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
@@ -1,305 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2011 Kolja Brix <brix@igpm.rwth-aachen.de>
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- // Copyright (C) 2011 Andreas Platen <andiplaten@gmx.de>
6
- // Copyright (C) 2012 Chen-Pang He <jdh8@ms63.hinet.net>
7
- //
8
- // This Source Code Form is subject to the terms of the Mozilla
9
- // Public License v. 2.0. If a copy of the MPL was not distributed
10
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
11
-
12
- #ifndef KRONECKER_TENSOR_PRODUCT_H
13
- #define KRONECKER_TENSOR_PRODUCT_H
14
-
15
- namespace Eigen {
16
-
17
- /*!
18
- * \ingroup KroneckerProduct_Module
19
- *
20
- * \brief The base class of dense and sparse Kronecker product.
21
- *
22
- * \tparam Derived is the derived type.
23
- */
24
- template<typename Derived>
25
- class KroneckerProductBase : public ReturnByValue<Derived>
26
- {
27
- private:
28
- typedef typename internal::traits<Derived> Traits;
29
- typedef typename Traits::Scalar Scalar;
30
-
31
- protected:
32
- typedef typename Traits::Lhs Lhs;
33
- typedef typename Traits::Rhs Rhs;
34
-
35
- public:
36
- /*! \brief Constructor. */
37
- KroneckerProductBase(const Lhs& A, const Rhs& B)
38
- : m_A(A), m_B(B)
39
- {}
40
-
41
- inline Index rows() const { return m_A.rows() * m_B.rows(); }
42
- inline Index cols() const { return m_A.cols() * m_B.cols(); }
43
-
44
- /*!
45
- * This overrides ReturnByValue::coeff because this function is
46
- * efficient enough.
47
- */
48
- Scalar coeff(Index row, Index col) const
49
- {
50
- return m_A.coeff(row / m_B.rows(), col / m_B.cols()) *
51
- m_B.coeff(row % m_B.rows(), col % m_B.cols());
52
- }
53
-
54
- /*!
55
- * This overrides ReturnByValue::coeff because this function is
56
- * efficient enough.
57
- */
58
- Scalar coeff(Index i) const
59
- {
60
- EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived);
61
- return m_A.coeff(i / m_A.size()) * m_B.coeff(i % m_A.size());
62
- }
63
-
64
- protected:
65
- typename Lhs::Nested m_A;
66
- typename Rhs::Nested m_B;
67
- };
68
-
69
- /*!
70
- * \ingroup KroneckerProduct_Module
71
- *
72
- * \brief Kronecker tensor product helper class for dense matrices
73
- *
74
- * This class is the return value of kroneckerProduct(MatrixBase,
75
- * MatrixBase). Use the function rather than construct this class
76
- * directly to avoid specifying template prarameters.
77
- *
78
- * \tparam Lhs Type of the left-hand side, a matrix expression.
79
- * \tparam Rhs Type of the rignt-hand side, a matrix expression.
80
- */
81
- template<typename Lhs, typename Rhs>
82
- class KroneckerProduct : public KroneckerProductBase<KroneckerProduct<Lhs,Rhs> >
83
- {
84
- private:
85
- typedef KroneckerProductBase<KroneckerProduct> Base;
86
- using Base::m_A;
87
- using Base::m_B;
88
-
89
- public:
90
- /*! \brief Constructor. */
91
- KroneckerProduct(const Lhs& A, const Rhs& B)
92
- : Base(A, B)
93
- {}
94
-
95
- /*! \brief Evaluate the Kronecker tensor product. */
96
- template<typename Dest> void evalTo(Dest& dst) const;
97
- };
98
-
99
- /*!
100
- * \ingroup KroneckerProduct_Module
101
- *
102
- * \brief Kronecker tensor product helper class for sparse matrices
103
- *
104
- * If at least one of the operands is a sparse matrix expression,
105
- * then this class is returned and evaluates into a sparse matrix.
106
- *
107
- * This class is the return value of kroneckerProduct(EigenBase,
108
- * EigenBase). Use the function rather than construct this class
109
- * directly to avoid specifying template prarameters.
110
- *
111
- * \tparam Lhs Type of the left-hand side, a matrix expression.
112
- * \tparam Rhs Type of the rignt-hand side, a matrix expression.
