type
72
- RealRowVectorType;
73
- typedef HouseholderSequence<
74
- MatrixType, typename internal::remove_all<
75
- typename HCoeffsType::ConjugateReturnType>::type>
76
- HouseholderSequenceType;
77
- typedef typename MatrixType::PlainObject PlainObject;
78
-
79
- private:
80
- typedef typename PermutationType::Index PermIndexType;
81
-
82
- public:
83
- /**
84
- * \brief Default Constructor.
85
- *
86
- * The default constructor is useful in cases in which the user intends to
87
- * perform decompositions via
88
- * \c CompleteOrthogonalDecomposition::compute(const* MatrixType&).
89
- */
90
- CompleteOrthogonalDecomposition() : m_cpqr(), m_zCoeffs(), m_temp() {}
91
-
92
- /** \brief Default Constructor with memory preallocation
93
- *
94
- * Like the default constructor but with preallocation of the internal data
95
- * according to the specified problem \a size.
96
- * \sa CompleteOrthogonalDecomposition()
97
- */
98
- CompleteOrthogonalDecomposition(Index rows, Index cols)
99
- : m_cpqr(rows, cols), m_zCoeffs((std::min)(rows, cols)), m_temp(cols) {}
100
-
101
- /** \brief Constructs a complete orthogonal decomposition from a given
102
- * matrix.
103
- *
104
- * This constructor computes the complete orthogonal decomposition of the
105
- * matrix \a matrix by calling the method compute(). The default
106
- * threshold for rank determination will be used. It is a short cut for:
107
- *
108
- * \code
109
- * CompleteOrthogonalDecomposition<MatrixType> cod(matrix.rows(),
110
- * matrix.cols());
111
- * cod.setThreshold(Default);
112
- * cod.compute(matrix);
113
- * \endcode
114
- *
115
- * \sa compute()
116
- */
117
- template <typename InputType>
118
- explicit CompleteOrthogonalDecomposition(const EigenBase<InputType>& matrix)
119
- : m_cpqr(matrix.rows(), matrix.cols()),
120
- m_zCoeffs((std::min)(matrix.rows(), matrix.cols())),
121
- m_temp(matrix.cols())
122
- {
123
- compute(matrix.derived());
124
- }
125
-
126
- /** \brief Constructs a complete orthogonal decomposition from a given matrix
127
- *
128
- * This overloaded constructor is provided for \link InplaceDecomposition inplace decomposition \endlink when \c MatrixType is a Eigen::Ref.
129
- *
130
- * \sa CompleteOrthogonalDecomposition(const EigenBase&)
131
- */
132
- template<typename InputType>
133
- explicit CompleteOrthogonalDecomposition(EigenBase<InputType>& matrix)
134
- : m_cpqr(matrix.derived()),
135
- m_zCoeffs((std::min)(matrix.rows(), matrix.cols())),
136
- m_temp(matrix.cols())
137
- {
138
- computeInPlace();
139
- }
140
-
141
- #ifdef EIGEN_PARSED_BY_DOXYGEN
142
- /** This method computes the minimum-norm solution X to a least squares
143
- * problem \f[\mathrm{minimize} \|A X - B\|, \f] where \b A is the matrix of
144
- * which \c *this is the complete orthogonal decomposition.
145
- *
146
- * \param b the right-hand sides of the problem to solve.
147
- *
148
- * \returns a solution.
149
- *
150
- */
151
- template <typename Rhs>
152
- inline const Solve<CompleteOrthogonalDecomposition, Rhs> solve(
153
- const MatrixBase<Rhs>& b) const;
154
- #endif
155
-
156
- HouseholderSequenceType householderQ(void) const;
157
- HouseholderSequenceType matrixQ(void) const { return m_cpqr.householderQ(); }
158
-
159
- /** \returns the matrix \b Z.
160
- */
161
- MatrixType matrixZ() const {
162
- MatrixType Z = MatrixType::Identity(m_cpqr.cols(), m_cpqr.cols());
163
- applyZOnTheLeftInPlace<false>(Z);
164
- return Z;
165
- }
166
-
167
- /** \returns a reference to the matrix where the complete orthogonal
168
- * decomposition is stored
169
- */
170
- const MatrixType& matrixQTZ() const { return m_cpqr.matrixQR(); }
171
-
172
- /** \returns a reference to the matrix where the complete orthogonal
173
- * decomposition is stored.
