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
@@ -1,657 +0,0 @@
1
- // -*- coding: utf-8
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- // vim: set fileencoding=utf-8
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-
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
6
- //
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- // Copyright (C) 2009 Thomas Capricelli <orzel@freehackers.org>
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- //
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- // 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
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
12
-
13
- #ifndef EIGEN_LEVENBERGMARQUARDT__H
14
- #define EIGEN_LEVENBERGMARQUARDT__H
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-
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- namespace Eigen {
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-
18
- namespace LevenbergMarquardtSpace {
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- enum Status {
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- NotStarted = -2,
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- Running = -1,
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- ImproperInputParameters = 0,
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- RelativeReductionTooSmall = 1,
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- RelativeErrorTooSmall = 2,
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- RelativeErrorAndReductionTooSmall = 3,
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- CosinusTooSmall = 4,
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- TooManyFunctionEvaluation = 5,
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- FtolTooSmall = 6,
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- XtolTooSmall = 7,
30
- GtolTooSmall = 8,
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- UserAsked = 9
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- };
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- }
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-
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-
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-
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- /**
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- * \ingroup NonLinearOptimization_Module
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- * \brief Performs non linear optimization over a non-linear function,
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- * using a variant of the Levenberg Marquardt algorithm.
41
- *
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- * Check wikipedia for more information.
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- * http://en.wikipedia.org/wiki/Levenberg%E2%80%93Marquardt_algorithm
44
- */
45
- template<typename FunctorType, typename Scalar=double>
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- class LevenbergMarquardt
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- {
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- static Scalar sqrt_epsilon()
49
- {
50
- using std::sqrt;
51
- return sqrt(NumTraits<Scalar>::epsilon());
52
- }
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-
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- public:
55
- LevenbergMarquardt(FunctorType &_functor)
56
- : functor(_functor) { nfev = njev = iter = 0; fnorm = gnorm = 0.; useExternalScaling=false; }
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-
58
- typedef DenseIndex Index;
59
-
60
- struct Parameters {
61
- Parameters()
62
- : factor(Scalar(100.))
63
- , maxfev(400)
64
- , ftol(sqrt_epsilon())
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- , xtol(sqrt_epsilon())
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- , gtol(Scalar(0.))
67
- , epsfcn(Scalar(0.)) {}
68
- Scalar factor;
69
- Index maxfev; // maximum number of function evaluation
70
- Scalar ftol;
71
- Scalar xtol;
72
- Scalar gtol;
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- Scalar epsfcn;
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- };
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-
76
- typedef Matrix< Scalar, Dynamic, 1 > FVectorType;
77
- typedef Matrix< Scalar, Dynamic, Dynamic > JacobianType;
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-
79
- LevenbergMarquardtSpace::Status lmder1(
80
- FVectorType &x,
81
- const Scalar tol = sqrt_epsilon()
82
- );
83
-
84
- LevenbergMarquardtSpace::Status minimize(FVectorType &x);
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- LevenbergMarquardtSpace::Status minimizeInit(FVectorType &x);
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- LevenbergMarquardtSpace::Status minimizeOneStep(FVectorType &x);
87
-
88
- static LevenbergMarquardtSpace::Status lmdif1(
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- FunctorType &functor,
90
- FVectorType &x,
91
- Index *nfev,
92
- const Scalar tol = sqrt_epsilon()
93
- );
94
-
95
- LevenbergMarquardtSpace::Status lmstr1(
96
- FVectorType &x,
97
- const Scalar tol = sqrt_epsilon()
98
- );
99
-
100
- LevenbergMarquardtSpace::Status minimizeOptimumStorage(FVectorType &x);
101
- LevenbergMarquardtSpace::Status minimizeOptimumStorageInit(FVectorType &x);
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- LevenbergMarquardtSpace::Status minimizeOptimumStorageOneStep(FVectorType &x);
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-
104
- void resetParameters(void) { parameters = Parameters(); }
105
-
106
- Parameters parameters;
107
- FVectorType fvec, qtf, diag;
108
- JacobianType fjac;
109
- PermutationMatrix<Dynamic,Dynamic> permutation;
110
- Index nfev;
111
- Index njev;
112
- Index iter;
113
- Scalar fnorm, gnorm;
114
- bool useExternalScaling;
115
-
116
- Scalar lm_param(void) { return par; }
117
- private:
118
-
119
- FunctorType &functor;
120
- Index n;
121
- Index m;
122
- FVectorType wa1, wa2, wa3, wa4;
123
-
124
- Scalar par, sum;
125
- Scalar temp, temp1, temp2;
126
- Scalar delta;
127
- Scalar ratio;
128
- Scalar pnorm, xnorm, fnorm1, actred, dirder, prered;
129
-
130
- LevenbergMarquardt& operator=(const LevenbergMarquardt&);
131
- };
132
-
133
- template<typename FunctorType, typename Scalar>
134
- LevenbergMarquardtSpace::Status
135
- LevenbergMarquardt<FunctorType,Scalar>::lmder1(
136
- FVectorType &x,
137
- const Scalar tol
138
- )
139
- {
140
- n = x.size();
141
- m = functor.values();
142
-
143
- /* check the input parameters for errors. */
144
- if (n <= 0 || m < n || tol < 0.)
