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
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  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
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  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
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  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
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  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
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  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
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  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
@@ -1,713 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2008-2009 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_FULLPIVOTINGHOUSEHOLDERQR_H
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- #define EIGEN_FULLPIVOTINGHOUSEHOLDERQR_H
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-
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- namespace Eigen {
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-
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- namespace internal {
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-
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- template<typename _MatrixType> struct traits<FullPivHouseholderQR<_MatrixType> >
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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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- template<typename MatrixType> struct FullPivHouseholderQRMatrixQReturnType;
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-
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- template<typename MatrixType>
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- struct traits<FullPivHouseholderQRMatrixQReturnType<MatrixType> >
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- {
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- typedef typename MatrixType::PlainObject ReturnType;
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- };
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-
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- } // end namespace internal
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-
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- /** \ingroup QR_Module
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- *
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- * \class FullPivHouseholderQR
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- *
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- * \brief Householder rank-revealing QR decomposition of a matrix with full pivoting
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- *
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- * \tparam _MatrixType the type of the matrix of which we are computing the QR decomposition
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- *
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- * This class performs a rank-revealing QR decomposition of a matrix \b A into matrices \b P, \b P', \b Q and \b R
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- * such that
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- * \f[
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- * \mathbf{P} \, \mathbf{A} \, \mathbf{P}' = \mathbf{Q} \, \mathbf{R}
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- * \f]
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- * by using Householder transformations. Here, \b P and \b P' are permutation matrices, \b Q a unitary matrix
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- * and \b R an upper triangular matrix.
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- *
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- * This decomposition performs a very prudent full pivoting in order to be rank-revealing and achieve optimal
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- * numerical stability. The trade-off is that it is slower than HouseholderQR and ColPivHouseholderQR.
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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::fullPivHouseholderQr()
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- */
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- template<typename _MatrixType> class FullPivHouseholderQR
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- : public SolverBase<FullPivHouseholderQR<_MatrixType> >
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- {
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- public:
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-
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- typedef _MatrixType MatrixType;
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- typedef SolverBase<FullPivHouseholderQR> Base;
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- friend class SolverBase<FullPivHouseholderQR>;
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-
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- EIGEN_GENERIC_PUBLIC_INTERFACE(FullPivHouseholderQR)
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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 internal::FullPivHouseholderQRMatrixQReturnType<MatrixType> MatrixQReturnType;
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- typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
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- typedef Matrix<StorageIndex, 1,
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- EIGEN_SIZE_MIN_PREFER_DYNAMIC(ColsAtCompileTime,RowsAtCompileTime), RowMajor, 1,
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- EIGEN_SIZE_MIN_PREFER_FIXED(MaxColsAtCompileTime,MaxRowsAtCompileTime)> IntDiagSizeVectorType;
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- typedef PermutationMatrix<ColsAtCompileTime, MaxColsAtCompileTime> PermutationType;
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- typedef typename internal::plain_row_type<MatrixType>::type RowVectorType;
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- typedef typename internal::plain_col_type<MatrixType>::type ColVectorType;
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- typedef typename MatrixType::PlainObject PlainObject;
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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 FullPivHouseholderQR::compute(const MatrixType&).