174
- * \warning The strict lower part and \code cols() - rank() \endcode right
175
- * columns of this matrix contains internal values.
176
- * Only the upper triangular part should be referenced. To get it, use
177
- * \code matrixT().template triangularView<Upper>() \endcode
178
- * For rank-deficient matrices, use
179
- * \code
180
- * matrixR().topLeftCorner(rank(), rank()).template triangularView<Upper>()
181
- * \endcode
182
- */
183
- const MatrixType& matrixT() const { return m_cpqr.matrixQR(); }
184
-
185
- template <typename InputType>
186
- CompleteOrthogonalDecomposition& compute(const EigenBase<InputType>& matrix) {
187
- // Compute the column pivoted QR factorization A P = Q R.
188
- m_cpqr.compute(matrix);
189
- computeInPlace();
190
- return *this;
191
- }
192
-
193
- /** \returns a const reference to the column permutation matrix */
194
- const PermutationType& colsPermutation() const {
195
- return m_cpqr.colsPermutation();
196
- }
197
-
198
- /** \returns the absolute value of the determinant of the matrix of which
199
- * *this is the complete orthogonal decomposition. It has only linear
200
- * complexity (that is, O(n) where n is the dimension of the square matrix)
201
- * as the complete orthogonal decomposition has already been computed.
202
- *
203
- * \note This is only for square matrices.
204
- *
205
- * \warning a determinant can be very big or small, so for matrices
206
- * of large enough dimension, there is a risk of overflow/underflow.
207
- * One way to work around that is to use logAbsDeterminant() instead.
208
- *
209
- * \sa logAbsDeterminant(), MatrixBase::determinant()
210
- */
211
- typename MatrixType::RealScalar absDeterminant() const;
212
-
213
- /** \returns the natural log of the absolute value of the determinant of the
214
- * matrix of which *this is the complete orthogonal decomposition. It has
215
- * only linear complexity (that is, O(n) where n is the dimension of the
216
- * square matrix) as the complete orthogonal decomposition has already been
217
- * computed.
218
- *
219
- * \note This is only for square matrices.
220
- *
221
- * \note This method is useful to work around the risk of overflow/underflow
222
- * that's inherent to determinant computation.
223
- *
224
- * \sa absDeterminant(), MatrixBase::determinant()
225
- */
226
- typename MatrixType::RealScalar logAbsDeterminant() const;
227
-
228
- /** \returns the rank of the matrix of which *this is the complete orthogonal
229
- * decomposition.
230
- *
231
- * \note This method has to determine which pivots should be considered
232
- * nonzero. For that, it uses the threshold value that you can control by
233
- * calling setThreshold(const RealScalar&).
234
- */
235
- inline Index rank() const { return m_cpqr.rank(); }
236
-
237
- /** \returns the dimension of the kernel of the matrix of which *this is the
238
- * complete orthogonal decomposition.
239
- *
240
- * \note This method has to determine which pivots should be considered
241
- * nonzero. For that, it uses the threshold value that you can control by
242
- * calling setThreshold(const RealScalar&).
243
- */
244
- inline Index dimensionOfKernel() const { return m_cpqr.dimensionOfKernel(); }
245
-
246
- /** \returns true if the matrix of which *this is the decomposition represents
247
- * an injective linear map, i.e. has trivial kernel; false otherwise.
248
- *
249
- * \note This method has to determine which pivots should be considered
250
- * nonzero. For that, it uses the threshold value that you can control by
251
- * calling setThreshold(const RealScalar&).
252
- */
253
- inline bool isInjective() const { return m_cpqr.isInjective(); }
254
-
255
- /** \returns true if the matrix of which *this is the decomposition represents
256
- * a surjective linear map; false otherwise.
257
- *
258
- * \note This method has to determine which pivots should be considered
259
- * nonzero. For that, it uses the threshold value that you can control by
260
- * calling setThreshold(const RealScalar&).
261
- */
262
- inline bool isSurjective() const { return m_cpqr.isSurjective(); }
263
-
264
- /** \returns true if the matrix of which *this is the complete orthogonal
265
- * decomposition is invertible.
