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
@@ -1,91 +0,0 @@
1
- namespace Eigen {
2
-
3
- namespace internal {
4
-
5
- // TODO : once qrsolv2 is removed, use ColPivHouseholderQR or PermutationMatrix instead of ipvt
6
- template <typename Scalar>
7
- void qrsolv(
8
- Matrix< Scalar, Dynamic, Dynamic > &s,
9
- // TODO : use a PermutationMatrix once lmpar is no more:
10
- const VectorXi &ipvt,
11
- const Matrix< Scalar, Dynamic, 1 > &diag,
12
- const Matrix< Scalar, Dynamic, 1 > &qtb,
13
- Matrix< Scalar, Dynamic, 1 > &x,
14
- Matrix< Scalar, Dynamic, 1 > &sdiag)
15
-
16
- {
17
- typedef DenseIndex Index;
18
-
19
- /* Local variables */
20
- Index i, j, k, l;
21
- Scalar temp;
22
- Index n = s.cols();
23
- Matrix< Scalar, Dynamic, 1 > wa(n);
24
- JacobiRotation<Scalar> givens;
25
-
26
- /* Function Body */
27
- // the following will only change the lower triangular part of s, including
28
- // the diagonal, though the diagonal is restored afterward
29
-
30
- /* copy r and (q transpose)*b to preserve input and initialize s. */
31
- /* in particular, save the diagonal elements of r in x. */
32
- x = s.diagonal();
33
- wa = qtb;
34
-
35
- s.topLeftCorner(n,n).template triangularView<StrictlyLower>() = s.topLeftCorner(n,n).transpose();
36
-
37
- /* eliminate the diagonal matrix d using a givens rotation. */
38
- for (j = 0; j < n; ++j) {
39
-
40
- /* prepare the row of d to be eliminated, locating the */
41
- /* diagonal element using p from the qr factorization. */
42
- l = ipvt[j];
43
- if (diag[l] == 0.)
44
- break;
45
- sdiag.tail(n-j).setZero();
46
- sdiag[j] = diag[l];
47
-
48
- /* the transformations to eliminate the row of d */
49
- /* modify only a single element of (q transpose)*b */
50
- /* beyond the first n, which is initially zero. */
51
- Scalar qtbpj = 0.;
52
- for (k = j; k < n; ++k) {
53
- /* determine a givens rotation which eliminates the */
54
- /* appropriate element in the current row of d. */
55
- givens.makeGivens(-s(k,k), sdiag[k]);
56
-
57
- /* compute the modified diagonal element of r and */
58
- /* the modified element of ((q transpose)*b,0). */
59
- s(k,k) = givens.c() * s(k,k) + givens.s() * sdiag[k];
60
- temp = givens.c() * wa[k] + givens.s() * qtbpj;
61
- qtbpj = -givens.s() * wa[k] + givens.c() * qtbpj;
62
- wa[k] = temp;
63
-
64
- /* accumulate the transformation in the row of s. */
65
- for (i = k+1; i<n; ++i) {
66
- temp = givens.c() * s(i,k) + givens.s() * sdiag[i];
67
- sdiag[i] = -givens.s() * s(i,k) + givens.c() * sdiag[i];
68
- s(i,k) = temp;
69
- }
70
- }
71
- }
72
-
73
- /* solve the triangular system for z. if the system is */
74
- /* singular, then obtain a least squares solution. */
75
- Index nsing;
76
- for(nsing=0; nsing<n && sdiag[nsing]!=0; nsing++) {}
77
-
78
- wa.tail(n-nsing).setZero();
79
- s.topLeftCorner(nsing, nsing).transpose().template triangularView<Upper>().solveInPlace(wa.head(nsing));
80
-
81
- // restore
82
- sdiag = s.diagonal();
83
- s.diagonal() = x;
84
-
85
- /* permute the components of z back to components of x. */
86
- for (j = 0; j < n; ++j) x[ipvt[j]] = wa[j];
87
- }
88
-
89
- } // end namespace internal
90
-
91
- } // end namespace Eigen
@@ -1,30 +0,0 @@
1
- namespace Eigen {
2
-
3
- namespace internal {
4
