sequenzo 0.1.17__cp39-cp39-win_amd64.whl → 0.1.19__cp39-cp39-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of sequenzo might be problematic. Click here for more details.

Files changed (475) hide show
  1. sequenzo/__init__.py +64 -8
  2. sequenzo/big_data/clara/clara.py +1 -1
  3. sequenzo/big_data/clara/utils/get_weighted_diss.c +156 -156
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp39-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp39-win_amd64.pyd +0 -0
  7. sequenzo/clustering/hierarchical_clustering.py +304 -8
  8. sequenzo/define_sequence_data.py +44 -3
  9. sequenzo/dissimilarity_measures/c_code.cp39-win_amd64.pyd +0 -0
  10. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  11. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  12. sequenzo/dissimilarity_measures/src/DHDdistance.cpp +13 -37
  13. sequenzo/dissimilarity_measures/src/LCPdistance.cpp +13 -37
  14. sequenzo/dissimilarity_measures/src/OMdistance.cpp +12 -47
  15. sequenzo/dissimilarity_measures/src/OMspellDistance.cpp +103 -67
  16. sequenzo/dissimilarity_measures/src/dp_utils.h +160 -0
  17. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_arithmetic.hpp +41 -16
  18. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_complex.hpp +4 -0
  19. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_details.hpp +7 -0
  20. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_logical.hpp +10 -0
  21. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_math.hpp +127 -43
  22. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_memory.hpp +30 -2
  23. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_swizzle.hpp +174 -0
  24. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/common/xsimd_common_trigo.hpp +14 -5
  25. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx.hpp +111 -54
  26. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx2.hpp +131 -9
  27. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512bw.hpp +11 -113
  28. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512dq.hpp +39 -7
  29. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512f.hpp +336 -30
  30. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi.hpp +9 -37
  31. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_avx512vbmi2.hpp +58 -0
  32. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common.hpp +1 -0
  33. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_common_fwd.hpp +35 -2
  34. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_constants.hpp +3 -1
  35. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_emulated.hpp +17 -0
  36. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_avx.hpp +13 -0
  37. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma3_sse.hpp +18 -0
  38. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_fma4.hpp +13 -0
  39. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_isa.hpp +8 -0
  40. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon.hpp +363 -34
  41. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_neon64.hpp +7 -0
  42. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_rvv.hpp +13 -0
  43. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_scalar.hpp +41 -4
  44. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse2.hpp +252 -16
  45. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sse3.hpp +9 -0
  46. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_ssse3.hpp +12 -1
  47. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_sve.hpp +7 -0
  48. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_vsx.hpp +892 -0
  49. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/arch/xsimd_wasm.hpp +78 -1
  50. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_arch.hpp +3 -1
  51. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_config.hpp +13 -2
  52. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_cpuid.hpp +5 -0
  53. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/config/xsimd_inline.hpp +5 -1
  54. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_all_registers.hpp +2 -0
  55. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_api.hpp +64 -1
  56. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_batch.hpp +36 -0
  57. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_rvv_register.hpp +40 -31
  58. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_traits.hpp +8 -0
  59. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/types/xsimd_vsx_register.hpp +77 -0
  60. sequenzo/dissimilarity_measures/src/xsimd/include/xsimd/xsimd.hpp +6 -0
  61. sequenzo/dissimilarity_measures/src/xsimd/test/test_basic_math.cpp +6 -0
  62. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch.cpp +54 -2
  63. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_bool.cpp +8 -0
  64. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_cast.cpp +11 -4
  65. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_complex.cpp +18 -0
  66. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_int.cpp +8 -14
  67. sequenzo/dissimilarity_measures/src/xsimd/test/test_batch_manip.cpp +216 -173
  68. sequenzo/dissimilarity_measures/src/xsimd/test/test_load_store.cpp +6 -0
  69. sequenzo/dissimilarity_measures/src/xsimd/test/test_memory.cpp +1 -1
  70. sequenzo/dissimilarity_measures/src/xsimd/test/test_power.cpp +7 -4
  71. sequenzo/dissimilarity_measures/src/xsimd/test/test_select.cpp +6 -2
  72. sequenzo/dissimilarity_measures/src/xsimd/test/test_shuffle.cpp +32 -18
  73. sequenzo/dissimilarity_measures/src/xsimd/test/test_utils.hpp +21 -24
  74. sequenzo/dissimilarity_measures/src/xsimd/test/test_xsimd_api.cpp +69 -9
  75. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +156 -156
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp39-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +156 -156
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp39-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +156 -156
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp39-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +156 -156
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp39-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +156 -156
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp39-win_amd64.pyd +0 -0
  85. sequenzo/multidomain/cat.py +0 -53
  86. sequenzo/multidomain/idcd.py +0 -1
  87. sequenzo/openmp_setup.py +233 -0
  88. sequenzo/sequence_characteristics/__init__.py +4 -0
  89. sequenzo/sequence_characteristics/complexity_index.py +17 -57
  90. sequenzo/sequence_characteristics/overall_cross_sectional_entropy.py +177 -111
  91. sequenzo/sequence_characteristics/plot_characteristics.py +30 -11
  92. sequenzo/sequence_characteristics/simple_characteristics.py +1 -0
  93. sequenzo/sequence_characteristics/state_frequencies_and_entropy_per_sequence.py +9 -3
  94. sequenzo/sequence_characteristics/turbulence.py +47 -67
  95. sequenzo/sequence_characteristics/variance_of_spell_durations.py +19 -9
  96. sequenzo/sequence_characteristics/within_sequence_entropy.py +5 -58
  97. sequenzo/visualization/plot_sequence_index.py +58 -35
  98. sequenzo/visualization/plot_state_distribution.py +57 -36
  99. sequenzo/visualization/plot_transition_matrix.py +21 -22
  100. sequenzo/with_event_history_analysis/__init__.py +35 -0
  101. sequenzo/with_event_history_analysis/sequence_analysis_multi_state_model.py +850 -0
  102. sequenzo/with_event_history_analysis/sequence_history_analysis.py +283 -0
  103. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/METADATA +48 -14
  104. sequenzo-0.1.19.dist-info/RECORD +272 -0
  105. sequenzo/dissimilarity_measures/setup.py +0 -35
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  172. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  173. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  174. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  175. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  176. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  177. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  178. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  179. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  180. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  181. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  182. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  183. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  184. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  185. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  186. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  187. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  188. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  189. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  190. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  191. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  192. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  193. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  194. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  195. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  196. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  197. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  198. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  199. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  200. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  201. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  202. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  203. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  204. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  205. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  206. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  207. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  208. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  209. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  210. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  211. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  212. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  213. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  214. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  215. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  216. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  217. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  218. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  219. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  220. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  221. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  222. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  223. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  224. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  225. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  226. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  227. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  228. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  229. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  230. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  231. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  232. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  233. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  234. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  235. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  236. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  237. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  238. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  239. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  240. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  241. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  242. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  243. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  244. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  245. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  246. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  247. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  248. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  249. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  250. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  251. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  252. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  253. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  254. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  255. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  256. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  257. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  258. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  259. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  260. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  261. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  262. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  263. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  264. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  265. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  266. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  267. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  268. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  269. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  270. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  271. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  272. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  273. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  274. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  275. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  276. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  277. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  278. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  279. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  280. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  281. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  282. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  283. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  284. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  285. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  286. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  287. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  288. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  289. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  290. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  291. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
  292. sequenzo/dissimilarity_measures/src/eigen/test/gpu_common.h +0 -176
  293. sequenzo/dissimilarity_measures/src/eigen/test/main.h +0 -857
  294. sequenzo/dissimilarity_measures/src/eigen/test/packetmath_test_shared.h +0 -275
  295. sequenzo/dissimilarity_measures/src/eigen/test/product.h +0 -259
  296. sequenzo/dissimilarity_measures/src/eigen/test/random_without_cast_overflow.h +0 -152
  297. sequenzo/dissimilarity_measures/src/eigen/test/solverbase.h +0 -36
  298. sequenzo/dissimilarity_measures/src/eigen/test/sparse.h +0 -204
  299. sequenzo/dissimilarity_measures/src/eigen/test/sparse_solver.h +0 -699
  300. sequenzo/dissimilarity_measures/src/eigen/test/split_test_helper.h +0 -5994
  301. sequenzo/dissimilarity_measures/src/eigen/test/svd_common.h +0 -521
  302. sequenzo/dissimilarity_measures/src/eigen/test/svd_fill.h +0 -118
  303. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/Tensor.h +0 -554
  304. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorArgMax.h +0 -329
  305. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorAssign.h +0 -247
  306. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBase.h +0 -1176
  307. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBlock.h +0 -1559
  308. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorBroadcasting.h +0 -1093
  309. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorChipping.h +0 -518
  310. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConcatenation.h +0 -377
  311. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContraction.h +0 -1023
  312. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionBlocking.h +0 -73
  313. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionCuda.h +0 -6
  314. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionGpu.h +0 -1413
  315. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionMapper.h +0 -575
  316. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionSycl.h +0 -1650
  317. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorContractionThreadPool.h +0 -1679
  318. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConversion.h +0 -456
  319. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolution.h +0 -1132
  320. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorConvolutionSycl.h +0 -544
  321. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCostModel.h +0 -214
  322. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorCustomOp.h +0 -347
  323. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDevice.h +0 -137
  324. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceCuda.h +0 -6
  325. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceDefault.h +0 -104
  326. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceGpu.h +0 -389
  327. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceSycl.h +0 -1048
  328. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h +0 -409
  329. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensionList.h +0 -236
  330. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorDimensions.h +0 -490
  331. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvalTo.h +0 -236
  332. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorEvaluator.h +0 -983
  333. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExecutor.h +0 -703
  334. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorExpr.h +0 -388
  335. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFFT.h +0 -669
  336. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFixedSize.h +0 -379
  337. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForcedEval.h +0 -237
  338. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorForwardDeclarations.h +0 -191