145
- return LevenbergMarquardtSpace::ImproperInputParameters;
146
-
147
- resetParameters();
148
- parameters.ftol = tol;
149
- parameters.xtol = tol;
150
- parameters.maxfev = 100*(n+1);
151
-
152
- return minimize(x);
153
- }
154
-
155
-
156
- template<typename FunctorType, typename Scalar>
157
- LevenbergMarquardtSpace::Status
158
- LevenbergMarquardt<FunctorType,Scalar>::minimize(FVectorType &x)
159
- {
160
- LevenbergMarquardtSpace::Status status = minimizeInit(x);
161
- if (status==LevenbergMarquardtSpace::ImproperInputParameters)
162
- return status;
163
- do {
164
- status = minimizeOneStep(x);
165
- } while (status==LevenbergMarquardtSpace::Running);
166
- return status;
167
- }
168
-
169
- template<typename FunctorType, typename Scalar>
170
- LevenbergMarquardtSpace::Status
171
- LevenbergMarquardt<FunctorType,Scalar>::minimizeInit(FVectorType &x)
172
- {
173
- n = x.size();
174
- m = functor.values();
175
-
176
- wa1.resize(n); wa2.resize(n); wa3.resize(n);
177
- wa4.resize(m);
178
- fvec.resize(m);
179
- fjac.resize(m, n);
180
- if (!useExternalScaling)
181
- diag.resize(n);
182
- eigen_assert( (!useExternalScaling || diag.size()==n) && "When useExternalScaling is set, the caller must provide a valid 'diag'");
183
- qtf.resize(n);
184
-
185
- /* Function Body */
186
- nfev = 0;
187
- njev = 0;
188
-
189
- /* check the input parameters for errors. */
190
- if (n <= 0 || m < n || parameters.ftol < 0. || parameters.xtol < 0. || parameters.gtol < 0. || parameters.maxfev <= 0 || parameters.factor <= 0.)
191
- return LevenbergMarquardtSpace::ImproperInputParameters;
192
-
193
- if (useExternalScaling)
194
- for (Index j = 0; j < n; ++j)
195
- if (diag[j] <= 0.)
