sequenzo 0.1.17__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of sequenzo might be problematic. Click here for more details.

Files changed (423) hide show
  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 +155 -155
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-312-darwin.so +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-312-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +155 -155
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-312-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +155 -155
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-312-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +155 -155
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-312-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +155 -155
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-312-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +155 -155
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-312-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  214. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  215. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  216. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  217. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  218. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  219. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  220. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  221. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  222. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  223. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  224. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  225. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  226. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  227. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  228. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  229. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  230. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  231. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  232. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  233. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  234. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  235. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  236. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  237. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  238. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  239. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  240. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  241. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  242. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  243. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  244. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  245. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  246. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  247. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  248. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  249. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  250. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  251. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  252. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  253. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  254. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  255. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  256. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  257. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  258. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  259. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  260. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  261. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  262. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  263. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  264. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  265. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  266. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  267. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  268. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  269. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  270. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  271. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  272. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  273. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
  274. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h +0 -104
  275. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h +0 -389
  276. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h +0 -1048
  277. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h +0 -409
  278. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h +0 -236
  279. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h +0 -490
  280. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h +0 -236
  281. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h +0 -983
  282. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h +0 -703
  283. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h +0 -388
  284. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h +0 -669
  285. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h +0 -379
  286. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h +0 -237
  287. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h +0 -191
  288. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h +0 -488
  289. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h +0 -302
  290. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGlobalFunctions.h +0 -33
  291. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h +0 -99
  292. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h +0 -44
  293. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIO.h +0 -79
  294. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h +0 -603
  295. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h +0 -738
  296. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h +0 -247
  297. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h +0 -82
  298. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h +0 -263
  299. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h +0 -216
  300. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h +0 -98
  301. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h +0 -327
  302. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h +0 -311
  303. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h +0 -1102
  304. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h +0 -708
  305. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h +0 -291
  306. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h +0 -322
  307. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h +0 -998
  308. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h +0 -6
  309. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h +0 -966
  310. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h +0 -582
  311. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h +0 -454
  312. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h +0 -465
  313. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h +0 -528
  314. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScanSycl.h +0 -513
  315. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h +0 -471
  316. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h +0 -161
  317. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStriding.h +0 -346
  318. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTrace.h +0 -303
  319. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h +0 -264
  320. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h +0 -249
  321. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h +0 -629
  322. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/DynamicSymmetry.h +0 -293
  323. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/StaticSymmetry.h +0 -236
  324. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/Symmetry.h +0 -338
  325. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h +0 -669
  326. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/Barrier.h +0 -67
  327. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h +0 -249
  328. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h +0 -486
  329. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h +0 -236
  330. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadCancel.h +0 -23
  331. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h +0 -40
  332. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h +0 -301
  333. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h +0 -48
  334. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h +0 -20
  335. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Meta.h +0 -537