266
- *
267
- * \note This method has to determine which pivots should be considered
268
- * nonzero. For that, it uses the threshold value that you can control by
269
- * calling setThreshold(const RealScalar&).
270
- */
271
- inline bool isInvertible() const { return m_cpqr.isInvertible(); }
272
-
273
- /** \returns the pseudo-inverse of the matrix of which *this is the complete
274
- * orthogonal decomposition.
275
- * \warning: Do not compute \c this->pseudoInverse()*rhs to solve a linear systems.
276
- * It is more efficient and numerically stable to call \c this->solve(rhs).
277
- */
278
- inline const Inverse<CompleteOrthogonalDecomposition> pseudoInverse() const
279
- {
280
- eigen_assert(m_cpqr.m_isInitialized && "CompleteOrthogonalDecomposition is not initialized.");
281
- return Inverse<CompleteOrthogonalDecomposition>(*this);
282
- }
283
-
284
- inline Index rows() const { return m_cpqr.rows(); }
285
- inline Index cols() const { return m_cpqr.cols(); }
286
-
287
- /** \returns a const reference to the vector of Householder coefficients used
288
- * to represent the factor \c Q.
289
- *
290
- * For advanced uses only.
291
- */
292
- inline const HCoeffsType& hCoeffs() const { return m_cpqr.hCoeffs(); }
293
-
294
- /** \returns a const reference to the vector of Householder coefficients
295
- * used to represent the factor \c Z.
296
- *
297
- * For advanced uses only.
298
- */
299
- const HCoeffsType& zCoeffs() const { return m_zCoeffs; }
300
-
301
- /** Allows to prescribe a threshold to be used by certain methods, such as
302
- * rank(), who need to determine when pivots are to be considered nonzero.
303
- * Most be called before calling compute().
304
- *
305
- * When it needs to get the threshold value, Eigen calls threshold(). By
306
- * default, this uses a formula to automatically determine a reasonable
307
- * threshold. Once you have called the present method
308
- * setThreshold(const RealScalar&), your value is used instead.
309
- *
310
- * \param threshold The new value to use as the threshold.
311
- *
312
- * A pivot will be considered nonzero if its absolute value is strictly
313
- * greater than
314
- * \f$ \vert pivot \vert \leqslant threshold \times \vert maxpivot \vert \f$
315
- * where maxpivot is the biggest pivot.
316
- *
317
- * If you want to come back to the default behavior, call
318
- * setThreshold(Default_t)
319
- */
320
- CompleteOrthogonalDecomposition& setThreshold(const RealScalar& threshold) {
321
- m_cpqr.setThreshold(threshold);
322
- return *this;
323
- }
324
-
325
- /** Allows to come back to the default behavior, letting Eigen use its default
326
- * formula for determining the threshold.
327
- *
328
- * You should pass the special object Eigen::Default as parameter here.
329
- * \code qr.setThreshold(Eigen::Default); \endcode
330
- *
331
- * See the documentation of setThreshold(const RealScalar&).
332
- */
333
- CompleteOrthogonalDecomposition& setThreshold(Default_t) {
334
- m_cpqr.setThreshold(Default);
335
- return *this;
336
- }
337
-
338
- /** Returns the threshold that will be used by certain methods such as rank().
339
- *
340
- * See the documentation of setThreshold(const RealScalar&).
341
- */
342
- RealScalar threshold() const { return m_cpqr.threshold(); }
343
-
344
- /** \returns the number of nonzero pivots in the complete orthogonal
345
- * decomposition. Here nonzero is meant in the exact sense, not in a
346
- * fuzzy sense. So that notion isn't really intrinsically interesting,
347
- * but it is still useful when implementing algorithms.
348
- *
349
- * \sa rank()
350
- */
351
- inline Index nonzeroPivots() const { return m_cpqr.nonzeroPivots(); }
352
-
353
- /** \returns the absolute value of the biggest pivot, i.e. the biggest
354
- * diagonal coefficient of R.
355
- */
356
- inline RealScalar maxPivot() const { return m_cpqr.maxPivot(); }
357
-
358
- /** \brief Reports whether the complete orthogonal decomposition was
359
- * successful.
360
- *
361
- * \note This function always returns \c Success. It is provided for
362
- * compatibility
363
- * with other factorization routines.