196
- return LevenbergMarquardtSpace::ImproperInputParameters;
197
-
198
- /* evaluate the function at the starting point */
199
- /* and calculate its norm. */
200
- nfev = 1;
201
- if ( functor(x, fvec) < 0)
202
- return LevenbergMarquardtSpace::UserAsked;
203
- fnorm = fvec.stableNorm();
204
-
205
- /* initialize levenberg-marquardt parameter and iteration counter. */
206
- par = 0.;
207
- iter = 1;
208
-
209
- return LevenbergMarquardtSpace::NotStarted;
210
- }
211
-
212
- template<typename FunctorType, typename Scalar>
213
- LevenbergMarquardtSpace::Status
214
- LevenbergMarquardt<FunctorType,Scalar>::minimizeOneStep(FVectorType &x)
215
- {
216
- using std::abs;
217
- using std::sqrt;
218
-
219
- eigen_assert(x.size()==n); // check the caller is not cheating us
220
-
221
- /* calculate the jacobian matrix. */
222
- Index df_ret = functor.df(x, fjac);
223
- if (df_ret<0)
224
- return LevenbergMarquardtSpace::UserAsked;
225
- if (df_ret>0)
226
- // numerical diff, we evaluated the function df_ret times
227
- nfev += df_ret;
228
- else njev++;
229
-
230
- /* compute the qr factorization of the jacobian. */
231
- wa2 = fjac.colwise().blueNorm();
232
- ColPivHouseholderQR<JacobianType> qrfac(fjac);
233
- fjac = qrfac.matrixQR();
234
- permutation = qrfac.colsPermutation();
235
-
236
- /* on the first iteration and if external scaling is not used, scale according */
237
- /* to the norms of the columns of the initial jacobian. */
238
- if (iter == 1) {
239
- if (!useExternalScaling)
240
- for (Index j = 0; j < n; ++j)
241
- diag[j] = (wa2[j]==0.)? 1. : wa2[j];
242
-
243
- /* on the first iteration, calculate the norm of the scaled x */
244
- /* and initialize the step bound delta. */
245
- xnorm = diag.cwiseProduct(x).stableNorm();
246
- delta = parameters.factor * xnorm;
247
- if (delta == 0.)
248
- delta = parameters.factor;
249
- }
250
-
251
- /* form (q transpose)*fvec and store the first n components in */
252
- /* qtf. */
253
- wa4 = fvec;
254
- wa4.applyOnTheLeft(qrfac.householderQ().adjoint());
255
- qtf = wa4.head(n);
256
-
257
- /* compute the norm of the scaled gradient. */
258
- gnorm = 0.;
259
- if (fnorm != 0.)
260
- for (Index j = 0; j < n; ++j)
261
- if (wa2[permutation.indices()[j]] != 0.)
262
- gnorm = (std::max)(gnorm, abs( fjac.col(j).head(j+1).dot(qtf.head(j+1)/fnorm) / wa2[permutation.indices()[j]]));
263
-
264
- /* test for convergence of the gradient norm. */
265
- if (gnorm <= parameters.gtol)
266
- return LevenbergMarquardtSpace::CosinusTooSmall;
267
-
268
- /* rescale if necessary. */
269
- if (!useExternalScaling)
270
- diag = diag.cwiseMax(wa2);
271
-
272
- do {
273
-
274
- /* determine the levenberg-marquardt parameter. */
275
- internal::lmpar2<Scalar>(qrfac, diag, qtf, delta, par, wa1);
276
-
277
- /* store the direction p and x + p. calculate the norm of p. */
278
- wa1 = -wa1;
279
- wa2 = x + wa1;
280
- pnorm = diag.cwiseProduct(wa1).stableNorm();
281
-
282
- /* on the first iteration, adjust the initial step bound. */
283
- if (iter == 1)
284
- delta = (std::min)(delta,pnorm);
285
-
286
- /* evaluate the function at x + p and calculate its norm. */
287
- if ( functor(wa2, wa4) < 0)
288
- return LevenbergMarquardtSpace::UserAsked;
289
- ++nfev;
290
- fnorm1 = wa4.stableNorm();
291
-
292
- /* compute the scaled actual reduction. */
293
- actred = -1.;
294
- if (Scalar(.1) * fnorm1 < fnorm)
295
- actred = 1. - numext::abs2(fnorm1 / fnorm);
296
-
297
- /* compute the scaled predicted reduction and */
298
- /* the scaled directional derivative. */
299
- wa3 = fjac.template triangularView<Upper>() * (qrfac.colsPermutation().inverse() *wa1);
300
- temp1 = numext::abs2(wa3.stableNorm() / fnorm);
301
- temp2 = numext::abs2(sqrt(par) * pnorm / fnorm);
302
- prered = temp1 + temp2 / Scalar(.5);
303
- dirder = -(temp1 + temp2);
304
-
305
- /* compute the ratio of the actual to the predicted */
306
- /* reduction. */
307
- ratio = 0.;
308
- if (prered != 0.)
