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
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  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
@@ -1,877 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2006-2009 Benoit Jacob <jacob.benoit.1@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_LU_H
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- #define EIGEN_LU_H
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-
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- namespace Eigen {
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-
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- namespace internal {
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- template<typename _MatrixType> struct traits<FullPivLU<_MatrixType> >
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- : traits<_MatrixType>
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- {
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- typedef MatrixXpr XprKind;
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- typedef SolverStorage StorageKind;
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- typedef int StorageIndex;
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- enum { Flags = 0 };
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- };
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-
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- } // end namespace internal
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-
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- /** \ingroup LU_Module
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- *
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- * \class FullPivLU
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- *
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- * \brief LU decomposition of a matrix with complete pivoting, and related features
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- *
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- * \tparam _MatrixType the type of the matrix of which we are computing the LU decomposition
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- *
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- * This class represents a LU decomposition of any matrix, with complete pivoting: the matrix A is
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- * decomposed as \f$ A = P^{-1} L U Q^{-1} \f$ where L is unit-lower-triangular, U is
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- * upper-triangular, and P and Q are permutation matrices. This is a rank-revealing LU
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- * decomposition. The eigenvalues (diagonal coefficients) of U are sorted in such a way that any
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- * zeros are at the end.
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- *
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- * This decomposition provides the generic approach to solving systems of linear equations, computing
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- * the rank, invertibility, inverse, kernel, and determinant.
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- *
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- * This LU decomposition is very stable and well tested with large matrices. However there are use cases where the SVD
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- * decomposition is inherently more stable and/or flexible. For example, when computing the kernel of a matrix,
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- * working with the SVD allows to select the smallest singular values of the matrix, something that
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- * the LU decomposition doesn't see.
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- *
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- * The data of the LU decomposition can be directly accessed through the methods matrixLU(),
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- * permutationP(), permutationQ().
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- *
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- * As an example, here is how the original matrix can be retrieved:
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- * \include class_FullPivLU.cpp
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- * Output: \verbinclude class_FullPivLU.out
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- *
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- * This class supports the \link InplaceDecomposition inplace decomposition \endlink mechanism.
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- *
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- * \sa MatrixBase::fullPivLu(), MatrixBase::determinant(), MatrixBase::inverse()
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- */
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- template<typename _MatrixType> class FullPivLU
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- : public SolverBase<FullPivLU<_MatrixType> >
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- {
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- public:
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- typedef _MatrixType MatrixType;
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- typedef SolverBase<FullPivLU> Base;
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- friend class SolverBase<FullPivLU>;
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-
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- EIGEN_GENERIC_PUBLIC_INTERFACE(FullPivLU)
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- enum {
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- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
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- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
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- };
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- typedef typename internal::plain_row_type<MatrixType, StorageIndex>::type IntRowVectorType;
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- typedef typename internal::plain_col_type<MatrixType, StorageIndex>::type IntColVectorType;
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- typedef PermutationMatrix<ColsAtCompileTime, MaxColsAtCompileTime> PermutationQType;
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- typedef PermutationMatrix<RowsAtCompileTime, MaxRowsAtCompileTime> PermutationPType;
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- typedef typename MatrixType::PlainObject PlainObject;
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-
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- /**
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- * \brief Default Constructor.
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- *
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- * The default constructor is useful in cases in which the user intends to
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- * perform decompositions via LU::compute(const MatrixType&).
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- */
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- FullPivLU();
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-
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- /** \brief Default Constructor with memory preallocation
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- *
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- * Like the default constructor but with preallocation of the internal data
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- * according to the specified problem \a size.
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- * \sa FullPivLU()
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- */
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- FullPivLU(Index rows, Index cols);
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-
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- /** Constructor.
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- *
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- * \param matrix the matrix of which to compute the LU decomposition.
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- * It is required to be nonzero.
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- */
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- template<typename InputType>
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- explicit FullPivLU(const EigenBase<InputType>& matrix);
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-
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- /** \brief Constructs a LU factorization from a given matrix
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- *
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- * This overloaded constructor is provided for \link InplaceDecomposition inplace decomposition \endlink when \c MatrixType is a Eigen::Ref.
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- *
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- * \sa FullPivLU(const EigenBase&)
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- */
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- template<typename InputType>
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- explicit FullPivLU(EigenBase<InputType>& matrix);
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-
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- /** Computes the LU decomposition of the given matrix.
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- *
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- * \param matrix the matrix of which to compute the LU decomposition.
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- * It is required to be nonzero.
