sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-win_amd64.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
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  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  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
@@ -1,431 +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) 20010-2011 Hauke Heibel <hauke.heibel@gmail.com>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_SPLINE_FITTING_H
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- #define EIGEN_SPLINE_FITTING_H
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-
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- #include <algorithm>
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- #include <functional>
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- #include <numeric>
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- #include <vector>
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-
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- #include "SplineFwd.h"
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-
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- #include "../../../../Eigen/LU"
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- #include "../../../../Eigen/QR"
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-
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- namespace Eigen
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- {
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- /**
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- * \brief Computes knot averages.
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- * \ingroup Splines_Module
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- *
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- * The knots are computed as
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- * \f{align*}
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- * u_0 & = \hdots = u_p = 0 \\
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- * u_{m-p} & = \hdots = u_{m} = 1 \\
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- * u_{j+p} & = \frac{1}{p}\sum_{i=j}^{j+p-1}\bar{u}_i \quad\quad j=1,\hdots,n-p
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- * \f}
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- * where \f$p\f$ is the degree and \f$m+1\f$ the number knots
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- * of the desired interpolating spline.
37
- *
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- * \param[in] parameters The input parameters. During interpolation one for each data point.
39
- * \param[in] degree The spline degree which is used during the interpolation.
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- * \param[out] knots The output knot vector.
41
- *
42
- * \sa Les Piegl and Wayne Tiller, The NURBS book (2nd ed.), 1997, 9.2.1 Global Curve Interpolation to Point Data
43
- **/
44
- template <typename KnotVectorType>
45
- void KnotAveraging(const KnotVectorType& parameters, DenseIndex degree, KnotVectorType& knots)
46
- {
47
- knots.resize(parameters.size()+degree+1);
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-
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- for (DenseIndex j=1; j<parameters.size()-degree; ++j)
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- knots(j+degree) = parameters.segment(j,degree).mean();
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-
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- knots.segment(0,degree+1) = KnotVectorType::Zero(degree+1);
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- knots.segment(knots.size()-degree-1,degree+1) = KnotVectorType::Ones(degree+1);
54
- }
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-
56
- /**
57
- * \brief Computes knot averages when derivative constraints are present.
58
- * Note that this is a technical interpretation of the referenced article
59
- * since the algorithm contained therein is incorrect as written.
60
- * \ingroup Splines_Module
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- *
62
- * \param[in] parameters The parameters at which the interpolation B-Spline
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- * will intersect the given interpolation points. The parameters
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- * are assumed to be a non-decreasing sequence.
65
- * \param[in] degree The degree of the interpolating B-Spline. This must be
66
- * greater than zero.
67
- * \param[in] derivativeIndices The indices corresponding to parameters at
68
- * which there are derivative constraints. The indices are assumed
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- * to be a non-decreasing sequence.
70
- * \param[out] knots The calculated knot vector. These will be returned as a
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- * non-decreasing sequence
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- *
73
- * \sa Les A. Piegl, Khairan Rajab, Volha Smarodzinana. 2008.
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- * Curve interpolation with directional constraints for engineering design.
75
- * Engineering with Computers
76
- **/
77
- template <typename KnotVectorType, typename ParameterVectorType, typename IndexArray>
78
- void KnotAveragingWithDerivatives(const ParameterVectorType& parameters,
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- const unsigned int degree,
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- const IndexArray& derivativeIndices,
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- KnotVectorType& knots)
82
- {
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- typedef typename ParameterVectorType::Scalar Scalar;
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-
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- DenseIndex numParameters = parameters.size();
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- DenseIndex numDerivatives = derivativeIndices.size();
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-
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- if (numDerivatives < 1)
89
- {
90
- KnotAveraging(parameters, degree, knots);
91
- return;
92
- }
93
-
94
- DenseIndex startIndex;
95
- DenseIndex endIndex;
96
-
97
- DenseIndex numInternalDerivatives = numDerivatives;
98
-
99
- if (derivativeIndices[0] == 0)
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- {
101
- startIndex = 0;
102
- --numInternalDerivatives;
103
- }
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- else
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- {
106
- startIndex = 1;
107
- }
108
- if (derivativeIndices[numDerivatives - 1] == numParameters - 1)
109
- {
110
- endIndex = numParameters - degree;
111
- --numInternalDerivatives;
112
- }
113
- else
114
- {
115
- endIndex = numParameters - degree - 1;
116
- }
117
-
118
- // There are (endIndex - startIndex + 1) knots obtained from the averaging
119
- // and 2 for the first and last parameters.
