sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.19__cp39-cp39-win_amd64.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 (475) 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 +156 -156
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp39-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp39-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +156 -156
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp39-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  214. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  215. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  216. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  217. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  218. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  219. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  220. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  221. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  222. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  223. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  224. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  225. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  226. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  227. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  228. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  229. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  230. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  231. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  232. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  233. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  234. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  235. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  236. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  237. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  238. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  239. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  240. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  241. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  242. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  243. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  244. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  245. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  246. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  247. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  248. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  249. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  250. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  251. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  252. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  253. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  254. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  255. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  256. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  257. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  258. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  259. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  260. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  261. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  262. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  263. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  264. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  265. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  266. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  267. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  268. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  269. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  270. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  271. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  272. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  273. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  274. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  275. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  276. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  277. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  278. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  279. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  280. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  281. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  282. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  283. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  284. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  285. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  286. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  287. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  288. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  289. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  290. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  291. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
  292. sequenzo/dissimilarity_measures/src/eigen/test/gpu_common.h +0 -176
  293. sequenzo/dissimilarity_measures/src/eigen/test/main.h +0 -857
  294. sequenzo/dissimilarity_measures/src/eigen/test/packetmath_test_shared.h +0 -275
  295. sequenzo/dissimilarity_measures/src/eigen/test/product.h +0 -259
  296. sequenzo/dissimilarity_measures/src/eigen/test/random_without_cast_overflow.h +0 -152
  297. sequenzo/dissimilarity_measures/src/eigen/test/solverbase.h +0 -36
  298. sequenzo/dissimilarity_measures/src/eigen/test/sparse.h +0 -204
  299. sequenzo/dissimilarity_measures/src/eigen/test/sparse_solver.h +0 -699
  300. sequenzo/dissimilarity_measures/src/eigen/test/split_test_helper.h +0 -5994
  301. sequenzo/dissimilarity_measures/src/eigen/test/svd_common.h +0 -521
  302. sequenzo/dissimilarity_measures/src/eigen/test/svd_fill.h +0 -118
  303. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  304. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  305. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  306. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  307. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  308. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  309. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  310. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  311. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  312. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  313. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  314. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  315. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  316. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  317. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  318. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  319. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  320. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  321. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  322. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  323. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  324. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
  325. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h +0 -104
  326. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h +0 -389
  327. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h +0 -1048
  328. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h +0 -409
  329. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h +0 -236
  330. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h +0 -490
  331. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h +0 -236
  332. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h +0 -983
  333. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h +0 -703
  334. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h +0 -388
  335. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h +0 -669
  336. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h +0 -379
  337. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h +0 -237
  338. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h +0 -191
  339. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h +0 -488
  340. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h +0 -302
  341. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGlobalFunctions.h +0 -33
  342. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h +0 -99
  343. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h +0 -44
  344. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIO.h +0 -79
  345. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h +0 -603
  346. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h +0 -738
  347. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h +0 -247
  348. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h +0 -82
  349. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h +0 -263
  350. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h +0 -216
  351. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h +0 -98
  352. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h +0 -327
  353. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h +0 -311
  354. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h +0 -1102
  355. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h +0 -708
  356. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h +0 -291
  357. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h +0 -322
  358. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h +0 -998
  359. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h +0 -6
  360. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h +0 -966
  361. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h +0 -582
  362. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h +0 -454
  363. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h +0 -465
  364. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h +0 -528
  365. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScanSycl.h +0 -513
  366. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h +0 -471
  367. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h +0 -161
  368. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStriding.h +0 -346
  369. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTrace.h +0 -303
  370. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h +0 -264
  371. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h +0 -249
  372. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h +0 -629
  373. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/DynamicSymmetry.h +0 -293
  374. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/StaticSymmetry.h +0 -236
  375. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/Symmetry.h +0 -338
  376. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h +0 -669
  377. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/Barrier.h +0 -67
  378. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h +0 -249
  379. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h +0 -486
  380. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h +0 -236
  381. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadCancel.h +0 -23
  382. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h +0 -40
  383. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h +0 -301
  384. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h +0 -48
  385. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h +0 -20
  386. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Meta.h +0 -537
  387. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h +0 -88
  388. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/EmulateArray.h +0 -261
  389. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h +0 -158
  390. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h +0 -108
  391. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h +0 -730
  392. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffVector.h +0 -220
  393. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/BVAlgorithms.h +0 -293
  394. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/KdBVH.h +0 -223
  395. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h +0 -790
  396. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerAngles.h +0 -355
  397. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerSystem.h +0 -305
  398. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_fftw_impl.h +0 -261
  399. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_kissfft_impl.h +0 -449
  400. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h +0 -187
  401. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/DGMRES.h +0 -511
  402. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/GMRES.h +0 -335
  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IDRS.h +0 -436
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h +0 -90
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IterationController.h +0 -154
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/MINRES.h +0 -267
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/Scaling.h +0 -193
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h +0 -305
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h +0 -84
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMonestep.h +0 -202
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h +0 -160
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h +0 -188
  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
@@ -1,669 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2015 Jianwei Cui <thucjw@gmail.com>
5
- //
6
- // This Source Code Form is subject to the terms of the Mozilla
7
- // Public License v. 2.0. If a copy of the MPL was not distributed
8
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
-
10
- #ifndef EIGEN_CXX11_TENSOR_TENSOR_FFT_H
11
- #define EIGEN_CXX11_TENSOR_TENSOR_FFT_H
12
-
13
- namespace Eigen {
14
-
15
- /** \class TensorFFT
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Tensor FFT class.
