sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.19__cp39-cp39-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 +156 -156
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp39-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.cp39-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 +156 -156
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp39-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,705 +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) 2012, 2013 Chen-Pang He <jdh8@ms63.hinet.net>
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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_MATRIX_POWER
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- #define EIGEN_MATRIX_POWER
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-
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- namespace Eigen {
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-
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- template<typename MatrixType> class MatrixPower;
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-
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- /**
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- * \ingroup MatrixFunctions_Module
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- *
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- * \brief Proxy for the matrix power of some matrix.
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- *
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- * \tparam MatrixType type of the base, a matrix.
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- *
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- * This class holds the arguments to the matrix power until it is
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- * assigned or evaluated for some other reason (so the argument
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- * should not be changed in the meantime). It is the return type of
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- * MatrixPower::operator() and related functions and most of the
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- * time this is the only way it is used.
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- */
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- /* TODO This class is only used by MatrixPower, so it should be nested
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- * into MatrixPower, like MatrixPower::ReturnValue. However, my
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- * compiler complained about unused template parameter in the
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- * following declaration in namespace internal.
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- *
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- * template<typename MatrixType>
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- * struct traits<MatrixPower<MatrixType>::ReturnValue>;
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- */
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- template<typename MatrixType>
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- class MatrixPowerParenthesesReturnValue : public ReturnByValue< MatrixPowerParenthesesReturnValue<MatrixType> >
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- {
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- public:
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- typedef typename MatrixType::RealScalar RealScalar;
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-
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- /**
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- * \brief Constructor.
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- *
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- * \param[in] pow %MatrixPower storing the base.
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- * \param[in] p scalar, the exponent of the matrix power.
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- */
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- MatrixPowerParenthesesReturnValue(MatrixPower<MatrixType>& pow, RealScalar p) : m_pow(pow), m_p(p)
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- { }
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-
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- /**
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- * \brief Compute the matrix power.
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- *
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- * \param[out] result
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- */
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- template<typename ResultType>
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- inline void evalTo(ResultType& result) const
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- { m_pow.compute(result, m_p); }
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-
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- Index rows() const { return m_pow.rows(); }
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- Index cols() const { return m_pow.cols(); }
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-
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- private:
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- MatrixPower<MatrixType>& m_pow;
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- const RealScalar m_p;
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- };
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-
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- /**
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- * \ingroup MatrixFunctions_Module
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- *
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- * \brief Class for computing matrix powers.
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- *
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- * \tparam MatrixType type of the base, expected to be an instantiation
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- * of the Matrix class template.
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- *
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- * This class is capable of computing triangular real/complex matrices
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- * raised to a power in the interval \f$ (-1, 1) \f$.
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- *
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- * \note Currently this class is only used by MatrixPower. One may
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- * insist that this be nested into MatrixPower. This class is here to
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- * facilitate future development of triangular matrix functions.
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- */
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- template<typename MatrixType>
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- class MatrixPowerAtomic : internal::noncopyable
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- {
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- private:
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- enum {
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- RowsAtCompileTime = MatrixType::RowsAtCompileTime,
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- MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime
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- };
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- typedef typename MatrixType::Scalar Scalar;
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- typedef typename MatrixType::RealScalar RealScalar;
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- typedef std::complex<RealScalar> ComplexScalar;
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- typedef Block<MatrixType,Dynamic,Dynamic> ResultType;
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-
98
- const MatrixType& m_A;
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- RealScalar m_p;
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-
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- void computePade(int degree, const MatrixType& IminusT, ResultType& res) const;
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- void compute2x2(ResultType& res, RealScalar p) const;
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- void computeBig(ResultType& res) const;
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- static int getPadeDegree(float normIminusT);
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- static int getPadeDegree(double normIminusT);
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- static int getPadeDegree(long double normIminusT);
107
- static ComplexScalar computeSuperDiag(const ComplexScalar&, const ComplexScalar&, RealScalar p);
108
- static RealScalar computeSuperDiag(RealScalar, RealScalar, RealScalar p);
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-
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- public:
111
- /**
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- * \brief Constructor.
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- *
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- * \param[in] T the base of the matrix power.
115
- * \param[in] p the exponent of the matrix power, should be in
116
- * \f$ (-1, 1) \f$.
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- *
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- * The class stores a reference to T, so it should not be changed
119
- * (or destroyed) before evaluation. Only the upper triangular
120
- * part of T is read.