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- *
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- * \returns a reference to *this
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- */
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- template<typename InputType>
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- FullPivLU& compute(const EigenBase<InputType>& matrix) {
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- m_lu = matrix.derived();
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- computeInPlace();
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- return *this;
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- }
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-
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- /** \returns the LU decomposition matrix: the upper-triangular part is U, the
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- * unit-lower-triangular part is L (at least for square matrices; in the non-square
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- * case, special care is needed, see the documentation of class FullPivLU).
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- *
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- * \sa matrixL(), matrixU()
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- */
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- inline const MatrixType& matrixLU() const
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- {
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- eigen_assert(m_isInitialized && "LU is not initialized.");
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- return m_lu;
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- }
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-
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- /** \returns the number of nonzero pivots in the LU decomposition.
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- * Here nonzero is meant in the exact sense, not in a fuzzy sense.
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- * So that notion isn't really intrinsically interesting, but it is
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- * still useful when implementing algorithms.
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- *
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- * \sa rank()
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- */
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- inline Index nonzeroPivots() const
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- {
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- eigen_assert(m_isInitialized && "LU is not initialized.");
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- return m_nonzero_pivots;
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- }
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-
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- /** \returns the absolute value of the biggest pivot, i.e. the biggest
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- * diagonal coefficient of U.
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- */
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- RealScalar maxPivot() const { return m_maxpivot; }
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-
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- /** \returns the permutation matrix P
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- *
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- * \sa permutationQ()
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- */
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- EIGEN_DEVICE_FUNC inline const PermutationPType& permutationP() const
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- {
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- eigen_assert(m_isInitialized && "LU is not initialized.");
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- return m_p;
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- }
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-
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- /** \returns the permutation matrix Q
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- *
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- * \sa permutationP()
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- */
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- inline const PermutationQType& permutationQ() const
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- {
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- eigen_assert(m_isInitialized && "LU is not initialized.");
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- return m_q;
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- }
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-
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- /** \returns the kernel of the matrix, also called its null-space. The columns of the returned matrix
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- * will form a basis of the kernel.
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- *
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- * \note If the kernel has dimension zero, then the returned matrix is a column-vector filled with zeros.
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- *
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- * \note This method has to determine which pivots should be considered nonzero.
182
- * For that, it uses the threshold value that you can control by calling
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- * setThreshold(const RealScalar&).
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- *
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- * Example: \include FullPivLU_kernel.cpp
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- * Output: \verbinclude FullPivLU_kernel.out
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- *
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- * \sa image()
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- */
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- inline const internal::kernel_retval<FullPivLU> kernel() const
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- {
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- eigen_assert(m_isInitialized && "LU is not initialized.");
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- return internal::kernel_retval<FullPivLU>(*this);
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- }
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-
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- /** \returns the image of the matrix, also called its column-space. The columns of the returned matrix
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- * will form a basis of the image (column-space).
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- *
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- * \param originalMatrix the original matrix, of which *this is the LU decomposition.
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- * The reason why it is needed to pass it here, is that this allows
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- * a large optimization, as otherwise this method would need to reconstruct it
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- * from the LU decomposition.
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- *
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- * \note If the image has dimension zero, then the returned matrix is a column-vector filled with zeros.
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- *
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- * \note This method has to determine which pivots should be considered nonzero.
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- * For that, it uses the threshold value that you can control by calling
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- * setThreshold(const RealScalar&).
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- *
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- * Example: \include FullPivLU_image.cpp
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- * Output: \verbinclude FullPivLU_image.out
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- *
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- * \sa kernel()
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- */
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- inline const internal::image_retval<FullPivLU>
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- image(const MatrixType& originalMatrix) const
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- {
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- eigen_assert(m_isInitialized && "LU is not initialized.");
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- return internal::image_retval<FullPivLU>(*this, originalMatrix);
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- }
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-
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- #ifdef EIGEN_PARSED_BY_DOXYGEN
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- /** \return a solution x to the equation Ax=b, where A is the matrix of which
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- * *this is the LU decomposition.
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- *
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- * \param b the right-hand-side of the equation to solve. Can be a vector or a matrix,
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- * the only requirement in order for the equation to make sense is that
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- * b.rows()==A.rows(), where A is the matrix of which *this is the LU decomposition.
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- *
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- * \returns a solution.
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- *
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- * \note_about_checking_solutions
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- *
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- * \note_about_arbitrary_choice_of_solution
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- * \note_about_using_kernel_to_study_multiple_solutions
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- *
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- * Example: \include FullPivLU_solve.cpp
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- * Output: \verbinclude FullPivLU_solve.out
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- *
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- * \sa TriangularView::solve(), kernel(), inverse()
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- */
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- template<typename Rhs>
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- inline const Solve<FullPivLU, Rhs>
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- solve(const MatrixBase<Rhs>& b) const;
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- #endif
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-
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- /** \returns an estimate of the reciprocal condition number of the matrix of which \c *this is
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- the LU decomposition.