113
- */
114
- template<typename Lhs, typename Rhs>
115
- class KroneckerProductSparse : public KroneckerProductBase<KroneckerProductSparse<Lhs,Rhs> >
116
- {
117
- private:
118
- typedef KroneckerProductBase<KroneckerProductSparse> Base;
119
- using Base::m_A;
120
- using Base::m_B;
121
-
122
- public:
123
- /*! \brief Constructor. */
124
- KroneckerProductSparse(const Lhs& A, const Rhs& B)
125
- : Base(A, B)
126
- {}
127
-
128
- /*! \brief Evaluate the Kronecker tensor product. */
129
- template<typename Dest> void evalTo(Dest& dst) const;
130
- };
131
-
132
- template<typename Lhs, typename Rhs>
133
- template<typename Dest>
134
- void KroneckerProduct<Lhs,Rhs>::evalTo(Dest& dst) const
135
- {
136
- const int BlockRows = Rhs::RowsAtCompileTime,
137
- BlockCols = Rhs::ColsAtCompileTime;
138
- const Index Br = m_B.rows(),
139
- Bc = m_B.cols();
140
- for (Index i=0; i < m_A.rows(); ++i)
141
- for (Index j=0; j < m_A.cols(); ++j)
142
- Block<Dest,BlockRows,BlockCols>(dst,i*Br,j*Bc,Br,Bc) = m_A.coeff(i,j) * m_B;
143
- }
144
-
145
- template<typename Lhs, typename Rhs>
146
- template<typename Dest>
147
- void KroneckerProductSparse<Lhs,Rhs>::evalTo(Dest& dst) const
148
- {
149
- Index Br = m_B.rows(), Bc = m_B.cols();
150
- dst.resize(this->rows(), this->cols());
151
- dst.resizeNonZeros(0);
152
-
153
- // 1 - evaluate the operands if needed:
154
- typedef typename internal::nested_eval<Lhs,Dynamic>::type Lhs1;
155
- typedef typename internal::remove_all<Lhs1>::type Lhs1Cleaned;
156
- const Lhs1 lhs1(m_A);
157
- typedef typename internal::nested_eval<Rhs,Dynamic>::type Rhs1;
158
- typedef typename internal::remove_all<Rhs1>::type Rhs1Cleaned;
159
- const Rhs1 rhs1(m_B);
160
-
161
- // 2 - construct respective iterators
162
- typedef Eigen::InnerIterator<Lhs1Cleaned> LhsInnerIterator;
163
- typedef Eigen::InnerIterator<Rhs1Cleaned> RhsInnerIterator;
164
-
165
- // compute number of non-zeros per innervectors of dst
166
- {
167
- // TODO VectorXi is not necessarily big enough!
168
- VectorXi nnzA = VectorXi::Zero(Dest::IsRowMajor ? m_A.rows() : m_A.cols());
169
- for (Index kA=0; kA < m_A.outerSize(); ++kA)
170
- for (LhsInnerIterator itA(lhs1,kA); itA; ++itA)
171
- nnzA(Dest::IsRowMajor ? itA.row() : itA.col())++;
172
-
173
- VectorXi nnzB = VectorXi::Zero(Dest::IsRowMajor ? m_B.rows() : m_B.cols());
174
- for (Index kB=0; kB < m_B.outerSize(); ++kB)
175
- for (RhsInnerIterator itB(rhs1,kB); itB; ++itB)
176
- nnzB(Dest::IsRowMajor ? itB.row() : itB.col())++;
177
-
178
- Matrix<int,Dynamic,Dynamic,ColMajor> nnzAB = nnzB * nnzA.transpose();
179
- dst.reserve(VectorXi::Map(nnzAB.data(), nnzAB.size()));
180
- }
181
-
182
- for (Index kA=0; kA < m_A.outerSize(); ++kA)
183
- {
184
- for (Index kB=0; kB < m_B.outerSize(); ++kB)
185
- {
186
- for (LhsInnerIterator itA(lhs1,kA); itA; ++itA)
187
- {
188
- for (RhsInnerIterator itB(rhs1,kB); itB; ++itB)
189
- {
190
- Index i = itA.row() * Br + itB.row(),
191
- j = itA.col() * Bc + itB.col();
192
- dst.insert(i,j) = itA.value() * itB.value();
193
- }
194
- }
195
- }
196
- }
197
- }
198
-
199
- namespace internal {
200
-
201
- template<typename _Lhs, typename _Rhs>
202
- struct traits<KroneckerProduct<_Lhs,_Rhs> >
203
- {
204
- typedef typename remove_all<_Lhs>::type Lhs;
205