121
- */
122
- MatrixPowerAtomic(const MatrixType& T, RealScalar p);
123
-
124
- /**
125
- * \brief Compute the matrix power.
126
- *
127
- * \param[out] res \f$ A^p \f$ where A and p are specified in the
128
- * constructor.
129
- */
130
- void compute(ResultType& res) const;
131
- };
132
-
133
- template<typename MatrixType>
134
- MatrixPowerAtomic<MatrixType>::MatrixPowerAtomic(const MatrixType& T, RealScalar p) :
135
- m_A(T), m_p(p)
136
- {
137
- eigen_assert(T.rows() == T.cols());
138
- eigen_assert(p > -1 && p < 1);
139
- }
140
-
141
- template<typename MatrixType>
142
- void MatrixPowerAtomic<MatrixType>::compute(ResultType& res) const
143
- {
144
- using std::pow;
145
- switch (m_A.rows()) {
146
- case 0:
147
- break;
148
- case 1:
149
- res(0,0) = pow(m_A(0,0), m_p);
150
- break;
151
- case 2:
152
- compute2x2(res, m_p);
153
- break;
154
- default:
155
- computeBig(res);
156
- }
157
- }
158
-
159
- template<typename MatrixType>
160
- void MatrixPowerAtomic<MatrixType>::computePade(int degree, const MatrixType& IminusT, ResultType& res) const
161
- {
162
- int i = 2*degree;
163
- res = (m_p-RealScalar(degree)) / RealScalar(2*i-2) * IminusT;
164
-
165
- for (--i; i; --i) {
166
- res = (MatrixType::Identity(IminusT.rows(), IminusT.cols()) + res).template triangularView<Upper>()
167
- .solve((i==1 ? -m_p : i&1 ? (-m_p-RealScalar(i/2))/RealScalar(2*i) : (m_p-RealScalar(i/2))/RealScalar(2*i-2)) * IminusT).eval();
168
- }
169
- res += MatrixType::Identity(IminusT.rows(), IminusT.cols());
170
- }
171
-
172
- // This function assumes that res has the correct size (see bug 614)
173
- template<typename MatrixType>
174
- void MatrixPowerAtomic<MatrixType>::compute2x2(ResultType& res, RealScalar p) const
175
- {
176
- using std::abs;
177
- using std::pow;
178
- res.coeffRef(0,0) = pow(m_A.coeff(0,0), p);
179
-
180
- for (Index i=1; i < m_A.cols(); ++i) {
181
- res.coeffRef(i,i) = pow(m_A.coeff(i,i), p);
182
- if (m_A.coeff(i-1,i-1) == m_A.coeff(i,i))
183
- res.coeffRef(i-1,i) = p * pow(m_A.coeff(i,i), p-1);
184
- else if (2*abs(m_A.coeff(i-1,i-1)) < abs(m_A.coeff(i,i)) || 2*abs(m_A.coeff(i,i)) < abs(m_A.coeff(i-1,i-1)))
185
- res.coeffRef(i-1,i) = (res.coeff(i,i)-res.coeff(i-1,i-1)) / (m_A.coeff(i,i)-m_A.coeff(i-1,i-1));
186
- else
187
- res.coeffRef(i-1,i) = computeSuperDiag(m_A.coeff(i,i), m_A.coeff(i-1,i-1), p);
188
- res.coeffRef(i-1,i) *= m_A.coeff(i-1,i);
189
- }
190
- }
191
-
192
- template<typename MatrixType>
193
- void MatrixPowerAtomic<MatrixType>::computeBig(ResultType& res) const
194
- {
195
- using std::ldexp;
196
- const int digits = std::numeric_limits<RealScalar>::digits;
197
- const RealScalar maxNormForPade = RealScalar(
198
- digits <= 24? 4.3386528e-1L // single precision
199
- : digits <= 53? 2.789358995219730e-1L // double precision
200
- : digits <= 64? 2.4471944416607995472e-1L // extended precision
201
- : digits <= 106? 1.1016843812851143391275867258512e-1L // double-double
202
- : 9.134603732914548552537150753385375e-2L); // quadruple precision
203
- MatrixType IminusT, sqrtT, T = m_A.template triangularView<Upper>();
204
- RealScalar normIminusT;
205
- int degree, degree2, numberOfSquareRoots = 0;
206
- bool hasExtraSquareRoot = false;
207
-
208
- for (Index i=0; i < m_A.cols(); ++i)
209
- eigen_assert(m_A(i,i) != RealScalar(0));
