sequenzo 0.1.17__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

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  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +157 -157
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cpython-39-darwin.so +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/hierarchical_clustering.py +304 -8
  7. sequenzo/define_sequence_data.py +44 -3
  8. sequenzo/dissimilarity_measures/c_code.cpython-39-darwin.so +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  12. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  14. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  15. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  16. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  60. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +157 -157
  61. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cpython-39-darwin.so +0 -0
  62. sequenzo/dissimilarity_measures/utils/seqconc.c +157 -157
  63. sequenzo/dissimilarity_measures/utils/seqconc.cpython-39-darwin.so +0 -0
  64. sequenzo/dissimilarity_measures/utils/seqdss.c +157 -157
  65. sequenzo/dissimilarity_measures/utils/seqdss.cpython-39-darwin.so +0 -0
  66. sequenzo/dissimilarity_measures/utils/seqdur.c +157 -157
  67. sequenzo/dissimilarity_measures/utils/seqdur.cpython-39-darwin.so +0 -0
  68. sequenzo/dissimilarity_measures/utils/seqlength.c +157 -157
  69. sequenzo/dissimilarity_measures/utils/seqlength.cpython-39-darwin.so +0 -0
  70. sequenzo/multidomain/cat.py +0 -53
  71. sequenzo/multidomain/idcd.py +0 -1
  72. sequenzo/openmp_setup.py +233 -0
  73. sequenzo/sequence_characteristics/__init__.py +4 -0
  74. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  75. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  76. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  77. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  78. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  79. sequenzo/sequence_characteristics/turbulence.py +47 -67
  80. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  81. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  82. sequenzo/visualization/plot_sequence_index.py +58 -35
  83. sequenzo/visualization/plot_state_distribution.py +57 -36
  84. sequenzo/visualization/plot_transition_matrix.py +21 -22
  85. sequenzo/with_event_history_analysis/__init__.py +35 -0
  86. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  87. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  88. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  89. sequenzo-0.1.19.dist-info/RECORD +215 -0
  90. sequenzo/dissimilarity_measures/setup.py +0 -35
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
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  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  420. sequenzo-0.1.17.dist-info/RECORD +0 -537
  421. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  422. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  423. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,398 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2008-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
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_SPARSEMATRIXBASE_H
11
- #define EIGEN_SPARSEMATRIXBASE_H
12
-
13
- namespace Eigen {
14
-
15
- /** \ingroup SparseCore_Module
16
- *
17
- * \class SparseMatrixBase
18
- *
19
- * \brief Base class of any sparse matrices or sparse expressions
20
- *
21
- * \tparam Derived is the derived type, e.g. a sparse matrix type, or an expression, etc.
22
- *
23
- * This class can be extended with the help of the plugin mechanism described on the page
24
- * \ref TopicCustomizing_Plugins by defining the preprocessor symbol \c EIGEN_SPARSEMATRIXBASE_PLUGIN.
25
- */
26
- template<typename Derived> class SparseMatrixBase
27
- : public EigenBase<Derived>
28
- {
29
- public:
30
-
31
- typedef typename internal::traits<Derived>::Scalar Scalar;
32
-
33
- /** The numeric type of the expression' coefficients, e.g. float, double, int or std::complex<float>, etc.
34
- *
35
- * It is an alias for the Scalar type */
36
- typedef Scalar value_type;
37
-
38
- typedef typename internal::packet_traits<Scalar>::type PacketScalar;
39
- typedef typename internal::traits<Derived>::StorageKind StorageKind;
40
-
41
- /** The integer type used to \b store indices within a SparseMatrix.