- typedef typename remove_all<_Rhs>::type Rhs;
206
- typedef typename ScalarBinaryOpTraits<typename Lhs::Scalar, typename Rhs::Scalar>::ReturnType Scalar;
207
- typedef typename promote_index_type<typename Lhs::StorageIndex, typename Rhs::StorageIndex>::type StorageIndex;
208
-
209
- enum {
210
- Rows = size_at_compile_time<traits<Lhs>::RowsAtCompileTime, traits<Rhs>::RowsAtCompileTime>::ret,
211
- Cols = size_at_compile_time<traits<Lhs>::ColsAtCompileTime, traits<Rhs>::ColsAtCompileTime>::ret,
212
- MaxRows = size_at_compile_time<traits<Lhs>::MaxRowsAtCompileTime, traits<Rhs>::MaxRowsAtCompileTime>::ret,
213
- MaxCols = size_at_compile_time<traits<Lhs>::MaxColsAtCompileTime, traits<Rhs>::MaxColsAtCompileTime>::ret
214
- };
215
-
216
- typedef Matrix<Scalar,Rows,Cols> ReturnType;
217
- };
218
-
219
- template<typename _Lhs, typename _Rhs>
220
- struct traits<KroneckerProductSparse<_Lhs,_Rhs> >
221
- {
222
- typedef MatrixXpr XprKind;
223
- typedef typename remove_all<_Lhs>::type Lhs;
224
- typedef typename remove_all<_Rhs>::type Rhs;
225
- typedef typename ScalarBinaryOpTraits<typename Lhs::Scalar, typename Rhs::Scalar>::ReturnType Scalar;
226
- typedef typename cwise_promote_storage_type<typename traits<Lhs>::StorageKind, typename traits<Rhs>::StorageKind, scalar_product_op<typename Lhs::Scalar, typename Rhs::Scalar> >::ret StorageKind;
227
- typedef typename promote_index_type<typename Lhs::StorageIndex, typename Rhs::StorageIndex>::type StorageIndex;
228
-
229
- enum {
230
- LhsFlags = Lhs::Flags,
231
- RhsFlags = Rhs::Flags,
232
-
233
- RowsAtCompileTime = size_at_compile_time<traits<Lhs>::RowsAtCompileTime, traits<Rhs>::RowsAtCompileTime>::ret,
234
- ColsAtCompileTime = size_at_compile_time<traits<Lhs>::ColsAtCompileTime, traits<Rhs>::ColsAtCompileTime>::ret,
235
- MaxRowsAtCompileTime = size_at_compile_time<traits<Lhs>::MaxRowsAtCompileTime, traits<Rhs>::MaxRowsAtCompileTime>::ret,
236
- MaxColsAtCompileTime = size_at_compile_time<traits<Lhs>::MaxColsAtCompileTime, traits<Rhs>::MaxColsAtCompileTime>::ret,
237
-
238
- EvalToRowMajor = (int(LhsFlags) & int(RhsFlags) & RowMajorBit),
239
- RemovedBits = ~(EvalToRowMajor ? 0 : RowMajorBit),
240
-
241
- Flags = ((int(LhsFlags) | int(RhsFlags)) & HereditaryBits & RemovedBits)
242
- | EvalBeforeNestingBit,
243
- CoeffReadCost = HugeCost
244
- };
245
-
246
- typedef SparseMatrix<Scalar, 0, StorageIndex> ReturnType;
247
- };
248
-
249
- } // end namespace internal
250
-
251
- /*!
252
- * \ingroup KroneckerProduct_Module
253
- *
254
- * Computes Kronecker tensor product of two dense matrices
255
- *
256
- * \warning If you want to replace a matrix by its Kronecker product
257
- * with some matrix, do \b NOT do this:
258
- * \code
259
- * A = kroneckerProduct(A,B); // bug!!! caused by aliasing effect
260
- * \endcode
261
- * instead, use eval() to work around this:
262
- * \code
263
- * A = kroneckerProduct(A,B).eval();
264
- * \endcode
265
- *
266
- * \param a Dense matrix a
267
- * \param b Dense matrix b
268
- * \return Kronecker tensor product of a and b
269
- */
270
- template<typename A, typename B>
271
- KroneckerProduct<A,B> kroneckerProduct(const MatrixBase<A>& a, const MatrixBase<B>& b)
272
- {
273
- return KroneckerProduct<A, B>(a.derived(), b.derived());
274
- }
275
-
276
- /*!