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- */
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- inline RealScalar rcond() const
251
- {
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- eigen_assert(m_isInitialized && "PartialPivLU is not initialized.");
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- return internal::rcond_estimate_helper(m_l1_norm, *this);
254
- }
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-
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- /** \returns the determinant of the matrix of which
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- * *this is the LU decomposition. It has only linear complexity
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- * (that is, O(n) where n is the dimension of the square matrix)
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- * as the LU decomposition has already been computed.
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- *
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- * \note This is only for square matrices.
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- *
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- * \note For fixed-size matrices of size up to 4, MatrixBase::determinant() offers
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- * optimized paths.
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- *
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- * \warning a determinant can be very big or small, so for matrices
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- * of large enough dimension, there is a risk of overflow/underflow.
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- *
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- * \sa MatrixBase::determinant()
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- */
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- typename internal::traits<MatrixType>::Scalar determinant() const;
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-
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- /** Allows to prescribe a threshold to be used by certain methods, such as rank(),
274
- * who need to determine when pivots are to be considered nonzero. This is not used for the
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- * LU decomposition itself.
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- *
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- * When it needs to get the threshold value, Eigen calls threshold(). By default, this
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- * uses a formula to automatically determine a reasonable threshold.
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- * Once you have called the present method setThreshold(const RealScalar&),
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- * your value is used instead.
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- *
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- * \param threshold The new value to use as the threshold.
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- *
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- * A pivot will be considered nonzero if its absolute value is strictly greater than
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- * \f$ \vert pivot \vert \leqslant threshold \times \vert maxpivot \vert \f$
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- * where maxpivot is the biggest pivot.
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- *
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- * If you want to come back to the default behavior, call setThreshold(Default_t)
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- */
290
- FullPivLU& setThreshold(const RealScalar& threshold)
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- {
292
- m_usePrescribedThreshold = true;
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- m_prescribedThreshold = threshold;
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- return *this;
295
- }
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-
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- /** Allows to come back to the default behavior, letting Eigen use its default formula for
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- * determining the threshold.
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- *
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- * You should pass the special object Eigen::Default as parameter here.
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- * \code lu.setThreshold(Eigen::Default); \endcode
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- *
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- * See the documentation of setThreshold(const RealScalar&).
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- */
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- FullPivLU& setThreshold(Default_t)
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- {
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- m_usePrescribedThreshold = false;
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- return *this;
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- }
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-
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- /** Returns the threshold that will be used by certain methods such as rank().
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- *
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- * See the documentation of setThreshold(const RealScalar&).
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- */
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- RealScalar threshold() const
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- {
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- eigen_assert(m_isInitialized || m_usePrescribedThreshold);
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- return m_usePrescribedThreshold ? m_prescribedThreshold
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- // this formula comes from experimenting (see "LU precision tuning" thread on the list)
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- // and turns out to be identical to Higham's formula used already in LDLt.
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- : NumTraits<Scalar>::epsilon() * RealScalar(m_lu.diagonalSize());
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- }
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-
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- /** \returns the rank of the matrix of which *this is the LU decomposition.
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- *
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- * \note This method has to determine which pivots should be considered nonzero.
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- * For that, it uses the threshold value that you can control by calling
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- * setThreshold(const RealScalar&).
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- */
330
- inline Index rank() const
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- {
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- using std::abs;
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- eigen_assert(m_isInitialized && "LU is not initialized.");
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- RealScalar premultiplied_threshold = abs(m_maxpivot) * threshold();
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- Index result = 0;
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- for(Index i = 0; i < m_nonzero_pivots; ++i)
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- result += (abs(m_lu.coeff(i,i)) > premultiplied_threshold);
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- return result;
339
- }
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-
341
- /** \returns the dimension of the kernel of the matrix of which *this is the LU decomposition.
342
- *
343
- * \note This method has to determine which pivots should be considered nonzero.
344
- * For that, it uses the threshold value that you can control by calling
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- * setThreshold(const RealScalar&).
346
- */
347
- inline Index dimensionOfKernel() const
348
- {
349
- eigen_assert(m_isInitialized && "LU is not initialized.");
350
- return cols() - rank();
351
- }
352
-
353
- /** \returns true if the matrix of which *this is the LU decomposition represents an injective
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- * linear map, i.e. has trivial kernel; false otherwise.
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- *
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- * \note This method has to determine which pivots should be considered nonzero.
357
- * For that, it uses the threshold value that you can control by calling
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- * setThreshold(const RealScalar&).