42
- * For a \c SparseMatrix<Scalar,Options,IndexType> it an alias of the third template parameter \c IndexType. */
43
- typedef typename internal::traits<Derived>::StorageIndex StorageIndex;
44
-
45
- typedef typename internal::add_const_on_value_type_if_arithmetic<
46
- typename internal::packet_traits<Scalar>::type
47
- >::type PacketReturnType;
48
-
49
- typedef SparseMatrixBase StorageBaseType;
50
-
51
- typedef Matrix<StorageIndex,Dynamic,1> IndexVector;
52
- typedef Matrix<Scalar,Dynamic,1> ScalarVector;
53
-
54
- template<typename OtherDerived>
55
- Derived& operator=(const EigenBase<OtherDerived> &other);
56
-
57
- enum {
58
-
59
- RowsAtCompileTime = internal::traits<Derived>::RowsAtCompileTime,
60
- /**< The number of rows at compile-time. This is just a copy of the value provided
61
- * by the \a Derived type. If a value is not known at compile-time,
62
- * it is set to the \a Dynamic constant.
63
- * \sa MatrixBase::rows(), MatrixBase::cols(), ColsAtCompileTime, SizeAtCompileTime */
64
-
65
- ColsAtCompileTime = internal::traits<Derived>::ColsAtCompileTime,
66
- /**< The number of columns at compile-time. This is just a copy of the value provided
67
- * by the \a Derived type. If a value is not known at compile-time,
68
- * it is set to the \a Dynamic constant.
69
- * \sa MatrixBase::rows(), MatrixBase::cols(), RowsAtCompileTime, SizeAtCompileTime */
70
-
71
-
72
- SizeAtCompileTime = (internal::size_at_compile_time<internal::traits<Derived>::RowsAtCompileTime,
73
- internal::traits<Derived>::ColsAtCompileTime>::ret),
74
- /**< This is equal to the number of coefficients, i.e. the number of
75
- * rows times the number of columns, or to \a Dynamic if this is not
76
- * known at compile-time. \sa RowsAtCompileTime, ColsAtCompileTime */
77
-
78
- MaxRowsAtCompileTime = RowsAtCompileTime,
79
- MaxColsAtCompileTime = ColsAtCompileTime,
80
-
81
- MaxSizeAtCompileTime = (internal::size_at_compile_time<MaxRowsAtCompileTime,
82
- MaxColsAtCompileTime>::ret),
83
-
84
- IsVectorAtCompileTime = RowsAtCompileTime == 1 || ColsAtCompileTime == 1,
85
- /**< This is set to true if either the number of rows or the number of
86
- * columns is known at compile-time to be equal to 1. Indeed, in that case,
87
- * we are dealing with a column-vector (if there is only one column) or with
88
- * a row-vector (if there is only one row). */
89
-
90
- NumDimensions = int(MaxSizeAtCompileTime) == 1 ? 0 : bool(IsVectorAtCompileTime) ? 1 : 2,
91
- /**< This value is equal to Tensor::NumDimensions, i.e. 0 for scalars, 1 for vectors,
92
- * and 2 for matrices.
93
- */
94
-
95
- Flags = internal::traits<Derived>::Flags,
96
- /**< This stores expression \ref flags flags which may or may not be inherited by new expressions
97
- * constructed from this one. See the \ref flags "list of flags".
98
- */
99
-
100
- IsRowMajor = Flags&RowMajorBit ? 1 : 0,
101
-
102
- InnerSizeAtCompileTime = int(IsVectorAtCompileTime) ? int(SizeAtCompileTime)
103
- : int(IsRowMajor) ? int(ColsAtCompileTime) : int(RowsAtCompileTime),
104
-
105
- #ifndef EIGEN_PARSED_BY_DOXYGEN
106
- _HasDirectAccess = (int(Flags)&DirectAccessBit) ? 1 : 0 // workaround sunCC
107
- #endif
108
- };
109
-
110
- /** \internal the return type of MatrixBase::adjoint() */
111
- typedef typename internal::conditional<NumTraits<Scalar>::IsComplex,
112
- CwiseUnaryOp<internal::scalar_conjugate_op<Scalar>, Eigen::Transpose<const Derived> >,
113
- Transpose<const Derived>
114
- >::type AdjointReturnType;
115
- typedef Transpose<Derived> TransposeReturnType;
116
- typedef typename internal::add_const<Transpose<const Derived> >::type ConstTransposeReturnType;
117
-
118
- // FIXME storage order do not match evaluator storage order
119
- typedef SparseMatrix<Scalar, Flags&RowMajorBit ? RowMajor : ColMajor, StorageIndex> PlainObject;
120
-
121
- #ifndef EIGEN_PARSED_BY_DOXYGEN
122
- /** This is the "real scalar" type; if the \a Scalar type is already real numbers
123
- * (e.g. int, float or double) then \a RealScalar is just the same as \a Scalar. If
124
- * \a Scalar is \a std::complex<T> then RealScalar is \a T.