277
- * \ingroup KroneckerProduct_Module
278
- *
279
- * Computes Kronecker tensor product of two matrices, at least one of
280
- * which is sparse
281
- *
282
- * \warning If you want to replace a matrix by its Kronecker product
283
- * with some matrix, do \b NOT do this:
284
- * \code
285
- * A = kroneckerProduct(A,B); // bug!!! caused by aliasing effect
286
- * \endcode
287
- * instead, use eval() to work around this:
288
- * \code
289
- * A = kroneckerProduct(A,B).eval();
290
- * \endcode
291
- *
292
- * \param a Dense/sparse matrix a
293
- * \param b Dense/sparse matrix b
294
- * \return Kronecker tensor product of a and b, stored in a sparse
295
- * matrix
296
- */
297
- template<typename A, typename B>
298
- KroneckerProductSparse<A,B> kroneckerProduct(const EigenBase<A>& a, const EigenBase<B>& b)
299
- {
300
- return KroneckerProductSparse<A,B>(a.derived(), b.derived());
301
- }
302
-
303
- } // end namespace Eigen
304
-
305
- #endif // KRONECKER_TENSOR_PRODUCT_H
@@ -1,84 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // This code initially comes from MINPACK whose original authors are:
5
- // Copyright Jorge More - Argonne National Laboratory
6
- // Copyright Burt Garbow - Argonne National Laboratory
7
- // Copyright Ken Hillstrom - Argonne National Laboratory
8
- //
9
- // This Source Code Form is subject to the terms of the Minpack license
10
- // (a BSD-like license) described in the campaigned CopyrightMINPACK.txt file.
11
-
12
- #ifndef EIGEN_LMCOVAR_H
13
- #define EIGEN_LMCOVAR_H
14
-
15
- namespace Eigen {
16
-
17
- namespace internal {
18
-
19
- template <typename Scalar>
20
- void covar(
21
- Matrix< Scalar, Dynamic, Dynamic > &r,
22
- const VectorXi& ipvt,
23
- Scalar tol = std::sqrt(NumTraits<Scalar>::epsilon()) )
24
- {
25
- using std::abs;
26
- /* Local variables */
27
- Index i, j, k, l, ii, jj;
28
- bool sing;
29
- Scalar temp;
30
-
31
- /* Function Body */
32
- const Index n = r.cols();
33
- const Scalar tolr = tol * abs(r(0,0));
34
- Matrix< Scalar, Dynamic, 1 > wa(n);
35
- eigen_assert(ipvt.size()==n);
36
-
37
- /* form the inverse of r in the full upper triangle of r. */
38
- l = -1;
39
- for (k = 0; k < n; ++k)
40
- if (abs(r(k,k)) > tolr) {
41
- r(k,k) = 1. / r(k,k);
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- for (j = 0; j <= k-1; ++j) {
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- temp = r(k,k) * r(j,k);
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- r(j,k) = 0.;
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- r.col(k).head(j+1) -= r.col(j).head(j+1) * temp;
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- }
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- l = k;
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- }
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-
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- /* form the full upper triangle of the inverse of (r transpose)*r */
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- /* in the full upper triangle of r. */
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- for (k = 0; k <= l; ++k) {
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- for (j = 0; j <= k-1; ++j)
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- r.col(j).head(j+1) += r.col(k).head(j+1) * r(j,k);
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- r.col(k).head(k+1) *= r(k,k);
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- }
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-
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- /* form the full lower triangle of the covariance matrix */
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- /* in the strict lower triangle of r and in wa. */
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- for (j = 0; j < n; ++j) {
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- jj = ipvt[j];
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- sing = j > l;
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- for (i = 0; i <= j; ++i) {
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- if (sing)
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- r(i,j) = 0.;
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- ii = ipvt[i];
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- if (ii > jj)
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- r(ii,jj) = r(i,j);
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- if (ii < jj)
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- r(jj,ii) = r(i,j);
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- }
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- wa[jj] = r(j,j);
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- }
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-
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- /* symmetrize the covariance matrix in r. */
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- r.topLeftCorner(n,n).template triangularView<StrictlyUpper>() = r.topLeftCorner(n,n).transpose();
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- r.diagonal() = wa;
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- }
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-
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- } // end namespace internal
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-
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- } // end namespace Eigen
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-
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- #endif // EIGEN_LMCOVAR_H
@@ -1,202 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2009 Thomas Capricelli <orzel@freehackers.org>
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- //
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- // This code initially comes from MINPACK whose original authors are:
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- // Copyright Jorge More - Argonne National Laboratory
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- // Copyright Burt Garbow - Argonne National Laboratory
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- // Copyright Ken Hillstrom - Argonne National Laboratory
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- //
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- // This Source Code Form is subject to the terms of the Minpack license
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- // (a BSD-like license) described in the campaigned CopyrightMINPACK.txt file.
