sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-win_amd64.whl
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- sequenzo/__init__.py +64 -8
- sequenzo/big_data/clara/clara.py +1 -1
- sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
- sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
- sequenzo/clustering/KMedoids.py +39 -0
- sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
- sequenzo/clustering/hierarchical_clustering.py +304 -8
- sequenzo/define_sequence_data.py +44 -3
- sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
- sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
- sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
- sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
- sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
- sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
- sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
- sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
- sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
- sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
- sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
- sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
- sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
- sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
- sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
- sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
- sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
- sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
- sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
- sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
- sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
- sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
- sequenzo/multidomain/cat.py +0 -53
- sequenzo/multidomain/idcd.py +0 -1
- sequenzo/openmp_setup.py +233 -0
- sequenzo/sequence_characteristics/__init__.py +4 -0
- sequenzo/sequence_characteristics/complexity_index.py +17 -57
- sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
- sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
- sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
- sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
- sequenzo/sequence_characteristics/turbulence.py +47 -67
- sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
- sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
- sequenzo/visualization/plot_sequence_index.py +58 -35
- sequenzo/visualization/plot_state_distribution.py +57 -36
- sequenzo/visualization/plot_transition_matrix.py +21 -22
- sequenzo/with_event_history_analysis/__init__.py +35 -0
- sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
- sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
- {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
- sequenzo-0.1.19.dist-info/RECORD +272 -0
- sequenzo/dissimilarity_measures/setup.py +0 -35
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
- sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
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- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
- sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
- sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
- sequenzo-0.1.17.dist-info/RECORD +0 -631
- {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
- {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
- {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +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) 2015 Jianwei Cui <thucjw@gmail.com>
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//
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// This Source Code Form is subject to the terms of the Mozilla
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// Public License v. 2.0. If a copy of the MPL was not distributed
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// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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#ifndef EIGEN_CXX11_TENSOR_TENSOR_FFT_H
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#define EIGEN_CXX11_TENSOR_TENSOR_FFT_H
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namespace Eigen {
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/** \class TensorFFT
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* \ingroup CXX11_Tensor_Module
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*
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* \brief Tensor FFT class.
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*
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* TODO:
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* Vectorize the Cooley Tukey and the Bluestein algorithm
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* Add support for multithreaded evaluation
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* Improve the performance on GPU
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*/
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template <bool NeedUprade> struct MakeComplex {
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template <typename T>
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EIGEN_DEVICE_FUNC
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T operator() (const T& val) const { return val; }
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};
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template <> struct MakeComplex<true> {
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template <typename T>
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EIGEN_DEVICE_FUNC
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std::complex<T> operator() (const T& val) const { return std::complex<T>(val, 0); }
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};
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template <> struct MakeComplex<false> {
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template <typename T>
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EIGEN_DEVICE_FUNC
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std::complex<T> operator() (const std::complex<T>& val) const { return val; }
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};
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template <int ResultType> struct PartOf {
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template <typename T> T operator() (const T& val) const { return val; }
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};
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template <> struct PartOf<RealPart> {
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template <typename T> T operator() (const std::complex<T>& val) const { return val.real(); }
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};
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template <> struct PartOf<ImagPart> {
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template <typename T> T operator() (const std::complex<T>& val) const { return val.imag(); }
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};
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namespace internal {
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template <typename FFT, typename XprType, int FFTResultType, int FFTDir>
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struct traits<TensorFFTOp<FFT, XprType, FFTResultType, FFTDir> > : public traits<XprType> {
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typedef traits<XprType> XprTraits;
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typedef typename NumTraits<typename XprTraits::Scalar>::Real RealScalar;
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typedef typename std::complex<RealScalar> ComplexScalar;
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typedef typename XprTraits::Scalar InputScalar;
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typedef typename conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
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typedef typename XprTraits::StorageKind StorageKind;
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typedef typename XprTraits::Index Index;
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typedef typename XprType::Nested Nested;
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typedef typename remove_reference<Nested>::type _Nested;
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static const int NumDimensions = XprTraits::NumDimensions;
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static const int Layout = XprTraits::Layout;
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typedef typename traits<XprType>::PointerType PointerType;
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};
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template <typename FFT, typename XprType, int FFTResultType, int FFTDirection>
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struct eval<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>, Eigen::Dense> {
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typedef const TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>& type;
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};
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template <typename FFT, typename XprType, int FFTResultType, int FFTDirection>
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struct nested<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection>, 1, typename eval<TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection> >::type> {
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typedef TensorFFTOp<FFT, XprType, FFTResultType, FFTDirection> type;
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};
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} // end namespace internal
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template <typename FFT, typename XprType, int FFTResultType, int FFTDir>
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class TensorFFTOp : public TensorBase<TensorFFTOp<FFT, XprType, FFTResultType, FFTDir>, ReadOnlyAccessors> {
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public:
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typedef typename Eigen::internal::traits<TensorFFTOp>::Scalar Scalar;
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typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
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typedef typename std::complex<RealScalar> ComplexScalar;
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typedef typename internal::conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
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typedef OutputScalar CoeffReturnType;
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typedef typename Eigen::internal::nested<TensorFFTOp>::type Nested;
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typedef typename Eigen::internal::traits<TensorFFTOp>::StorageKind StorageKind;