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- */
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- FullPivHouseholderQR()
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- : m_qr(),
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- m_hCoeffs(),
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- m_rows_transpositions(),
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- m_cols_transpositions(),
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- m_cols_permutation(),
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- m_temp(),
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- m_isInitialized(false),
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- m_usePrescribedThreshold(false) {}
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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 FullPivHouseholderQR()
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- */
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- FullPivHouseholderQR(Index rows, Index cols)
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- : m_qr(rows, cols),
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- m_hCoeffs((std::min)(rows,cols)),
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- m_rows_transpositions((std::min)(rows,cols)),
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- m_cols_transpositions((std::min)(rows,cols)),
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- m_cols_permutation(cols),
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- m_temp(cols),
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- m_isInitialized(false),
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- m_usePrescribedThreshold(false) {}
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-
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- /** \brief Constructs a QR factorization from a given matrix
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- *
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- * This constructor computes the QR factorization of the matrix \a matrix by calling
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- * the method compute(). It is a short cut for:
119
- *
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- * \code
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- * FullPivHouseholderQR<MatrixType> qr(matrix.rows(), matrix.cols());
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- * qr.compute(matrix);
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- * \endcode
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- *
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- * \sa compute()
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- */
127
- template<typename InputType>
128
- explicit FullPivHouseholderQR(const EigenBase<InputType>& matrix)
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- : m_qr(matrix.rows(), matrix.cols()),
130
- m_hCoeffs((std::min)(matrix.rows(), matrix.cols())),
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- m_rows_transpositions((std::min)(matrix.rows(), matrix.cols())),
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- m_cols_transpositions((std::min)(matrix.rows(), matrix.cols())),
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- m_cols_permutation(matrix.cols()),
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- m_temp(matrix.cols()),
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- m_isInitialized(false),
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- m_usePrescribedThreshold(false)
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- {
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- compute(matrix.derived());
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- }
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-
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- /** \brief Constructs a QR 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 FullPivHouseholderQR(const EigenBase&)
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- */
147
- template<typename InputType>
148
- explicit FullPivHouseholderQR(EigenBase<InputType>& matrix)
149
- : m_qr(matrix.derived()),
150
- m_hCoeffs((std::min)(matrix.rows(), matrix.cols())),
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- m_rows_transpositions((std::min)(matrix.rows(), matrix.cols())),
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- m_cols_transpositions((std::min)(matrix.rows(), matrix.cols())),
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- m_cols_permutation(matrix.cols()),
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- m_temp(matrix.cols()),
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- m_isInitialized(false),
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- m_usePrescribedThreshold(false)
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- {
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- computeInPlace();
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- }
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-
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- #ifdef EIGEN_PARSED_BY_DOXYGEN
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- /** This method finds a solution x to the equation Ax=b, where A is the matrix of which
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- * \c *this is the QR decomposition.
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- *
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- * \param b the right-hand-side of the equation to solve.
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- *
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- * \returns the exact or least-square solution if the rank is greater or equal to the number of columns of A,
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- * and an arbitrary solution otherwise.
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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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- *
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- * Example: \include FullPivHouseholderQR_solve.cpp
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- * Output: \verbinclude FullPivHouseholderQR_solve.out
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- */
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- template<typename Rhs>
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- inline const Solve<FullPivHouseholderQR, 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 Expression object representing the matrix Q
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- */
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- MatrixQReturnType matrixQ(void) const;
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-
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- /** \returns a reference to the matrix where the Householder QR decomposition is stored
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- */
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- const MatrixType& matrixQR() const
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- {
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- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
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- return m_qr;
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- }
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-
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- template<typename InputType>
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- FullPivHouseholderQR& compute(const EigenBase<InputType>& matrix);
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-
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- /** \returns a const reference to the column permutation matrix */
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- const PermutationType& colsPermutation() const
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- {
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- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
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- return m_cols_permutation;
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- }
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-
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- /** \returns a const reference to the vector of indices representing the rows transpositions */
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- const IntDiagSizeVectorType& rowsTranspositions() const
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- {
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- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
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- return m_rows_transpositions;
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- }
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-
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- /** \returns the absolute value of the determinant of the matrix of which
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- * *this is the QR 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 QR 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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- * \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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- * One way to work around that is to use logAbsDeterminant() instead.
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- *
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- * \sa logAbsDeterminant(), MatrixBase::determinant()
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- */
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- typename MatrixType::RealScalar absDeterminant() const;
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-
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- /** \returns the natural log of the absolute value of the determinant of the matrix of which
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- * *this is the QR 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 QR 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 This method is useful to work around the risk of overflow/underflow that's inherent
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- * to determinant computation.