210
-
211
- while (true) {
212
- IminusT = MatrixType::Identity(m_A.rows(), m_A.cols()) - T;
213
- normIminusT = IminusT.cwiseAbs().colwise().sum().maxCoeff();
214
- if (normIminusT < maxNormForPade) {
215
- degree = getPadeDegree(normIminusT);
216
- degree2 = getPadeDegree(normIminusT/2);
217
- if (degree - degree2 <= 1 || hasExtraSquareRoot)
218
- break;
219
- hasExtraSquareRoot = true;
220
- }
221
- matrix_sqrt_triangular(T, sqrtT);
222
- T = sqrtT.template triangularView<Upper>();
223
- ++numberOfSquareRoots;
224
- }
225
- computePade(degree, IminusT, res);
226
-
227
- for (; numberOfSquareRoots; --numberOfSquareRoots) {
228
- compute2x2(res, ldexp(m_p, -numberOfSquareRoots));
229
- res = res.template triangularView<Upper>() * res;
230
- }
231
- compute2x2(res, m_p);
232
- }
233
-
234
- template<typename MatrixType>
235
- inline int MatrixPowerAtomic<MatrixType>::getPadeDegree(float normIminusT)
236
- {
237
- const float maxNormForPade[] = { 2.8064004e-1f /* degree = 3 */ , 4.3386528e-1f };
238
- int degree = 3;
239
- for (; degree <= 4; ++degree)
240
- if (normIminusT <= maxNormForPade[degree - 3])
241
- break;
242
- return degree;
243
- }
244
-
245
- template<typename MatrixType>
246
- inline int MatrixPowerAtomic<MatrixType>::getPadeDegree(double normIminusT)
247
- {
248
- const double maxNormForPade[] = { 1.884160592658218e-2 /* degree = 3 */ , 6.038881904059573e-2, 1.239917516308172e-1,
249
- 1.999045567181744e-1, 2.789358995219730e-1 };
250
- int degree = 3;
251
- for (; degree <= 7; ++degree)
252
- if (normIminusT <= maxNormForPade[degree - 3])
253
- break;
254
- return degree;
255
- }
256
-
257
- template<typename MatrixType>
258
- inline int MatrixPowerAtomic<MatrixType>::getPadeDegree(long double normIminusT)
259
- {
260
- #if LDBL_MANT_DIG == 53
261
- const int maxPadeDegree = 7;
262
- const double maxNormForPade[] = { 1.884160592658218e-2L /* degree = 3 */ , 6.038881904059573e-2L, 1.239917516308172e-1L,
263
- 1.999045567181744e-1L, 2.789358995219730e-1L };
264
- #elif LDBL_MANT_DIG <= 64
265
- const int maxPadeDegree = 8;
266
- const long double maxNormForPade[] = { 6.3854693117491799460e-3L /* degree = 3 */ , 2.6394893435456973676e-2L,
267
- 6.4216043030404063729e-2L, 1.1701165502926694307e-1L, 1.7904284231268670284e-1L, 2.4471944416607995472e-1L };
268
- #elif LDBL_MANT_DIG <= 106
269
- const int maxPadeDegree = 10;
270
- const double maxNormForPade[] = { 1.0007161601787493236741409687186e-4L /* degree = 3 */ ,
271
- 1.0007161601787493236741409687186e-3L, 4.7069769360887572939882574746264e-3L, 1.3220386624169159689406653101695e-2L,
272
- 2.8063482381631737920612944054906e-2L, 4.9625993951953473052385361085058e-2L, 7.7367040706027886224557538328171e-2L,
273
- 1.1016843812851143391275867258512e-1L };
274
- #else
275
- const int maxPadeDegree = 10;
276
- const double maxNormForPade[] = { 5.524506147036624377378713555116378e-5L /* degree = 3 */ ,
277
- 6.640600568157479679823602193345995e-4L, 3.227716520106894279249709728084626e-3L,
278
- 9.619593944683432960546978734646284e-3L, 2.134595382433742403911124458161147e-2L,
279
- 3.908166513900489428442993794761185e-2L, 6.266780814639442865832535460550138e-2L,
280
- 9.134603732914548552537150753385375e-2L };
281
- #endif
282
- int degree = 3;
283
- for (; degree <= maxPadeDegree; ++degree)