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typedef typename Eigen::internal::traits<TensorFFTOp>::Index Index;
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EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorFFTOp(const XprType& expr, const FFT& fft)
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: m_xpr(expr), m_fft(fft) {}
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EIGEN_DEVICE_FUNC
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const FFT& fft() const { return m_fft; }
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EIGEN_DEVICE_FUNC
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const typename internal::remove_all<typename XprType::Nested>::type& expression() const {
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return m_xpr;
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}
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protected:
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typename XprType::Nested m_xpr;
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const FFT m_fft;
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};
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// Eval as rvalue
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template <typename FFT, typename ArgType, typename Device, int FFTResultType, int FFTDir>
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struct TensorEvaluator<const TensorFFTOp<FFT, ArgType, FFTResultType, FFTDir>, Device> {
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typedef TensorFFTOp<FFT, ArgType, FFTResultType, FFTDir> XprType;
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typedef typename XprType::Index Index;
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static const int NumDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
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typedef DSizes<Index, NumDims> Dimensions;
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typedef typename XprType::Scalar Scalar;
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typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
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typedef typename std::complex<RealScalar> ComplexScalar;
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typedef typename TensorEvaluator<ArgType, Device>::Dimensions InputDimensions;
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typedef internal::traits<XprType> XprTraits;
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typedef typename XprTraits::Scalar InputScalar;
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typedef typename internal::conditional<FFTResultType == RealPart || FFTResultType == ImagPart, RealScalar, ComplexScalar>::type OutputScalar;
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typedef OutputScalar CoeffReturnType;
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typedef typename PacketType<OutputScalar, Device>::type PacketReturnType;
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static const int PacketSize = internal::unpacket_traits<PacketReturnType>::size;
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typedef StorageMemory<CoeffReturnType, Device> Storage;
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typedef typename Storage::Type EvaluatorPointerType;
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enum {
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IsAligned = false,
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PacketAccess = true,
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BlockAccess = false,
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PreferBlockAccess = false,
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Layout = TensorEvaluator<ArgType, Device>::Layout,
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CoordAccess = false,
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RawAccess = false
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};
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//===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
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typedef internal::TensorBlockNotImplemented TensorBlock;
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//===--------------------------------------------------------------------===//
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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) {
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const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
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for (int i = 0; i < NumDims; ++i) {
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eigen_assert(input_dims[i] > 0);
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m_dimensions[i] = input_dims[i];
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}
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if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
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m_strides[0] = 1;
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for (int i = 1; i < NumDims; ++i) {
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m_strides[i] = m_strides[i - 1] * m_dimensions[i - 1];
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}
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} else {
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m_strides[NumDims - 1] = 1;
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for (int i = NumDims - 2; i >= 0; --i) {
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m_strides[i] = m_strides[i + 1] * m_dimensions[i + 1];
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}
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}
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m_size = m_dimensions.TotalSize();
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}
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EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const {
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}
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EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType data) {
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m_impl.evalSubExprsIfNeeded(NULL);
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if (data) {
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evalToBuf(data);
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return false;
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} else {
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m_data = (EvaluatorPointerType)m_device.get((CoeffReturnType*)(m_device.allocate_temp(sizeof(CoeffReturnType) * m_size)));
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evalToBuf(m_data);
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return true;
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}
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}
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EIGEN_STRONG_INLINE void cleanup() {
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if (m_data) {
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m_device.deallocate(m_data);
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m_data = NULL;
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}
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m_impl.cleanup();
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}
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EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE CoeffReturnType coeff(Index index) const {
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return m_data[index];
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}
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template <int LoadMode>
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EIGEN_DEVICE_FUNC EIGEN_ALWAYS_INLINE PacketReturnType
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packet(Index index) const {
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return internal::ploadt<PacketReturnType, LoadMode>(m_data + index);
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}
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EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
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costPerCoeff(bool vectorized) const {
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return TensorOpCost(sizeof(CoeffReturnType), 0, 0, vectorized, PacketSize);
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}
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EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return m_data; }
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#ifdef EIGEN_USE_SYCL
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// binding placeholder accessors to a command group handler for SYCL
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EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
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m_data.bind(cgh);
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}
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#endif
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private:
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EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void evalToBuf(EvaluatorPointerType data) {
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const bool write_to_out = internal::is_same<OutputScalar, ComplexScalar>::value;
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ComplexScalar* buf = write_to_out ? (ComplexScalar*)data : (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * m_size);
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for (Index i = 0; i < m_size; ++i) {
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buf[i] = MakeComplex<internal::is_same<InputScalar, RealScalar>::value>()(m_impl.coeff(i));
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}
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for (size_t i = 0; i < m_fft.size(); ++i) {
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Index dim = m_fft[i];
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eigen_assert(dim >= 0 && dim < NumDims);
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Index line_len = m_dimensions[dim];
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eigen_assert(line_len >= 1);
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ComplexScalar* line_buf = (ComplexScalar*)m_device.allocate(sizeof(ComplexScalar) * line_len);
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const bool is_power_of_two = isPowerOfTwo(line_len);
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const Index good_composite = is_power_of_two ? 0 : findGoodComposite(line_len);
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|
-
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
|