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- *
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- * \sa absDeterminant(), MatrixBase::determinant()
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- */
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- typename MatrixType::RealScalar logAbsDeterminant() const;
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-
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- /** \returns the rank of the matrix of which *this is the QR 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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- */
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- inline Index rank() const
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- {
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- using std::abs;
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- eigen_assert(m_isInitialized && "FullPivHouseholderQR 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_qr.coeff(i,i)) > premultiplied_threshold);
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- return result;
255
- }
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-
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- /** \returns the dimension of the kernel of the matrix of which *this is the QR decomposition.
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- *
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- * \note This method has to determine which pivots should be considered nonzero.
260
- * For that, it uses the threshold value that you can control by calling
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- * setThreshold(const RealScalar&).
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- */
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- inline Index dimensionOfKernel() const
264
- {
265
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
266
- return cols() - rank();
267
- }
268
-
269
- /** \returns true if the matrix of which *this is the QR decomposition represents an injective
270
- * linear map, i.e. has trivial kernel; false otherwise.
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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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- */
276
- inline bool isInjective() const
277
- {
278
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
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- return rank() == cols();
280
- }
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-
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- /** \returns true if the matrix of which *this is the QR 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
290
- {
291
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
292
- return rank() == rows();
293
- }
294
-
295
- /** \returns true if the matrix of which *this is the QR decomposition is invertible.
296
- *
297
- * \note This method has to determine which pivots should be considered nonzero.
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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 isInvertible() const
302
- {
303
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
304
- return isInjective() && isSurjective();
305
- }
306
-
307
- /** \returns the inverse of the matrix of which *this is the QR decomposition.
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- *
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- * \note If this matrix is not invertible, the returned matrix has undefined coefficients.
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- * Use isInvertible() to first determine whether this matrix is invertible.
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- */
312
- inline const Inverse<FullPivHouseholderQR> inverse() const
313
- {
314
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
315
- return Inverse<FullPivHouseholderQR>(*this);
316
- }
317
-
318
- inline Index rows() const { return m_qr.rows(); }
319
- inline Index cols() const { return m_qr.cols(); }
320
-
321
- /** \returns a const reference to the vector of Householder coefficients used to represent the factor \c Q.
322
- *
323
- * For advanced uses only.
324
- */
325
- const HCoeffsType& hCoeffs() const { return m_hCoeffs; }
326
-
327
- /** Allows to prescribe a threshold to be used by certain methods, such as rank(),
328
- * who need to determine when pivots are to be considered nonzero. This is not used for the
329
- * QR decomposition itself.
330
- *
331
- * When it needs to get the threshold value, Eigen calls threshold(). By default, this
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- * uses a formula to automatically determine a reasonable threshold.
333
- * Once you have called the present method setThreshold(const RealScalar&),
334
- * your value is used instead.
335
- *
336
- * \param threshold The new value to use as the threshold.
337
- *
338
- * A pivot will be considered nonzero if its absolute value is strictly greater than
339
- * \f$ \vert pivot \vert \leqslant threshold \times \vert maxpivot \vert \f$
340
- * where maxpivot is the biggest pivot.
341
- *
342
- * If you want to come back to the default behavior, call setThreshold(Default_t)
343
- */
344
- FullPivHouseholderQR& setThreshold(const RealScalar& threshold)
345
- {
346
- m_usePrescribedThreshold = true;
347
- m_prescribedThreshold = threshold;
348
- return *this;
349
- }
350
-
351
- /** Allows to come back to the default behavior, letting Eigen use its default formula for
352
- * determining the threshold.
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- *
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- * You should pass the special object Eigen::Default as parameter here.
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- * \code qr.setThreshold(Eigen::Default); \endcode
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- *
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- * See the documentation of setThreshold(const RealScalar&).
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- */
359
- FullPivHouseholderQR& setThreshold(Default_t)
360
- {
361
- m_usePrescribedThreshold = false;
362
- return *this;
363
- }
364
-
365
- /** Returns the threshold that will be used by certain methods such as rank().
366
- *
367
- * See the documentation of setThreshold(const RealScalar&).