120
- DenseIndex numAverageKnots = endIndex - startIndex + 3;
121
- KnotVectorType averageKnots(numAverageKnots);
122
- averageKnots[0] = parameters[0];
123
-
124
- int newKnotIndex = 0;
125
- for (DenseIndex i = startIndex; i <= endIndex; ++i)
126
- averageKnots[++newKnotIndex] = parameters.segment(i, degree).mean();
127
- averageKnots[++newKnotIndex] = parameters[numParameters - 1];
128
-
129
- newKnotIndex = -1;
130
-
131
- ParameterVectorType temporaryParameters(numParameters + 1);
132
- KnotVectorType derivativeKnots(numInternalDerivatives);
133
- for (DenseIndex i = 0; i < numAverageKnots - 1; ++i)
134
- {
135
- temporaryParameters[0] = averageKnots[i];
136
- ParameterVectorType parameterIndices(numParameters);
137
- int temporaryParameterIndex = 1;
138
- for (DenseIndex j = 0; j < numParameters; ++j)
139
- {
140
- Scalar parameter = parameters[j];
141
- if (parameter >= averageKnots[i] && parameter < averageKnots[i + 1])
142
- {
143
- parameterIndices[temporaryParameterIndex] = j;
144
- temporaryParameters[temporaryParameterIndex++] = parameter;
145
- }
146
- }
147
- temporaryParameters[temporaryParameterIndex] = averageKnots[i + 1];
148
-
149
- for (int j = 0; j <= temporaryParameterIndex - 2; ++j)
150
- {
151
- for (DenseIndex k = 0; k < derivativeIndices.size(); ++k)
152
- {
153
- if (parameterIndices[j + 1] == derivativeIndices[k]
154
- && parameterIndices[j + 1] != 0
155
- && parameterIndices[j + 1] != numParameters - 1)
156
- {
157
- derivativeKnots[++newKnotIndex] = temporaryParameters.segment(j, 3).mean();
158
- break;
159
- }
160
- }
161
- }
162
- }
163
-
164
- KnotVectorType temporaryKnots(averageKnots.size() + derivativeKnots.size());
165
-
166
- std::merge(averageKnots.data(), averageKnots.data() + averageKnots.size(),
167
- derivativeKnots.data(), derivativeKnots.data() + derivativeKnots.size(),
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- temporaryKnots.data());
169
-
170
- // Number of knots (one for each point and derivative) plus spline order.
171
- DenseIndex numKnots = numParameters + numDerivatives + degree + 1;
172
- knots.resize(numKnots);
173
-
174
- knots.head(degree).fill(temporaryKnots[0]);
175
- knots.tail(degree).fill(temporaryKnots.template tail<1>()[0]);
176
- knots.segment(degree, temporaryKnots.size()) = temporaryKnots;
177
- }
178
-
179
- /**
180
- * \brief Computes chord length parameters which are required for spline interpolation.
181
- * \ingroup Splines_Module
182
- *
183
- * \param[in] pts The data points to which a spline should be fit.
184
- * \param[out] chord_lengths The resulting chord length vector.
185
- *
186
- * \sa Les Piegl and Wayne Tiller, The NURBS book (2nd ed.), 1997, 9.2.1 Global Curve Interpolation to Point Data
187
- **/
188
- template <typename PointArrayType, typename KnotVectorType>
189
- void ChordLengths(const PointArrayType& pts, KnotVectorType& chord_lengths)
190
- {
191
- typedef typename KnotVectorType::Scalar Scalar;
192
-
193
- const DenseIndex n = pts.cols();
194
-
195
- // 1. compute the column-wise norms
196
- chord_lengths.resize(pts.cols());
197
- chord_lengths[0] = 0;
198
- chord_lengths.rightCols(n-1) = (pts.array().leftCols(n-1) - pts.array().rightCols(n-1)).matrix().colwise().norm();
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-
200
- // 2. compute the partial sums
201
- std::partial_sum(chord_lengths.data(), chord_lengths.data()+n, chord_lengths.data());
202
-
203
- // 3. normalize the data
204
- chord_lengths /= chord_lengths(n-1);
205
- chord_lengths(n-1) = Scalar(1);
206
- }
207
-
208
- /**
209
- * \brief Spline fitting methods.
