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
@@ -1,261 +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