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- */
360
- inline bool isInjective() const
361
- {
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- eigen_assert(m_isInitialized && "LU is not initialized.");
363
- return rank() == cols();
364
- }
365
-
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- /** \returns true if the matrix of which *this is the LU decomposition represents a surjective
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- * linear map; false otherwise.
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- *
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- * \note This method has to determine which pivots should be considered nonzero.
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- * For that, it uses the threshold value that you can control by calling
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- * setThreshold(const RealScalar&).
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- */
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- inline bool isSurjective() const
374
- {
375
- eigen_assert(m_isInitialized && "LU is not initialized.");
376
- return rank() == rows();
377
- }
378
-
379
- /** \returns true if the matrix of which *this is the LU decomposition is invertible.
380
- *
381
- * \note This method has to determine which pivots should be considered nonzero.
382
- * For that, it uses the threshold value that you can control by calling
383
- * setThreshold(const RealScalar&).
384
- */
385
- inline bool isInvertible() const
386
- {
387
- eigen_assert(m_isInitialized && "LU is not initialized.");
388
- return isInjective() && (m_lu.rows() == m_lu.cols());
389
- }
390
-
391
- /** \returns the inverse of the matrix of which *this is the LU decomposition.
392
- *
393
- * \note If this matrix is not invertible, the returned matrix has undefined coefficients.
394
- * Use isInvertible() to first determine whether this matrix is invertible.
395
- *
396
- * \sa MatrixBase::inverse()
397
- */
398
- inline const Inverse<FullPivLU> inverse() const
399
- {
400
- eigen_assert(m_isInitialized && "LU is not initialized.");
401
- eigen_assert(m_lu.rows() == m_lu.cols() && "You can't take the inverse of a non-square matrix!");
402
- return Inverse<FullPivLU>(*this);
403
- }
404
-
405
- MatrixType reconstructedMatrix() const;
406
-
407
- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
408
- inline Index rows() const EIGEN_NOEXCEPT { return m_lu.rows(); }
409
- EIGEN_DEVICE_FUNC EIGEN_CONSTEXPR
410
- inline Index cols() const EIGEN_NOEXCEPT { return m_lu.cols(); }
411
-
412
- #ifndef EIGEN_PARSED_BY_DOXYGEN
413
- template<typename RhsType, typename DstType>
414
- void _solve_impl(const RhsType &rhs, DstType &dst) const;
415
-
416
- template<bool Conjugate, typename RhsType, typename DstType>
417
- void _solve_impl_transposed(const RhsType &rhs, DstType &dst) const;
418
- #endif
419
-
420
- protected:
421
-
422
- static void check_template_parameters()
423
- {
424
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
425
- }
426
-
427
- void computeInPlace();
428
-
429
- MatrixType m_lu;
430
- PermutationPType m_p;
431
- PermutationQType m_q;
432
- IntColVectorType m_rowsTranspositions;
433
- IntRowVectorType m_colsTranspositions;
434
- Index m_nonzero_pivots;
435
- RealScalar m_l1_norm;
436
- RealScalar m_maxpivot, m_prescribedThreshold;
437
- signed char m_det_pq;
438
- bool m_isInitialized, m_usePrescribedThreshold;
439
- };
440
-
441
- template<typename MatrixType>
442
- FullPivLU<MatrixType>::FullPivLU()
443
- : m_isInitialized(false), m_usePrescribedThreshold(false)
444
- {
445
- }
446
-
447
- template<typename MatrixType>
448
- FullPivLU<MatrixType>::FullPivLU(Index rows, Index cols)
449
- : m_lu(rows, cols),
450
- m_p(rows),
451
- m_q(cols),
452
- m_rowsTranspositions(rows),
453
- m_colsTranspositions(cols),
454
- m_isInitialized(false),
455
- m_usePrescribedThreshold(false)
456
- {
457
- }
458
-
459
- template<typename MatrixType>
460
- template<typename InputType>
461
- FullPivLU<MatrixType>::FullPivLU(const EigenBase<InputType>& matrix)
462
- : m_lu(matrix.rows(), matrix.cols()),
463
- m_p(matrix.rows()),
464
- m_q(matrix.cols()),
465
- m_rowsTranspositions(matrix.rows()),
466
- m_colsTranspositions(matrix.cols()),
467
- m_isInitialized(false),
468
- m_usePrescribedThreshold(false)
469
- {
470
- compute(matrix.derived());
471
- }
472
-
473
- template<typename MatrixType>
474
- template<typename InputType>
475
- FullPivLU<MatrixType>::FullPivLU(EigenBase<InputType>& matrix)
476
- : m_lu(matrix.derived()),
477
- m_p(matrix.rows()),
478
- m_q(matrix.cols()),
479
- m_rowsTranspositions(matrix.rows()),
480
- m_colsTranspositions(matrix.cols()),
481
- m_isInitialized(false),
482
- m_usePrescribedThreshold(false)
483
- {
484
- computeInPlace();
485
- }
486
-
487
- template<typename MatrixType>
488
- void FullPivLU<MatrixType>::computeInPlace()
489
- {
490
- check_template_parameters();
491
-
492
- // the permutations are stored as int indices, so just to be sure:
493
- eigen_assert(m_lu.rows()<=NumTraits<int>::highest() && m_lu.cols()<=NumTraits<int>::highest());
494
-
495
- m_l1_norm = m_lu.cwiseAbs().colwise().sum().maxCoeff();
496
-
497
- const Index size = m_lu.diagonalSize();
498
- const Index rows = m_lu.rows();
499
- const Index cols = m_lu.cols();
500
-
501
- // will store the transpositions, before we accumulate them at the end.