210
- * \ingroup Splines_Module
211
- **/
212
- template <typename SplineType>
213
- struct SplineFitting
214
- {
215
- typedef typename SplineType::KnotVectorType KnotVectorType;
216
- typedef typename SplineType::ParameterVectorType ParameterVectorType;
217
-
218
- /**
219
- * \brief Fits an interpolating Spline to the given data points.
220
- *
221
- * \param pts The points for which an interpolating spline will be computed.
222
- * \param degree The degree of the interpolating spline.
223
- *
224
- * \returns A spline interpolating the initially provided points.
225
- **/
226
- template <typename PointArrayType>
227
- static SplineType Interpolate(const PointArrayType& pts, DenseIndex degree);
228
-
229
- /**
230
- * \brief Fits an interpolating Spline to the given data points.
231
- *
232
- * \param pts The points for which an interpolating spline will be computed.
233
- * \param degree The degree of the interpolating spline.
234
- * \param knot_parameters The knot parameters for the interpolation.
235
- *
236
- * \returns A spline interpolating the initially provided points.
237
- **/
238
- template <typename PointArrayType>
239
- static SplineType Interpolate(const PointArrayType& pts, DenseIndex degree, const KnotVectorType& knot_parameters);
240
-
241
- /**
242
- * \brief Fits an interpolating spline to the given data points and
243
- * derivatives.
244
- *
245
- * \param points The points for which an interpolating spline will be computed.
246
- * \param derivatives The desired derivatives of the interpolating spline at interpolation
247
- * points.
248
- * \param derivativeIndices An array indicating which point each derivative belongs to. This
249
- * must be the same size as @a derivatives.
250
- * \param degree The degree of the interpolating spline.
251
- *
252
- * \returns A spline interpolating @a points with @a derivatives at those points.
253
- *
254
- * \sa Les A. Piegl, Khairan Rajab, Volha Smarodzinana. 2008.
255
- * Curve interpolation with directional constraints for engineering design.
256
- * Engineering with Computers
257
- **/
258
- template <typename PointArrayType, typename IndexArray>
259
- static SplineType InterpolateWithDerivatives(const PointArrayType& points,
260
- const PointArrayType& derivatives,
261
- const IndexArray& derivativeIndices,
262
- const unsigned int degree);
263
-
264
- /**
265
- * \brief Fits an interpolating spline to the given data points and derivatives.
266
- *
267
- * \param points The points for which an interpolating spline will be computed.
268
- * \param derivatives The desired derivatives of the interpolating spline at interpolation points.
269
- * \param derivativeIndices An array indicating which point each derivative belongs to. This
270
- * must be the same size as @a derivatives.
271
- * \param degree The degree of the interpolating spline.
272
- * \param parameters The parameters corresponding to the interpolation points.
273
- *
274
- * \returns A spline interpolating @a points with @a derivatives at those points.
275
- *
276
- * \sa Les A. Piegl, Khairan Rajab, Volha Smarodzinana. 2008.
277
- * Curve interpolation with directional constraints for engineering design.
278
- * Engineering with Computers
279
- */
280
- template <typename PointArrayType, typename IndexArray>
281
- static SplineType InterpolateWithDerivatives(const PointArrayType& points,
282
- const PointArrayType& derivatives,
283
- const IndexArray& derivativeIndices,
284
- const unsigned int degree,
285
- const ParameterVectorType& parameters);
286
- };
287
-
288
- template <typename SplineType>
289
- template <typename PointArrayType>
290
- SplineType SplineFitting<SplineType>::Interpolate(const PointArrayType& pts, DenseIndex degree, const KnotVectorType& knot_parameters)
291
- {
292
- typedef typename SplineType::KnotVectorType::Scalar Scalar;
293
- typedef typename SplineType::ControlPointVectorType ControlPointVectorType;
294
-
295
- typedef Matrix<Scalar,Dynamic,Dynamic> MatrixType;
296
-
297
- KnotVectorType knots;
298
- KnotAveraging(knot_parameters, degree, knots);
299
-
300
- DenseIndex n = pts.cols();
301
- MatrixType A = MatrixType::Zero(n,n);
302
- for (DenseIndex i=1; i<n-1; ++i)
303
- {
304
- const DenseIndex span = SplineType::Span(knot_parameters[i], degree, knots);
305
-
306
- // The segment call should somehow be told the spline order at compile time.