364
- * \returns \c Success
365
- */
366
- ComputationInfo info() const {
367
- eigen_assert(m_cpqr.m_isInitialized && "Decomposition is not initialized.");
368
- return Success;
369
- }
370
-
371
- #ifndef EIGEN_PARSED_BY_DOXYGEN
372
- template <typename RhsType, typename DstType>
373
- void _solve_impl(const RhsType& rhs, DstType& dst) const;
374
-
375
- template<bool Conjugate, typename RhsType, typename DstType>
376
- void _solve_impl_transposed(const RhsType &rhs, DstType &dst) const;
377
- #endif
378
-
379
- protected:
380
- static void check_template_parameters() {
381
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
382
- }
383
-
384
- template<bool Transpose_, typename Rhs>
385
- void _check_solve_assertion(const Rhs& b) const {
386
- EIGEN_ONLY_USED_FOR_DEBUG(b);
387
- eigen_assert(m_cpqr.m_isInitialized && "CompleteOrthogonalDecomposition is not initialized.");
388
- eigen_assert((Transpose_?derived().cols():derived().rows())==b.rows() && "CompleteOrthogonalDecomposition::solve(): invalid number of rows of the right hand side matrix b");
389
- }
390
-
391
- void computeInPlace();
392
-
393
- /** Overwrites \b rhs with \f$ \mathbf{Z} * \mathbf{rhs} \f$ or
394
- * \f$ \mathbf{\overline Z} * \mathbf{rhs} \f$ if \c Conjugate
395
- * is set to \c true.
396
- */
397
- template <bool Conjugate, typename Rhs>
398
- void applyZOnTheLeftInPlace(Rhs& rhs) const;
399
-
400
- /** Overwrites \b rhs with \f$ \mathbf{Z}^* * \mathbf{rhs} \f$.
401
- */
402
- template <typename Rhs>
403
- void applyZAdjointOnTheLeftInPlace(Rhs& rhs) const;
404
-
405
- ColPivHouseholderQR<MatrixType> m_cpqr;
406
- HCoeffsType m_zCoeffs;
407
- RowVectorType m_temp;
408
- };
409
-
410
- template <typename MatrixType>
411
- typename MatrixType::RealScalar
412
- CompleteOrthogonalDecomposition<MatrixType>::absDeterminant() const {
413
- return m_cpqr.absDeterminant();
414
- }
415
-
416
- template <typename MatrixType>
417
- typename MatrixType::RealScalar
418
- CompleteOrthogonalDecomposition<MatrixType>::logAbsDeterminant() const {
419
- return m_cpqr.logAbsDeterminant();
420
- }
421
-
422
- /** Performs the complete orthogonal decomposition of the given matrix \a
423
- * matrix. The result of the factorization is stored into \c *this, and a
424
- * reference to \c *this is returned.
425
- *
426
- * \sa class CompleteOrthogonalDecomposition,
427
- * CompleteOrthogonalDecomposition(const MatrixType&)
428
- */
429
- template <typename MatrixType>
430
- void CompleteOrthogonalDecomposition<MatrixType>::computeInPlace()
431
- {
432
- check_template_parameters();
433
-
434
- // the column permutation is stored as int indices, so just to be sure:
435
- eigen_assert(m_cpqr.cols() <= NumTraits<int>::highest());
436
-
437
- const Index rank = m_cpqr.rank();
438
- const Index cols = m_cpqr.cols();
439
- const Index rows = m_cpqr.rows();
440
- m_zCoeffs.resize((std::min)(rows, cols));
441
- m_temp.resize(cols);
442
-
443
- if (rank < cols) {
444
- // We have reduced the (permuted) matrix to the form
445
- // [R11 R12]
446
- // [ 0 R22]
447
- // where R11 is r-by-r (r = rank) upper triangular, R12 is
448
- // r-by-(n-r), and R22 is empty or the norm of R22 is negligible.
449
- // We now compute the complete orthogonal decomposition by applying
450
- // Householder transformations from the right to the upper trapezoidal
451
- // matrix X = [R11 R12] to zero out R12 and obtain the factorization
452
- // [R11 R12] = [T11 0] * Z, where T11 is r-by-r upper triangular and
453
- // Z = Z(0) * Z(1) ... Z(r-1) is an n-by-n orthogonal matrix.
454
- // We store the data representing Z in R12 and m_zCoeffs.
