sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,545 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2009 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 2010 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_HOUSEHOLDER_SEQUENCE_H
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- #define EIGEN_HOUSEHOLDER_SEQUENCE_H
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-
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- namespace Eigen {
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-
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- /** \ingroup Householder_Module
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- * \householder_module
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- * \class HouseholderSequence
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- * \brief Sequence of Householder reflections acting on subspaces with decreasing size
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- * \tparam VectorsType type of matrix containing the Householder vectors
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- * \tparam CoeffsType type of vector containing the Householder coefficients
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- * \tparam Side either OnTheLeft (the default) or OnTheRight
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- *
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- * This class represents a product sequence of Householder reflections where the first Householder reflection
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- * acts on the whole space, the second Householder reflection leaves the one-dimensional subspace spanned by
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- * the first unit vector invariant, the third Householder reflection leaves the two-dimensional subspace
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- * spanned by the first two unit vectors invariant, and so on up to the last reflection which leaves all but
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- * one dimensions invariant and acts only on the last dimension. Such sequences of Householder reflections
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- * are used in several algorithms to zero out certain parts of a matrix. Indeed, the methods
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- * HessenbergDecomposition::matrixQ(), Tridiagonalization::matrixQ(), HouseholderQR::householderQ(),
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- * and ColPivHouseholderQR::householderQ() all return a %HouseholderSequence.
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- *
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- * More precisely, the class %HouseholderSequence represents an \f$ n \times n \f$ matrix \f$ H \f$ of the
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- * form \f$ H = \prod_{i=0}^{n-1} H_i \f$ where the i-th Householder reflection is \f$ H_i = I - h_i v_i
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- * v_i^* \f$. The i-th Householder coefficient \f$ h_i \f$ is a scalar and the i-th Householder vector \f$
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- * v_i \f$ is a vector of the form
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- * \f[
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- * v_i = [\underbrace{0, \ldots, 0}_{i-1\mbox{ zeros}}, 1, \underbrace{*, \ldots,*}_{n-i\mbox{ arbitrary entries}} ].
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- * \f]
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- * The last \f$ n-i \f$ entries of \f$ v_i \f$ are called the essential part of the Householder vector.
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- *
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- * Typical usages are listed below, where H is a HouseholderSequence:
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- * \code
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- * A.applyOnTheRight(H); // A = A * H
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- * A.applyOnTheLeft(H); // A = H * A
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- * A.applyOnTheRight(H.adjoint()); // A = A * H^*
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- * A.applyOnTheLeft(H.adjoint()); // A = H^* * A
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- * MatrixXd Q = H; // conversion to a dense matrix
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- * \endcode
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- * In addition to the adjoint, you can also apply the inverse (=adjoint), the transpose, and the conjugate operators.
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- *
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- * See the documentation for HouseholderSequence(const VectorsType&, const CoeffsType&) for an example.