368
- */
369
- RealScalar threshold() const
370
- {
371
- eigen_assert(m_isInitialized || m_usePrescribedThreshold);
372
- return m_usePrescribedThreshold ? m_prescribedThreshold
373
- // this formula comes from experimenting (see "LU precision tuning" thread on the list)
374
- // and turns out to be identical to Higham's formula used already in LDLt.
375
- : NumTraits<Scalar>::epsilon() * RealScalar(m_qr.diagonalSize());
376
- }
377
-
378
- /** \returns the number of nonzero pivots in the QR decomposition.
379
- * Here nonzero is meant in the exact sense, not in a fuzzy sense.
380
- * So that notion isn't really intrinsically interesting, but it is
381
- * still useful when implementing algorithms.
382
- *
383
- * \sa rank()
384
- */
385
- inline Index nonzeroPivots() const
386
- {
387
- eigen_assert(m_isInitialized && "LU is not initialized.");
388
- return m_nonzero_pivots;
389
- }
390
-
391
- /** \returns the absolute value of the biggest pivot, i.e. the biggest
392
- * diagonal coefficient of U.
393
- */
394
- RealScalar maxPivot() const { return m_maxpivot; }
395
-
396
- #ifndef EIGEN_PARSED_BY_DOXYGEN
397
- template<typename RhsType, typename DstType>
398
- void _solve_impl(const RhsType &rhs, DstType &dst) const;
399
-
400
- template<bool Conjugate, typename RhsType, typename DstType>
401
- void _solve_impl_transposed(const RhsType &rhs, DstType &dst) const;
402
- #endif
403
-
404
- protected:
405
-
406
- static void check_template_parameters()
407
- {
408
- EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
409
- }
410
-
411
- void computeInPlace();
412
-
413
- MatrixType m_qr;
414
- HCoeffsType m_hCoeffs;
415
- IntDiagSizeVectorType m_rows_transpositions;
416
- IntDiagSizeVectorType m_cols_transpositions;
417
- PermutationType m_cols_permutation;
418
- RowVectorType m_temp;
419
- bool m_isInitialized, m_usePrescribedThreshold;
420
- RealScalar m_prescribedThreshold, m_maxpivot;
421
- Index m_nonzero_pivots;
422
- RealScalar m_precision;
423
- Index m_det_pq;
424
- };
425
-
426
- template<typename MatrixType>
427
- typename MatrixType::RealScalar FullPivHouseholderQR<MatrixType>::absDeterminant() const
428
- {
429
- using std::abs;
430
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
431
- eigen_assert(m_qr.rows() == m_qr.cols() && "You can't take the determinant of a non-square matrix!");
432
- return abs(m_qr.diagonal().prod());
433
- }
434
-
435
- template<typename MatrixType>
436
- typename MatrixType::RealScalar FullPivHouseholderQR<MatrixType>::logAbsDeterminant() const
437
- {
438
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
439
- eigen_assert(m_qr.rows() == m_qr.cols() && "You can't take the determinant of a non-square matrix!");
440
- return m_qr.diagonal().cwiseAbs().array().log().sum();
441
- }
442
-
443
- /** Performs the QR factorization of the given matrix \a matrix. The result of
444
- * the factorization is stored into \c *this, and a reference to \c *this
445
- * is returned.