19
- *
20
- * TODO:
21
- * Vectorize the Cooley Tukey and the Bluestein algorithm
22
- * Add support for multithreaded evaluation
23
- * Improve the performance on GPU
24
- */
25
-
26
- template <bool NeedUprade> struct MakeComplex {
27
- template <typename T>
28
- EIGEN_DEVICE_FUNC
29
- T operator() (const T& val) const { return val; }
30
- };
31
-
32
- template <> struct MakeComplex<true> {
33
- template <typename T>
34
- EIGEN_DEVICE_FUNC
35
- std::complex<T> operator() (const T& val) const { return std::complex<T>(val, 0); }
36
- };
37
-
38
- template <> struct MakeComplex<false> {
39
- template <typename T>
40
- EIGEN_DEVICE_FUNC
41
- std::complex<T> operator() (const std::complex<T>& val) const { return val; }
42
- };
43
-
44
- template <int ResultType> struct PartOf {
45
- template <typename T> T operator() (const T& val) const { return val; }
46
- };
47
-
48
- template <> struct PartOf<RealPart> {
49
- template <typename T> T operator() (const std::complex<T>& val) const { return val.real(); }
50
- };
51
-
52
- template <> struct PartOf<ImagPart> {
53
- template <typename T> T operator() (const std::complex<T>& val) const { return val.imag(); }
54
- };
55
-
56
- namespace internal {
57
- template <typename FFT, typename XprType, int FFTResultType, int FFTDir>
58
- struct traits<TensorFFTOp<FFT, XprType, FFTResultType, FFTDir> > : public traits<XprType> {
59
- typedef traits<XprType> XprTraits;
60
- typedef typename NumTraits<typename XprTraits::Scalar>::Real RealScalar;
61
- typedef typename std::complex<RealScalar> ComplexScalar;
62
- typedef typename XprTraits::Scalar InputScalar;
63
- typedef typename conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
64
- typedef typename XprTraits::StorageKind StorageKind;
65
- typedef typename XprTraits::Index Index;
66
- typedef typename XprType::Nested Nested;
67
- typedef typename remove_reference<Nested>::type _Nested;
68
- static const int NumDimensions = XprTraits::NumDimensions;
69
- static const int Layout = XprTraits::Layout;
70
- typedef typename traits<XprType>::PointerType PointerType;
71
- };
72
-
73
- template <typename FFT, typename XprType, int FFTResultType, int FFTDirection>
74
- struct eval<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>, Eigen::Dense> {
75
- typedef const TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>& type;
76
- };
77
-
78
- template <typename FFT, typename XprType, int FFTResultType, int FFTDirection>
79
- struct nested<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>, 1, typename eval<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection> >::type> {
80
- typedef TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection> type;
81
- };
82
-
83
- } // end namespace internal
84
-
85
- template <typename FFT, typename XprType, int FFTResultType, int FFTDir>
86
- class TensorFFTOp : public TensorBase<TensorFFTOp<FFT, XprType, FFTResultType, FFTDir>, ReadOnlyAccessors> {
87
- public:
88
- typedef typename Eigen::internal::traits<TensorFFTOp>::Scalar Scalar;
89
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
90
- typedef typename std::complex<RealScalar> ComplexScalar;
91
- typedef typename internal::conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
92
- typedef OutputScalar CoeffReturnType;
93
- typedef typename Eigen::internal::nested<TensorFFTOp>::type Nested;
94
- typedef typename Eigen::internal::traits<TensorFFTOp>::StorageKind StorageKind;
95
- typedef typename Eigen::internal::traits<TensorFFTOp>::Index Index;