  336. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h +0 -88
  337. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/EmulateArray.h +0 -261
  338. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h +0 -158
  339. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h +0 -108
  340. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h +0 -730
  341. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffVector.h +0 -220
  342. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/BVAlgorithms.h +0 -293
  343. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/KdBVH.h +0 -223
  344. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h +0 -790
  345. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerAngles.h +0 -355
  346. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerSystem.h +0 -305
  347. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_fftw_impl.h +0 -261
  348. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_kissfft_impl.h +0 -449
  349. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h +0 -187
  350. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/DGMRES.h +0 -511
  351. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/GMRES.h +0 -335
  352. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IDRS.h +0 -436
  353. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h +0 -90
  354. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IterationController.h +0 -154
  355. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/MINRES.h +0 -267
  356. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/Scaling.h +0 -193
  357. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h +0 -305
  358. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h +0 -84
  359. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMonestep.h +0 -202
  360. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h +0 -160
  361. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h +0 -188
  362. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  363. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  364. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  365. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  366. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  367. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  368. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  369. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  370. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  371. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  372. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  373. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  374. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  375. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  376. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  377. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  378. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  379. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  380. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  381. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  382. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  383. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  384. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  385. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  386. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  387. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  388. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  389. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  390. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  391. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  392. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  393. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  394. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  395. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  396. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  397. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  398. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  399. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  400. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  401. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  402. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,261 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2009 Mark Borgerding mark a borgerding net