284
- if (normIminusT <= maxNormForPade[degree - 3])
285
- break;
286
- return degree;
287
- }
288
-
289
- template<typename MatrixType>
290
- inline typename MatrixPowerAtomic<MatrixType>::ComplexScalar
291
- MatrixPowerAtomic<MatrixType>::computeSuperDiag(const ComplexScalar& curr, const ComplexScalar& prev, RealScalar p)
292
- {
293
- using std::ceil;
294
- using std::exp;
295
- using std::log;
296
- using std::sinh;
297
-
298
- ComplexScalar logCurr = log(curr);
299
- ComplexScalar logPrev = log(prev);
300
- RealScalar unwindingNumber = ceil((numext::imag(logCurr - logPrev) - RealScalar(EIGEN_PI)) / RealScalar(2*EIGEN_PI));
301
- ComplexScalar w = numext::log1p((curr-prev)/prev)/RealScalar(2) + ComplexScalar(0, RealScalar(EIGEN_PI)*unwindingNumber);
302
- return RealScalar(2) * exp(RealScalar(0.5) * p * (logCurr + logPrev)) * sinh(p * w) / (curr - prev);
303
- }
304
-
305
- template<typename MatrixType>
306
- inline typename MatrixPowerAtomic<MatrixType>::RealScalar
307
- MatrixPowerAtomic<MatrixType>::computeSuperDiag(RealScalar curr, RealScalar prev, RealScalar p)
308
- {
309
- using std::exp;
310
- using std::log;
311
- using std::sinh;
312
-
313
- RealScalar w = numext::log1p((curr-prev)/prev)/RealScalar(2);
314
- return 2 * exp(p * (log(curr) + log(prev)) / 2) * sinh(p * w) / (curr - prev);
315
- }
316
-
317
- /**
318
- * \ingroup MatrixFunctions_Module
319
- *
320
- * \brief Class for computing matrix powers.
321
- *
322
- * \tparam MatrixType type of the base, expected to be an instantiation
323
- * of the Matrix class template.
324
- *
325
- * This class is capable of computing real/complex matrices raised to
326
- * an arbitrary real power. Meanwhile, it saves the result of Schur
327
- * decomposition if an non-integral power has even been calculated.
328
- * Therefore, if you want to compute multiple (>= 2) matrix powers
329
- * for the same matrix, using the class directly is more efficient than
330
- * calling MatrixBase::pow().
331
- *
332
- * Example:
333
- * \include MatrixPower_optimal.cpp
334
- * Output: \verbinclude MatrixPower_optimal.out
335
- */
336
- template<typename MatrixType>
337
- class MatrixPower : internal::noncopyable
338
- {
339
- private:
340
- typedef typename MatrixType::Scalar Scalar;
341
- typedef typename MatrixType::RealScalar RealScalar;
342
-
343
- public:
344
- /**
345
- * \brief Constructor.
346
- *
347
- * \param[in] A the base of the matrix power.
348
- *
349
- * The class stores a reference to A, so it should not be changed
350
- * (or destroyed) before evaluation.
351
- */
352
- explicit MatrixPower(const MatrixType& A) :
353
- m_A(A),
354
- m_conditionNumber(0),
355
- m_rank(A.cols()),
356
- m_nulls(0)
357
- { eigen_assert(A.rows() == A.cols()); }
358
-
359
- /**
360
- * \brief Returns the matrix power.
361
- *
362
- * \param[in] p exponent, a real scalar.
363
- * \return The expression \f$ A^p \f$, where A is specified in the
364
- * constructor.
365
- */
366
- const MatrixPowerParenthesesReturnValue<MatrixType> operator()(RealScalar p)
367
- { return MatrixPowerParenthesesReturnValue<MatrixType>(*this, p); }
368
-
369
- /**
370
- * \brief Compute the matrix power.
371
- *
372
- * \param[in] p exponent, a real scalar.
373
- * \param[out] res \f$ A^p \f$ where A is specified in the
374
- * constructor.