125
- *
126
- * \sa class NumTraits
127
- */
128
- typedef typename NumTraits<Scalar>::Real RealScalar;
129
-
130
- /** \internal the return type of coeff()
131
- */
132
- typedef typename internal::conditional<_HasDirectAccess, const Scalar&, Scalar>::type CoeffReturnType;
133
-
134
- /** \internal Represents a matrix with all coefficients equal to one another*/
135
- typedef CwiseNullaryOp<internal::scalar_constant_op<Scalar>,Matrix<Scalar,Dynamic,Dynamic> > ConstantReturnType;
136
-
137
- /** type of the equivalent dense matrix */
138
- typedef Matrix<Scalar,RowsAtCompileTime,ColsAtCompileTime> DenseMatrixType;
139
- /** type of the equivalent square matrix */
140
- typedef Matrix<Scalar,EIGEN_SIZE_MAX(RowsAtCompileTime,ColsAtCompileTime),
141
- EIGEN_SIZE_MAX(RowsAtCompileTime,ColsAtCompileTime)> SquareMatrixType;
142
-
143
- inline const Derived& derived() const { return *static_cast<const Derived*>(this); }
144
- inline Derived& derived() { return *static_cast<Derived*>(this); }
145
- inline Derived& const_cast_derived() const
146
- { return *static_cast<Derived*>(const_cast<SparseMatrixBase*>(this)); }
147
-
148
- typedef EigenBase<Derived> Base;
149
-
150
- #endif // not EIGEN_PARSED_BY_DOXYGEN
151
-
152
- #define EIGEN_CURRENT_STORAGE_BASE_CLASS Eigen::SparseMatrixBase
153
- #ifdef EIGEN_PARSED_BY_DOXYGEN
154
- #define EIGEN_DOC_UNARY_ADDONS(METHOD,OP) /** <p>This method does not change the sparsity of \c *this: the OP is applied to explicitly stored coefficients only. \sa SparseCompressedBase::coeffs() </p> */
155
- #define EIGEN_DOC_BLOCK_ADDONS_NOT_INNER_PANEL /** <p> \warning This method returns a read-only expression for any sparse matrices. \sa \ref TutorialSparse_SubMatrices "Sparse block operations" </p> */
156
- #define EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF(COND) /** <p> \warning This method returns a read-write expression for COND sparse matrices only. Otherwise, the returned expression is read-only. \sa \ref TutorialSparse_SubMatrices "Sparse block operations" </p> */
157
- #else
158
- #define EIGEN_DOC_UNARY_ADDONS(X,Y)
159
- #define EIGEN_DOC_BLOCK_ADDONS_NOT_INNER_PANEL
160
- #define EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF(COND)
161
- #endif
162
- # include "../plugins/CommonCwiseUnaryOps.h"
163
- # include "../plugins/CommonCwiseBinaryOps.h"
164
- # include "../plugins/MatrixCwiseUnaryOps.h"
165
- # include "../plugins/MatrixCwiseBinaryOps.h"
166
- # include "../plugins/BlockMethods.h"
167
- # ifdef EIGEN_SPARSEMATRIXBASE_PLUGIN
168
- # include EIGEN_SPARSEMATRIXBASE_PLUGIN
169
- # endif
170
- #undef EIGEN_CURRENT_STORAGE_BASE_CLASS
171
- #undef EIGEN_DOC_UNARY_ADDONS
172
- #undef EIGEN_DOC_BLOCK_ADDONS_NOT_INNER_PANEL
173
- #undef EIGEN_DOC_BLOCK_ADDONS_INNER_PANEL_IF
174
-
175
- /** \returns the number of rows. \sa cols() */
176
- inline Index rows() const { return derived().rows(); }
177
- /** \returns the number of columns. \sa rows() */
178
- inline Index cols() const { return derived().cols(); }
179
- /** \returns the number of coefficients, which is \a rows()*cols().