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- *
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- * \sa MatrixBase::applyOnTheLeft(), MatrixBase::applyOnTheRight()
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- */
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-
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- namespace internal {
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-
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- template<typename VectorsType, typename CoeffsType, int Side>
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- struct traits<HouseholderSequence<VectorsType,CoeffsType,Side> >
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- {
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- typedef typename VectorsType::Scalar Scalar;
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- typedef typename VectorsType::StorageIndex StorageIndex;
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- typedef typename VectorsType::StorageKind StorageKind;
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- enum {
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- RowsAtCompileTime = Side==OnTheLeft ? traits<VectorsType>::RowsAtCompileTime
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- : traits<VectorsType>::ColsAtCompileTime,
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- ColsAtCompileTime = RowsAtCompileTime,
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- MaxRowsAtCompileTime = Side==OnTheLeft ? traits<VectorsType>::MaxRowsAtCompileTime
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- : traits<VectorsType>::MaxColsAtCompileTime,
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- MaxColsAtCompileTime = MaxRowsAtCompileTime,
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- Flags = 0
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- };
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- };
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-
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- struct HouseholderSequenceShape {};
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-
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- template<typename VectorsType, typename CoeffsType, int Side>
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- struct evaluator_traits<HouseholderSequence<VectorsType,CoeffsType,Side> >
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- : public evaluator_traits_base<HouseholderSequence<VectorsType,CoeffsType,Side> >
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- {
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- typedef HouseholderSequenceShape Shape;
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- };
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-
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- template<typename VectorsType, typename CoeffsType, int Side>
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- struct hseq_side_dependent_impl
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- {
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- typedef Block<const VectorsType, Dynamic, 1> EssentialVectorType;
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- typedef HouseholderSequence<VectorsType, CoeffsType, OnTheLeft> HouseholderSequenceType;
90
- static EIGEN_DEVICE_FUNC inline const EssentialVectorType essentialVector(const HouseholderSequenceType& h, Index k)
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- {
92
- Index start = k+1+h.m_shift;
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- return Block<const VectorsType,Dynamic,1>(h.m_vectors, start, k, h.rows()-start, 1);
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- }
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- };
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-
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- template<typename VectorsType, typename CoeffsType>
98
- struct hseq_side_dependent_impl<VectorsType, CoeffsType, OnTheRight>
99
- {
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- typedef Transpose<Block<const VectorsType, 1, Dynamic> > EssentialVectorType;
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- typedef HouseholderSequence<VectorsType, CoeffsType, OnTheRight> HouseholderSequenceType;
102
- static inline const EssentialVectorType essentialVector(const HouseholderSequenceType& h, Index k)
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- {
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- Index start = k+1+h.m_shift;
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- return Block<const VectorsType,1,Dynamic>(h.m_vectors, k, start, 1, h.rows()-start).transpose();
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- }
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- };
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-
109
- template<typename OtherScalarType, typename MatrixType> struct matrix_type_times_scalar_type
110
- {
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- typedef typename ScalarBinaryOpTraits<OtherScalarType, typename MatrixType::Scalar>::ReturnType
112
- ResultScalar;
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- typedef Matrix<ResultScalar, MatrixType::RowsAtCompileTime, MatrixType::ColsAtCompileTime,
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- 0, MatrixType::MaxRowsAtCompileTime, MatrixType::MaxColsAtCompileTime> Type;
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- };
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-
117
- } // end namespace internal
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-
119
- template<typename VectorsType, typename CoeffsType, int Side> class HouseholderSequence
120
- : public EigenBase<HouseholderSequence<VectorsType,CoeffsType,Side> >
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- {
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- typedef typename internal::hseq_side_dependent_impl<VectorsType,CoeffsType,Side>::EssentialVectorType EssentialVectorType;
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-
124
- public:
125
- enum {
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- RowsAtCompileTime = internal::traits<HouseholderSequence>::RowsAtCompileTime,
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- ColsAtCompileTime = internal::traits<HouseholderSequence>::ColsAtCompileTime,
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- MaxRowsAtCompileTime = internal::traits<HouseholderSequence>::MaxRowsAtCompileTime,
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- MaxColsAtCompileTime = internal::traits<HouseholderSequence>::MaxColsAtCompileTime
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- };
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- typedef typename internal::traits<HouseholderSequence>::Scalar Scalar;
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-
133
- typedef HouseholderSequence<
134
- typename internal::conditional<NumTraits<Scalar>::IsComplex,
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- typename internal::remove_all<typename VectorsType::ConjugateReturnType>::type,
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- VectorsType>::type,
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- typename internal::conditional<NumTraits<Scalar>::IsComplex,
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- typename internal::remove_all<typename CoeffsType::ConjugateReturnType>::type,
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- CoeffsType>::type,
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- Side
141
- > ConjugateReturnType;
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-
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- typedef HouseholderSequence<
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- VectorsType,
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- typename internal::conditional<NumTraits<Scalar>::IsComplex,
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- typename internal::remove_all<typename CoeffsType::ConjugateReturnType>::type,
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- CoeffsType>::type,
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- Side
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- > AdjointReturnType;
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-
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- typedef HouseholderSequence<
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- typename internal::conditional<NumTraits<Scalar>::IsComplex,
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- typename internal::remove_all<typename VectorsType::ConjugateReturnType>::type,
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- VectorsType>::type,
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- CoeffsType,
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- Side
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- > TransposeReturnType;
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-
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- typedef HouseholderSequence<
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- typename internal::add_const<VectorsType>::type,
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- typename internal::add_const<CoeffsType>::type,
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- Side
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- > ConstHouseholderSequence;
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-
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- /** \brief Constructor.