96
-
97
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorFFTOp(const XprType& expr, const FFT& fft)
98
- : m_xpr(expr), m_fft(fft) {}
99
-
100
- EIGEN_DEVICE_FUNC
101
- const FFT& fft() const { return m_fft; }
102
-
103
- EIGEN_DEVICE_FUNC
104
- const typename internal::remove_all<typename XprType::Nested>::type& expression() const {
105
- return m_xpr;
106
- }
107
-
108
- protected:
109
- typename XprType::Nested m_xpr;
110
- const FFT m_fft;
111
- };
112
-
113
- // Eval as rvalue
114
- template <typename FFT, typename ArgType, typename Device, int FFTResultType, int FFTDir>
115
- struct TensorEvaluator<const TensorFFTOp<FFT, ArgType, FFTResultType, FFTDir>, Device> {
116
- typedef TensorFFTOp<FFT, ArgType, FFTResultType, FFTDir> XprType;
117
- typedef typename XprType::Index Index;
118
- static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
119
- typedef DSizes<Index, NumDims> Dimensions;
120
- typedef typename XprType::Scalar Scalar;
121
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
122
- typedef typename std::complex<RealScalar> ComplexScalar;
123
- typedef typename TensorEvaluator<ArgType, Device>::Dimensions InputDimensions;
124
- typedef internal::traits<XprType> XprTraits;
125
- typedef typename XprTraits::Scalar InputScalar;
126
- typedef typename internal::conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
127
- typedef OutputScalar CoeffReturnType;
128
- typedef typename PacketType<OutputScalar, Device>::type PacketReturnType;
129
- static const int PacketSize = internal::unpacket_traits<PacketReturnType>::size;
130
- typedef StorageMemory<CoeffReturnType, Device> Storage;
131
- typedef typename Storage::Type EvaluatorPointerType;
132
-
133
- enum {
134
- IsAligned = false,
135
- PacketAccess = true,
136
- BlockAccess = false,
137
- PreferBlockAccess = false,
138
- Layout = TensorEvaluator<ArgType, Device>::Layout,
139
- CoordAccess = false,
140
- RawAccess = false
141
- };
142
-
143
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
144
- typedef internal::TensorBlockNotImplemented TensorBlock;
145
- //===--------------------------------------------------------------------===//
146
-
147
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device) : m_fft(op.fft()), m_impl(op.expression(), device), m_data(NULL), m_device(device) {
148
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
149
- for (int i = 0; i < NumDims; ++i) {
150
- eigen_assert(input_dims[i] > 0);
151
- m_dimensions[i] = input_dims[i];
152
- }
153
-
154
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
155
- m_strides[0] = 1;
156
- for (int i = 1; i < NumDims; ++i) {
157
- m_strides[i] = m_strides[i - 1] * m_dimensions[i - 1];
158
- }
159
- } else {
160
- m_strides[NumDims - 1] = 1;
161
- for (int i = NumDims - 2; i >= 0; --i) {
162
- m_strides[i] = m_strides[i + 1] * m_dimensions[i + 1];
163
- }
164
- }
165
- m_size = m_dimensions.TotalSize();
166
- }
167
-
168
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const {
169
- return m_dimensions;
170
- }
171
-
172
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType data) {
173
- m_impl.evalSubExprsIfNeeded(NULL);
174
- if (data) {
175
- evalToBuf(data);
176
- return false;
177
- } else {
178
- m_data = (EvaluatorPointerType)m_device.get((CoeffReturnType*)(m_device.allocate_temp(sizeof(CoeffReturnType) * m_size)));
179
- evalToBuf(m_data);
180
- return true;
181
- }
182
- }
183
-
184
- EIGEN_STRONG_INLINE void cleanup() {
185