307
- A.row(i).segment(span-degree, degree+1) = SplineType::BasisFunctions(knot_parameters[i], degree, knots);
308
- }
309
- A(0,0) = 1.0;
310
- A(n-1,n-1) = 1.0;
311
-
312
- HouseholderQR<MatrixType> qr(A);
313
-
314
- // Here, we are creating a temporary due to an Eigen issue.
315
- ControlPointVectorType ctrls = qr.solve(MatrixType(pts.transpose())).transpose();
316
-
317
- return SplineType(knots, ctrls);
318
- }
319
-
320
- template <typename SplineType>
321
- template <typename PointArrayType>
322
- SplineType SplineFitting<SplineType>::Interpolate(const PointArrayType& pts, DenseIndex degree)
323
- {
324
- KnotVectorType chord_lengths; // knot parameters
325
- ChordLengths(pts, chord_lengths);
326
- return Interpolate(pts, degree, chord_lengths);
327
- }
328
-
329
- template <typename SplineType>
330
- template <typename PointArrayType, typename IndexArray>
331
- SplineType
332
- SplineFitting<SplineType>::InterpolateWithDerivatives(const PointArrayType& points,
333
- const PointArrayType& derivatives,
334
- const IndexArray& derivativeIndices,
335
- const unsigned int degree,
336
- const ParameterVectorType& parameters)
337
- {
338
- typedef typename SplineType::KnotVectorType::Scalar Scalar;
339
- typedef typename SplineType::ControlPointVectorType ControlPointVectorType;
340
-
341
- typedef Matrix<Scalar, Dynamic, Dynamic> MatrixType;
342
-
343
- const DenseIndex n = points.cols() + derivatives.cols();
344
-
345
- KnotVectorType knots;
346
-
347
- KnotAveragingWithDerivatives(parameters, degree, derivativeIndices, knots);
348
-
349
- // fill matrix
350
- MatrixType A = MatrixType::Zero(n, n);
351
-
352
- // Use these dimensions for quicker populating, then transpose for solving.
353
- MatrixType b(points.rows(), n);
354
-
355
- DenseIndex startRow;
356
- DenseIndex derivativeStart;
357
-
358
- // End derivatives.
359
- if (derivativeIndices[0] == 0)
360
- {
361
- A.template block<1, 2>(1, 0) << -1, 1;
362
-
363
- Scalar y = (knots(degree + 1) - knots(0)) / degree;
364
- b.col(1) = y*derivatives.col(0);
365
-
366
- startRow = 2;
367
- derivativeStart = 1;
368
- }
369
- else
370
- {
371
- startRow = 1;
372
- derivativeStart = 0;
373
- }
374
- if (derivativeIndices[derivatives.cols() - 1] == points.cols() - 1)
375
- {
376
- A.template block<1, 2>(n - 2, n - 2) << -1, 1;
377
-
378
- Scalar y = (knots(knots.size() - 1) - knots(knots.size() - (degree + 2))) / degree;
379
- b.col(b.cols() - 2) = y*derivatives.col(derivatives.cols() - 1);
380
- }
381
-
382
- DenseIndex row = startRow;
383
- DenseIndex derivativeIndex = derivativeStart;
384
- for (DenseIndex i = 1; i < parameters.size() - 1; ++i)
385
- {
386
- const DenseIndex span = SplineType::Span(parameters[i], degree, knots);
387
-
388
- if (derivativeIndex < derivativeIndices.size() && derivativeIndices[derivativeIndex] == i)
389
- {
390
- A.block(row, span - degree, 2, degree + 1)
391
- = SplineType::BasisFunctionDerivatives(parameters[i], 1, degree, knots);
392
-
393
- b.col(row++) = points.col(i);
394
- b.col(row++) = derivatives.col(derivativeIndex++);
395
- }
396
- else
397
- {
398
- A.row(row).segment(span - degree, degree + 1)
399
- = SplineType::BasisFunctions(parameters[i], degree, knots);
400
- b.col(row++) = points.col(i);
401
- }
402
- }
403
- b.col(0) = points.col(0);
404
- b.col(b.cols() - 1) = points.col(points.cols() - 1);
405
- A(0,0) = 1;
406
- A(n - 1, n - 1) = 1;
407
-
408
- // Solve