502
- // can't accumulate on-the-fly because that will be done in reverse order for the rows.
503
- m_rowsTranspositions.resize(m_lu.rows());
504
- m_colsTranspositions.resize(m_lu.cols());
505
- Index number_of_transpositions = 0; // number of NONTRIVIAL transpositions, i.e. m_rowsTranspositions[i]!=i
506
-
507
- m_nonzero_pivots = size; // the generic case is that in which all pivots are nonzero (invertible case)
508
- m_maxpivot = RealScalar(0);
509
-
510
- for(Index k = 0; k < size; ++k)
511
- {
512
- // First, we need to find the pivot.
513
-
514
- // biggest coefficient in the remaining bottom-right corner (starting at row k, col k)
515
- Index row_of_biggest_in_corner, col_of_biggest_in_corner;
516
- typedef internal::scalar_score_coeff_op<Scalar> Scoring;
517
- typedef typename Scoring::result_type Score;
518
- Score biggest_in_corner;
519
- biggest_in_corner = m_lu.bottomRightCorner(rows-k, cols-k)
520
- .unaryExpr(Scoring())
521
- .maxCoeff(&row_of_biggest_in_corner, &col_of_biggest_in_corner);
522
- row_of_biggest_in_corner += k; // correct the values! since they were computed in the corner,
523
- col_of_biggest_in_corner += k; // need to add k to them.
524
-
525
- if(biggest_in_corner==Score(0))
526
- {
527
- // before exiting, make sure to initialize the still uninitialized transpositions
528
- // in a sane state without destroying what we already have.
529
- m_nonzero_pivots = k;
530
- for(Index i = k; i < size; ++i)
531
- {
532
- m_rowsTranspositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
533
- m_colsTranspositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
534
- }
535
- break;
536
- }
537
-
538
- RealScalar abs_pivot = internal::abs_knowing_score<Scalar>()(m_lu(row_of_biggest_in_corner, col_of_biggest_in_corner), biggest_in_corner);
539
- if(abs_pivot > m_maxpivot) m_maxpivot = abs_pivot;
540
-
541
- // Now that we've found the pivot, we need to apply the row/col swaps to
542
- // bring it to the location (k,k).
543
-
544
- m_rowsTranspositions.coeffRef(k) = internal::convert_index<StorageIndex>(row_of_biggest_in_corner);
545
- m_colsTranspositions.coeffRef(k) = internal::convert_index<StorageIndex>(col_of_biggest_in_corner);
546
- if(k != row_of_biggest_in_corner) {
547
- m_lu.row(k).swap(m_lu.row(row_of_biggest_in_corner));
548
- ++number_of_transpositions;
549
- }
550
- if(k != col_of_biggest_in_corner) {
551
- m_lu.col(k).swap(m_lu.col(col_of_biggest_in_corner));
552
- ++number_of_transpositions;
553
- }
554
-
555
- // Now that the pivot is at the right location, we update the remaining
556
- // bottom-right corner by Gaussian elimination.
557
-
558
- if(k<rows-1)
559
- m_lu.col(k).tail(rows-k-1) /= m_lu.coeff(k,k);
560
- if(k<size-1)
561
- m_lu.block(k+1,k+1,rows-k-1,cols-k-1).noalias() -= m_lu.col(k).tail(rows-k-1) * m_lu.row(k).tail(cols-k-1);
562
- }
563
-
564
- // the main loop is over, we still have to accumulate the transpositions to find the
565
- // permutations P and Q
566
-
567
- m_p.setIdentity(rows);
568
- for(Index k = size-1; k >= 0; --k)
569
- m_p.applyTranspositionOnTheRight(k, m_rowsTranspositions.coeff(k));
570
-
571
- m_q.setIdentity(cols);
572
- for(Index k = 0; k < size; ++k)
573
- m_q.applyTranspositionOnTheRight(k, m_colsTranspositions.coeff(k));
574
-
575
- m_det_pq = (number_of_transpositions%2) ? -1 : 1;
576
-
577
- m_isInitialized = true;
578
- }
579
-
580
- template<typename MatrixType>
581
- typename internal::traits<MatrixType>::Scalar FullPivLU<MatrixType>::determinant() const
582
- {
583
- eigen_assert(m_isInitialized && "LU is not initialized.");
584
- eigen_assert(m_lu.rows() == m_lu.cols() && "You can't take the determinant of a non-square matrix!");
585
- return Scalar(m_det_pq) * Scalar(m_lu.diagonal().prod());
586
- }
587
-
588
- /** \returns the matrix represented by the decomposition,
589
- * i.e., it returns the product: \f$ P^{-1} L U Q^{-1} \f$.