180
- * \sa rows(), cols(). */
181
- inline Index size() const { return rows() * cols(); }
182
- /** \returns true if either the number of rows or the number of columns is equal to 1.
183
- * In other words, this function returns
184
- * \code rows()==1 || cols()==1 \endcode
185
- * \sa rows(), cols(), IsVectorAtCompileTime. */
186
- inline bool isVector() const { return rows()==1 || cols()==1; }
187
- /** \returns the size of the storage major dimension,
188
- * i.e., the number of columns for a columns major matrix, and the number of rows otherwise */
189
- Index outerSize() const { return (int(Flags)&RowMajorBit) ? this->rows() : this->cols(); }
190
- /** \returns the size of the inner dimension according to the storage order,
191
- * i.e., the number of rows for a columns major matrix, and the number of cols otherwise */
192
- Index innerSize() const { return (int(Flags)&RowMajorBit) ? this->cols() : this->rows(); }
193
-
194
- bool isRValue() const { return m_isRValue; }
195
- Derived& markAsRValue() { m_isRValue = true; return derived(); }
196
-
197
- SparseMatrixBase() : m_isRValue(false) { /* TODO check flags */ }
198
-
199
-
200
- template<typename OtherDerived>
201
- Derived& operator=(const ReturnByValue<OtherDerived>& other);
202
-
203
- template<typename OtherDerived>
204
- inline Derived& operator=(const SparseMatrixBase<OtherDerived>& other);
205
-
206
- inline Derived& operator=(const Derived& other);
207
-
208
- protected:
209
-
210
- template<typename OtherDerived>
211
- inline Derived& assign(const OtherDerived& other);
212
-
213
- template<typename OtherDerived>
214
- inline void assignGeneric(const OtherDerived& other);
215
-
216
- public:
217
-
218
- friend std::ostream & operator << (std::ostream & s, const SparseMatrixBase& m)
219
- {
220
- typedef typename Derived::Nested Nested;
221
- typedef typename internal::remove_all<Nested>::type NestedCleaned;
222
-
223
- if (Flags&RowMajorBit)
224
- {
225
- Nested nm(m.derived());
226
- internal::evaluator<NestedCleaned> thisEval(nm);
227
- for (Index row=0; row<nm.outerSize(); ++row)
228
- {
229
- Index col = 0;
230
- for (typename internal::evaluator<NestedCleaned>::InnerIterator it(thisEval, row); it; ++it)
231
- {
232
- for ( ; col<it.index(); ++col)
233
- s << "0 ";
234
- s << it.value() << " ";
235
- ++col;
236
- }
237
- for ( ; col<m.cols(); ++col)
238
- s << "0 ";
239
- s << std::endl;
240
- }
241
- }
242
- else
243
- {
244
- Nested nm(m.derived());
245
- internal::evaluator<NestedCleaned> thisEval(nm);
246
- if (m.cols() == 1) {
247
- Index row = 0;
248
- for (typename internal::evaluator<NestedCleaned>::InnerIterator it(thisEval, 0); it; ++it)
249
- {
250
- for ( ; row<it.index(); ++row)
251
- s << "0" << std::endl;
252
- s << it.value() << std::endl;
253
- ++row;
254
- }
255
- for ( ; row<m.rows(); ++row)
256
- s << "0" << std::endl;
257
- }
258
- else
259
- {
260
- SparseMatrix<Scalar, RowMajorBit, StorageIndex> trans = m;
261
- s << static_cast<const SparseMatrixBase<SparseMatrix<Scalar, RowMajorBit, StorageIndex> >&>(trans);
262
- }
263
- }
264
- return s;
265
- }
266
-
267
- template<typename OtherDerived>
268
- Derived& operator+=(const SparseMatrixBase<OtherDerived>& other);
269
- template<typename OtherDerived>
270