- if (m_data) {
186
- m_device.deallocate(m_data);
187
- m_data = NULL;
188
- }
189
- m_impl.cleanup();
190
- }
191
-
192
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE CoeffReturnType coeff(Index index) const {
193
- return m_data[index];
194
- }
195
-
196
- template <int LoadMode>
197
- EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketReturnType
198
- packet(Index index) const {
199
- return internal::ploadt<PacketReturnType, LoadMode>(m_data + index);
200
- }
201
-
202
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
203
- costPerCoeff(bool vectorized) const {
204
- return TensorOpCost(sizeof(CoeffReturnType), 0, 0, vectorized, PacketSize);
205
- }
206
-
207
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return m_data; }
208
- #ifdef EIGEN_USE_SYCL
209
- // binding placeholder accessors to a command group handler for SYCL
210
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
211
- m_data.bind(cgh);
212
- }
213
- #endif
214
-
215
- private:
216
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalToBuf(EvaluatorPointerType data) {
217
- const bool write_to_out = internal::is_same<OutputScalar, ComplexScalar>::value;
218
- ComplexScalar* buf = write_to_out ? (ComplexScalar*)data : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * m_size);
219
-
220
- for (Index i = 0; i < m_size; ++i) {
221
- buf[i] = MakeComplex<internal::is_same<InputScalar, RealScalar>::value>()(m_impl.coeff(i));
222
- }
223
-
224
- for (size_t i = 0; i < m_fft.size(); ++i) {
225
- Index dim = m_fft[i];
226
- eigen_assert(dim >= 0 && dim < NumDims);
227
- Index line_len = m_dimensions[dim];
228
- eigen_assert(line_len >= 1);
229
- ComplexScalar* line_buf = (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * line_len);
230
- const bool is_power_of_two = isPowerOfTwo(line_len);
231
- const Index good_composite = is_power_of_two ? 0 : findGoodComposite(line_len);
232
- const Index log_len = is_power_of_two ? getLog2(line_len) : getLog2(good_composite);
233
-
234
- ComplexScalar* a = is_power_of_two ? NULL : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * good_composite);
235
- ComplexScalar* b = is_power_of_two ? NULL : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * good_composite);
236
- ComplexScalar* pos_j_base_powered = is_power_of_two ? NULL : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * (line_len + 1));
237
- if (!is_power_of_two) {
238
- // Compute twiddle factors
239
- // t_n = exp(sqrt(-1) * pi * n^2 / line_len)
240
- // for n = 0, 1,..., line_len-1.
241
- // For n > 2 we use the recurrence t_n = t_{n-1}^2 / t_{n-2} * t_1^2
242
-
243
- // The recurrence is correct in exact arithmetic, but causes
244
- // numerical issues for large transforms, especially in
245
- // single-precision floating point.
246
- //
247
- // pos_j_base_powered[0] = ComplexScalar(1, 0);
248
- // if (line_len > 1) {
249
- // const ComplexScalar pos_j_base = ComplexScalar(
250
- // numext::cos(M_PI / line_len), numext::sin(M_PI / line_len));
251
- // pos_j_base_powered[1] = pos_j_base;
252
- // if (line_len > 2) {
253
- // const ComplexScalar pos_j_base_sq = pos_j_base * pos_j_base;
254
- // for (int i = 2; i < line_len + 1; ++i) {
255
- // pos_j_base_powered[i] = pos_j_base_powered[i - 1] *
256
- // pos_j_base_powered[i - 1] /
257
- // pos_j_base_powered[i - 2] *
258
- // pos_j_base_sq;
259
- // }
260
- // }
261
- // }
262
- // TODO(rmlarsen): Find a way to use Eigen's vectorized sin
263
- // and cosine functions here.