590
- * This function is provided for debug purposes. */
591
- template<typename MatrixType>
592
- MatrixType FullPivLU<MatrixType>::reconstructedMatrix() const
593
- {
594
- eigen_assert(m_isInitialized && "LU is not initialized.");
595
- const Index smalldim = (std::min)(m_lu.rows(), m_lu.cols());
596
- // LU
597
- MatrixType res(m_lu.rows(),m_lu.cols());
598
- // FIXME the .toDenseMatrix() should not be needed...
599
- res = m_lu.leftCols(smalldim)
600
- .template triangularView<UnitLower>().toDenseMatrix()
601
- * m_lu.topRows(smalldim)
602
- .template triangularView<Upper>().toDenseMatrix();
603
-
604
- // P^{-1}(LU)
605
- res = m_p.inverse() * res;
606
-
607
- // (P^{-1}LU)Q^{-1}
608
- res = res * m_q.inverse();
609
-
610
- return res;
611
- }
612
-
613
- /********* Implementation of kernel() **************************************************/
614
-
615
- namespace internal {
616
- template<typename _MatrixType>
617
- struct kernel_retval<FullPivLU<_MatrixType> >
618
- : kernel_retval_base<FullPivLU<_MatrixType> >
619
- {
620
- EIGEN_MAKE_KERNEL_HELPERS(FullPivLU<_MatrixType>)
621
-
622
- enum { MaxSmallDimAtCompileTime = EIGEN_SIZE_MIN_PREFER_FIXED(
623
- MatrixType::MaxColsAtCompileTime,
624
- MatrixType::MaxRowsAtCompileTime)
625
- };
626
-
627
- template<typename Dest> void evalTo(Dest& dst) const
628
- {
629
- using std::abs;
630
- const Index cols = dec().matrixLU().cols(), dimker = cols - rank();
631
- if(dimker == 0)
632
- {
633
- // The Kernel is just {0}, so it doesn't have a basis properly speaking, but let's
634
- // avoid crashing/asserting as that depends on floating point calculations. Let's
635
- // just return a single column vector filled with zeros.
636
- dst.setZero();
637
- return;
638
- }
639
-
640
- /* Let us use the following lemma:
641
- *
642
- * Lemma: If the matrix A has the LU decomposition PAQ = LU,
643
- * then Ker A = Q(Ker U).
644
- *
645
- * Proof: trivial: just keep in mind that P, Q, L are invertible.
646
- */
647
-
648
- /* Thus, all we need to do is to compute Ker U, and then apply Q.
649
- *
650
- * U is upper triangular, with eigenvalues sorted so that any zeros appear at the end.
651
- * Thus, the diagonal of U ends with exactly
652
- * dimKer zero's. Let us use that to construct dimKer linearly
653
- * independent vectors in Ker U.
654
- */
655
-
656
- Matrix<Index, Dynamic, 1, 0, MaxSmallDimAtCompileTime, 1> pivots(rank());
657
- RealScalar premultiplied_threshold = dec().maxPivot() * dec().threshold();
658
- Index p = 0;
659
- for(Index i = 0; i < dec().nonzeroPivots(); ++i)
660
- if(abs(dec().matrixLU().coeff(i,i)) > premultiplied_threshold)
661
- pivots.coeffRef(p++) = i;
662
- eigen_internal_assert(p == rank());
663
-
664
- // we construct a temporaty trapezoid matrix m, by taking the U matrix and
665
- // permuting the rows and cols to bring the nonnegligible pivots to the top of
666
- // the main diagonal. We need that to be able to apply our triangular solvers.