- Derived& operator-=(const SparseMatrixBase<OtherDerived>& other);
271
-
272
- template<typename OtherDerived>
273
- Derived& operator+=(const DiagonalBase<OtherDerived>& other);
274
- template<typename OtherDerived>
275
- Derived& operator-=(const DiagonalBase<OtherDerived>& other);
276
-
277
- template<typename OtherDerived>
278
- Derived& operator+=(const EigenBase<OtherDerived> &other);
279
- template<typename OtherDerived>
280
- Derived& operator-=(const EigenBase<OtherDerived> &other);
281
-
282
- Derived& operator*=(const Scalar& other);
283
- Derived& operator/=(const Scalar& other);
284
-
285
- template<typename OtherDerived> struct CwiseProductDenseReturnType {
286
- typedef CwiseBinaryOp<internal::scalar_product_op<typename ScalarBinaryOpTraits<
287
- typename internal::traits<Derived>::Scalar,
288
- typename internal::traits<OtherDerived>::Scalar
289
- >::ReturnType>,
290
- const Derived,
291
- const OtherDerived
292
- > Type;
293
- };
294
-
295
- template<typename OtherDerived>
296
- EIGEN_STRONG_INLINE const typename CwiseProductDenseReturnType<OtherDerived>::Type
297
- cwiseProduct(const MatrixBase<OtherDerived> &other) const;
298
-
299
- // sparse * diagonal
300
- template<typename OtherDerived>
301
- const Product<Derived,OtherDerived>
302
- operator*(const DiagonalBase<OtherDerived> &other) const
303
- { return Product<Derived,OtherDerived>(derived(), other.derived()); }
304
-
305
- // diagonal * sparse
306
- template<typename OtherDerived> friend
307
- const Product<OtherDerived,Derived>
308
- operator*(const DiagonalBase<OtherDerived> &lhs, const SparseMatrixBase& rhs)
309
- { return Product<OtherDerived,Derived>(lhs.derived(), rhs.derived()); }
310
-
311
- // sparse * sparse
312
- template<typename OtherDerived>
313
- const Product<Derived,OtherDerived,AliasFreeProduct>
314
- operator*(const SparseMatrixBase<OtherDerived> &other) const;
315
-
316
- // sparse * dense
317
- template<typename OtherDerived>
318
- const Product<Derived,OtherDerived>
319
- operator*(const MatrixBase<OtherDerived> &other) const
320
- { return Product<Derived,OtherDerived>(derived(), other.derived()); }
321
-
322
- // dense * sparse
323
- template<typename OtherDerived> friend
324
- const Product<OtherDerived,Derived>
325
- operator*(const MatrixBase<OtherDerived> &lhs, const SparseMatrixBase& rhs)
326
- { return Product<OtherDerived,Derived>(lhs.derived(), rhs.derived()); }
327
-
328
- /** \returns an expression of P H P^-1 where H is the matrix represented by \c *this */
329
- SparseSymmetricPermutationProduct<Derived,Upper|Lower> twistedBy(const PermutationMatrix<Dynamic,Dynamic,StorageIndex>& perm) const
330
- {
331
- return SparseSymmetricPermutationProduct<Derived,Upper|Lower>(derived(), perm);
332
- }
333
-
334
- template<typename OtherDerived>
335
- Derived& operator*=(const SparseMatrixBase<OtherDerived>& other);
336
-
337
- template<int Mode>
338
- inline const TriangularView<const Derived, Mode> triangularView() const;
339
-
340
- template<unsigned int UpLo> struct SelfAdjointViewReturnType { typedef SparseSelfAdjointView<Derived, UpLo> Type; };
341
- template<unsigned int UpLo> struct ConstSelfAdjointViewReturnType { typedef const SparseSelfAdjointView<const Derived, UpLo> Type; };
342
-
343