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
- namespace Eigen {
11
-
12
- namespace internal {
13
-
14
- // FFTW uses non-const arguments
15
- // so we must use ugly const_cast calls for all the args it uses
16
- //
17
- // This should be safe as long as
18
- // 1. we use FFTW_ESTIMATE for all our planning
19
- // see the FFTW docs section 4.3.2 "Planner Flags"
20
- // 2. fftw_complex is compatible with std::complex
21
- // This assumes std::complex<T> layout is array of size 2 with real,imag
22
- template <typename T>
23
- inline
24
- T * fftw_cast(const T* p)
25
- {
26
- return const_cast<T*>( p);
27
- }
28
-
29
- inline
30
- fftw_complex * fftw_cast( const std::complex<double> * p)
31
- {
32
- return const_cast<fftw_complex*>( reinterpret_cast<const fftw_complex*>(p) );
33
- }
34
-
35
- inline
36
- fftwf_complex * fftw_cast( const std::complex<float> * p)
37
- {
38
- return const_cast<fftwf_complex*>( reinterpret_cast<const fftwf_complex*>(p) );
39
- }
40
-
41
- inline
42
- fftwl_complex * fftw_cast( const std::complex<long double> * p)
43
- {
44
- return const_cast<fftwl_complex*>( reinterpret_cast<const fftwl_complex*>(p) );
45
- }
46
-
47
- template <typename T>
48
- struct fftw_plan {};
49
-
50
- template <>
51
- struct fftw_plan<float>
52
- {
53
- typedef float scalar_type;
54
- typedef fftwf_complex complex_type;
55
- fftwf_plan m_plan;
56
- fftw_plan() :m_plan(NULL) {}
57
- ~fftw_plan() {if (m_plan) fftwf_destroy_plan(m_plan);}
58
-
59
- inline
60
- void fwd(complex_type * dst,complex_type * src,int nfft) {
61
- if (m_plan==NULL) m_plan = fftwf_plan_dft_1d(nfft,src,dst, FFTW_FORWARD, FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
62
- fftwf_execute_dft( m_plan, src,dst);
63
- }
64
- inline
65
- void inv(complex_type * dst,complex_type * src,int nfft) {
66
- if (m_plan==NULL) m_plan = fftwf_plan_dft_1d(nfft,src,dst, FFTW_BACKWARD , FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
67
- fftwf_execute_dft( m_plan, src,dst);
68
- }
69
- inline
70
- void fwd(complex_type * dst,scalar_type * src,int nfft) {
71
- if (m_plan==NULL) m_plan = fftwf_plan_dft_r2c_1d(nfft,src,dst,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
72
- fftwf_execute_dft_r2c( m_plan,src,dst);
73
- }
74
- inline
75
- void inv(scalar_type * dst,complex_type * src,int nfft) {
76
- if (m_plan==NULL)
77
- m_plan = fftwf_plan_dft_c2r_1d(nfft,src,dst,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
78
- fftwf_execute_dft_c2r( m_plan, src,dst);
79
- }
80
-
81
- inline
82
- void fwd2( complex_type * dst,complex_type * src,int n0,int n1) {
83
- if (m_plan==NULL) m_plan = fftwf_plan_dft_2d(n0,n1,src,dst,FFTW_FORWARD,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
84
- fftwf_execute_dft( m_plan, src,dst);
85
- }
86
- inline
87
- void inv2( complex_type * dst,complex_type * src,int n0,int n1) {
88
- if (m_plan==NULL) m_plan = fftwf_plan_dft_2d(n0,n1,src,dst,FFTW_BACKWARD,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
89
- fftwf_execute_dft( m_plan, src,dst);
90
- }
91
-
92
- };
93
- template <>
94
- struct fftw_plan<double>
95
- {
96
- typedef double scalar_type;
97
- typedef fftw_complex complex_type;
98
- ::fftw_plan m_plan;
99
- fftw_plan() :m_plan(NULL) {}
100
- ~fftw_plan() {if (m_plan) fftw_destroy_plan(m_plan);}
101
-
102
- inline
103
- void fwd(complex_type * dst,complex_type * src,int nfft) {
104
- if (m_plan==NULL) m_plan = fftw_plan_dft_1d(nfft,src,dst, FFTW_FORWARD, FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
105
- fftw_execute_dft( m_plan, src,dst);
106
- }
107
- inline
108
- void inv(complex_type * dst,complex_type * src,int nfft) {
109
- if (m_plan==NULL) m_plan = fftw_plan_dft_1d(nfft,src,dst, FFTW_BACKWARD , FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
110
- fftw_execute_dft( m_plan, src,dst);
111
- }
112
- inline
113
- void fwd(complex_type * dst,scalar_type * src,int nfft) {
114
- if (m_plan==NULL) m_plan = fftw_plan_dft_r2c_1d(nfft,src,dst,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
115
- fftw_execute_dft_r2c( m_plan,src,dst);
116
- }
117
- inline
118
- void inv(scalar_type * dst,complex_type * src,int nfft) {
119
- if (m_plan==NULL)
120
- m_plan = fftw_plan_dft_c2r_1d(nfft,src,dst,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
121
- fftw_execute_dft_c2r( m_plan, src,dst);
122
- }
123
- inline
124
- void fwd2( complex_type * dst,complex_type * src,int n0,int n1) {
125