-
5
- // TODO : move this to GivensQR once there's such a thing in Eigen
6
-
7
- template <typename Scalar>
8
- void r1mpyq(DenseIndex m, DenseIndex n, Scalar *a, const std::vector<JacobiRotation<Scalar> > &v_givens, const std::vector<JacobiRotation<Scalar> > &w_givens)
9
- {
10
- typedef DenseIndex Index;
11
-
12
- /* apply the first set of givens rotations to a. */
13
- for (Index j = n-2; j>=0; --j)
14
- for (Index i = 0; i<m; ++i) {
15
- Scalar temp = v_givens[j].c() * a[i+m*j] - v_givens[j].s() * a[i+m*(n-1)];
16
- a[i+m*(n-1)] = v_givens[j].s() * a[i+m*j] + v_givens[j].c() * a[i+m*(n-1)];
17
- a[i+m*j] = temp;
18
- }
19
- /* apply the second set of givens rotations to a. */
20
- for (Index j = 0; j<n-1; ++j)
21
- for (Index i = 0; i<m; ++i) {
22
- Scalar temp = w_givens[j].c() * a[i+m*j] + w_givens[j].s() * a[i+m*(n-1)];
23
- a[i+m*(n-1)] = -w_givens[j].s() * a[i+m*j] + w_givens[j].c() * a[i+m*(n-1)];
24
- a[i+m*j] = temp;
25
- }
26
- }
27
-
28
- } // end namespace internal
29
-
30
- } // end namespace Eigen
@@ -1,99 +0,0 @@
1
- namespace Eigen {
2
-
3
- namespace internal {
4
-
5
- template <typename Scalar>
6
- void r1updt(
7
- Matrix< Scalar, Dynamic, Dynamic > &s,
8
- const Matrix< Scalar, Dynamic, 1> &u,
9
- std::vector<JacobiRotation<Scalar> > &v_givens,
10
- std::vector<JacobiRotation<Scalar> > &w_givens,
11
- Matrix< Scalar, Dynamic, 1> &v,
12
- Matrix< Scalar, Dynamic, 1> &w,
13
- bool *sing)
14
- {
15
- typedef DenseIndex Index;
16
- const JacobiRotation<Scalar> IdentityRotation = JacobiRotation<Scalar>(1,0);
17
-
18
- /* Local variables */
19
- const Index m = s.rows();
20
- const Index n = s.cols();
21
- Index i, j=1;
22
- Scalar temp;
23
- JacobiRotation<Scalar> givens;
24
-
25
- // r1updt had a broader usecase, but we don't use it here. And, more
26
- // importantly, we can not test it.
27
- eigen_assert(m==n);
28
- eigen_assert(u.size()==m);
29
- eigen_assert(v.size()==n);
30
- eigen_assert(w.size()==n);
31
-
32
- /* move the nontrivial part of the last column of s into w. */
33
- w[n-1] = s(n-1,n-1);
34
-
35
- /* rotate the vector v into a multiple of the n-th unit vector */
36
- /* in such a way that a spike is introduced into w. */
37
- for (j=n-2; j>=0; --j) {
38
- w[j] = 0.;
39
- if (v[j] != 0.) {
40
- /* determine a givens rotation which eliminates the */
41
- /* j-th element of v. */
42
- givens.makeGivens(-v[n-1], v[j]);
43
-
44
- /* apply the transformation to v and store the information */
45
- /* necessary to recover the givens rotation. */
46
- v[n-1] = givens.s() * v[j] + givens.c() * v[n-1];
47
- v_givens[j] = givens;
48
-
49
- /* apply the transformation to s and extend the spike in w. */
50
- for (i = j; i < m; ++i) {
51
- temp = givens.c() * s(j,i) - givens.s() * w[i];
52
- w[i] = givens.s() * s(j,i) + givens.c() * w[i];
53
- s(j,i) = temp;
54
- }
55
- } else
56
- v_givens[j] = IdentityRotation;
57
- }
58
-
59
- /* add the spike from the rank 1 update to w. */
60
- w += v[n-1] * u;
61
-
62
- /* eliminate the spike. */
63
- *sing = false;
64
- for (j = 0; j < n-1; ++j) {
65
- if (w[j] != 0.) {
66
- /* determine a givens rotation which eliminates the */
67
- /* j-th element of the spike. */
68
- givens.makeGivens(-s(j,j), w[j]);
69
-
70