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- * \param[in] v %Matrix containing the essential parts of the Householder vectors
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- * \param[in] h Vector containing the Householder coefficients
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- *
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- * Constructs the Householder sequence with coefficients given by \p h and vectors given by \p v. The
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- * i-th Householder coefficient \f$ h_i \f$ is given by \p h(i) and the essential part of the i-th
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- * Householder vector \f$ v_i \f$ is given by \p v(k,i) with \p k > \p i (the subdiagonal part of the
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- * i-th column). If \p v has fewer columns than rows, then the Householder sequence contains as many
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- * Householder reflections as there are columns.
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- *
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- * \note The %HouseholderSequence object stores \p v and \p h by reference.
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- *
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- * Example: \include HouseholderSequence_HouseholderSequence.cpp
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- * Output: \verbinclude HouseholderSequence_HouseholderSequence.out
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- *
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- * \sa setLength(), setShift()
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- */
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- EIGEN_DEVICE_FUNC
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- HouseholderSequence(const VectorsType& v, const CoeffsType& h)
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- : m_vectors(v), m_coeffs(h), m_reverse(false), m_length(v.diagonalSize()),
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- m_shift(0)
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- {
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- }
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-
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- /** \brief Copy constructor. */
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- EIGEN_DEVICE_FUNC
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- HouseholderSequence(const HouseholderSequence& other)
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- : m_vectors(other.m_vectors),
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- m_coeffs(other.m_coeffs),
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- m_reverse(other.m_reverse),
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- m_length(other.m_length),
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- m_shift(other.m_shift)
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- {
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- }
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-
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- /** \brief Number of rows of transformation viewed as a matrix.
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- * \returns Number of rows
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- * \details This equals the dimension of the space that the transformation acts on.
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- */
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- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
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- Index rows() const EIGEN_NOEXCEPT { return Side==OnTheLeft ? m_vectors.rows() : m_vectors.cols(); }
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-
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- /** \brief Number of columns of transformation viewed as a matrix.
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- * \returns Number of columns
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- * \details This equals the dimension of the space that the transformation acts on.
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- */
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- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
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- Index cols() const EIGEN_NOEXCEPT { return rows(); }
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-
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- /** \brief Essential part of a Householder vector.
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- * \param[in] k Index of Householder reflection
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- * \returns Vector containing non-trivial entries of k-th Householder vector
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- *
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- * This function returns the essential part of the Householder vector \f$ v_i \f$. This is a vector of
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- * length \f$ n-i \f$ containing the last \f$ n-i \f$ entries of the vector
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- * \f[
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- * v_i = [\underbrace{0, \ldots, 0}_{i-1\mbox{ zeros}}, 1, \underbrace{*, \ldots,*}_{n-i\mbox{ arbitrary entries}} ].
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- * \f]
223
- * The index \f$ i \f$ equals \p k + shift(), corresponding to the k-th column of the matrix \p v
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- * passed to the constructor.