375
- */
376
- template<typename ResultType>
377
- void compute(ResultType& res, RealScalar p);
378
-
379
- Index rows() const { return m_A.rows(); }
380
- Index cols() const { return m_A.cols(); }
381
-
382
- private:
383
- typedef std::complex<RealScalar> ComplexScalar;
384
- typedef Matrix<ComplexScalar, Dynamic, Dynamic, 0,
385
- MatrixType::RowsAtCompileTime, MatrixType::ColsAtCompileTime> ComplexMatrix;
386
-
387
- /** \brief Reference to the base of matrix power. */
388
- typename MatrixType::Nested m_A;
389
-
390
- /** \brief Temporary storage. */
391
- MatrixType m_tmp;
392
-
393
- /** \brief Store the result of Schur decomposition. */
394
- ComplexMatrix m_T, m_U;
395
-
396
- /** \brief Store fractional power of m_T. */
397
- ComplexMatrix m_fT;
398
-
399
- /**
400
- * \brief Condition number of m_A.
401
- *
402
- * It is initialized as 0 to avoid performing unnecessary Schur
403
- * decomposition, which is the bottleneck.
404
- */
405
- RealScalar m_conditionNumber;
406
-
407
- /** \brief Rank of m_A. */
408
- Index m_rank;
409
-
410
- /** \brief Rank deficiency of m_A. */
411
- Index m_nulls;
412
-
413
- /**
414
- * \brief Split p into integral part and fractional part.
415
- *
416
- * \param[in] p The exponent.
417
- * \param[out] p The fractional part ranging in \f$ (-1, 1) \f$.
418
- * \param[out] intpart The integral part.
419
- *
420
- * Only if the fractional part is nonzero, it calls initialize().
421
- */
422
- void split(RealScalar& p, RealScalar& intpart);
423
-
424
- /** \brief Perform Schur decomposition for fractional power. */
425
- void initialize();
426
-
427
- template<typename ResultType>
428
- void computeIntPower(ResultType& res, RealScalar p);
429
-
430
- template<typename ResultType>
431
- void computeFracPower(ResultType& res, RealScalar p);
432
-
433
- template<int Rows, int Cols, int Options, int MaxRows, int MaxCols>
434
- static void revertSchur(
435
- Matrix<ComplexScalar, Rows, Cols, Options, MaxRows, MaxCols>& res,
436
- const ComplexMatrix& T,
437
- const ComplexMatrix& U);
438
-
439
- template<int Rows, int Cols, int Options, int MaxRows, int MaxCols>
440
- static void revertSchur(
441
- Matrix<RealScalar, Rows, Cols, Options, MaxRows, MaxCols>& res,
442
- const ComplexMatrix& T,
443
- const ComplexMatrix& U);
444
- };
445
-
446
- template<typename MatrixType>
447
- template<typename ResultType>
448
- void MatrixPower<MatrixType>::compute(ResultType& res, RealScalar p)
449
- {
450
- using std::pow;
451
- switch (cols()) {
452
- case 0:
453
- break;
454
- case 1:
455
- res(0,0) = pow(m_A.coeff(0,0), p);
456
- break;
457
- default:
458
- RealScalar intpart;
459
- split(p, intpart);
460
-
461
- res = MatrixType::Identity(rows(), cols());
462
- computeIntPower(res, intpart);
463
- if (p) computeFracPower(res, p);
464
- }
465
- }
466
-
467
- template<typename MatrixType>
468
- void MatrixPower<MatrixType>::split(RealScalar& p, RealScalar& intpart)
469
- {
470
- using std::floor;
471
- using std::pow;
472
-
473
- intpart = floor(p);
474
- p -= intpart;
475
-
476
- // Perform Schur decomposition if it is not yet performed and the power is
477
- // not an integer.
478
- if (!m_conditionNumber && p)
479
- initialize();
480
-
481
- // Choose the more stable of intpart = floor(p) and intpart = ceil(p).
482
- if (p > RealScalar(0.5) && p > (1-p) * pow(m_conditionNumber, p)) {
483
- --p;
484
- ++intpart;
485
- }
486
- }
487
-
488
- template<typename MatrixType>
489
- void MatrixPower<MatrixType>::initialize()
490
- {
491
- const ComplexSchur<MatrixType> schurOfA(m_A);
492
- JacobiRotation<ComplexScalar> rot;
493
- ComplexScalar eigenvalue;
494
-
495
- m_fT.resizeLike(m_A);
496
- m_T = schurOfA.matrixT();
497
- m_U = schurOfA.matrixU();
498
- m_conditionNumber = m_T.diagonal().array().abs().maxCoeff() / m_T.diagonal().array().abs().minCoeff();
499
-
500
- // Move zero eigenvalues to the bottom right corner.