667
- // FIXME when we get triangularView-for-rectangular-matrices, this can be simplified
668
- Matrix<typename MatrixType::Scalar, Dynamic, Dynamic, MatrixType::Options,
669
- MaxSmallDimAtCompileTime, MatrixType::MaxColsAtCompileTime>
670
- m(dec().matrixLU().block(0, 0, rank(), cols));
671
- for(Index i = 0; i < rank(); ++i)
672
- {
673
- if(i) m.row(i).head(i).setZero();
674
- m.row(i).tail(cols-i) = dec().matrixLU().row(pivots.coeff(i)).tail(cols-i);
675
- }
676
- m.block(0, 0, rank(), rank());
677
- m.block(0, 0, rank(), rank()).template triangularView<StrictlyLower>().setZero();
678
- for(Index i = 0; i < rank(); ++i)
679
- m.col(i).swap(m.col(pivots.coeff(i)));
680
-
681
- // ok, we have our trapezoid matrix, we can apply the triangular solver.
682
- // notice that the math behind this suggests that we should apply this to the
683
- // negative of the RHS, but for performance we just put the negative sign elsewhere, see below.
684
- m.topLeftCorner(rank(), rank())
685
- .template triangularView<Upper>().solveInPlace(
686
- m.topRightCorner(rank(), dimker)
687
- );
688
-
689
- // now we must undo the column permutation that we had applied!
690
- for(Index i = rank()-1; i >= 0; --i)
691
- m.col(i).swap(m.col(pivots.coeff(i)));
692
-
693
- // see the negative sign in the next line, that's what we were talking about above.
694
- for(Index i = 0; i < rank(); ++i) dst.row(dec().permutationQ().indices().coeff(i)) = -m.row(i).tail(dimker);
695
- for(Index i = rank(); i < cols; ++i) dst.row(dec().permutationQ().indices().coeff(i)).setZero();
696
- for(Index k = 0; k < dimker; ++k) dst.coeffRef(dec().permutationQ().indices().coeff(rank()+k), k) = Scalar(1);
697
- }
698
- };
699
-
700
- /***** Implementation of image() *****************************************************/
701
-
702
- template<typename _MatrixType>
703
- struct image_retval<FullPivLU<_MatrixType> >
704
- : image_retval_base<FullPivLU<_MatrixType> >
705
- {
706
- EIGEN_MAKE_IMAGE_HELPERS(FullPivLU<_MatrixType>)
707
-
708
- enum { MaxSmallDimAtCompileTime = EIGEN_SIZE_MIN_PREFER_FIXED(
709
- MatrixType::MaxColsAtCompileTime,
710
- MatrixType::MaxRowsAtCompileTime)
711
- };
712
-
713
- template<typename Dest> void evalTo(Dest& dst) const
714
- {
715
- using std::abs;
716
- if(rank() == 0)
717
- {
718
- // The Image is just {0}, so it doesn't have a basis properly speaking, but let's
719
- // avoid crashing/asserting as that depends on floating point calculations. Let's
720
- // just return a single column vector filled with zeros.
721
- dst.setZero();
722
- return;
723
- }
724
-
725
- Matrix<Index, Dynamic, 1, 0, MaxSmallDimAtCompileTime, 1> pivots(rank());
726
- RealScalar premultiplied_threshold = dec().maxPivot() * dec().threshold();
727
- Index p = 0;
728
- for(Index i = 0; i < dec().nonzeroPivots(); ++i)
729
- if(abs(dec().matrixLU().coeff(i,i)) > premultiplied_threshold)
730
- pivots.coeffRef(p++) = i;
731
- eigen_internal_assert(p == rank());
732
-
733
- for(Index i = 0; i < rank(); ++i)
734
- dst.col(i) = originalMatrix().col(dec().permutationQ().indices().coeff(pivots.coeff(i)));
735
- }
736
- };
737
-
738
- /***** Implementation of solve() *****************************************************/
739
-
740
- } // end namespace internal
741
-
742
- #ifndef EIGEN_PARSED_BY_DOXYGEN
743
- template<typename _MatrixType>
744
- template<typename RhsType, typename DstType>
745
- void FullPivLU<_MatrixType>::_solve_impl(const RhsType &rhs, DstType &dst) const
746
- {
747
- /* The decomposition PAQ = LU can be rewritten as A = P^{-1} L U Q^{-1}.
748
- * So we proceed as follows:
749
- * Step 1: compute c = P * rhs.
750
- * Step 2: replace c by the solution x to Lx = c. Exists because L is invertible.
751
- * Step 3: replace c by the solution x to Ux = c. May or may not exist.