- if (m_plan==NULL) m_plan = fftw_plan_dft_2d(n0,n1,src,dst,FFTW_FORWARD,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
126
- fftw_execute_dft( m_plan, src,dst);
127
- }
128
- inline
129
- void inv2( complex_type * dst,complex_type * src,int n0,int n1) {
130
- if (m_plan==NULL) m_plan = fftw_plan_dft_2d(n0,n1,src,dst,FFTW_BACKWARD,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
131
- fftw_execute_dft( m_plan, src,dst);
132
- }
133
- };
134
- template <>
135
- struct fftw_plan<long double>
136
- {
137
- typedef long double scalar_type;
138
- typedef fftwl_complex complex_type;
139
- fftwl_plan m_plan;
140
- fftw_plan() :m_plan(NULL) {}
141
- ~fftw_plan() {if (m_plan) fftwl_destroy_plan(m_plan);}
142
-
143
- inline
144
- void fwd(complex_type * dst,complex_type * src,int nfft) {
145
- if (m_plan==NULL) m_plan = fftwl_plan_dft_1d(nfft,src,dst, FFTW_FORWARD, FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
146
- fftwl_execute_dft( m_plan, src,dst);
147
- }
148
- inline
149
- void inv(complex_type * dst,complex_type * src,int nfft) {
150
- if (m_plan==NULL) m_plan = fftwl_plan_dft_1d(nfft,src,dst, FFTW_BACKWARD , FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
151
- fftwl_execute_dft( m_plan, src,dst);
152
- }
153
- inline
154
- void fwd(complex_type * dst,scalar_type * src,int nfft) {
155
- if (m_plan==NULL) m_plan = fftwl_plan_dft_r2c_1d(nfft,src,dst,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
156
- fftwl_execute_dft_r2c( m_plan,src,dst);
157
- }
158
- inline
159
- void inv(scalar_type * dst,complex_type * src,int nfft) {
160
- if (m_plan==NULL)
161
- m_plan = fftwl_plan_dft_c2r_1d(nfft,src,dst,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
162
- fftwl_execute_dft_c2r( m_plan, src,dst);
163
- }
164
- inline
165
- void fwd2( complex_type * dst,complex_type * src,int n0,int n1) {
166
- if (m_plan==NULL) m_plan = fftwl_plan_dft_2d(n0,n1,src,dst,FFTW_FORWARD,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
167
- fftwl_execute_dft( m_plan, src,dst);
168
- }
169
- inline
170
- void inv2( complex_type * dst,complex_type * src,int n0,int n1) {
171
- if (m_plan==NULL) m_plan = fftwl_plan_dft_2d(n0,n1,src,dst,FFTW_BACKWARD,FFTW_ESTIMATE|FFTW_PRESERVE_INPUT);
172
- fftwl_execute_dft( m_plan, src,dst);
173
- }
174
- };
175
-
176
- template <typename _Scalar>
177
- struct fftw_impl
178
- {
179
- typedef _Scalar Scalar;
180
- typedef std::complex<Scalar> Complex;
181
-
182
- inline
183
- void clear()
184
- {
185
- m_plans.clear();
186
- }
187
-
188
- // complex-to-complex forward FFT
189
- inline
190
- void fwd( Complex * dst,const Complex *src,int nfft)
191
- {
192
- get_plan(nfft,false,dst,src).fwd(fftw_cast(dst), fftw_cast(src),nfft );
193
- }
194
-
195
- // real-to-complex forward FFT
196
- inline
197
- void fwd( Complex * dst,const Scalar * src,int nfft)
198
- {
199
- get_plan(nfft,false,dst,src).fwd(fftw_cast(dst), fftw_cast(src) ,nfft);
200
- }
201
-
202
- // 2-d complex-to-complex
203
- inline
204
- void fwd2(Complex * dst, const Complex * src, int n0,int n1)
205
- {
206
- get_plan(n0,n1,false,dst,src).fwd2(fftw_cast(dst), fftw_cast(src) ,n0,n1);
207
- }
208
-
209
- // inverse complex-to-complex
210
- inline
211
- void inv(Complex * dst,const Complex *src,int nfft)
212
- {
213
- get_plan(nfft,true,dst,src).inv(fftw_cast(dst), fftw_cast(src),nfft );
214
- }
215
-
216
- // half-complex to scalar
217
- inline
218
- void inv( Scalar * dst,const Complex * src,int nfft)
219
- {
220
- get_plan(nfft,true,dst,src).inv(fftw_cast(dst), fftw_cast(src),nfft );
221
- }
222
-
223
- // 2-d complex-to-complex
224
- inline
225
- void inv2(Complex * dst, const Complex * src, int n0,int n1)
226
- {
227
- get_plan(n0,n1,true,dst,src).inv2(fftw_cast(dst), fftw_cast(src) ,n0,n1);
228
- }
229
-
230
-
231
- protected:
232
- typedef fftw_plan<Scalar> PlanData;
233
-
234
- typedef Eigen::numext::int64_t int64_t;
235
-
236
- typedef std::map<int64_t,PlanData> PlanMap;
237
-
238
- PlanMap m_plans;
239
-
240
- inline
241
- PlanData & get_plan(int nfft,bool inverse,void * dst,const void * src)
242
- {
243
- bool inplace = (dst==src);
244
- bool aligned = ( (reinterpret_cast<size_t>(src)&15) | (reinterpret_cast<size_t>(dst)&15) ) == 0;
245
- int64_t key = ( (nfft<<3 ) | (inverse<<2) | (inplace<<1) | aligned ) << 1;
246
- return m_plans[key];
247
- }
248
-
249
- inline
250
- PlanData & get_plan(int n0,int n1,bool inverse,void * dst,const void * src)
251
- {
252
- bool inplace = (dst==src);
253