446
- *
447
- * \sa class FullPivHouseholderQR, FullPivHouseholderQR(const MatrixType&)
448
- */
449
- template<typename MatrixType>
450
- template<typename InputType>
451
- FullPivHouseholderQR<MatrixType>& FullPivHouseholderQR<MatrixType>::compute(const EigenBase<InputType>& matrix)
452
- {
453
- m_qr = matrix.derived();
454
- computeInPlace();
455
- return *this;
456
- }
457
-
458
- template<typename MatrixType>
459
- void FullPivHouseholderQR<MatrixType>::computeInPlace()
460
- {
461
- check_template_parameters();
462
-
463
- using std::abs;
464
- Index rows = m_qr.rows();
465
- Index cols = m_qr.cols();
466
- Index size = (std::min)(rows,cols);
467
-
468
-
469
- m_hCoeffs.resize(size);
470
-
471
- m_temp.resize(cols);
472
-
473
- m_precision = NumTraits<Scalar>::epsilon() * RealScalar(size);
474
-
475
- m_rows_transpositions.resize(size);
476
- m_cols_transpositions.resize(size);
477
- Index number_of_transpositions = 0;
478
-
479
- RealScalar biggest(0);
480
-
481
- m_nonzero_pivots = size; // the generic case is that in which all pivots are nonzero (invertible case)
482
- m_maxpivot = RealScalar(0);
483
-
484
- for (Index k = 0; k < size; ++k)
485
- {
486
- Index row_of_biggest_in_corner, col_of_biggest_in_corner;
487
- typedef internal::scalar_score_coeff_op<Scalar> Scoring;
488
- typedef typename Scoring::result_type Score;
489
-
490
- Score score = m_qr.bottomRightCorner(rows-k, cols-k)
491
- .unaryExpr(Scoring())
492
- .maxCoeff(&row_of_biggest_in_corner, &col_of_biggest_in_corner);
493
- row_of_biggest_in_corner += k;
494
- col_of_biggest_in_corner += k;
495
- RealScalar biggest_in_corner = internal::abs_knowing_score<Scalar>()(m_qr(row_of_biggest_in_corner, col_of_biggest_in_corner), score);
496
- if(k==0) biggest = biggest_in_corner;
497
-
498
- // if the corner is negligible, then we have less than full rank, and we can finish early
499
- if(internal::isMuchSmallerThan(biggest_in_corner, biggest, m_precision))
500
- {
501
- m_nonzero_pivots = k;
502
- for(Index i = k; i < size; i++)
503
- {
504
- m_rows_transpositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
505
- m_cols_transpositions.coeffRef(i) = internal::convert_index<StorageIndex>(i);
506
- m_hCoeffs.coeffRef(i) = Scalar(0);
507
- }
508
- break;
509
- }
510
-
511
- m_rows_transpositions.coeffRef(k) = internal::convert_index<StorageIndex>(row_of_biggest_in_corner);
512
- m_cols_transpositions.coeffRef(k) = internal::convert_index<StorageIndex>(col_of_biggest_in_corner);
513
- if(k != row_of_biggest_in_corner) {
514
- m_qr.row(k).tail(cols-k).swap(m_qr.row(row_of_biggest_in_corner).tail(cols-k));
515
- ++number_of_transpositions;
516
- }
517
- if(k != col_of_biggest_in_corner) {
518
- m_qr.col(k).swap(m_qr.col(col_of_biggest_in_corner));
519
- ++number_of_transpositions;
520
- }
521
-
522
- RealScalar beta;
523
- m_qr.col(k).tail(rows-k).makeHouseholderInPlace(m_hCoeffs.coeffRef(k), beta);
524
- m_qr.coeffRef(k,k) = beta;
525
-
526
- // remember the maximum absolute value of diagonal coefficients
527
- if(abs(beta) > m_maxpivot) m_maxpivot = abs(beta);
528
-
529
- m_qr.bottomRightCorner(rows-k, cols-k-1)
530
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(rows-k-1), m_hCoeffs.coeffRef(k), &m_temp.coeffRef(k+1));
531
- }
532
-
533
- m_cols_permutation.setIdentity(cols);
534
- for(Index k = 0; k < size; ++k)
535
- m_cols_permutation.applyTranspositionOnTheRight(k, m_cols_transpositions.coeff(k));
536
-
537
- m_det_pq = (number_of_transpositions%2) ? -1 : 1;
538
- m_isInitialized = true;
539
- }
540
-
541
- #ifndef EIGEN_PARSED_BY_DOXYGEN
542
- template<typename _MatrixType>
543
- template<typename RhsType, typename DstType>
544
- void FullPivHouseholderQR<_MatrixType>::_solve_impl(const RhsType &rhs, DstType &dst) const
545
- {
546
- const Index l_rank = rank();
547
-
548
- // FIXME introduce nonzeroPivots() and use it here. and more generally,
549
- // make the same improvements in this dec as in FullPivLU.