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-
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- #ifndef EIGEN_LMONESTEP_H
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- #define EIGEN_LMONESTEP_H
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-
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- namespace Eigen {
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-
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- template<typename FunctorType>
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- LevenbergMarquardtSpace::Status
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- LevenbergMarquardt<FunctorType>::minimizeOneStep(FVectorType &x)
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- {
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- using std::abs;
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- using std::sqrt;
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- RealScalar temp, temp1,temp2;
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- RealScalar ratio;
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- RealScalar pnorm, xnorm, fnorm1, actred, dirder, prered;
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- eigen_assert(x.size()==n); // check the caller is not cheating us
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-
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- temp = 0.0; xnorm = 0.0;
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- /* calculate the jacobian matrix. */
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- Index df_ret = m_functor.df(x, m_fjac);
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- if (df_ret<0)
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- return LevenbergMarquardtSpace::UserAsked;
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- if (df_ret>0)
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- // numerical diff, we evaluated the function df_ret times
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- m_nfev += df_ret;
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- else m_njev++;
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-
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- /* compute the qr factorization of the jacobian. */
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- for (int j = 0; j < x.size(); ++j)
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- m_wa2(j) = m_fjac.col(j).blueNorm();
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- QRSolver qrfac(m_fjac);
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- if(qrfac.info() != Success) {
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- m_info = NumericalIssue;
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- return LevenbergMarquardtSpace::ImproperInputParameters;
47
- }
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- // Make a copy of the first factor with the associated permutation
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- m_rfactor = qrfac.matrixR();
50
- m_permutation = (qrfac.colsPermutation());
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-
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- /* on the first iteration and if external scaling is not used, scale according */
53
- /* to the norms of the columns of the initial jacobian. */
54
- if (m_iter == 1) {
55
- if (!m_useExternalScaling)
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- for (Index j = 0; j < n; ++j)
57
- m_diag[j] = (m_wa2[j]==0.)? 1. : m_wa2[j];
58
-
59
- /* on the first iteration, calculate the norm of the scaled x */
60
- /* and initialize the step bound m_delta. */
61
- xnorm = m_diag.cwiseProduct(x).stableNorm();
62
- m_delta = m_factor * xnorm;
63
- if (m_delta == 0.)
64
- m_delta = m_factor;
65
- }
66
-
67
- /* form (q transpose)*m_fvec and store the first n components in */
68
- /* m_qtf. */
69
- m_wa4 = m_fvec;
70
- m_wa4 = qrfac.matrixQ().adjoint() * m_fvec;
71
- m_qtf = m_wa4.head(n);
72
-
73
- /* compute the norm of the scaled gradient. */
74
- m_gnorm = 0.;
75
- if (m_fnorm != 0.)
76
- for (Index j = 0; j < n; ++j)
77
- if (m_wa2[m_permutation.indices()[j]] != 0.)
78
- m_gnorm = (std::max)(m_gnorm, abs( m_rfactor.col(j).head(j+1).dot(m_qtf.head(j+1)/m_fnorm) / m_wa2[m_permutation.indices()[j]]));
79
-
80
- /* test for convergence of the gradient norm. */
81
- if (m_gnorm <= m_gtol) {
82
- m_info = Success;
83
- return LevenbergMarquardtSpace::CosinusTooSmall;
84
- }
85
-
86
- /* rescale if necessary. */
87
- if (!m_useExternalScaling)
88
- m_diag = m_diag.cwiseMax(m_wa2);
89
-
90
- do {
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- /* determine the levenberg-marquardt parameter. */
92
- internal::lmpar2(qrfac, m_diag, m_qtf, m_delta, m_par, m_wa1);
93
-
94
- /* store the direction p and x + p. calculate the norm of p. */
95
- m_wa1 = -m_wa1;
96
- m_wa2 = x + m_wa1;
97
- pnorm = m_diag.cwiseProduct(m_wa1).stableNorm();
98
-
99
- /* on the first iteration, adjust the initial step bound. */
100
- if (m_iter == 1)
101
- m_delta = (std::min)(m_delta,pnorm);
102
-
103
- /* evaluate the function at x + p and calculate its norm. */
104
- if ( m_functor(m_wa2, m_wa4) < 0)
105
- return LevenbergMarquardtSpace::UserAsked;
106
- ++m_nfev;
107
- fnorm1 = m_wa4.stableNorm();
108
-
109
- /* compute the scaled actual reduction. */
110
- actred = -1.;
111
- if (Scalar(.1) * fnorm1 < m_fnorm)
112
- actred = 1. - numext::abs2(fnorm1 / m_fnorm);
113
-
114
- /* compute the scaled predicted reduction and */
115
- /* the scaled directional derivative. */
116
- m_wa3 = m_rfactor.template triangularView<Upper>() * (m_permutation.inverse() *m_wa1);
117
- temp1 = numext::abs2(m_wa3.stableNorm() / m_fnorm);
118
- temp2 = numext::abs2(sqrt(m_par) * pnorm / m_fnorm);
119
- prered = temp1 + temp2 / Scalar(.5);
120
- dirder = -(temp1 + temp2);
121
-
122
- /* compute the ratio of the actual to the predicted */
123
- /* reduction. */
124
- ratio = 0.;
125
- if (prered != 0.)