- bool aligned = ( (reinterpret_cast<size_t>(src)&15) | (reinterpret_cast<size_t>(dst)&15) ) == 0;
254
- int64_t key = ( ( (((int64_t)n0) << 30)|(n1<<3 ) | (inverse<<2) | (inplace<<1) | aligned ) << 1 ) + 1;
255
- return m_plans[key];
256
- }
257
- };
258
-
259
- } // end namespace internal
260
-
261
- } // end namespace Eigen
@@ -1,449 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2009 Mark Borgerding mark a borgerding net
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
- namespace Eigen {
11
-
12
- namespace internal {
13
-
14
- // This FFT implementation was derived from kissfft http:sourceforge.net/projects/kissfft
15
- // Copyright 2003-2009 Mark Borgerding
16
-
17
- template <typename _Scalar>
18
- struct kiss_cpx_fft
19
- {
20
- typedef _Scalar Scalar;
21
- typedef std::complex<Scalar> Complex;
22
- std::vector<Complex> m_twiddles;
23
- std::vector<int> m_stageRadix;
24
- std::vector<int> m_stageRemainder;
25
- std::vector<Complex> m_scratchBuf;
26
- bool m_inverse;
27
-
28
- inline void make_twiddles(int nfft, bool inverse)
29
- {
30
- using numext::sin;
31
- using numext::cos;
32
- m_inverse = inverse;
33
- m_twiddles.resize(nfft);
34
- double phinc = 0.25 * double(EIGEN_PI) / nfft;
35
- Scalar flip = inverse ? Scalar(1) : Scalar(-1);
36
- m_twiddles[0] = Complex(Scalar(1), Scalar(0));
37
- if ((nfft&1)==0)
38
- m_twiddles[nfft/2] = Complex(Scalar(-1), Scalar(0));
39
- int i=1;
40
- for (;i*8<nfft;++i)
41
- {
42
- Scalar c = Scalar(cos(i*8*phinc));
43
- Scalar s = Scalar(sin(i*8*phinc));
44
- m_twiddles[i] = Complex(c, s*flip);
45
- m_twiddles[nfft-i] = Complex(c, -s*flip);
46
- }
47
- for (;i*4<nfft;++i)
48
- {
49
- Scalar c = Scalar(cos((2*nfft-8*i)*phinc));
50
- Scalar s = Scalar(sin((2*nfft-8*i)*phinc));
51
- m_twiddles[i] = Complex(s, c*flip);
52
- m_twiddles[nfft-i] = Complex(s, -c*flip);
53
- }
54
- for (;i*8<3*nfft;++i)
55
- {
56
- Scalar c = Scalar(cos((8*i-2*nfft)*phinc));
57
- Scalar s = Scalar(sin((8*i-2*nfft)*phinc));
58
- m_twiddles[i] = Complex(-s, c*flip);
59
- m_twiddles[nfft-i] = Complex(-s, -c*flip);
60
- }
61
- for (;i*2<nfft;++i)
62
- {
63
- Scalar c = Scalar(cos((4*nfft-8*i)*phinc));
64
- Scalar s = Scalar(sin((4*nfft-8*i)*phinc));
65
- m_twiddles[i] = Complex(-c, s*flip);
66
- m_twiddles[nfft-i] = Complex(-c, -s*flip);
67
- }
68
- }
69
-
70
- void factorize(int nfft)
71
- {
72
- //start factoring out 4's, then 2's, then 3,5,7,9,...
73
- int n= nfft;
74
- int p=4;
75
- do {
76
- while (n % p) {
77
- switch (p) {
78
- case 4: p = 2; break;
79
- case 2: p = 3; break;
80
- default: p += 2; break;
81
- }
82
- if (p*p>n)
83
- p=n;// impossible to have a factor > sqrt(n)
84
- }
85
- n /= p;
86
- m_stageRadix.push_back(p);
87
- m_stageRemainder.push_back(n);
88
- if ( p > 5 )
89
- m_scratchBuf.resize(p); // scratchbuf will be needed in bfly_generic
90
- }while(n>1);
91
- }
92
-
93
- template <typename _Src>
94
- inline
95
- void work( int stage,Complex * xout, const _Src * xin, size_t fstride,size_t in_stride)
96
- {
97
- int p = m_stageRadix[stage];
98
- int m = m_stageRemainder[stage];
99
- Complex * Fout_beg = xout;
100
- Complex * Fout_end = xout + p*m;
101
-
102
- if (m>1) {
103
- do{
104
- // recursive call:
105
- // DFT of size m*p performed by doing
106
- // p instances of smaller DFTs of size m,
107
- // each one takes a decimated version of the input
108
- work(stage+1, xout , xin, fstride*p,in_stride);
109
- xin += fstride*in_stride;
110
- }while( (xout += m) != Fout_end );
111
- }else{
112
- do{
113
- *xout = *xin;
114
- xin += fstride*in_stride;
115
- }while(++xout != Fout_end );
116
- }
117
- xout=Fout_beg;
118
-
119
- // recombine the p smaller DFTs
120
- switch (p) {
121
- case 2: bfly2(xout,fstride,m); break;
122
- case 3: bfly3(xout,fstride,m); break;
123
- case 4: bfly4(xout,fstride,m); break;
124
- case 5: bfly5(xout,fstride,m); break;
125
- default: bfly_generic(xout,fstride,m,p); break;
126
- }
127
- }
128
-
129
- inline
130
- void bfly2( Complex * Fout, const size_t fstride, int m)
131
- {
132
- for (int k=0;k<m;++k) {
133
- Complex t = Fout[m+k] * m_twiddles[k*fstride];
134
- Fout[m+k] = Fout[k] - t;
135
- Fout[k] += t;
136
- }
137
- }
138
-
139
- inline
140
- void bfly4( Complex * Fout, const size_t fstride, const size_t m)
141
- {
142
- Complex scratch[6];
143
- int negative_if_inverse = m_inverse * -2 +1;
144
- for (size_t k=0;k<m;++k) {
145
- scratch[0] = Fout[k+m] * m_twiddles[k*fstride];
146
- scratch[1] = Fout[k+2*m] * m_twiddles[k*fstride*2];