550
- if(l_rank==0)
551
- {
552
- dst.setZero();
553
- return;
554
- }
555
-
556
- typename RhsType::PlainObject c(rhs);
557
-
558
- Matrix<typename RhsType::Scalar,1,RhsType::ColsAtCompileTime> temp(rhs.cols());
559
- for (Index k = 0; k < l_rank; ++k)
560
- {
561
- Index remainingSize = rows()-k;
562
- c.row(k).swap(c.row(m_rows_transpositions.coeff(k)));
563
- c.bottomRightCorner(remainingSize, rhs.cols())
564
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(remainingSize-1),
565
- m_hCoeffs.coeff(k), &temp.coeffRef(0));
566
- }
567
-
568
- m_qr.topLeftCorner(l_rank, l_rank)
569
- .template triangularView<Upper>()
570
- .solveInPlace(c.topRows(l_rank));
571
-
572
- for(Index i = 0; i < l_rank; ++i) dst.row(m_cols_permutation.indices().coeff(i)) = c.row(i);
573
- for(Index i = l_rank; i < cols(); ++i) dst.row(m_cols_permutation.indices().coeff(i)).setZero();
574
- }
575
-
576
- template<typename _MatrixType>
577
- template<bool Conjugate, typename RhsType, typename DstType>
578
- void FullPivHouseholderQR<_MatrixType>::_solve_impl_transposed(const RhsType &rhs, DstType &dst) const
579
- {
580
- const Index l_rank = rank();
581
-
582
- if(l_rank == 0)
583
- {
584
- dst.setZero();
585
- return;
586
- }
587
-
588
- typename RhsType::PlainObject c(m_cols_permutation.transpose()*rhs);
589
-
590
- m_qr.topLeftCorner(l_rank, l_rank)
591
- .template triangularView<Upper>()
592
- .transpose().template conjugateIf<Conjugate>()
593
- .solveInPlace(c.topRows(l_rank));
594
-
595
- dst.topRows(l_rank) = c.topRows(l_rank);
596
- dst.bottomRows(rows()-l_rank).setZero();
597
-
598
- Matrix<Scalar, 1, DstType::ColsAtCompileTime> temp(dst.cols());
599
- const Index size = (std::min)(rows(), cols());
600
- for (Index k = size-1; k >= 0; --k)
601
- {
602
- Index remainingSize = rows()-k;
603
-
604
- dst.bottomRightCorner(remainingSize, dst.cols())
605
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(remainingSize-1).template conjugateIf<!Conjugate>(),
606
- m_hCoeffs.template conjugateIf<Conjugate>().coeff(k), &temp.coeffRef(0));
607
-
608
- dst.row(k).swap(dst.row(m_rows_transpositions.coeff(k)));
609
- }
610
- }
611
- #endif
612
-
613
- namespace internal {
614
-
615
- template<typename DstXprType, typename MatrixType>
616
- struct Assignment<DstXprType, Inverse<FullPivHouseholderQR<MatrixType> >, internal::assign_op<typename DstXprType::Scalar,typename FullPivHouseholderQR<MatrixType>::Scalar>, Dense2Dense>
617
- {
618
- typedef FullPivHouseholderQR<MatrixType> QrType;
619
- typedef Inverse<QrType> SrcXprType;
620
- static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename QrType::Scalar> &)
621
- {
622
- dst = src.nestedExpression().solve(MatrixType::Identity(src.rows(), src.cols()));
623
- }
624
- };
625
-
626
- /** \ingroup QR_Module
627
- *
628
- * \brief Expression type for return value of FullPivHouseholderQR::matrixQ()
629
- *
630
- * \tparam MatrixType type of underlying dense matrix
631
- */
632
- template<typename MatrixType> struct FullPivHouseholderQRMatrixQReturnType
633