501
- for (Index i = cols()-1; i>=0; --i) {
502
- if (m_rank <= 2)
503
- return;
504
- if (m_T.coeff(i,i) == RealScalar(0)) {
505
- for (Index j=i+1; j < m_rank; ++j) {
506
- eigenvalue = m_T.coeff(j,j);
507
- rot.makeGivens(m_T.coeff(j-1,j), eigenvalue);
508
- m_T.applyOnTheRight(j-1, j, rot);
509
- m_T.applyOnTheLeft(j-1, j, rot.adjoint());
510
- m_T.coeffRef(j-1,j-1) = eigenvalue;
511
- m_T.coeffRef(j,j) = RealScalar(0);
512
- m_U.applyOnTheRight(j-1, j, rot);
513
- }
514
- --m_rank;
515
- }
516
- }
517
-
518
- m_nulls = rows() - m_rank;
519
- if (m_nulls) {
520
- eigen_assert(m_T.bottomRightCorner(m_nulls, m_nulls).isZero()
521
- && "Base of matrix power should be invertible or with a semisimple zero eigenvalue.");
522
- m_fT.bottomRows(m_nulls).fill(RealScalar(0));
523
- }
524
- }
525
-
526
- template<typename MatrixType>
527
- template<typename ResultType>
528
- void MatrixPower<MatrixType>::computeIntPower(ResultType& res, RealScalar p)
529
- {
530
- using std::abs;
531
- using std::fmod;
532
- RealScalar pp = abs(p);
533
-
534
- if (p<0)
535
- m_tmp = m_A.inverse();
536
- else
537
- m_tmp = m_A;
538
-
539
- while (true) {
540
- if (fmod(pp, 2) >= 1)
541
- res = m_tmp * res;
542
- pp /= 2;
543
- if (pp < 1)
544
- break;
545
- m_tmp *= m_tmp;
546
- }
547
- }
548
-
549
- template<typename MatrixType>
550
- template<typename ResultType>
551
- void MatrixPower<MatrixType>::computeFracPower(ResultType& res, RealScalar p)
552
- {
553
- Block<ComplexMatrix,Dynamic,Dynamic> blockTp(m_fT, 0, 0, m_rank, m_rank);
554
- eigen_assert(m_conditionNumber);
555
- eigen_assert(m_rank + m_nulls == rows());
556
-
557
- MatrixPowerAtomic<ComplexMatrix>(m_T.topLeftCorner(m_rank, m_rank), p).compute(blockTp);
558
- if (m_nulls) {
559
- m_fT.topRightCorner(m_rank, m_nulls) = m_T.topLeftCorner(m_rank, m_rank).template triangularView<Upper>()
560
- .solve(blockTp * m_T.topRightCorner(m_rank, m_nulls));
561
- }
562
- revertSchur(m_tmp, m_fT, m_U);
563
- res = m_tmp * res;
564
- }
565
-
566
- template<typename MatrixType>
567
- template<int Rows, int Cols, int Options, int MaxRows, int MaxCols>
568
- inline void MatrixPower<MatrixType>::revertSchur(
569
- Matrix<ComplexScalar, Rows, Cols, Options, MaxRows, MaxCols>& res,
570
- const ComplexMatrix& T,
571
- const ComplexMatrix& U)
572
- { res.noalias() = U * (T.template triangularView<Upper>() * U.adjoint()); }
573
-
574
- template<typename MatrixType>
575
- template<int Rows, int Cols, int Options, int MaxRows, int MaxCols>
576
- inline void MatrixPower<MatrixType>::revertSchur(
577
- Matrix<RealScalar, Rows, Cols, Options, MaxRows, MaxCols>& res,
578
- const ComplexMatrix& T,
579
- const ComplexMatrix& U)
580
- { res.noalias() = (U * (T.template triangularView<Upper>() * U.adjoint())).real(); }
581
-
582
- /**
583
- * \ingroup MatrixFunctions_Module
584
- *
585
- * \brief Proxy for the matrix power of some matrix (expression).
586
- *
587
- * \tparam Derived type of the base, a matrix (expression).
588
- *
589
- * This class holds the arguments to the matrix power until it is
590
- * assigned or evaluated for some other reason (so the argument
591
- * should not be changed in the meantime). It is the return type of
592
- * MatrixBase::pow() and related functions and most of the
593
- * time this is the only way it is used.