264
- for (int j = 0; j < line_len + 1; ++j) {
265
- double arg = ((EIGEN_PI * j) * j) / line_len;
266
- std::complex<double> tmp(numext::cos(arg), numext::sin(arg));
267
- pos_j_base_powered[j] = static_cast<ComplexScalar>(tmp);
268
- }
269
- }
270
-
271
- for (Index partial_index = 0; partial_index < m_size / line_len; ++partial_index) {
272
- const Index base_offset = getBaseOffsetFromIndex(partial_index, dim);
273
-
274
- // get data into line_buf
275
- const Index stride = m_strides[dim];
276
- if (stride == 1) {
277
- m_device.memcpy(line_buf, &buf[base_offset], line_len*sizeof(ComplexScalar));
278
- } else {
279
- Index offset = base_offset;
280
- for (int j = 0; j < line_len; ++j, offset += stride) {
281
- line_buf[j] = buf[offset];
282
- }
283
- }
284
-
285
- // process the line
286
- if (is_power_of_two) {
287
- processDataLineCooleyTukey(line_buf, line_len, log_len);
288
- }
289
- else {
290
- processDataLineBluestein(line_buf, line_len, good_composite, log_len, a, b, pos_j_base_powered);
291
- }
292
-
293
- // write back
294
- if (FFTDir == FFT_FORWARD && stride == 1) {
295
- m_device.memcpy(&buf[base_offset], line_buf, line_len*sizeof(ComplexScalar));
296
- } else {
297
- Index offset = base_offset;
298
- const ComplexScalar div_factor = ComplexScalar(1.0 / line_len, 0);
299
- for (int j = 0; j < line_len; ++j, offset += stride) {
300
- buf[offset] = (FFTDir == FFT_FORWARD) ? line_buf[j] : line_buf[j] * div_factor;
301
- }
302
- }
303
- }
304
- m_device.deallocate(line_buf);
305
- if (!is_power_of_two) {
306
- m_device.deallocate(a);
307
- m_device.deallocate(b);
308
- m_device.deallocate(pos_j_base_powered);
309
- }
310
- }
311
-
312
- if(!write_to_out) {
313
- for (Index i = 0; i < m_size; ++i) {
314
- data[i] = PartOf<FFTResultType>()(buf[i]);
315
- }
316
- m_device.deallocate(buf);
317
- }
318
- }
319
-
320
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static bool isPowerOfTwo(Index x) {
321
- eigen_assert(x > 0);
322
- return !(x & (x - 1));
323
- }
324
-
325
- // The composite number for padding, used in Bluestein's FFT algorithm
326
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static Index findGoodComposite(Index n) {
327
- Index i = 2;
328
- while (i < 2 * n - 1) i *= 2;
329
- return i;
330
- }
331
-
332
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static Index getLog2(Index m) {
333
- Index log2m = 0;
334
- while (m >>= 1) log2m++;
335
- return log2m;
336
- }
337
-
338
- // Call Cooley Tukey algorithm directly, data length must be power of 2
339
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void processDataLineCooleyTukey(ComplexScalar* line_buf, Index line_len, Index log_len) {
340
- eigen_assert(isPowerOfTwo(line_len));
341
- scramble_FFT(line_buf, line_len);
342
- compute_1D_Butterfly<FFTDir>(line_buf, line_len, log_len);
343
- }
344
-
345
- // Call Bluestein's FFT algorithm, m is a good composite number greater than (2 * n - 1), used as the padding length
346
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void processDataLineBluestein(ComplexScalar* line_buf, Index line_len, Index good_composite, Index log_len, ComplexScalar* a, ComplexScalar* b, const ComplexScalar* pos_j_base_powered) {
347
- Index n = line_len;
348
- Index m = good_composite;
349
- ComplexScalar* data = line_buf;
350
-
351
- for (Index i = 0; i < n; ++i) {
352
- if(FFTDir == FFT_FORWARD) {
353
- a[i] = data[i] * numext::conj(pos_j_base_powered[i]);
354
- }
355
- else {
356
- a[i] = data[i] * pos_j_base_powered[i];
357
- }
358
- }
359
- for (Index i = n; i < m; ++i) {