- /* apply the transformation to s and reduce the spike in w. */
71
- for (i = j; i < m; ++i) {
72
- temp = givens.c() * s(j,i) + givens.s() * w[i];
73
- w[i] = -givens.s() * s(j,i) + givens.c() * w[i];
74
- s(j,i) = temp;
75
- }
76
-
77
- /* store the information necessary to recover the */
78
- /* givens rotation. */
79
- w_givens[j] = givens;
80
- } else
81
- v_givens[j] = IdentityRotation;
82
-
83
- /* test for zero diagonal elements in the output s. */
84
- if (s(j,j) == 0.) {
85
- *sing = true;
86
- }
87
- }
88
- /* move w back into the last column of the output s. */
89
- s(n-1,n-1) = w[n-1];
90
-
91
- if (s(j,j) == 0.) {
92
- *sing = true;
93
- }
94
- return;
95
- }
96
-
97
- } // end namespace internal
98
-
99
- } // end namespace Eigen
@@ -1,49 +0,0 @@
1
- namespace Eigen {
2
-
3
- namespace internal {
4
-
5
- template <typename Scalar>
6
- void rwupdt(
7
- Matrix< Scalar, Dynamic, Dynamic > &r,
8
- const Matrix< Scalar, Dynamic, 1> &w,
9
- Matrix< Scalar, Dynamic, 1> &b,
10
- Scalar alpha)
11
- {
12
- typedef DenseIndex Index;
13
-
14
- const Index n = r.cols();
15
- eigen_assert(r.rows()>=n);
16
- std::vector<JacobiRotation<Scalar> > givens(n);
17
-
18
- /* Local variables */
19
- Scalar temp, rowj;
20
-
21
- /* Function Body */
22
- for (Index j = 0; j < n; ++j) {
23
- rowj = w[j];
24
-
25
- /* apply the previous transformations to */
26
- /* r(i,j), i=0,1,...,j-1, and to w(j). */
27
- for (Index i = 0; i < j; ++i) {
28
- temp = givens[i].c() * r(i,j) + givens[i].s() * rowj;
29
- rowj = -givens[i].s() * r(i,j) + givens[i].c() * rowj;
30
- r(i,j) = temp;
31
- }
32
-
33
- /* determine a givens rotation which eliminates w(j). */
34
- givens[j].makeGivens(-r(j,j), rowj);
35
-
36
- if (rowj == 0.)
37
- continue; // givens[j] is identity
38
-
39
- /* apply the current transformation to r(j,j), b(j), and alpha. */
40
- r(j,j) = givens[j].c() * r(j,j) + givens[j].s() * rowj;
41
- temp = givens[j].c() * b[j] + givens[j].s() * alpha;
42
- alpha = -givens[j].s() * b[j] + givens[j].c() * alpha;
43
- b[j] = temp;
44
- }
45
- }
46
-
47
- } // end namespace internal
48
-
49
- } // end namespace Eigen
@@ -1,130 +0,0 @@
1
- // -*- coding: utf-8
2
- // vim: set fileencoding=utf-8
3
-
4
- // This file is part of Eigen, a lightweight C++ template library
5
- // for linear algebra.
6
- //
7
- // Copyright (C) 2009 Thomas Capricelli <orzel@freehackers.org>
8
- //
9
- // This Source Code Form is subject to the terms of the Mozilla
10
- // Public License v. 2.0. If a copy of the MPL was not distributed
11
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
12
-
13
- #ifndef EIGEN_NUMERICAL_DIFF_H
14
- #define EIGEN_NUMERICAL_DIFF_H
15
-
16
- namespace Eigen {
17
-
18
- enum NumericalDiffMode {
19
- Forward,
20
- Central
21
- };
22
-
23
-
24
- /**
25
- * This class allows you to add a method df() to your functor, which will
26
- * use numerical differentiation to compute an approximate of the
27
- * derivative for the functor. Of course, if you have an analytical form
28
- * for the derivative, you should rather implement df() by yourself.
29
- *
30
- * More information on
31
- * http://en.wikipedia.org/wiki/Numerical_differentiation
32
- *
33
- * Currently only "Forward" and "Central" scheme are implemented.