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- *
226
- * \sa setShift(), shift()
227
- */
228
- EIGEN_DEVICE_FUNC
229
- const EssentialVectorType essentialVector(Index k) const
230
- {
231
- eigen_assert(k >= 0 && k < m_length);
232
- return internal::hseq_side_dependent_impl<VectorsType,CoeffsType,Side>::essentialVector(*this, k);
233
- }
234
-
235
- /** \brief %Transpose of the Householder sequence. */
236
- TransposeReturnType transpose() const
237
- {
238
- return TransposeReturnType(m_vectors.conjugate(), m_coeffs)
239
- .setReverseFlag(!m_reverse)
240
- .setLength(m_length)
241
- .setShift(m_shift);
242
- }
243
-
244
- /** \brief Complex conjugate of the Householder sequence. */
245
- ConjugateReturnType conjugate() const
246
- {
247
- return ConjugateReturnType(m_vectors.conjugate(), m_coeffs.conjugate())
248
- .setReverseFlag(m_reverse)
249
- .setLength(m_length)
250
- .setShift(m_shift);
251
- }
252
-
253
- /** \returns an expression of the complex conjugate of \c *this if Cond==true,
254
- * returns \c *this otherwise.
255
- */
256
- template<bool Cond>
257
- EIGEN_DEVICE_FUNC
258
- inline typename internal::conditional<Cond,ConjugateReturnType,ConstHouseholderSequence>::type
259
- conjugateIf() const
260
- {
261
- typedef typename internal::conditional<Cond,ConjugateReturnType,ConstHouseholderSequence>::type ReturnType;
262
- return ReturnType(m_vectors.template conjugateIf<Cond>(), m_coeffs.template conjugateIf<Cond>());
263
- }
264
-
265
- /** \brief Adjoint (conjugate transpose) of the Householder sequence. */
266
- AdjointReturnType adjoint() const
267
- {
268
- return AdjointReturnType(m_vectors, m_coeffs.conjugate())
269
- .setReverseFlag(!m_reverse)
270
- .setLength(m_length)
271
- .setShift(m_shift);
272
- }
273
-
274
- /** \brief Inverse of the Householder sequence (equals the adjoint). */
275
- AdjointReturnType inverse() const { return adjoint(); }
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-
277
- /** \internal */
278
- template<typename DestType>
279
- inline EIGEN_DEVICE_FUNC
280
- void evalTo(DestType& dst) const
281
- {
282
- Matrix<Scalar, DestType::RowsAtCompileTime, 1,
283
- AutoAlign|ColMajor, DestType::MaxRowsAtCompileTime, 1> workspace(rows());
284
- evalTo(dst, workspace);
285
- }
286
-
287
- /** \internal */
288
- template<typename Dest, typename Workspace>
289
- EIGEN_DEVICE_FUNC
290
- void evalTo(Dest& dst, Workspace& workspace) const
291
- {
292
- workspace.resize(rows());
293
- Index vecs = m_length;
294
- if(internal::is_same_dense(dst,m_vectors))
295
- {
296
- // in-place
297
- dst.diagonal().setOnes();
298
- dst.template triangularView<StrictlyUpper>().setZero();
299
- for(Index k = vecs-1; k >= 0; --k)
300
- {
301
- Index cornerSize = rows() - k - m_shift;
302
- if(m_reverse)
303
- dst.bottomRightCorner(cornerSize, cornerSize)
304
- .applyHouseholderOnTheRight(essentialVector(k), m_coeffs.coeff(k), workspace.data());
305
- else
306
- dst.bottomRightCorner(cornerSize, cornerSize)
307
- .applyHouseholderOnTheLeft(essentialVector(k), m_coeffs.coeff(k), workspace.data());
308
-
309
- // clear the off diagonal vector
310
- dst.col(k).tail(rows()-k-1).setZero();
311
- }
312
- // clear the remaining columns if needed
313
- for(Index k = 0; k<cols()-vecs ; ++k)
314
- dst.col(k).tail(rows()-k-1).setZero();
315
- }
316
- else if(m_length>BlockSize)
317
- {
318
- dst.setIdentity(rows(), rows());
319
- if(m_reverse)
320
- applyThisOnTheLeft(dst,workspace,true);
321
- else
322
- applyThisOnTheLeft(dst,workspace,true);
323
- }
324
- else
325
- {
326
- dst.setIdentity(rows(), rows());
327
- for(Index k = vecs-1; k >= 0; --k)