360
- a[i] = ComplexScalar(0, 0);
361
- }
362
-
363
- for (Index i = 0; i < n; ++i) {
364
- if(FFTDir == FFT_FORWARD) {
365
- b[i] = pos_j_base_powered[i];
366
- }
367
- else {
368
- b[i] = numext::conj(pos_j_base_powered[i]);
369
- }
370
- }
371
- for (Index i = n; i < m - n; ++i) {
372
- b[i] = ComplexScalar(0, 0);
373
- }
374
- for (Index i = m - n; i < m; ++i) {
375
- if(FFTDir == FFT_FORWARD) {
376
- b[i] = pos_j_base_powered[m-i];
377
- }
378
- else {
379
- b[i] = numext::conj(pos_j_base_powered[m-i]);
380
- }
381
- }
382
-
383
- scramble_FFT(a, m);
384
- compute_1D_Butterfly<FFT_FORWARD>(a, m, log_len);
385
-
386
- scramble_FFT(b, m);
387
- compute_1D_Butterfly<FFT_FORWARD>(b, m, log_len);
388
-
389
- for (Index i = 0; i < m; ++i) {
390
- a[i] *= b[i];
391
- }
392
-
393
- scramble_FFT(a, m);
394
- compute_1D_Butterfly<FFT_REVERSE>(a, m, log_len);
395
-
396
- //Do the scaling after ifft
397
- for (Index i = 0; i < m; ++i) {
398
- a[i] /= m;
399
- }
400
-
401
- for (Index i = 0; i < n; ++i) {
402
- if(FFTDir == FFT_FORWARD) {
403
- data[i] = a[i] * numext::conj(pos_j_base_powered[i]);
404
- }
405
- else {
406
- data[i] = a[i] * pos_j_base_powered[i];
407
- }
408
- }
409
- }
410
-
411
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE static void scramble_FFT(ComplexScalar* data, Index n) {
412
- eigen_assert(isPowerOfTwo(n));
413
- Index j = 1;
414
- for (Index i = 1; i < n; ++i){
415
- if (j > i) {
416
- std::swap(data[j-1], data[i-1]);
417
- }
418
- Index m = n >> 1;
419
- while (m >= 2 && j > m) {
420
- j -= m;
421
- m >>= 1;
422
- }
423
- j += m;
424
- }
425
- }
426
-
427
- template <int Dir>
428
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_2(ComplexScalar* data) {
429
- ComplexScalar tmp = data[1];
430
- data[1] = data[0] - data[1];
431
- data[0] += tmp;
432
- }
433
-
434
- template <int Dir>
435
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_4(ComplexScalar* data) {
436
- ComplexScalar tmp[4];
437
- tmp[0] = data[0] + data[1];
438
- tmp[1] = data[0] - data[1];
439
- tmp[2] = data[2] + data[3];
440
- if (Dir == FFT_FORWARD) {
441
- tmp[3] = ComplexScalar(0.0, -1.0) * (data[2] - data[3]);
442
- } else {
443
- tmp[3] = ComplexScalar(0.0, 1.0) * (data[2] - data[3]);
444
- }
445
- data[0] = tmp[0] + tmp[2];
446
- data[1] = tmp[1] + tmp[3];
447
- data[2] = tmp[0] - tmp[2];
448
- data[3] = tmp[1] - tmp[3];
449
- }
450
-
451
- template <int Dir>
452
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_8(ComplexScalar* data) {
453
- ComplexScalar tmp_1[8];
454
- ComplexScalar tmp_2[8];
455
-
456
- tmp_1[0] = data[0] + data[1];
457
- tmp_1[1] = data[0] - data[1];
458
- tmp_1[2] = data[2] + data[3];
459
- if (Dir == FFT_FORWARD) {
460
- tmp_1[3] = (data[2] - data[3]) * ComplexScalar(0, -1);
461
- } else {
462
- tmp_1[3] = (data[2] - data[3]) * ComplexScalar(0, 1);
463
- }
464
- tmp_1[4] = data[4] + data[5];
465
- tmp_1[5] = data[4] - data[5];
466
- tmp_1[6] = data[6] + data[7];
467
- if (Dir == FFT_FORWARD) {
468
- tmp_1[7] = (data[6] - data[7]) * ComplexScalar(0, -1);
469
- } else {
470
- tmp_1[7] = (data[6] - data[7]) * ComplexScalar(0, 1);
471
- }
472
- tmp_2[0] = tmp_1[0] + tmp_1[2];
473
- tmp_2[1] = tmp_1[1] + tmp_1[3];
474
- tmp_2[2] = tmp_1[0] - tmp_1[2];
475
- tmp_2[3] = tmp_1[1] - tmp_1[3];
476
- tmp_2[4] = tmp_1[4] + tmp_1[6];
477
- // SQRT2DIV2 = sqrt(2)/2
478
- #define SQRT2DIV2 0.7071067811865476
479
- if (Dir == FFT_FORWARD) {
480
- tmp_2[5] = (tmp_1[5] + tmp_1[7]) * ComplexScalar(SQRT2DIV2, -SQRT2DIV2);
481
- tmp_2[6] = (tmp_1[4] - tmp_1[6]) * ComplexScalar(0, -1);