309
- ratio = actred / prered;
310
-
311
- /* update the step bound. */
312
- if (ratio <= Scalar(.25)) {
313
- if (actred >= 0.)
314
- temp = Scalar(.5);
315
- if (actred < 0.)
316
- temp = Scalar(.5) * dirder / (dirder + Scalar(.5) * actred);
317
- if (Scalar(.1) * fnorm1 >= fnorm || temp < Scalar(.1))
318
- temp = Scalar(.1);
319
- /* Computing MIN */
320
- delta = temp * (std::min)(delta, pnorm / Scalar(.1));
321
- par /= temp;
322
- } else if (!(par != 0. && ratio < Scalar(.75))) {
323
- delta = pnorm / Scalar(.5);
324
- par = Scalar(.5) * par;
325
- }
326
-
327
- /* test for successful iteration. */
328
- if (ratio >= Scalar(1e-4)) {
329
- /* successful iteration. update x, fvec, and their norms. */
330
- x = wa2;
331
- wa2 = diag.cwiseProduct(x);
332
- fvec = wa4;
333
- xnorm = wa2.stableNorm();
334
- fnorm = fnorm1;
335
- ++iter;
336
- }
337
-
338
- /* tests for convergence. */
339
- if (abs(actred) <= parameters.ftol && prered <= parameters.ftol && Scalar(.5) * ratio <= 1. && delta <= parameters.xtol * xnorm)
340
- return LevenbergMarquardtSpace::RelativeErrorAndReductionTooSmall;
341
- if (abs(actred) <= parameters.ftol && prered <= parameters.ftol && Scalar(.5) * ratio <= 1.)
342
- return LevenbergMarquardtSpace::RelativeReductionTooSmall;
343
- if (delta <= parameters.xtol * xnorm)
344
- return LevenbergMarquardtSpace::RelativeErrorTooSmall;
345
-
346
- /* tests for termination and stringent tolerances. */
347
- if (nfev >= parameters.maxfev)
348
- return LevenbergMarquardtSpace::TooManyFunctionEvaluation;
349
- if (abs(actred) <= NumTraits<Scalar>::epsilon() && prered <= NumTraits<Scalar>::epsilon() && Scalar(.5) * ratio <= 1.)
350
- return LevenbergMarquardtSpace::FtolTooSmall;
351
- if (delta <= NumTraits<Scalar>::epsilon() * xnorm)
352
- return LevenbergMarquardtSpace::XtolTooSmall;
353
- if (gnorm <= NumTraits<Scalar>::epsilon())
354
- return LevenbergMarquardtSpace::GtolTooSmall;
355
-
356
- } while (ratio < Scalar(1e-4));
357
-
358
- return LevenbergMarquardtSpace::Running;
359
- }
360
-
361
- template<typename FunctorType, typename Scalar>
362
- LevenbergMarquardtSpace::Status
363
- LevenbergMarquardt<FunctorType,Scalar>::lmstr1(
364
- FVectorType &x,
365
- const Scalar tol
366
- )
367
- {
368
- n = x.size();
369
- m = functor.values();
370
-
371
- /* check the input parameters for errors. */
372
- if (n <= 0 || m < n || tol < 0.)
373
- return LevenbergMarquardtSpace::ImproperInputParameters;
374
-
375
- resetParameters();
376
- parameters.ftol = tol;
377
- parameters.xtol = tol;
378
- parameters.maxfev = 100*(n+1);
379
-
380
- return minimizeOptimumStorage(x);
381
- }
382
-
383
- template<typename FunctorType, typename Scalar>
384
- LevenbergMarquardtSpace::Status
385
- LevenbergMarquardt<FunctorType,Scalar>::minimizeOptimumStorageInit(FVectorType &x)
386
- {
387
- n = x.size();
388
- m = functor.values();
389
-
390
- wa1.resize(n); wa2.resize(n); wa3.resize(n);
391
- wa4.resize(m);
392
- fvec.resize(m);
393
- // Only R is stored in fjac. Q is only used to compute 'qtf', which is
394
- // Q.transpose()*rhs. qtf will be updated using givens rotation,
395
- // instead of storing them in Q.