455
- for (Index k = rank - 1; k >= 0; --k) {
456
- if (k != rank - 1) {
457
- // Given the API for Householder reflectors, it is more convenient if
458
- // we swap the leading parts of columns k and r-1 (zero-based) to form
459
- // the matrix X_k = [X(0:k, k), X(0:k, r:n)]
460
- m_cpqr.m_qr.col(k).head(k + 1).swap(
461
- m_cpqr.m_qr.col(rank - 1).head(k + 1));
462
- }
463
- // Construct Householder reflector Z(k) to zero out the last row of X_k,
464
- // i.e. choose Z(k) such that
465
- // [X(k, k), X(k, r:n)] * Z(k) = [beta, 0, .., 0].
466
- RealScalar beta;
467
- m_cpqr.m_qr.row(k)
468
- .tail(cols - rank + 1)
469
- .makeHouseholderInPlace(m_zCoeffs(k), beta);
470
- m_cpqr.m_qr(k, rank - 1) = beta;
471
- if (k > 0) {
472
- // Apply Z(k) to the first k rows of X_k
473
- m_cpqr.m_qr.topRightCorner(k, cols - rank + 1)
474
- .applyHouseholderOnTheRight(
475
- m_cpqr.m_qr.row(k).tail(cols - rank).adjoint(), m_zCoeffs(k),
476
- &m_temp(0));
477
- }
478
- if (k != rank - 1) {
479
- // Swap X(0:k,k) back to its proper location.
480
- m_cpqr.m_qr.col(k).head(k + 1).swap(
481
- m_cpqr.m_qr.col(rank - 1).head(k + 1));
482
- }
483
- }
484
- }
485
- }
486
-
487
- template <typename MatrixType>
488
- template <bool Conjugate, typename Rhs>
489
- void CompleteOrthogonalDecomposition<MatrixType>::applyZOnTheLeftInPlace(
490
- Rhs& rhs) const {
491
- const Index cols = this->cols();
492
- const Index nrhs = rhs.cols();
493
- const Index rank = this->rank();
494
- Matrix<typename Rhs::Scalar, Dynamic, 1> temp((std::max)(cols, nrhs));
495
- for (Index k = rank-1; k >= 0; --k) {
496
- if (k != rank - 1) {
497
- rhs.row(k).swap(rhs.row(rank - 1));
498
- }
499
- rhs.middleRows(rank - 1, cols - rank + 1)
500
- .applyHouseholderOnTheLeft(
501
- matrixQTZ().row(k).tail(cols - rank).transpose().template conjugateIf<!Conjugate>(), zCoeffs().template conjugateIf<Conjugate>()(k),
502
- &temp(0));
503
- if (k != rank - 1) {
504
- rhs.row(k).swap(rhs.row(rank - 1));
505
- }
506
- }
507
- }
508
-
509
- template <typename MatrixType>
510
- template <typename Rhs>
511
- void CompleteOrthogonalDecomposition<MatrixType>::applyZAdjointOnTheLeftInPlace(
512
- Rhs& rhs) const {
513
- const Index cols = this->cols();
514
- const Index nrhs = rhs.cols();
515
- const Index rank = this->rank();
516
- Matrix<typename Rhs::Scalar, Dynamic, 1> temp((std::max)(cols, nrhs));
517
- for (Index k = 0; k < rank; ++k) {
518
- if (k != rank - 1) {
519
- rhs.row(k).swap(rhs.row(rank - 1));
520
- }
521
- rhs.middleRows(rank - 1, cols - rank + 1)
522
- .applyHouseholderOnTheLeft(
523
- matrixQTZ().row(k).tail(cols - rank).adjoint(), zCoeffs()(k),
524
- &temp(0));
525
- if (k != rank - 1) {
526
- rhs.row(k).swap(rhs.row(rank - 1));
527
- }
528
- }
529
- }
530
-
531
- #ifndef EIGEN_PARSED_BY_DOXYGEN
532
- template <typename _MatrixType>
533
- template <typename RhsType, typename DstType>
534
- void CompleteOrthogonalDecomposition<_MatrixType>::_solve_impl(
535
- const RhsType& rhs, DstType& dst) const {
536
- const Index rank = this->rank();
537
- if (rank == 0) {
538
- dst.setZero();
539
- return;
540
- }
541
-
542
- // Compute c = Q^* * rhs
543
- typename RhsType::PlainObject c(rhs);
544
- c.applyOnTheLeft(matrixQ().setLength(rank).adjoint());
545
-
546
- // Solve T z = c(1:rank, :)
547
- dst.topRows(rank) = matrixT()
548
- .topLeftCorner(rank, rank)
549
- .template triangularView<Upper>()
550
- .solve(c.topRows(rank));
551
-
552
- const Index cols = this->cols();
553
- if (rank < cols) {
554
- // Compute y = Z^* * [ z ]
555
- // [ 0 ]
556
- dst.bottomRows(cols - rank).setZero();
557
- applyZAdjointOnTheLeftInPlace(dst);
558
- }
559
-
560
- // Undo permutation to get x = P^{-1} * y.