328
- {
329
- Index cornerSize = rows() - k - m_shift;
330
- if(m_reverse)
331
- dst.bottomRightCorner(cornerSize, cornerSize)
332
- .applyHouseholderOnTheRight(essentialVector(k), m_coeffs.coeff(k), workspace.data());
333
- else
334
- dst.bottomRightCorner(cornerSize, cornerSize)
335
- .applyHouseholderOnTheLeft(essentialVector(k), m_coeffs.coeff(k), workspace.data());
336
- }
337
- }
338
- }
339
-
340
- /** \internal */
341
- template<typename Dest> inline void applyThisOnTheRight(Dest& dst) const
342
- {
343
- Matrix<Scalar,1,Dest::RowsAtCompileTime,RowMajor,1,Dest::MaxRowsAtCompileTime> workspace(dst.rows());
344
- applyThisOnTheRight(dst, workspace);
345
- }
346
-
347
- /** \internal */
348
- template<typename Dest, typename Workspace>
349
- inline void applyThisOnTheRight(Dest& dst, Workspace& workspace) const
350
- {
351
- workspace.resize(dst.rows());
352
- for(Index k = 0; k < m_length; ++k)
353
- {
354
- Index actual_k = m_reverse ? m_length-k-1 : k;
355
- dst.rightCols(rows()-m_shift-actual_k)
356
- .applyHouseholderOnTheRight(essentialVector(actual_k), m_coeffs.coeff(actual_k), workspace.data());
357
- }
358
- }
359
-
360
- /** \internal */
361
- template<typename Dest> inline void applyThisOnTheLeft(Dest& dst, bool inputIsIdentity = false) const
362
- {
363
- Matrix<Scalar,1,Dest::ColsAtCompileTime,RowMajor,1,Dest::MaxColsAtCompileTime> workspace;
364
- applyThisOnTheLeft(dst, workspace, inputIsIdentity);
365
- }
366
-
367
- /** \internal */
368
- template<typename Dest, typename Workspace>
369
- inline void applyThisOnTheLeft(Dest& dst, Workspace& workspace, bool inputIsIdentity = false) const
370
- {
371
- if(inputIsIdentity && m_reverse)
372
- inputIsIdentity = false;
373
- // if the entries are large enough, then apply the reflectors by block
374
- if(m_length>=BlockSize && dst.cols()>1)
375
- {
376
- // Make sure we have at least 2 useful blocks, otherwise it is point-less:
377
- Index blockSize = m_length<Index(2*BlockSize) ? (m_length+1)/2 : Index(BlockSize);
378
- for(Index i = 0; i < m_length; i+=blockSize)
379
- {
380
- Index end = m_reverse ? (std::min)(m_length,i+blockSize) : m_length-i;
381
- Index k = m_reverse ? i : (std::max)(Index(0),end-blockSize);
382
- Index bs = end-k;
383
- Index start = k + m_shift;
384
-
385
- typedef Block<typename internal::remove_all<VectorsType>::type,Dynamic,Dynamic> SubVectorsType;
386
- SubVectorsType sub_vecs1(m_vectors.const_cast_derived(), Side==OnTheRight ? k : start,
387
- Side==OnTheRight ? start : k,
388
- Side==OnTheRight ? bs : m_vectors.rows()-start,
389
- Side==OnTheRight ? m_vectors.cols()-start : bs);
390
- typename internal::conditional<Side==OnTheRight, Transpose<SubVectorsType>, SubVectorsType&>::type sub_vecs(sub_vecs1);
391
-
392
- Index dstStart = dst.rows()-rows()+m_shift+k;
393
- Index dstRows = rows()-m_shift-k;
394
- Block<Dest,Dynamic,Dynamic> sub_dst(dst,
395
- dstStart,
396
- inputIsIdentity ? dstStart : 0,
397
- dstRows,
398
- inputIsIdentity ? dstRows : dst.cols());
399
- apply_block_householder_on_the_left(sub_dst, sub_vecs, m_coeffs.segment(k, bs), !m_reverse);
400
- }
401
- }
402
- else
403
- {
404
- workspace.resize(dst.cols());
405
- for(Index k = 0; k < m_length; ++k)
406
- {
407
- Index actual_k = m_reverse ? k : m_length-k-1;
408
- Index dstStart = rows()-m_shift-actual_k;
409
- dst.bottomRightCorner(dstStart, inputIsIdentity ? dstStart : dst.cols())
410
- .applyHouseholderOnTheLeft(essentialVector(actual_k), m_coeffs.coeff(actual_k), workspace.data());
411
- }
412
- }
413
- }
414
-
415
- /** \brief Computes the product of a Householder sequence with a matrix.