126
- ratio = actred / prered;
127
-
128
- /* update the step bound. */
129
- if (ratio <= Scalar(.25)) {
130
- if (actred >= 0.)
131
- temp = RealScalar(.5);
132
- if (actred < 0.)
133
- temp = RealScalar(.5) * dirder / (dirder + RealScalar(.5) * actred);
134
- if (RealScalar(.1) * fnorm1 >= m_fnorm || temp < RealScalar(.1))
135
- temp = Scalar(.1);
136
- /* Computing MIN */
137
- m_delta = temp * (std::min)(m_delta, pnorm / RealScalar(.1));
138
- m_par /= temp;
139
- } else if (!(m_par != 0. && ratio < RealScalar(.75))) {
140
- m_delta = pnorm / RealScalar(.5);
141
- m_par = RealScalar(.5) * m_par;
142
- }
143
-
144
- /* test for successful iteration. */
145
- if (ratio >= RealScalar(1e-4)) {
146
- /* successful iteration. update x, m_fvec, and their norms. */
147
- x = m_wa2;
148
- m_wa2 = m_diag.cwiseProduct(x);
149
- m_fvec = m_wa4;
150
- xnorm = m_wa2.stableNorm();
151
- m_fnorm = fnorm1;
152
- ++m_iter;
153
- }
154
-
155
- /* tests for convergence. */
156
- if (abs(actred) <= m_ftol && prered <= m_ftol && Scalar(.5) * ratio <= 1. && m_delta <= m_xtol * xnorm)
157
- {
158
- m_info = Success;
159
- return LevenbergMarquardtSpace::RelativeErrorAndReductionTooSmall;
160
- }
161
- if (abs(actred) <= m_ftol && prered <= m_ftol && Scalar(.5) * ratio <= 1.)
162
- {
163
- m_info = Success;
164
- return LevenbergMarquardtSpace::RelativeReductionTooSmall;
165
- }
166
- if (m_delta <= m_xtol * xnorm)
167
- {
168
- m_info = Success;
169
- return LevenbergMarquardtSpace::RelativeErrorTooSmall;
170
- }
171
-
172
- /* tests for termination and stringent tolerances. */
173
- if (m_nfev >= m_maxfev)
174
- {
175
- m_info = NoConvergence;
176
- return LevenbergMarquardtSpace::TooManyFunctionEvaluation;
177
- }
178
- if (abs(actred) <= NumTraits<Scalar>::epsilon() && prered <= NumTraits<Scalar>::epsilon() && Scalar(.5) * ratio <= 1.)
179
- {
180
- m_info = Success;
181
- return LevenbergMarquardtSpace::FtolTooSmall;
182
- }
183
- if (m_delta <= NumTraits<Scalar>::epsilon() * xnorm)
184
- {
185
- m_info = Success;
186
- return LevenbergMarquardtSpace::XtolTooSmall;
187
- }
188
- if (m_gnorm <= NumTraits<Scalar>::epsilon())
189
- {
190
- m_info = Success;
191
- return LevenbergMarquardtSpace::GtolTooSmall;
192
- }
193
-
194
- } while (ratio < Scalar(1e-4));
195
-
196
- return LevenbergMarquardtSpace::Running;
197
- }
198
-
199
-
200
- } // end namespace Eigen
201
-
202
- #endif // EIGEN_LMONESTEP_H