396
- // The purpose it to only use a nxn matrix, instead of mxn here, so
397
- // that we can handle cases where m>>n :
398
- fjac.resize(n, n);
399
- if (!useExternalScaling)
400
- diag.resize(n);
401
- eigen_assert( (!useExternalScaling || diag.size()==n) && "When useExternalScaling is set, the caller must provide a valid 'diag'");
402
- qtf.resize(n);
403
-
404
- /* Function Body */
405
- nfev = 0;
406
- njev = 0;
407
-
408
- /* check the input parameters for errors. */
409
- if (n <= 0 || m < n || parameters.ftol < 0. || parameters.xtol < 0. || parameters.gtol < 0. || parameters.maxfev <= 0 || parameters.factor <= 0.)
410
- return LevenbergMarquardtSpace::ImproperInputParameters;
411
-
412
- if (useExternalScaling)
413
- for (Index j = 0; j < n; ++j)
414
- if (diag[j] <= 0.)
415
- return LevenbergMarquardtSpace::ImproperInputParameters;
416
-
417
- /* evaluate the function at the starting point */
418
- /* and calculate its norm. */
419
- nfev = 1;
420
- if ( functor(x, fvec) < 0)
421
- return LevenbergMarquardtSpace::UserAsked;
422
- fnorm = fvec.stableNorm();
423
-
424
- /* initialize levenberg-marquardt parameter and iteration counter. */
425
- par = 0.;
426
- iter = 1;
427
-
428
- return LevenbergMarquardtSpace::NotStarted;
429
- }
430
-
431
-
432
- template<typename FunctorType, typename Scalar>
433
- LevenbergMarquardtSpace::Status
434
- LevenbergMarquardt<FunctorType,Scalar>::minimizeOptimumStorageOneStep(FVectorType &x)
435
- {
436
- using std::abs;
437
- using std::sqrt;
438
-
439
- eigen_assert(x.size()==n); // check the caller is not cheating us
440
-
441
- Index i, j;
442
- bool sing;
443
-
444
- /* compute the qr factorization of the jacobian matrix */
445
- /* calculated one row at a time, while simultaneously */
446
- /* forming (q transpose)*fvec and storing the first */
447
- /* n components in qtf. */
448
- qtf.fill(0.);
449
- fjac.fill(0.);
450
- Index rownb = 2;
451
- for (i = 0; i < m; ++i) {
452
- if (functor.df(x, wa3, rownb) < 0) return LevenbergMarquardtSpace::UserAsked;
453
- internal::rwupdt<Scalar>(fjac, wa3, qtf, fvec[i]);
454
- ++rownb;
455
- }
456
- ++njev;
457
-
458
- /* if the jacobian is rank deficient, call qrfac to */
459
- /* reorder its columns and update the components of qtf. */
460
- sing = false;
461
- for (j = 0; j < n; ++j) {
462
- if (fjac(j,j) == 0.)
463
- sing = true;
464
- wa2[j] = fjac.col(j).head(j).stableNorm();
465
- }
466
- permutation.setIdentity(n);
467
- if (sing) {
468
- wa2 = fjac.colwise().blueNorm();
469
- // TODO We have no unit test covering this code path, do not modify
470
- // until it is carefully tested
471
- ColPivHouseholderQR<JacobianType> qrfac(fjac);
472
- fjac = qrfac.matrixQR();
473
- wa1 = fjac.diagonal();
474
- fjac.diagonal() = qrfac.hCoeffs();
475
- permutation = qrfac.colsPermutation();
476
- // TODO : avoid this:
477
- for(Index ii=0; ii< fjac.cols(); ii++) fjac.col(ii).segment(ii+1, fjac.rows()-ii-1) *= fjac(ii,ii); // rescale vectors
478
-
479
- for (j = 0; j < n; ++j) {
480
- if (fjac(j,j) != 0.) {
481
- sum = 0.;
482
- for (i = j; i < n; ++i)
483
- sum += fjac(i,j) * qtf[i];
484
- temp = -sum / fjac(j,j);
485
- for (i = j; i < n; ++i)
486
- qtf[i] += fjac(i,j) * temp;
487
- }
488
- fjac(j,j) = wa1[j];
489
- }
490
- }
491
-
492
- /* on the first iteration and if external scaling is not used, scale according */
493
- /* to the norms of the columns of the initial jacobian. */
494
- if (iter == 1) {
495
- if (!useExternalScaling)
496
- for (j = 0; j < n; ++j)
497
- diag[j] = (wa2[j]==0.)? 1. : wa2[j];
498
-
499
- /* on the first iteration, calculate the norm of the scaled x */
500
- /* and initialize the step bound delta. */
501
- xnorm = diag.cwiseProduct(x).stableNorm();
502
- delta = parameters.factor * xnorm;
503
- if (delta == 0.)