- template<unsigned int UpLo> inline
344
- typename ConstSelfAdjointViewReturnType<UpLo>::Type selfadjointView() const;
345
- template<unsigned int UpLo> inline
346
- typename SelfAdjointViewReturnType<UpLo>::Type selfadjointView();
347
-
348
- template<typename OtherDerived> Scalar dot(const MatrixBase<OtherDerived>& other) const;
349
- template<typename OtherDerived> Scalar dot(const SparseMatrixBase<OtherDerived>& other) const;
350
- RealScalar squaredNorm() const;
351
- RealScalar norm() const;
352
- RealScalar blueNorm() const;
353
-
354
- TransposeReturnType transpose() { return TransposeReturnType(derived()); }
355
- const ConstTransposeReturnType transpose() const { return ConstTransposeReturnType(derived()); }
356
- const AdjointReturnType adjoint() const { return AdjointReturnType(transpose()); }
357
-
358
- DenseMatrixType toDense() const
359
- {
360
- return DenseMatrixType(derived());
361
- }
362
-
363
- template<typename OtherDerived>
364
- bool isApprox(const SparseMatrixBase<OtherDerived>& other,
365
- const RealScalar& prec = NumTraits<Scalar>::dummy_precision()) const;
366
-
367
- template<typename OtherDerived>
368
- bool isApprox(const MatrixBase<OtherDerived>& other,
369
- const RealScalar& prec = NumTraits<Scalar>::dummy_precision()) const
370
- { return toDense().isApprox(other,prec); }
371
-
372
- /** \returns the matrix or vector obtained by evaluating this expression.
373
- *
374
- * Notice that in the case of a plain matrix or vector (not an expression) this function just returns
375
- * a const reference, in order to avoid a useless copy.
376
- */
377
- inline const typename internal::eval<Derived>::type eval() const
378
- { return typename internal::eval<Derived>::type(derived()); }
379
-
380
- Scalar sum() const;
381
-
382
- inline const SparseView<Derived>
383
- pruned(const Scalar& reference = Scalar(0), const RealScalar& epsilon = NumTraits<Scalar>::dummy_precision()) const;
384
-
385
- protected:
386
-
387
- bool m_isRValue;
388
-
389
- static inline StorageIndex convert_index(const Index idx) {
390
- return internal::convert_index<StorageIndex>(idx);
391
- }
392
- private:
393
- template<typename Dest> void evalTo(Dest &) const;
394
- };
395
-
396
- } // end namespace Eigen
397
-
398
- #endif // EIGEN_SPARSEMATRIXBASE_H
@@ -1,178 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2012 Gael Guennebaud <gael.guennebaud@inria.fr>
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_SPARSE_PERMUTATION_H
11
- #define EIGEN_SPARSE_PERMUTATION_H
12
-
13
- // This file implements sparse * permutation products
14
-
15
- namespace Eigen {
16
-
17
- namespace internal {
18
-
19
- template<typename ExpressionType, int Side, bool Transposed>
20
- struct permutation_matrix_product<ExpressionType, Side, Transposed, SparseShape>
21
- {
22
- typedef typename nested_eval<ExpressionType, 1>::type MatrixType;
23
- typedef typename remove_all<MatrixType>::type MatrixTypeCleaned;
24
-
25
- typedef typename MatrixTypeCleaned::Scalar Scalar;
26
- typedef typename MatrixTypeCleaned::StorageIndex StorageIndex;
27
-
28
- enum {
29
- SrcStorageOrder = MatrixTypeCleaned::Flags&RowMajorBit ? RowMajor : ColMajor,
30
- MoveOuter = SrcStorageOrder==RowMajor ? Side==OnTheLeft : Side==OnTheRight