- : public ReturnByValue<FullPivHouseholderQRMatrixQReturnType<MatrixType> >
634
- {
635
- public:
636
- typedef typename FullPivHouseholderQR<MatrixType>::IntDiagSizeVectorType IntDiagSizeVectorType;
637
- typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
638
- typedef Matrix<typename MatrixType::Scalar, 1, MatrixType::RowsAtCompileTime, RowMajor, 1,
639
- MatrixType::MaxRowsAtCompileTime> WorkVectorType;
640
-
641
- FullPivHouseholderQRMatrixQReturnType(const MatrixType& qr,
642
- const HCoeffsType& hCoeffs,
643
- const IntDiagSizeVectorType& rowsTranspositions)
644
- : m_qr(qr),
645
- m_hCoeffs(hCoeffs),
646
- m_rowsTranspositions(rowsTranspositions)
647
- {}
648
-
649
- template <typename ResultType>
650
- void evalTo(ResultType& result) const
651
- {
652
- const Index rows = m_qr.rows();
653
- WorkVectorType workspace(rows);
654
- evalTo(result, workspace);
655
- }
656
-
657
- template <typename ResultType>
658
- void evalTo(ResultType& result, WorkVectorType& workspace) const
659
- {
660
- using numext::conj;
661
- // compute the product H'_0 H'_1 ... H'_n-1,
662
- // where H_k is the k-th Householder transformation I - h_k v_k v_k'
663
- // and v_k is the k-th Householder vector [1,m_qr(k+1,k), m_qr(k+2,k), ...]
664
- const Index rows = m_qr.rows();
665
- const Index cols = m_qr.cols();
666
- const Index size = (std::min)(rows, cols);
667
- workspace.resize(rows);
668
- result.setIdentity(rows, rows);
669
- for (Index k = size-1; k >= 0; k--)
670
- {
671
- result.block(k, k, rows-k, rows-k)
672
- .applyHouseholderOnTheLeft(m_qr.col(k).tail(rows-k-1), conj(m_hCoeffs.coeff(k)), &workspace.coeffRef(k));
673
- result.row(k).swap(result.row(m_rowsTranspositions.coeff(k)));
674
- }
675
- }
676
-
677
- Index rows() const { return m_qr.rows(); }
678
- Index cols() const { return m_qr.rows(); }
679
-
680
- protected:
681
- typename MatrixType::Nested m_qr;
682
- typename HCoeffsType::Nested m_hCoeffs;
683
- typename IntDiagSizeVectorType::Nested m_rowsTranspositions;
684
- };
685
-
686
- // template<typename MatrixType>
687
- // struct evaluator<FullPivHouseholderQRMatrixQReturnType<MatrixType> >
688
- // : public evaluator<ReturnByValue<FullPivHouseholderQRMatrixQReturnType<MatrixType> > >
689
- // {};
690
-
691
- } // end namespace internal
692
-
693
- template<typename MatrixType>
694
- inline typename FullPivHouseholderQR<MatrixType>::MatrixQReturnType FullPivHouseholderQR<MatrixType>::matrixQ() const
695
- {
696
- eigen_assert(m_isInitialized && "FullPivHouseholderQR is not initialized.");
697
- return MatrixQReturnType(m_qr, m_hCoeffs, m_rows_transpositions);
698
- }
699
-
700
- /** \return the full-pivoting Householder QR decomposition of \c *this.
701
- *
702
- * \sa class FullPivHouseholderQR
703
- */
704
- template<typename Derived>
705
- const FullPivHouseholderQR<typename MatrixBase<Derived>::PlainObject>
706
- MatrixBase<Derived>::fullPivHouseholderQr() const
707
- {
708
- return FullPivHouseholderQR<PlainObject>(eval());
709
- }
710
-
711
- } // end namespace Eigen
712
-
713
- #endif // EIGEN_FULLPIVOTINGHOUSEHOLDERQR_H