504
- delta = parameters.factor;
505
- }
506
-
507
- /* compute the norm of the scaled gradient. */
508
- gnorm = 0.;
509
- if (fnorm != 0.)
510
- for (j = 0; j < n; ++j)
511
- if (wa2[permutation.indices()[j]] != 0.)
512
- gnorm = (std::max)(gnorm, abs( fjac.col(j).head(j+1).dot(qtf.head(j+1)/fnorm) / wa2[permutation.indices()[j]]));
513
-
514
- /* test for convergence of the gradient norm. */
515
- if (gnorm <= parameters.gtol)
516
- return LevenbergMarquardtSpace::CosinusTooSmall;
517
-
518
- /* rescale if necessary. */
519
- if (!useExternalScaling)
520
- diag = diag.cwiseMax(wa2);
521
-
522
- do {
523
-
524
- /* determine the levenberg-marquardt parameter. */
525
- internal::lmpar<Scalar>(fjac, permutation.indices(), diag, qtf, delta, par, wa1);
526
-
527
- /* store the direction p and x + p. calculate the norm of p. */
528
- wa1 = -wa1;
529
- wa2 = x + wa1;
530
- pnorm = diag.cwiseProduct(wa1).stableNorm();
531
-
532
- /* on the first iteration, adjust the initial step bound. */
533
- if (iter == 1)
534
- delta = (std::min)(delta,pnorm);
535
-
536
- /* evaluate the function at x + p and calculate its norm. */
537
- if ( functor(wa2, wa4) < 0)
538
- return LevenbergMarquardtSpace::UserAsked;
539
- ++nfev;
540
- fnorm1 = wa4.stableNorm();
541
-
542
- /* compute the scaled actual reduction. */
543
- actred = -1.;
544
- if (Scalar(.1) * fnorm1 < fnorm)
545
- actred = 1. - numext::abs2(fnorm1 / fnorm);
546
-
547
- /* compute the scaled predicted reduction and */
548
- /* the scaled directional derivative. */
549
- wa3 = fjac.topLeftCorner(n,n).template triangularView<Upper>() * (permutation.inverse() * wa1);
550
- temp1 = numext::abs2(wa3.stableNorm() / fnorm);
551
- temp2 = numext::abs2(sqrt(par) * pnorm / fnorm);
552
- prered = temp1 + temp2 / Scalar(.5);
553
- dirder = -(temp1 + temp2);
554
-
555
- /* compute the ratio of the actual to the predicted */
556
- /* reduction. */
557
- ratio = 0.;
558
- if (prered != 0.)
559
- ratio = actred / prered;
560
-
561
- /* update the step bound. */
562
- if (ratio <= Scalar(.25)) {
563
- if (actred >= 0.)
564
- temp = Scalar(.5);
565
- if (actred < 0.)