31
- };
32
-
33
- typedef typename internal::conditional<MoveOuter,
34
- SparseMatrix<Scalar,SrcStorageOrder,StorageIndex>,
35
- SparseMatrix<Scalar,int(SrcStorageOrder)==RowMajor?ColMajor:RowMajor,StorageIndex> >::type ReturnType;
36
-
37
- template<typename Dest,typename PermutationType>
38
- static inline void run(Dest& dst, const PermutationType& perm, const ExpressionType& xpr)
39
- {
40
- MatrixType mat(xpr);
41
- if(MoveOuter)
42
- {
43
- SparseMatrix<Scalar,SrcStorageOrder,StorageIndex> tmp(mat.rows(), mat.cols());
44
- Matrix<StorageIndex,Dynamic,1> sizes(mat.outerSize());
45
- for(Index j=0; j<mat.outerSize(); ++j)
46
- {
47
- Index jp = perm.indices().coeff(j);
48
- sizes[((Side==OnTheLeft) ^ Transposed) ? jp : j] = StorageIndex(mat.innerVector(((Side==OnTheRight) ^ Transposed) ? jp : j).nonZeros());
49
- }
50
- tmp.reserve(sizes);
51
- for(Index j=0; j<mat.outerSize(); ++j)
52
- {
53
- Index jp = perm.indices().coeff(j);
54
- Index jsrc = ((Side==OnTheRight) ^ Transposed) ? jp : j;
55
- Index jdst = ((Side==OnTheLeft) ^ Transposed) ? jp : j;
56
- for(typename MatrixTypeCleaned::InnerIterator it(mat,jsrc); it; ++it)
57
- tmp.insertByOuterInner(jdst,it.index()) = it.value();
58
- }
59
- dst = tmp;
60
- }
61
- else
62
- {
63
- SparseMatrix<Scalar,int(SrcStorageOrder)==RowMajor?ColMajor:RowMajor,StorageIndex> tmp(mat.rows(), mat.cols());
64
- Matrix<StorageIndex,Dynamic,1> sizes(tmp.outerSize());
65
- sizes.setZero();
66
- PermutationMatrix<Dynamic,Dynamic,StorageIndex> perm_cpy;
67
- if((Side==OnTheLeft) ^ Transposed)
68
- perm_cpy = perm;
69
- else
70
- perm_cpy = perm.transpose();
71
-
72
- for(Index j=0; j<mat.outerSize(); ++j)
73
- for(typename MatrixTypeCleaned::InnerIterator it(mat,j); it; ++it)
74
- sizes[perm_cpy.indices().coeff(it.index())]++;
75
- tmp.reserve(sizes);
76
- for(Index j=0; j<mat.outerSize(); ++j)
77
- for(typename MatrixTypeCleaned::InnerIterator it(mat,j); it; ++it)
78
- tmp.insertByOuterInner(perm_cpy.indices().coeff(it.index()),j) = it.value();
79
- dst = tmp;
80
- }
81
- }
82
- };
83
-
84
- }
85
-
86
- namespace internal {
87
-
88
- template <int ProductTag> struct product_promote_storage_type<Sparse, PermutationStorage, ProductTag> { typedef Sparse ret; };
89
- template <int ProductTag> struct product_promote_storage_type<PermutationStorage, Sparse, ProductTag> { typedef Sparse ret; };
90
-
91
- // TODO, the following two overloads are only needed to define the right temporary type through
92
- // typename traits<permutation_sparse_matrix_product<Rhs,Lhs,OnTheRight,false> >::ReturnType
93
- // whereas it should be correctly handled by traits<Product<> >::PlainObject
94
-
95
- template<typename Lhs, typename Rhs, int ProductTag>
96
- struct product_evaluator<Product<Lhs, Rhs, AliasFreeProduct>, ProductTag, PermutationShape, SparseShape>
97
- : public evaluator<typename permutation_matrix_product<Rhs,OnTheLeft,false,SparseShape>::ReturnType>
98
- {
99
- typedef Product<Lhs, Rhs, AliasFreeProduct> XprType;
100
- typedef typename permutation_matrix_product<Rhs,OnTheLeft,false,SparseShape>::ReturnType PlainObject;
101
- typedef evaluator<PlainObject> Base;
102
-
103
- enum {
104
- Flags = Base::Flags | EvalBeforeNestingBit
105
- };
106
-
107
- explicit product_evaluator(const XprType& xpr)