416
- * \param[in] other %Matrix being multiplied.
417
- * \returns Expression object representing the product.
418
- *
419
- * This function computes \f$ HM \f$ where \f$ H \f$ is the Householder sequence represented by \p *this
420
- * and \f$ M \f$ is the matrix \p other.
421
- */
422
- template<typename OtherDerived>
423
- typename internal::matrix_type_times_scalar_type<Scalar, OtherDerived>::Type operator*(const MatrixBase<OtherDerived>& other) const
424
- {
425
- typename internal::matrix_type_times_scalar_type<Scalar, OtherDerived>::Type
426
- res(other.template cast<typename internal::matrix_type_times_scalar_type<Scalar,OtherDerived>::ResultScalar>());
427
- applyThisOnTheLeft(res, internal::is_identity<OtherDerived>::value && res.rows()==res.cols());
428
- return res;
429
- }
430
-
431
- template<typename _VectorsType, typename _CoeffsType, int _Side> friend struct internal::hseq_side_dependent_impl;
432
-
433
- /** \brief Sets the length of the Householder sequence.
434
- * \param [in] length New value for the length.
435
- *
436
- * By default, the length \f$ n \f$ of the Householder sequence \f$ H = H_0 H_1 \ldots H_{n-1} \f$ is set
437
- * to the number of columns of the matrix \p v passed to the constructor, or the number of rows if that
438
- * is smaller. After this function is called, the length equals \p length.
439
- *
440
- * \sa length()
441
- */
442
- EIGEN_DEVICE_FUNC
443
- HouseholderSequence& setLength(Index length)
444
- {
445
- m_length = length;
446
- return *this;
447
- }
448
-
449
- /** \brief Sets the shift of the Householder sequence.
450
- * \param [in] shift New value for the shift.
451
- *
452
- * By default, a %HouseholderSequence object represents \f$ H = H_0 H_1 \ldots H_{n-1} \f$ and the i-th
453
- * column of the matrix \p v passed to the constructor corresponds to the i-th Householder
454
- * reflection. After this function is called, the object represents \f$ H = H_{\mathrm{shift}}
455
- * H_{\mathrm{shift}+1} \ldots H_{n-1} \f$ and the i-th column of \p v corresponds to the (shift+i)-th
456
- * Householder reflection.
457
- *
458
- * \sa shift()
459
- */
460
- EIGEN_DEVICE_FUNC
461
- HouseholderSequence& setShift(Index shift)
462
- {
463
- m_shift = shift;
464
- return *this;
465
- }
466
-
467
- EIGEN_DEVICE_FUNC
468
- Index length() const { return m_length; } /**< \brief Returns the length of the Householder sequence. */
469
-
470
- EIGEN_DEVICE_FUNC
471
- Index shift() const { return m_shift; } /**< \brief Returns the shift of the Householder sequence. */
472
-
473
- /* Necessary for .adjoint() and .conjugate() */
474
- template <typename VectorsType2, typename CoeffsType2, int Side2> friend class HouseholderSequence;
475
-
476
- protected:
477
-
478
- /** \internal
479
- * \brief Sets the reverse flag.