409
- FullPivLU<MatrixType> lu(A);
410
- ControlPointVectorType controlPoints = lu.solve(MatrixType(b.transpose())).transpose();
411
-
412
- SplineType spline(knots, controlPoints);
413
-
414
- return spline;
415
- }
416
-
417
- template <typename SplineType>
418
- template <typename PointArrayType, typename IndexArray>
419
- SplineType
420
- SplineFitting<SplineType>::InterpolateWithDerivatives(const PointArrayType& points,
421
- const PointArrayType& derivatives,
422
- const IndexArray& derivativeIndices,
423
- const unsigned int degree)
424
- {
425
- ParameterVectorType parameters;
426
- ChordLengths(points, parameters);
427
- return InterpolateWithDerivatives(points, derivatives, derivativeIndices, degree, parameters);
428
- }
429
- }
430
-
431
- #endif // EIGEN_SPLINE_FITTING_H
@@ -1,93 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 20010-2011 Hauke Heibel <hauke.heibel@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_SPLINES_FWD_H
11
- #define EIGEN_SPLINES_FWD_H
12
-
13
- #include "../../../../Eigen/Core"
14
-
15
- namespace Eigen
16
- {
17
- template <typename Scalar, int Dim, int Degree = Dynamic> class Spline;
18
-
19
- template < typename SplineType, int DerivativeOrder = Dynamic > struct SplineTraits {};
20
-
21
- /**
22
- * \ingroup Splines_Module
23
- * \brief Compile-time attributes of the Spline class for Dynamic degree.
24
- **/
25
- template <typename _Scalar, int _Dim, int _Degree>
26
- struct SplineTraits< Spline<_Scalar, _Dim, _Degree>, Dynamic >
27
- {
28
- typedef _Scalar Scalar; /*!< The spline curve's scalar type. */
29
- enum { Dimension = _Dim /*!< The spline curve's dimension. */ };
30
- enum { Degree = _Degree /*!< The spline curve's degree. */ };
31
-
32
- enum { OrderAtCompileTime = _Degree==Dynamic ? Dynamic : _Degree+1 /*!< The spline curve's order at compile-time. */ };
33
- enum { NumOfDerivativesAtCompileTime = OrderAtCompileTime /*!< The number of derivatives defined for the current spline. */ };
34
-
35
- enum { DerivativeMemoryLayout = Dimension==1 ? RowMajor : ColMajor /*!< The derivative type's memory layout. */ };
36
-
37
- /** \brief The data type used to store non-zero basis functions. */
38
- typedef Array<Scalar,1,OrderAtCompileTime> BasisVectorType;
39
-
40
- /** \brief The data type used to store the values of the basis function derivatives. */
41
- typedef Array<Scalar,Dynamic,Dynamic,RowMajor,NumOfDerivativesAtCompileTime,OrderAtCompileTime> BasisDerivativeType;
42
-
43
- /** \brief The data type used to store the spline's derivative values. */
44
- typedef Array<Scalar,Dimension,Dynamic,DerivativeMemoryLayout,Dimension,NumOfDerivativesAtCompileTime> DerivativeType;
45
-
46
- /** \brief The point type the spline is representing. */
47
- typedef Array<Scalar,Dimension,1> PointType;
48
-
49
- /** \brief The data type used to store knot vectors. */
50
- typedef Array<Scalar,1,Dynamic> KnotVectorType;
51
-
52
- /** \brief The data type used to store parameter vectors. */
53
- typedef Array<Scalar,1,Dynamic> ParameterVectorType;
54
-
55
- /** \brief The data type representing the spline's control points. */
56
- typedef Array<Scalar,Dimension,Dynamic> ControlPointVectorType;
57
- };
58
-
59
- /**
60
- * \ingroup Splines_Module
61
- * \brief Compile-time attributes of the Spline class for fixed degree.
62
- *
63
- * The traits class inherits all attributes from the SplineTraits of Dynamic degree.