561
- dst = colsPermutation() * dst;
562
- }
563
-
564
- template<typename _MatrixType>
565
- template<bool Conjugate, typename RhsType, typename DstType>
566
- void CompleteOrthogonalDecomposition<_MatrixType>::_solve_impl_transposed(const RhsType &rhs, DstType &dst) const
567
- {
568
- const Index rank = this->rank();
569
-
570
- if (rank == 0) {
571
- dst.setZero();
572
- return;
573
- }
574
-
575
- typename RhsType::PlainObject c(colsPermutation().transpose()*rhs);
576
-
577
- if (rank < cols()) {
578
- applyZOnTheLeftInPlace<!Conjugate>(c);
579
- }
580
-
581
- matrixT().topLeftCorner(rank, rank)
582
- .template triangularView<Upper>()
583
- .transpose().template conjugateIf<Conjugate>()
584
- .solveInPlace(c.topRows(rank));
585
-
586
- dst.topRows(rank) = c.topRows(rank);
587
- dst.bottomRows(rows()-rank).setZero();
588
-
589
- dst.applyOnTheLeft(householderQ().setLength(rank).template conjugateIf<!Conjugate>() );
590
- }
591
- #endif
592
-
593
- namespace internal {
594
-
595
- template<typename MatrixType>
596
- struct traits<Inverse<CompleteOrthogonalDecomposition<MatrixType> > >
597
- : traits<typename Transpose<typename MatrixType::PlainObject>::PlainObject>
598
- {
599
- enum { Flags = 0 };
600
- };
601
-
602
- template<typename DstXprType, typename MatrixType>
603
- struct Assignment<DstXprType, Inverse<CompleteOrthogonalDecomposition<MatrixType> >, internal::assign_op<typename DstXprType::Scalar,typename CompleteOrthogonalDecomposition<MatrixType>::Scalar>, Dense2Dense>
604
- {
605
- typedef CompleteOrthogonalDecomposition<MatrixType> CodType;
606
- typedef Inverse<CodType> SrcXprType;
607
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename CodType::Scalar> &)
608
- {
609
- typedef Matrix<typename CodType::Scalar, CodType::RowsAtCompileTime, CodType::RowsAtCompileTime, 0, CodType::MaxRowsAtCompileTime, CodType::MaxRowsAtCompileTime> IdentityMatrixType;
610
- dst = src.nestedExpression().solve(IdentityMatrixType::Identity(src.cols(), src.cols()));
611
- }
612
- };
613
-
614
- } // end namespace internal
615
-
616
- /** \returns the matrix Q as a sequence of householder transformations */
617
- template <typename MatrixType>
618
- typename CompleteOrthogonalDecomposition<MatrixType>::HouseholderSequenceType
619
- CompleteOrthogonalDecomposition<MatrixType>::householderQ() const {
620
- return m_cpqr.householderQ();
621
- }
622
-
623
- /** \return the complete orthogonal decomposition of \c *this.
624
- *
625
- * \sa class CompleteOrthogonalDecomposition
626
- */
627
- template <typename Derived>
628
- const CompleteOrthogonalDecomposition<typename MatrixBase<Derived>::PlainObject>
629
- MatrixBase<Derived>::completeOrthogonalDecomposition() const {
630
- return CompleteOrthogonalDecomposition<PlainObject>(eval());
631
- }
632
-
633
- } // end namespace Eigen
634
-
635
- #endif // EIGEN_COMPLETEORTHOGONALDECOMPOSITION_H