sequenzo 0.1.18__cp39-cp39-win_amd64.whl → 0.1.20__cp39-cp39-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +156 -156
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp39-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp39-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +156 -156
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp39-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,261 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2009 Mark Borgerding mark a borgerding net
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- namespace Eigen {
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-
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- namespace internal {
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-
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- // FFTW uses non-const arguments
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- // so we must use ugly const_cast calls for all the args it uses
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- //
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