480
- * \param [in] reverse New value of the reverse flag.
481
- *
482
- * By default, the reverse flag is not set. If the reverse flag is set, then this object represents
483
- * \f$ H^r = H_{n-1} \ldots H_1 H_0 \f$ instead of \f$ H = H_0 H_1 \ldots H_{n-1} \f$.
484
- * \note For real valued HouseholderSequence this is equivalent to transposing \f$ H \f$.
485
- *
486
- * \sa reverseFlag(), transpose(), adjoint()
487
- */
488
- HouseholderSequence& setReverseFlag(bool reverse)
489
- {
490
- m_reverse = reverse;
491
- return *this;
492
- }
493
-
494
- bool reverseFlag() const { return m_reverse; } /**< \internal \brief Returns the reverse flag. */
495
-
496
- typename VectorsType::Nested m_vectors;
497
- typename CoeffsType::Nested m_coeffs;
498
- bool m_reverse;
499
- Index m_length;
500
- Index m_shift;
501
- enum { BlockSize = 48 };
502
- };
503
-
504
- /** \brief Computes the product of a matrix with a Householder sequence.
505
- * \param[in] other %Matrix being multiplied.
506
- * \param[in] h %HouseholderSequence being multiplied.
507
- * \returns Expression object representing the product.
508
- *
509
- * This function computes \f$ MH \f$ where \f$ M \f$ is the matrix \p other and \f$ H \f$ is the
510
- * Householder sequence represented by \p h.
511
- */
512
- template<typename OtherDerived, typename VectorsType, typename CoeffsType, int Side>
513
- typename internal::matrix_type_times_scalar_type<typename VectorsType::Scalar,OtherDerived>::Type operator*(const MatrixBase<OtherDerived>& other, const HouseholderSequence<VectorsType,CoeffsType,Side>& h)
514
- {
515
- typename internal::matrix_type_times_scalar_type<typename VectorsType::Scalar,OtherDerived>::Type
516
- res(other.template cast<typename internal::matrix_type_times_scalar_type<typename VectorsType::Scalar,OtherDerived>::ResultScalar>());
517
- h.applyThisOnTheRight(res);
518
- return res;
519
- }
520
-
521
- /** \ingroup Householder_Module \householder_module
522
- * \brief Convenience function for constructing a Householder sequence.
523
- * \returns A HouseholderSequence constructed from the specified arguments.
524
- */
525
- template<typename VectorsType, typename CoeffsType>
526
- HouseholderSequence<VectorsType,CoeffsType> householderSequence(const VectorsType& v, const CoeffsType& h)
527
- {
528
- return HouseholderSequence<VectorsType,CoeffsType,OnTheLeft>(v, h);
529
- }
530
-
531
- /** \ingroup Householder_Module \householder_module
532
- * \brief Convenience function for constructing a Householder sequence.
533
- * \returns A HouseholderSequence constructed from the specified arguments.
534
- * \details This function differs from householderSequence() in that the template argument \p OnTheSide of
535
- * the constructed HouseholderSequence is set to OnTheRight, instead of the default OnTheLeft.
536
- */
537
- template<typename VectorsType, typename CoeffsType>
538
- HouseholderSequence<VectorsType,CoeffsType,OnTheRight> rightHouseholderSequence(const VectorsType& v, const CoeffsType& h)
539
- {
540
- return HouseholderSequence<VectorsType,CoeffsType,OnTheRight>(v, h);
541
- }
542
-
543
- } // end namespace Eigen
544
-
545
- #endif // EIGEN_HOUSEHOLDER_SEQUENCE_H