64
- **/
65
- template < typename _Scalar, int _Dim, int _Degree, int _DerivativeOrder >
66
- struct SplineTraits< Spline<_Scalar, _Dim, _Degree>, _DerivativeOrder > : public SplineTraits< Spline<_Scalar, _Dim, _Degree> >
67
- {
68
- enum { OrderAtCompileTime = _Degree==Dynamic ? Dynamic : _Degree+1 /*!< The spline curve's order at compile-time. */ };
69
- enum { NumOfDerivativesAtCompileTime = _DerivativeOrder==Dynamic ? Dynamic : _DerivativeOrder+1 /*!< The number of derivatives defined for the current spline. */ };
70
-
71
- enum { DerivativeMemoryLayout = _Dim==1 ? RowMajor : ColMajor /*!< The derivative type's memory layout. */ };
72
-
73
- /** \brief The data type used to store the values of the basis function derivatives. */
74
- typedef Array<_Scalar,Dynamic,Dynamic,RowMajor,NumOfDerivativesAtCompileTime,OrderAtCompileTime> BasisDerivativeType;
75
-
76
- /** \brief The data type used to store the spline's derivative values. */
77
- typedef Array<_Scalar,_Dim,Dynamic,DerivativeMemoryLayout,_Dim,NumOfDerivativesAtCompileTime> DerivativeType;
78
- };
79
-
80
- /** \brief 2D float B-spline with dynamic degree. */
81
- typedef Spline<float,2> Spline2f;
82
-
83
- /** \brief 3D float B-spline with dynamic degree. */
84
- typedef Spline<float,3> Spline3f;
85
-
86
- /** \brief 2D double B-spline with dynamic degree. */
87
- typedef Spline<double,2> Spline2d;
88
-
89
- /** \brief 3D double B-spline with dynamic degree. */
90
- typedef Spline<double,3> Spline3d;
91
- }
92
-
93
- #endif // EIGEN_SPLINES_FWD_H
@@ -1,67 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2009-2011 Jitse Niesen <jitse@maths.leeds.ac.uk>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #include "main.h"
11
- #include <unsupported/Eigen/MatrixFunctions>
12
-
13
- // For complex matrices, any matrix is fine.
14
- template<typename MatrixType, int IsComplex = NumTraits<typename internal::traits<MatrixType>::Scalar>::IsComplex>
15
- struct processTriangularMatrix
16
- {
17
- static void run(MatrixType&, MatrixType&, const MatrixType&)
18
- { }
19
- };
20
-
21
- // For real matrices, make sure none of the eigenvalues are negative.
22
- template<typename MatrixType>
23
- struct processTriangularMatrix<MatrixType,0>
24
- {
25
- static void run(MatrixType& m, MatrixType& T, const MatrixType& U)
26
- {
27
- const Index size = m.cols();
28
-
29
- for (Index i=0; i < size; ++i) {
30
- if (i == size - 1 || T.coeff(i+1,i) == 0)
31
- T.coeffRef(i,i) = std::abs(T.coeff(i,i));
32
- else
33
- ++i;
34
- }
35
- m = U * T * U.transpose();
36
- }
37
- };
38
-
39
- template <typename MatrixType, int IsComplex = NumTraits<typename internal::traits<MatrixType>::Scalar>::IsComplex>
40
- struct generateTestMatrix;
41
-
42
- template <typename MatrixType>
43
- struct generateTestMatrix<MatrixType,0>
44
- {
45
- static void run(MatrixType& result, typename MatrixType::Index size)
46
- {
47
- result = MatrixType::Random(size, size);
48
- RealSchur<MatrixType> schur(result);
49
- MatrixType T = schur.matrixT();
50
- processTriangularMatrix<MatrixType>::run(result, T, schur.matrixU());
51
- }
52
- };
53
-
54
- template <typename MatrixType>
55
- struct generateTestMatrix<MatrixType,1>
56
- {
57
- static void run(MatrixType& result, typename MatrixType::Index size)
58
- {
59
- result = MatrixType::Random(size, size);
60
- }
61
- };
62
-
63
- template <typename Derived, typename OtherDerived>
64
- typename Derived::RealScalar relerr(const MatrixBase<Derived>& A, const MatrixBase<OtherDerived>& B)
65
- {
66
- return std::sqrt((A - B).cwiseAbs2().sum() / (std::min)(A.cwiseAbs2().sum(), B.cwiseAbs2().sum()));
67
- }