482
- tmp_2[7] = (tmp_1[5] - tmp_1[7]) * ComplexScalar(-SQRT2DIV2, -SQRT2DIV2);
483
- } else {
484
- tmp_2[5] = (tmp_1[5] + tmp_1[7]) * ComplexScalar(SQRT2DIV2, SQRT2DIV2);
485
- tmp_2[6] = (tmp_1[4] - tmp_1[6]) * ComplexScalar(0, 1);
486
- tmp_2[7] = (tmp_1[5] - tmp_1[7]) * ComplexScalar(-SQRT2DIV2, SQRT2DIV2);
487
- }
488
- data[0] = tmp_2[0] + tmp_2[4];
489
- data[1] = tmp_2[1] + tmp_2[5];
490
- data[2] = tmp_2[2] + tmp_2[6];
491
- data[3] = tmp_2[3] + tmp_2[7];
492
- data[4] = tmp_2[0] - tmp_2[4];
493
- data[5] = tmp_2[1] - tmp_2[5];
494
- data[6] = tmp_2[2] - tmp_2[6];
495
- data[7] = tmp_2[3] - tmp_2[7];
496
- }
497
-
498
- template <int Dir>
499
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void butterfly_1D_merge(
500
- ComplexScalar* data, Index n, Index n_power_of_2) {
501
- // Original code:
502
- // RealScalar wtemp = std::sin(M_PI/n);
503
- // RealScalar wpi = -std::sin(2 * M_PI/n);
504
- const RealScalar wtemp = m_sin_PI_div_n_LUT[n_power_of_2];
505
- const RealScalar wpi = (Dir == FFT_FORWARD)
506
- ? m_minus_sin_2_PI_div_n_LUT[n_power_of_2]
507
- : -m_minus_sin_2_PI_div_n_LUT[n_power_of_2];
508
-
509
- const ComplexScalar wp(wtemp, wpi);
510
- const ComplexScalar wp_one = wp + ComplexScalar(1, 0);
511
- const ComplexScalar wp_one_2 = wp_one * wp_one;
512
- const ComplexScalar wp_one_3 = wp_one_2 * wp_one;
513
- const ComplexScalar wp_one_4 = wp_one_3 * wp_one;
514
- const Index n2 = n / 2;
515
- ComplexScalar w(1.0, 0.0);
516
- for (Index i = 0; i < n2; i += 4) {
517
- ComplexScalar temp0(data[i + n2] * w);
518
- ComplexScalar temp1(data[i + 1 + n2] * w * wp_one);
519
- ComplexScalar temp2(data[i + 2 + n2] * w * wp_one_2);
520
- ComplexScalar temp3(data[i + 3 + n2] * w * wp_one_3);
521
- w = w * wp_one_4;
522
-
523
- data[i + n2] = data[i] - temp0;
524
- data[i] += temp0;
525
-
526
- data[i + 1 + n2] = data[i + 1] - temp1;
527
- data[i + 1] += temp1;
528
-
529
- data[i + 2 + n2] = data[i + 2] - temp2;
530
- data[i + 2] += temp2;
531
-
532
- data[i + 3 + n2] = data[i + 3] - temp3;
533
- data[i + 3] += temp3;
534
- }
535
- }
536
-
537
- template <int Dir>
538
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void compute_1D_Butterfly(
539
- ComplexScalar* data, Index n, Index n_power_of_2) {
540
- eigen_assert(isPowerOfTwo(n));
541
- if (n > 8) {
542
- compute_1D_Butterfly<Dir>(data, n / 2, n_power_of_2 - 1);
543
- compute_1D_Butterfly<Dir>(data + n / 2, n / 2, n_power_of_2 - 1);
544
- butterfly_1D_merge<Dir>(data, n, n_power_of_2);
545
- } else if (n == 8) {
546
- butterfly_8<Dir>(data);
547
- } else if (n == 4) {
548
- butterfly_4<Dir>(data);
549
- } else if (n == 2) {
550
- butterfly_2<Dir>(data);
551
- }
552
- }
553
-
554
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index getBaseOffsetFromIndex(Index index, Index omitted_dim) const {
555
- Index result = 0;
556
-
557
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
558
- for (int i = NumDims - 1; i > omitted_dim; --i) {
559
- const Index partial_m_stride = m_strides[i] / m_dimensions[omitted_dim];
560
- const Index idx = index / partial_m_stride;
561
- index -= idx * partial_m_stride;
562
- result += idx * m_strides[i];
563
- }
564
- result += index;
565
- }
566
- else {
567
- for (Index i = 0; i < omitted_dim; ++i) {
568
- const Index partial_m_stride = m_strides[i] / m_dimensions[omitted_dim];
569
- const Index idx = index / partial_m_stride;
570
- index -= idx * partial_m_stride;
571
- result += idx * m_strides[i];
572
- }
573
- result += index;
574
- }
575
- // Value of index_coords[omitted_dim] is not determined to this step