752
- * Step 4: result = Q * c;
753
- */
754
-
755
- const Index rows = this->rows(),
756
- cols = this->cols(),
757
- nonzero_pivots = this->rank();
758
- const Index smalldim = (std::min)(rows, cols);
759
-
760
- if(nonzero_pivots == 0)
761
- {
762
- dst.setZero();
763
- return;
764
- }
765
-
766
- typename RhsType::PlainObject c(rhs.rows(), rhs.cols());
767
-
768
- // Step 1
769
- c = permutationP() * rhs;
770
-
771
- // Step 2
772
- m_lu.topLeftCorner(smalldim,smalldim)
773
- .template triangularView<UnitLower>()
774
- .solveInPlace(c.topRows(smalldim));
775
- if(rows>cols)
776
- c.bottomRows(rows-cols) -= m_lu.bottomRows(rows-cols) * c.topRows(cols);
777
-
778
- // Step 3
779
- m_lu.topLeftCorner(nonzero_pivots, nonzero_pivots)
780
- .template triangularView<Upper>()
781
- .solveInPlace(c.topRows(nonzero_pivots));
782
-
783
- // Step 4
784
- for(Index i = 0; i < nonzero_pivots; ++i)
785
- dst.row(permutationQ().indices().coeff(i)) = c.row(i);
786
- for(Index i = nonzero_pivots; i < m_lu.cols(); ++i)
787
- dst.row(permutationQ().indices().coeff(i)).setZero();
788
- }
789
-
790
- template<typename _MatrixType>
791
- template<bool Conjugate, typename RhsType, typename DstType>
792
- void FullPivLU<_MatrixType>::_solve_impl_transposed(const RhsType &rhs, DstType &dst) const
793
- {
794
- /* The decomposition PAQ = LU can be rewritten as A = P^{-1} L U Q^{-1},
795
- * and since permutations are real and unitary, we can write this
796
- * as A^T = Q U^T L^T P,
797
- * So we proceed as follows:
798
- * Step 1: compute c = Q^T rhs.
799
- * Step 2: replace c by the solution x to U^T x = c. May or may not exist.
800
- * Step 3: replace c by the solution x to L^T x = c.
801
- * Step 4: result = P^T c.
802
- * If Conjugate is true, replace "^T" by "^*" above.
803
- */
804
-
805
- const Index rows = this->rows(), cols = this->cols(),
806
- nonzero_pivots = this->rank();
807
- const Index smalldim = (std::min)(rows, cols);
808
-
809
- if(nonzero_pivots == 0)
810
- {
811
- dst.setZero();
812
- return;
813
- }
814
-
815
- typename RhsType::PlainObject c(rhs.rows(), rhs.cols());
816
-
817
- // Step 1
818
- c = permutationQ().inverse() * rhs;
819
-
820
- // Step 2
821
- m_lu.topLeftCorner(nonzero_pivots, nonzero_pivots)
822
- .template triangularView<Upper>()
823
- .transpose()
824
- .template conjugateIf<Conjugate>()
825
- .solveInPlace(c.topRows(nonzero_pivots));
826
-
827
- // Step 3
828
- m_lu.topLeftCorner(smalldim, smalldim)
829
- .template triangularView<UnitLower>()
830
- .transpose()
831
- .template conjugateIf<Conjugate>()
832
- .solveInPlace(c.topRows(smalldim));
833
-
834
- // Step 4
835
- PermutationPType invp = permutationP().inverse().eval();
836
- for(Index i = 0; i < smalldim; ++i)
837
- dst.row(invp.indices().coeff(i)) = c.row(i);
838
- for(Index i = smalldim; i < rows; ++i)
839
- dst.row(invp.indices().coeff(i)).setZero();
840
- }
841
-
842
- #endif
843
-
844
- namespace internal {
845
-
846
-
847
- /***** Implementation of inverse() *****************************************************/
848
- template<typename DstXprType, typename MatrixType>
849
- struct Assignment<DstXprType, Inverse<FullPivLU<MatrixType> >, internal::assign_op<typename DstXprType::Scalar,typename FullPivLU<MatrixType>::Scalar>, Dense2Dense>
850
- {
851
- typedef FullPivLU<MatrixType> LuType;
852
- typedef Inverse<LuType> SrcXprType;
853
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename MatrixType::Scalar> &)
854
- {
855
- dst = src.nestedExpression().solve(MatrixType::Identity(src.rows(), src.cols()));
856
- }
857
- };
858
- } // end namespace internal
859
-
860
- /******* MatrixBase methods *****************************************************************/
861
-
862
- /** \lu_module
863
- *
864
- * \return the full-pivoting LU decomposition of \c *this.
865
- *
866
- * \sa class FullPivLU
867
- */
868
- template<typename Derived>
869
- inline const FullPivLU<typename MatrixBase<Derived>::PlainObject>
870
- MatrixBase<Derived>::fullPivLu() const
871
- {
872
- return FullPivLU<PlainObject>(eval());
873
- }
874
-
875
- } // end namespace Eigen
876
-
877
- #endif // EIGEN_LU_H