147
- scratch[2] = Fout[k+3*m] * m_twiddles[k*fstride*3];
148
- scratch[5] = Fout[k] - scratch[1];
149
-
150
- Fout[k] += scratch[1];
151
- scratch[3] = scratch[0] + scratch[2];
152
- scratch[4] = scratch[0] - scratch[2];
153
- scratch[4] = Complex( scratch[4].imag()*negative_if_inverse , -scratch[4].real()* negative_if_inverse );
154
-
155
- Fout[k+2*m] = Fout[k] - scratch[3];
156
- Fout[k] += scratch[3];
157
- Fout[k+m] = scratch[5] + scratch[4];
158
- Fout[k+3*m] = scratch[5] - scratch[4];
159
- }
160
- }
161
-
162
- inline
163
- void bfly3( Complex * Fout, const size_t fstride, const size_t m)
164
- {
165
- size_t k=m;
166
- const size_t m2 = 2*m;
167
- Complex *tw1,*tw2;
168
- Complex scratch[5];
169
- Complex epi3;
170
- epi3 = m_twiddles[fstride*m];
171
-
172
- tw1=tw2=&m_twiddles[0];
173
-
174
- do{
175
- scratch[1]=Fout[m] * *tw1;
176
- scratch[2]=Fout[m2] * *tw2;
177
-
178
- scratch[3]=scratch[1]+scratch[2];
179
- scratch[0]=scratch[1]-scratch[2];
180
- tw1 += fstride;
181
- tw2 += fstride*2;
182
- Fout[m] = Complex( Fout->real() - Scalar(.5)*scratch[3].real() , Fout->imag() - Scalar(.5)*scratch[3].imag() );
183
- scratch[0] *= epi3.imag();
184
- *Fout += scratch[3];
185
- Fout[m2] = Complex( Fout[m].real() + scratch[0].imag() , Fout[m].imag() - scratch[0].real() );
186
- Fout[m] += Complex( -scratch[0].imag(),scratch[0].real() );
187
- ++Fout;
188
- }while(--k);
189
- }
190
-
191
- inline
192
- void bfly5( Complex * Fout, const size_t fstride, const size_t m)
193
- {
194
- Complex *Fout0,*Fout1,*Fout2,*Fout3,*Fout4;
195
- size_t u;
196
- Complex scratch[13];
197
- Complex * twiddles = &m_twiddles[0];
198
- Complex *tw;
199
- Complex ya,yb;
200
- ya = twiddles[fstride*m];
201
- yb = twiddles[fstride*2*m];
202
-
203
- Fout0=Fout;
204
- Fout1=Fout0+m;
205
- Fout2=Fout0+2*m;
206
- Fout3=Fout0+3*m;
207
- Fout4=Fout0+4*m;
208
-
209
- tw=twiddles;
210
- for ( u=0; u<m; ++u ) {
211
- scratch[0] = *Fout0;
212
-
213
- scratch[1] = *Fout1 * tw[u*fstride];
214
- scratch[2] = *Fout2 * tw[2*u*fstride];
215
- scratch[3] = *Fout3 * tw[3*u*fstride];
216
- scratch[4] = *Fout4 * tw[4*u*fstride];
217
-
218
- scratch[7] = scratch[1] + scratch[4];
219
- scratch[10] = scratch[1] - scratch[4];
220
- scratch[8] = scratch[2] + scratch[3];
221
- scratch[9] = scratch[2] - scratch[3];
222
-
223
- *Fout0 += scratch[7];
224
- *Fout0 += scratch[8];
225
-
226
- scratch[5] = scratch[0] + Complex(
227
- (scratch[7].real()*ya.real() ) + (scratch[8].real() *yb.real() ),
228
- (scratch[7].imag()*ya.real()) + (scratch[8].imag()*yb.real())
229
- );
230
-
231
- scratch[6] = Complex(
232
- (scratch[10].imag()*ya.imag()) + (scratch[9].imag()*yb.imag()),
233
- -(scratch[10].real()*ya.imag()) - (scratch[9].real()*yb.imag())
234
- );
235
-
236
- *Fout1 = scratch[5] - scratch[6];
237
- *Fout4 = scratch[5] + scratch[6];
238
-
239
- scratch[11] = scratch[0] +
240
- Complex(
241
- (scratch[7].real()*yb.real()) + (scratch[8].real()*ya.real()),
242
- (scratch[7].imag()*yb.real()) + (scratch[8].imag()*ya.real())
243
- );
244
-
245
- scratch[12] = Complex(
246
- -(scratch[10].imag()*yb.imag()) + (scratch[9].imag()*ya.imag()),
247
- (scratch[10].real()*yb.imag()) - (scratch[9].real()*ya.imag())
248
- );
249
-
250
- *Fout2=scratch[11]+scratch[12];
251
- *Fout3=scratch[11]-scratch[12];
252
-
253
- ++Fout0;++Fout1;++Fout2;++Fout3;++Fout4;
254
- }
255
- }
256
-
257
- /* perform the butterfly for one stage of a mixed radix FFT */
258
- inline
259
- void bfly_generic(
260
- Complex * Fout,
261
- const size_t fstride,
262
- int m,
263
- int p
264
- )
265
- {
266
- int u,k,q1,q;
267
- Complex * twiddles = &m_twiddles[0];
268
- Complex t;
269
- int Norig = static_cast<int>(m_twiddles.size());
270
- Complex * scratchbuf = &m_scratchBuf[0];
271
-
272
- for ( u=0; u<m; ++u ) {
273
- k=u;
274
- for ( q1=0 ; q1<p ; ++q1 ) {
275
- scratchbuf[q1] = Fout[ k ];
276
- k += m;
277
- }
278
-
279
- k=u;
280
- for ( q1=0 ; q1<p ; ++q1 ) {
281
- int twidx=0;
282
- Fout[ k ] = scratchbuf[0];
283
- for (q=1;q<p;++q ) {
284
- twidx += static_cast<int>(fstride) * k;
285
- if (twidx>=Norig) twidx-=Norig;
286
- t=scratchbuf[q] * twiddles[twidx];
287
- Fout[ k ] += t;
288
- }
289
- k += m;
290
- }
291
- }
292
- }
293
- };
294
-
295
- template <typename _Scalar>
296
- struct kissfft_impl
297
- {
298
- typedef _Scalar Scalar;
299
- typedef std::complex<Scalar> Complex;
300
-
301
- void clear()
302
- {
303
- m_plans.clear();
304
- m_realTwiddles.clear();