34
- */
35
- template<typename _Functor, NumericalDiffMode mode=Forward>
36
- class NumericalDiff : public _Functor
37
- {
38
- public:
39
- typedef _Functor Functor;
40
- typedef typename Functor::Scalar Scalar;
41
- typedef typename Functor::InputType InputType;
42
- typedef typename Functor::ValueType ValueType;
43
- typedef typename Functor::JacobianType JacobianType;
44
-
45
- NumericalDiff(Scalar _epsfcn=0.) : Functor(), epsfcn(_epsfcn) {}
46
- NumericalDiff(const Functor& f, Scalar _epsfcn=0.) : Functor(f), epsfcn(_epsfcn) {}
47
-
48
- // forward constructors
49
- template<typename T0>
50
- NumericalDiff(const T0& a0) : Functor(a0), epsfcn(0) {}
51
- template<typename T0, typename T1>
52
- NumericalDiff(const T0& a0, const T1& a1) : Functor(a0, a1), epsfcn(0) {}
53
- template<typename T0, typename T1, typename T2>
54
- NumericalDiff(const T0& a0, const T1& a1, const T2& a2) : Functor(a0, a1, a2), epsfcn(0) {}
55
-
56
- enum {
57
- InputsAtCompileTime = Functor::InputsAtCompileTime,
58
- ValuesAtCompileTime = Functor::ValuesAtCompileTime
59
- };
60
-
61
- /**
62
- * return the number of evaluation of functor
63
- */
64
- int df(const InputType& _x, JacobianType &jac) const
65
- {
66
- using std::sqrt;
67
- using std::abs;
68
- /* Local variables */
69
- Scalar h;
70
- int nfev=0;
71
- const typename InputType::Index n = _x.size();
72
- const Scalar eps = sqrt(((std::max)(epsfcn,NumTraits<Scalar>::epsilon() )));
73
- ValueType val1, val2;
74
- InputType x = _x;
75
- // TODO : we should do this only if the size is not already known
76
- val1.resize(Functor::values());
77
- val2.resize(Functor::values());
78
-
79
- // initialization
80
- switch(mode) {
81
- case Forward:
82
- // compute f(x)
83
- Functor::operator()(x, val1); nfev++;
84
- break;
85
- case Central:
86
- // do nothing
87
- break;
88
- default:
89
- eigen_assert(false);
90
- };
91
-
92
- // Function Body
93
- for (int j = 0; j < n; ++j) {
94
- h = eps * abs(x[j]);
95
- if (h == 0.) {
96
- h = eps;
97
- }
98
- switch(mode) {
99
- case Forward:
100
- x[j] += h;
101
- Functor::operator()(x, val2);
102
- nfev++;
103
- x[j] = _x[j];
104
- jac.col(j) = (val2-val1)/h;
105
- break;
106
- case Central:
107
- x[j] += h;
108
- Functor::operator()(x, val2); nfev++;
109
- x[j] -= 2*h;
110
- Functor::operator()(x, val1); nfev++;
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- x[j] = _x[j];
112
- jac.col(j) = (val2-val1)/(2*h);
113
- break;
114
- default:
115
- eigen_assert(false);
116
- };
117
- }
118
- return nfev;
119
- }
120
- private:
121
- Scalar epsfcn;
122
-
123
- NumericalDiff& operator=(const NumericalDiff&);
124
- };
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-
126
- } // end namespace Eigen
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-
128
- //vim: ai ts=4 sts=4 et sw=4
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- #endif // EIGEN_NUMERICAL_DIFF_H
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-
@@ -1,280 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
3
- //
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- // Copyright (C) 2010 Manuel Yguel <manuel.yguel@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_COMPANION_H
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- #define EIGEN_COMPANION_H
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-
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- // This file requires the user to include
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- // * Eigen/Core
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- // * Eigen/src/PolynomialSolver.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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- #ifndef EIGEN_PARSED_BY_DOXYGEN
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-
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- template<int Size>
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- struct decrement_if_fixed_size
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- {
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- enum {
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- ret = (Size == Dynamic) ? Dynamic : Size-1 };
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- };
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-
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- #endif
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-
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- template< typename _Scalar, int _Deg >
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- class companion
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- {
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- public:
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- EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_Deg==Dynamic ? Dynamic : _Deg)
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-
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- enum {
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- Deg = _Deg,