594
- */
595
- template<typename Derived>
596
- class MatrixPowerReturnValue : public ReturnByValue< MatrixPowerReturnValue<Derived> >
597
- {
598
- public:
599
- typedef typename Derived::PlainObject PlainObject;
600
- typedef typename Derived::RealScalar RealScalar;
601
-
602
- /**
603
- * \brief Constructor.
604
- *
605
- * \param[in] A %Matrix (expression), the base of the matrix power.
606
- * \param[in] p real scalar, the exponent of the matrix power.
607
- */
608
- MatrixPowerReturnValue(const Derived& A, RealScalar p) : m_A(A), m_p(p)
609
- { }
610
-
611
- /**
612
- * \brief Compute the matrix power.
613
- *
614
- * \param[out] result \f$ A^p \f$ where \p A and \p p are as in the
615
- * constructor.
616
- */
617
- template<typename ResultType>
618
- inline void evalTo(ResultType& result) const
619
- { MatrixPower<PlainObject>(m_A.eval()).compute(result, m_p); }
620
-
621
- Index rows() const { return m_A.rows(); }
622
- Index cols() const { return m_A.cols(); }
623
-
624
- private:
625
- const Derived& m_A;
626
- const RealScalar m_p;
627
- };
628
-
629
- /**
630
- * \ingroup MatrixFunctions_Module
631
- *
632
- * \brief Proxy for the matrix power of some matrix (expression).
633
- *
634
- * \tparam Derived type of the base, a matrix (expression).
635
- *
636
- * This class holds the arguments to the matrix power until it is
637
- * assigned or evaluated for some other reason (so the argument
638
- * should not be changed in the meantime). It is the return type of
639
- * MatrixBase::pow() and related functions and most of the
640
- * time this is the only way it is used.
641
- */
642
- template<typename Derived>
643
- class MatrixComplexPowerReturnValue : public ReturnByValue< MatrixComplexPowerReturnValue<Derived> >
644
- {
645
- public:
646
- typedef typename Derived::PlainObject PlainObject;
647
- typedef typename std::complex<typename Derived::RealScalar> ComplexScalar;
648
-
649
- /**
650
- * \brief Constructor.
651
- *
652
- * \param[in] A %Matrix (expression), the base of the matrix power.
653
- * \param[in] p complex scalar, the exponent of the matrix power.
654
- */
655
- MatrixComplexPowerReturnValue(const Derived& A, const ComplexScalar& p) : m_A(A), m_p(p)
656
- { }
657
-
658
- /**
659
- * \brief Compute the matrix power.
660
- *
661
- * Because \p p is complex, \f$ A^p \f$ is simply evaluated as \f$
662
- * \exp(p \log(A)) \f$.
663
- *
664
- * \param[out] result \f$ A^p \f$ where \p A and \p p are as in the
665
- * constructor.
666
- */
667
- template<typename ResultType>
668
- inline void evalTo(ResultType& result) const
669
- { result = (m_p * m_A.log()).exp(); }
670
-
671
- Index rows() const { return m_A.rows(); }
672
- Index cols() const { return m_A.cols(); }
673
-
674
- private:
675
- const Derived& m_A;
676
- const ComplexScalar m_p;
677
- };
678
-
679
- namespace internal {
680
-
681
- template<typename MatrixPowerType>
682
- struct traits< MatrixPowerParenthesesReturnValue<MatrixPowerType> >
683
- { typedef typename MatrixPowerType::PlainObject ReturnType; };
684
-
685
- template<typename Derived>
686
- struct traits< MatrixPowerReturnValue<Derived> >
687
- { typedef typename Derived::PlainObject ReturnType; };
688
-
689
- template<typename Derived>
690
- struct traits< MatrixComplexPowerReturnValue<Derived> >
691
- { typedef typename Derived::PlainObject ReturnType; };
692
-
693
- }
694
-
695
- template<typename Derived>
696
- const MatrixPowerReturnValue<Derived> MatrixBase<Derived>::pow(const RealScalar& p) const
697
- { return MatrixPowerReturnValue<Derived>(derived(), p); }
698
-
699
- template<typename Derived>
700
- const MatrixComplexPowerReturnValue<Derived> MatrixBase<Derived>::pow(const std::complex<RealScalar>& p) const
701
- { return MatrixComplexPowerReturnValue<Derived>(derived(), p); }
702
-
703
- } // namespace Eigen
704
-
705
- #endif // EIGEN_MATRIX_POWER