305
- }
306
-
307
- inline
308
- void fwd( Complex * dst,const Complex *src,int nfft)
309
- {
310
- get_plan(nfft,false).work(0, dst, src, 1,1);
311
- }
312
-
313
- inline
314
- void fwd2( Complex * dst,const Complex *src,int n0,int n1)
315
- {
316
- EIGEN_UNUSED_VARIABLE(dst);
317
- EIGEN_UNUSED_VARIABLE(src);
318
- EIGEN_UNUSED_VARIABLE(n0);
319
- EIGEN_UNUSED_VARIABLE(n1);
320
- }
321
-
322
- inline
323
- void inv2( Complex * dst,const Complex *src,int n0,int n1)
324
- {
325
- EIGEN_UNUSED_VARIABLE(dst);
326
- EIGEN_UNUSED_VARIABLE(src);
327
- EIGEN_UNUSED_VARIABLE(n0);
328
- EIGEN_UNUSED_VARIABLE(n1);
329
- }
330
-
331
- // real-to-complex forward FFT
332
- // perform two FFTs of src even and src odd
333
- // then twiddle to recombine them into the half-spectrum format
334
- // then fill in the conjugate symmetric half
335
- inline
336
- void fwd( Complex * dst,const Scalar * src,int nfft)
337
- {
338
- if ( nfft&3 ) {
339
- // use generic mode for odd
340
- m_tmpBuf1.resize(nfft);
341
- get_plan(nfft,false).work(0, &m_tmpBuf1[0], src, 1,1);
342
- std::copy(m_tmpBuf1.begin(),m_tmpBuf1.begin()+(nfft>>1)+1,dst );
343
- }else{
344
- int ncfft = nfft>>1;
345
- int ncfft2 = nfft>>2;
346
- Complex * rtw = real_twiddles(ncfft2);
347
-
348
- // use optimized mode for even real
349
- fwd( dst, reinterpret_cast<const Complex*> (src), ncfft);
350
- Complex dc(dst[0].real() + dst[0].imag());
351
- Complex nyquist(dst[0].real() - dst[0].imag());
352
- int k;
353
- for ( k=1;k <= ncfft2 ; ++k ) {
354
- Complex fpk = dst[k];
355
- Complex fpnk = conj(dst[ncfft-k]);
356
- Complex f1k = fpk + fpnk;
357
- Complex f2k = fpk - fpnk;
358
- Complex tw= f2k * rtw[k-1];
359
- dst[k] = (f1k + tw) * Scalar(.5);
360
- dst[ncfft-k] = conj(f1k -tw)*Scalar(.5);
361
- }
362
- dst[0] = dc;
363
- dst[ncfft] = nyquist;
364
- }
365
- }
366
-
367
- // inverse complex-to-complex
368
- inline
369
- void inv(Complex * dst,const Complex *src,int nfft)
370
- {
371
- get_plan(nfft,true).work(0, dst, src, 1,1);
372
- }
373
-
374
- // half-complex to scalar
375
- inline
376
- void inv( Scalar * dst,const Complex * src,int nfft)
377
- {
378
- if (nfft&3) {
379
- m_tmpBuf1.resize(nfft);
380
- m_tmpBuf2.resize(nfft);
381
- std::copy(src,src+(nfft>>1)+1,m_tmpBuf1.begin() );
382
- for (int k=1;k<(nfft>>1)+1;++k)
383
- m_tmpBuf1[nfft-k] = conj(m_tmpBuf1[k]);
384
- inv(&m_tmpBuf2[0],&m_tmpBuf1[0],nfft);
385
- for (int k=0;k<nfft;++k)
386
- dst[k] = m_tmpBuf2[k].real();
387
- }else{
388
- // optimized version for multiple of 4
389
- int ncfft = nfft>>1;
390
- int ncfft2 = nfft>>2;
391
- Complex * rtw = real_twiddles(ncfft2);
392
- m_tmpBuf1.resize(ncfft);
393
- m_tmpBuf1[0] = Complex( src[0].real() + src[ncfft].real(), src[0].real() - src[ncfft].real() );
394
- for (int k = 1; k <= ncfft / 2; ++k) {
395
- Complex fk = src[k];
396
- Complex fnkc = conj(src[ncfft-k]);
397
- Complex fek = fk + fnkc;
398
- Complex tmp = fk - fnkc;
399
- Complex fok = tmp * conj(rtw[k-1]);
400
- m_tmpBuf1[k] = fek + fok;
401
- m_tmpBuf1[ncfft-k] = conj(fek - fok);
402
- }
403
- get_plan(ncfft,true).work(0, reinterpret_cast<Complex*>(dst), &m_tmpBuf1[0], 1,1);
404
- }
405
- }
406
-
407
- protected:
408
- typedef kiss_cpx_fft<Scalar> PlanData;
409
- typedef std::map<int,PlanData> PlanMap;
410
-
411
- PlanMap m_plans;
412
- std::map<int, std::vector<Complex> > m_realTwiddles;
413
- std::vector<Complex> m_tmpBuf1;
414
- std::vector<Complex> m_tmpBuf2;
415
-
416
- inline
417
- int PlanKey(int nfft, bool isinverse) const { return (nfft<<1) | int(isinverse); }
418
-
419
- inline
420
- PlanData & get_plan(int nfft, bool inverse)
421
- {
422
- // TODO look for PlanKey(nfft, ! inverse) and conjugate the twiddles
423
- PlanData & pd = m_plans[ PlanKey(nfft,inverse) ];
424
- if ( pd.m_twiddles.size() == 0 ) {
425
- pd.make_twiddles(nfft,inverse);
426
- pd.factorize(nfft);
427
- }
428
- return pd;
429
- }
430
-
431
- inline
432
- Complex * real_twiddles(int ncfft2)
433
- {
434
- using std::acos;
435
- std::vector<Complex> & twidref = m_realTwiddles[ncfft2];// creates new if not there
436
- if ( (int)twidref.size() != ncfft2 ) {
437
- twidref.resize(ncfft2);
438
- int ncfft= ncfft2<<1;
439
- Scalar pi = acos( Scalar(-1) );
440
- for (int k=1;k<=ncfft2;++k)
441
- twidref[k-1] = exp( Complex(0,-pi * (Scalar(k) / ncfft + Scalar(.5)) ) );
442
- }
443
- return &twidref[0];
444
- }
445
- };
446
-
447
- } // end namespace internal
448
-
449
- } // end namespace Eigen