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- Deg_1=decrement_if_fixed_size<Deg>::ret
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- };
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-
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- typedef _Scalar Scalar;
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- typedef typename NumTraits<Scalar>::Real RealScalar;
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- typedef Matrix<Scalar, Deg, 1> RightColumn;
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- //typedef DiagonalMatrix< Scalar, Deg_1, Deg_1 > BottomLeftDiagonal;
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- typedef Matrix<Scalar, Deg_1, 1> BottomLeftDiagonal;
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-
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- typedef Matrix<Scalar, Deg, Deg> DenseCompanionMatrixType;
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- typedef Matrix< Scalar, _Deg, Deg_1 > LeftBlock;
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- typedef Matrix< Scalar, Deg_1, Deg_1 > BottomLeftBlock;
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- typedef Matrix< Scalar, 1, Deg_1 > LeftBlockFirstRow;
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-
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- typedef DenseIndex Index;
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-
56
- public:
57
- EIGEN_STRONG_INLINE const _Scalar operator()(Index row, Index col ) const
58
- {
59
- if( m_bl_diag.rows() > col )
60
- {
61
- if( 0 < row ){ return m_bl_diag[col]; }
62
- else{ return 0; }
63
- }
64
- else{ return m_monic[row]; }
65
- }
66
-
67
- public:
68
- template<typename VectorType>
69
- void setPolynomial( const VectorType& poly )
70
- {
71
- const Index deg = poly.size()-1;
72
- m_monic = -poly.head(deg)/poly[deg];
73
- m_bl_diag.setOnes(deg-1);
74
- }
75
-
76
- template<typename VectorType>
77
- companion( const VectorType& poly ){
78
- setPolynomial( poly ); }
79
-
80
- public:
81
- DenseCompanionMatrixType denseMatrix() const
82
- {
83
- const Index deg = m_monic.size();
84
- const Index deg_1 = deg-1;
85
- DenseCompanionMatrixType companMat(deg,deg);
86
- companMat <<
87
- ( LeftBlock(deg,deg_1)
88
- << LeftBlockFirstRow::Zero(1,deg_1),
89
- BottomLeftBlock::Identity(deg-1,deg-1)*m_bl_diag.asDiagonal() ).finished()
90
- , m_monic;
91
- return companMat;
92
- }
93
-
94
-
95
-
96
- protected:
97
- /** Helper function for the balancing algorithm.
98
- * \returns true if the row and the column, having colNorm and rowNorm
99
- * as norms, are balanced, false otherwise.
100
- * colB and rowB are respectively the multipliers for
101
- * the column and the row in order to balance them.
102
- * */
103
- bool balanced( RealScalar colNorm, RealScalar rowNorm,
104
- bool& isBalanced, RealScalar& colB, RealScalar& rowB );
105
-
106
- /** Helper function for the balancing algorithm.
107
- * \returns true if the row and the column, having colNorm and rowNorm
108
- * as norms, are balanced, false otherwise.
109
- * colB and rowB are respectively the multipliers for
110
- * the column and the row in order to balance them.
111
- * */
112
- bool balancedR( RealScalar colNorm, RealScalar rowNorm,
113
- bool& isBalanced, RealScalar& colB, RealScalar& rowB );
114
-
115
- public:
116
- /**
117
- * Balancing algorithm from B. N. PARLETT and C. REINSCH (1969)
118
- * "Balancing a matrix for calculation of eigenvalues and eigenvectors"
119
- * adapted to the case of companion matrices.
120
- * A matrix with non zero row and non zero column is balanced
121
- * for a certain norm if the i-th row and the i-th column
122
- * have same norm for all i.
123
- */
124
- void balance();
125
-
126
- protected:
127
- RightColumn m_monic;
128
- BottomLeftDiagonal m_bl_diag;
129
- };
130
-
131
-
132
-
133
- template< typename _Scalar, int _Deg >
134
- inline
135
- bool companion<_Scalar,_Deg>::balanced( RealScalar colNorm, RealScalar rowNorm,
136
- bool& isBalanced, RealScalar& colB, RealScalar& rowB )
137
- {
138
- if( RealScalar(0) == colNorm || RealScalar(0) == rowNorm
139
- || !(numext::isfinite)(colNorm) || !(numext::isfinite)(rowNorm)){
140
- return true;
141
- }
142
- else
143
- {
144
- //To find the balancing coefficients, if the radix is 2,
145
- //one finds \f$ \sigma \f$ such that
146
- // \f$ 2^{2\sigma-1} < rowNorm / colNorm \le 2^{2\sigma+1} \f$
147
- // then the balancing coefficient for the row is \f$ 1/2^{\sigma} \f$
148
- // and the balancing coefficient for the column is \f$ 2^{\sigma} \f$
149
- const RealScalar radix = RealScalar(2);
150
- const RealScalar radix2 = RealScalar(4);
151
-
152
- rowB = rowNorm / radix;
153
- colB = RealScalar(1);
154
- const RealScalar s = colNorm + rowNorm;
155
-
156
- // Find sigma s.t. rowNorm / 2 <= 2^(2*sigma) * colNorm
157
- RealScalar scout = colNorm;
158
- while (scout < rowB)
159
- {
160
- colB *= radix;
161
- scout *= radix2;
162
- }
163
-
164
- // We now have an upper-bound for sigma, try to lower it.