566
- temp = Scalar(.5) * dirder / (dirder + Scalar(.5) * actred);
567
- if (Scalar(.1) * fnorm1 >= fnorm || temp < Scalar(.1))
568
- temp = Scalar(.1);
569
- /* Computing MIN */
570
- delta = temp * (std::min)(delta, pnorm / Scalar(.1));
571
- par /= temp;
572
- } else if (!(par != 0. && ratio < Scalar(.75))) {
573
- delta = pnorm / Scalar(.5);
574
- par = Scalar(.5) * par;
575
- }
576
-
577
- /* test for successful iteration. */
578
- if (ratio >= Scalar(1e-4)) {
579
- /* successful iteration. update x, fvec, and their norms. */
580
- x = wa2;
581
- wa2 = diag.cwiseProduct(x);
582
- fvec = wa4;
583
- xnorm = wa2.stableNorm();
584
- fnorm = fnorm1;
585
- ++iter;
586
- }
587
-
588
- /* tests for convergence. */
589
- if (abs(actred) <= parameters.ftol && prered <= parameters.ftol && Scalar(.5) * ratio <= 1. && delta <= parameters.xtol * xnorm)
590
- return LevenbergMarquardtSpace::RelativeErrorAndReductionTooSmall;
591
- if (abs(actred) <= parameters.ftol && prered <= parameters.ftol && Scalar(.5) * ratio <= 1.)
592
- return LevenbergMarquardtSpace::RelativeReductionTooSmall;
593
- if (delta <= parameters.xtol * xnorm)
594
- return LevenbergMarquardtSpace::RelativeErrorTooSmall;
595
-
596
- /* tests for termination and stringent tolerances. */
597
- if (nfev >= parameters.maxfev)
598
- return LevenbergMarquardtSpace::TooManyFunctionEvaluation;
599
- if (abs(actred) <= NumTraits<Scalar>::epsilon() && prered <= NumTraits<Scalar>::epsilon() && Scalar(.5) * ratio <= 1.)
600
- return LevenbergMarquardtSpace::FtolTooSmall;
601
- if (delta <= NumTraits<Scalar>::epsilon() * xnorm)
602
- return LevenbergMarquardtSpace::XtolTooSmall;
603
- if (gnorm <= NumTraits<Scalar>::epsilon())
604
- return LevenbergMarquardtSpace::GtolTooSmall;
605
-
606
- } while (ratio < Scalar(1e-4));
607
-
608
- return LevenbergMarquardtSpace::Running;
609
- }
610
-
611
- template<typename FunctorType, typename Scalar>
612
- LevenbergMarquardtSpace::Status
613
- LevenbergMarquardt<FunctorType,Scalar>::minimizeOptimumStorage(FVectorType &x)
614
- {
615
- LevenbergMarquardtSpace::Status status = minimizeOptimumStorageInit(x);
616
- if (status==LevenbergMarquardtSpace::ImproperInputParameters)
617
- return status;
618
- do {
619
- status = minimizeOptimumStorageOneStep(x);
620
- } while (status==LevenbergMarquardtSpace::Running);
621
- return status;
622
- }
623
-
624
- template<typename FunctorType, typename Scalar>
625
- LevenbergMarquardtSpace::Status
626
- LevenbergMarquardt<FunctorType,Scalar>::lmdif1(
627
- FunctorType &functor,
628
- FVectorType &x,
629
- Index *nfev,
630
- const Scalar tol
631
- )
632
- {
633
- Index n = x.size();
634
- Index m = functor.values();
635
-
636
- /* check the input parameters for errors. */
637
- if (n <= 0 || m < n || tol < 0.)
638
- return LevenbergMarquardtSpace::ImproperInputParameters;
639
-
640
- NumericalDiff<FunctorType> numDiff(functor);
641
- // embedded LevenbergMarquardt
642
- LevenbergMarquardt<NumericalDiff<FunctorType>, Scalar > lm(numDiff);
643
- lm.parameters.ftol = tol;
644
- lm.parameters.xtol = tol;
645
- lm.parameters.maxfev = 200*(n+1);
646
-
647
- LevenbergMarquardtSpace::Status info = LevenbergMarquardtSpace::Status(lm.minimize(x));
648
- if (nfev)
649
- * nfev = lm.nfev;
650
- return info;
651
- }
652
-
653
- } // end namespace Eigen
654
-
655
- #endif // EIGEN_LEVENBERGMARQUARDT__H
656
-
657
- //vim: ai ts=4 sts=4 et sw=4