108
- : m_result(xpr.rows(), xpr.cols())
109
- {
110
- ::new (static_cast<Base*>(this)) Base(m_result);
111
- generic_product_impl<Lhs, Rhs, PermutationShape, SparseShape, ProductTag>::evalTo(m_result, xpr.lhs(), xpr.rhs());
112
- }
113
-
114
- protected:
115
- PlainObject m_result;
116
- };
117
-
118
- template<typename Lhs, typename Rhs, int ProductTag>
119
- struct product_evaluator<Product<Lhs, Rhs, AliasFreeProduct>, ProductTag, SparseShape, PermutationShape >
120
- : public evaluator<typename permutation_matrix_product<Lhs,OnTheRight,false,SparseShape>::ReturnType>
121
- {
122
- typedef Product<Lhs, Rhs, AliasFreeProduct> XprType;
123
- typedef typename permutation_matrix_product<Lhs,OnTheRight,false,SparseShape>::ReturnType PlainObject;
124
- typedef evaluator<PlainObject> Base;
125
-
126
- enum {
127
- Flags = Base::Flags | EvalBeforeNestingBit
128
- };
129
-
130
- explicit product_evaluator(const XprType& xpr)
131
- : m_result(xpr.rows(), xpr.cols())
132
- {
133
- ::new (static_cast<Base*>(this)) Base(m_result);
134
- generic_product_impl<Lhs, Rhs, SparseShape, PermutationShape, ProductTag>::evalTo(m_result, xpr.lhs(), xpr.rhs());
135
- }
136
-
137
- protected:
138
- PlainObject m_result;
139
- };
140
-
141
- } // end namespace internal
142
-
143
- /** \returns the matrix with the permutation applied to the columns
144
- */
145
- template<typename SparseDerived, typename PermDerived>
146
- inline const Product<SparseDerived, PermDerived, AliasFreeProduct>
147
- operator*(const SparseMatrixBase<SparseDerived>& matrix, const PermutationBase<PermDerived>& perm)
148
- { return Product<SparseDerived, PermDerived, AliasFreeProduct>(matrix.derived(), perm.derived()); }
149
-
150
- /** \returns the matrix with the permutation applied to the rows
151
- */
152
- template<typename SparseDerived, typename PermDerived>
153
- inline const Product<PermDerived, SparseDerived, AliasFreeProduct>
154
- operator*( const PermutationBase<PermDerived>& perm, const SparseMatrixBase<SparseDerived>& matrix)
155
- { return Product<PermDerived, SparseDerived, AliasFreeProduct>(perm.derived(), matrix.derived()); }
156
-
157
-
158
- /** \returns the matrix with the inverse permutation applied to the columns.
159
- */
160
- template<typename SparseDerived, typename PermutationType>
161
- inline const Product<SparseDerived, Inverse<PermutationType>, AliasFreeProduct>
162
- operator*(const SparseMatrixBase<SparseDerived>& matrix, const InverseImpl<PermutationType, PermutationStorage>& tperm)
163
- {
164
- return Product<SparseDerived, Inverse<PermutationType>, AliasFreeProduct>(matrix.derived(), tperm.derived());
165
- }
166
-
167
- /** \returns the matrix with the inverse permutation applied to the rows.
168
- */
169
- template<typename SparseDerived, typename PermutationType>
170
- inline const Product<Inverse<PermutationType>, SparseDerived, AliasFreeProduct>
171
- operator*(const InverseImpl<PermutationType,PermutationStorage>& tperm, const SparseMatrixBase<SparseDerived>& matrix)
172
- {
173
- return Product<Inverse<PermutationType>, SparseDerived, AliasFreeProduct>(tperm.derived(), matrix.derived());
174
- }
175
-
176
- } // end namespace Eigen
177
-
178
- #endif // EIGEN_SPARSE_SELFADJOINTVIEW_H