576
- return result;
577
- }
578
-
579
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index getIndexFromOffset(Index base, Index omitted_dim, Index offset) const {
580
- Index result = base + offset * m_strides[omitted_dim] ;
581
- return result;
582
- }
583
-
584
- protected:
585
- Index m_size;
586
- const FFT EIGEN_DEVICE_REF m_fft;
587
- Dimensions m_dimensions;
588
- array<Index, NumDims> m_strides;
589
- TensorEvaluator<ArgType, Device> m_impl;
590
- EvaluatorPointerType m_data;
591
- const Device EIGEN_DEVICE_REF m_device;
592
-
593
- // This will support a maximum FFT size of 2^32 for each dimension
594
- // m_sin_PI_div_n_LUT[i] = (-2) * std::sin(M_PI / std::pow(2,i)) ^ 2;
595
- const RealScalar m_sin_PI_div_n_LUT[32] = {
596
- RealScalar(0.0),
597
- RealScalar(-2),
598
- RealScalar(-0.999999999999999),
599
- RealScalar(-0.292893218813453),
600
- RealScalar(-0.0761204674887130),
601
- RealScalar(-0.0192147195967696),
602
- RealScalar(-0.00481527332780311),
603
- RealScalar(-0.00120454379482761),
604
- RealScalar(-3.01181303795779e-04),
605
- RealScalar(-7.52981608554592e-05),
606
- RealScalar(-1.88247173988574e-05),
607
- RealScalar(-4.70619042382852e-06),
608
- RealScalar(-1.17654829809007e-06),
609
- RealScalar(-2.94137117780840e-07),
610
- RealScalar(-7.35342821488550e-08),
611
- RealScalar(-1.83835707061916e-08),
612
- RealScalar(-4.59589268710903e-09),
613
- RealScalar(-1.14897317243732e-09),
614
- RealScalar(-2.87243293150586e-10),
615
- RealScalar( -7.18108232902250e-11),
616
- RealScalar(-1.79527058227174e-11),
617
- RealScalar(-4.48817645568941e-12),
618
- RealScalar(-1.12204411392298e-12),
619
- RealScalar(-2.80511028480785e-13),
620
- RealScalar(-7.01277571201985e-14),
621
- RealScalar(-1.75319392800498e-14),
622
- RealScalar(-4.38298482001247e-15),
623
- RealScalar(-1.09574620500312e-15),
624
- RealScalar(-2.73936551250781e-16),
625
- RealScalar(-6.84841378126949e-17),
626
- RealScalar(-1.71210344531737e-17),
627
- RealScalar(-4.28025861329343e-18)
628
- };
629
-
630
- // m_minus_sin_2_PI_div_n_LUT[i] = -std::sin(2 * M_PI / std::pow(2,i));
631
- const RealScalar m_minus_sin_2_PI_div_n_LUT[32] = {
632
- RealScalar(0.0),
633
- RealScalar(0.0),
634
- RealScalar(-1.00000000000000e+00),
635
- RealScalar(-7.07106781186547e-01),
636
- RealScalar(-3.82683432365090e-01),
637
- RealScalar(-1.95090322016128e-01),
638
- RealScalar(-9.80171403295606e-02),
639
- RealScalar(-4.90676743274180e-02),
640
- RealScalar(-2.45412285229123e-02),
641
- RealScalar(-1.22715382857199e-02),
642
- RealScalar(-6.13588464915448e-03),
643
- RealScalar(-3.06795676296598e-03),
644
- RealScalar(-1.53398018628477e-03),
645
- RealScalar(-7.66990318742704e-04),
646
- RealScalar(-3.83495187571396e-04),
647
- RealScalar(-1.91747597310703e-04),
648
- RealScalar(-9.58737990959773e-05),
649
- RealScalar(-4.79368996030669e-05),
650
- RealScalar(-2.39684498084182e-05),
651
- RealScalar(-1.19842249050697e-05),
652
- RealScalar(-5.99211245264243e-06),
653
- RealScalar(-2.99605622633466e-06),
654
- RealScalar(-1.49802811316901e-06),
655
- RealScalar(-7.49014056584716e-07),
656
- RealScalar(-3.74507028292384e-07),
657
- RealScalar(-1.87253514146195e-07),
658
- RealScalar(-9.36267570730981e-08),
659
- RealScalar(-4.68133785365491e-08),
660
- RealScalar(-2.34066892682746e-08),
661
- RealScalar(-1.17033446341373e-08),
662
- RealScalar(-5.85167231706864e-09),
663
- RealScalar(-2.92583615853432e-09)
664
- };
665
- };
666
-
667
- } // end namespace Eigen
668
-
669
- #endif // EIGEN_CXX11_TENSOR_TENSOR_FFT_H