165
- // Find sigma s.t. 2^(2*sigma) * colNorm / 2 < rowNorm
166
- scout = colNorm * (colB / radix) * colB; // Avoid overflow.
167
- while (scout >= rowNorm)
168
- {
169
- colB /= radix;
170
- scout /= radix2;
171
- }
172
-
173
- // This line is used to avoid insubstantial balancing.
174
- if ((rowNorm + radix * scout) < RealScalar(0.95) * s * colB)
175
- {
176
- isBalanced = false;
177
- rowB = RealScalar(1) / colB;
178
- return false;
179
- }
180
- else
181
- {
182
- return true;
183
- }
184
- }
185
- }
186
-
187
- template< typename _Scalar, int _Deg >
188
- inline
189
- bool companion<_Scalar,_Deg>::balancedR( RealScalar colNorm, RealScalar rowNorm,
190
- bool& isBalanced, RealScalar& colB, RealScalar& rowB )
191
- {
192
- if( RealScalar(0) == colNorm || RealScalar(0) == rowNorm ){ return true; }
193
- else
194
- {
195
- /**
196
- * Set the norm of the column and the row to the geometric mean
197
- * of the row and column norm
198
- */
199
- const RealScalar q = colNorm/rowNorm;
200
- if( !isApprox( q, _Scalar(1) ) )
201
- {
202
- rowB = sqrt( colNorm/rowNorm );
203
- colB = RealScalar(1)/rowB;
204
-
205
- isBalanced = false;
206
- return false;
207
- }
208
- else{
209
- return true; }
210
- }
211
- }
212
-
213
-
214
- template< typename _Scalar, int _Deg >
215
- void companion<_Scalar,_Deg>::balance()
216
- {
217
- using std::abs;
218
- EIGEN_STATIC_ASSERT( Deg == Dynamic || 1 < Deg, YOU_MADE_A_PROGRAMMING_MISTAKE );
219
- const Index deg = m_monic.size();
220
- const Index deg_1 = deg-1;
221
-
222
- bool hasConverged=false;
223
- while( !hasConverged )
224
- {
225
- hasConverged = true;
226
- RealScalar colNorm,rowNorm;
227
- RealScalar colB,rowB;
228
-
229
- //First row, first column excluding the diagonal
230
- //==============================================
231
- colNorm = abs(m_bl_diag[0]);
232
- rowNorm = abs(m_monic[0]);
233
-
234
- //Compute balancing of the row and the column
235
- if( !balanced( colNorm, rowNorm, hasConverged, colB, rowB ) )
236
- {
237
- m_bl_diag[0] *= colB;
238
- m_monic[0] *= rowB;
239
- }
240
-
241
- //Middle rows and columns excluding the diagonal
242
- //==============================================
243
- for( Index i=1; i<deg_1; ++i )
244
- {
245
- // column norm, excluding the diagonal
246
- colNorm = abs(m_bl_diag[i]);
247
-
248
- // row norm, excluding the diagonal
249
- rowNorm = abs(m_bl_diag[i-1]) + abs(m_monic[i]);
250
-
251
- //Compute balancing of the row and the column
252
- if( !balanced( colNorm, rowNorm, hasConverged, colB, rowB ) )
253
- {
254
- m_bl_diag[i] *= colB;
255
- m_bl_diag[i-1] *= rowB;
256
- m_monic[i] *= rowB;
257
- }
258
- }
259
-
260
- //Last row, last column excluding the diagonal
261
- //============================================
262
- const Index ebl = m_bl_diag.size()-1;
263
- VectorBlock<RightColumn,Deg_1> headMonic( m_monic, 0, deg_1 );
264
- colNorm = headMonic.array().abs().sum();
265
- rowNorm = abs( m_bl_diag[ebl] );
266
-
267
- //Compute balancing of the row and the column
268
- if( !balanced( colNorm, rowNorm, hasConverged, colB, rowB ) )
269
- {
270
- headMonic *= colB;
271
- m_bl_diag[ebl] *= rowB;
272
- }
273
- }
274
- }
275
-
276
- } // end namespace internal
277
-
278
- } // end namespace Eigen
279
-
280
- #endif // EIGEN_COMPANION_H