  339. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorFunctors.h +0 -488
  340. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGenerator.h +0 -302
  341. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGlobalFunctions.h +0 -33
  342. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaDefines.h +0 -99
  343. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorGpuHipCudaUndefines.h +0 -44
  344. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIO.h +0 -79
  345. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorImagePatch.h +0 -603
  346. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIndexList.h +0 -738
  347. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInflation.h +0 -247
  348. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorInitializer.h +0 -82
  349. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorIntDiv.h +0 -263
  350. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorLayoutSwap.h +0 -216
  351. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMacros.h +0 -98
  352. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMap.h +0 -327
  353. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMeta.h +0 -311
  354. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorMorphing.h +0 -1102
  355. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPadding.h +0 -708
  356. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorPatch.h +0 -291
  357. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRandom.h +0 -322
  358. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReduction.h +0 -998
  359. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionCuda.h +0 -6
  360. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionGpu.h +0 -966
  361. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReductionSycl.h +0 -582
  362. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorRef.h +0 -454
  363. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorReverse.h +0 -465
  364. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScan.h +0 -528
  365. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorScanSycl.h +0 -513
  366. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorShuffling.h +0 -471
  367. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h +0 -161
  368. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorStriding.h +0 -346
  369. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTrace.h +0 -303
  370. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h +0 -264
  371. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorUInt128.h +0 -249
  372. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/Tensor/TensorVolumePatch.h +0 -629
  373. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/DynamicSymmetry.h +0 -293
  374. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/StaticSymmetry.h +0 -236
  375. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/Symmetry.h +0 -338
  376. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/TensorSymmetry/util/TemplateGroupTheory.h +0 -669
  377. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/Barrier.h +0 -67
  378. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/EventCount.h +0 -249
  379. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/NonBlockingThreadPool.h +0 -486
  380. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/RunQueue.h +0 -236
  381. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadCancel.h +0 -23
  382. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadEnvironment.h +0 -40
  383. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadLocal.h +0 -301
  384. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadPoolInterface.h +0 -48
  385. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/ThreadPool/ThreadYield.h +0 -20
  386. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Meta.h +0 -537
  387. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/CXX11Workarounds.h +0 -88
  388. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/EmulateArray.h +0 -261
  389. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/CXX11/src/util/MaxSizeVector.h +0 -158
  390. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffJacobian.h +0 -108
  391. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h +0 -730
  392. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/AutoDiff/AutoDiffVector.h +0 -220
  393. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/BVAlgorithms.h +0 -293
  394. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/BVH/KdBVH.h +0 -223
  395. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Eigenvalues/ArpackSelfAdjointEigenSolver.h +0 -790
  396. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerAngles.h +0 -355
  397. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/EulerAngles/EulerSystem.h +0 -305
  398. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_fftw_impl.h +0 -261
  399. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/FFT/ei_kissfft_impl.h +0 -449
  400. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h +0 -187
  401. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/DGMRES.h +0 -511
  402. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/GMRES.h +0 -335
  403. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IDRS.h +0 -436
  404. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h +0 -90
  405. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/IterationController.h +0 -154
  406. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/MINRES.h +0 -267
  407. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/IterativeSolvers/Scaling.h +0 -193
  408. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h +0 -305
  409. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMcovar.h +0 -84
  410. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMonestep.h +0 -202
  411. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h +0 -160
  412. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h +0 -188
  413. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LevenbergMarquardt.h +0 -396
  414. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h +0 -441
  415. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h +0 -569
  416. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h +0 -373
  417. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixPower.h +0 -705
  418. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h +0 -368
  419. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MatrixFunctions/StemFunction.h +0 -117
  420. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/MoreVectorization/MathFunctions.h +0 -95
  421. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h +0 -601
  422. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h +0 -657
  423. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/chkder.h +0 -66
  424. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/covar.h +0 -70
  425. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/dogleg.h +0 -107
  426. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h +0 -79
  427. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/lmpar.h +0 -298
  428. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h +0 -91
  429. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h +0 -30
  430. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/r1updt.h +0 -99
  431. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h +0 -49
  432. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h +0 -130
  433. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/Companion.h +0 -280
  434. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h +0 -428
  435. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h +0 -143
  436. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h +0 -352
  437. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrix.h +0 -862
  438. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h +0 -212
  439. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineProduct.h +0 -295
  440. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineStorage.h +0 -259
  441. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Skyline/SkylineUtil.h +0 -89
  442. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h +0 -122
  443. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h +0 -1079
  444. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h +0 -404
  445. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MarketIO.h +0 -282
  446. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h +0 -247
  447. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/RandomSetter.h +0 -349
  448. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsArrayAPI.h +0 -286
  449. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsBFloat16.h +0 -68
  450. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsFunctors.h +0 -357
  451. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsHalf.h +0 -66
  452. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsImpl.h +0 -1959
  453. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/BesselFunctionsPacketMath.h +0 -118
  454. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/HipVectorCompatibility.h +0 -67
  455. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsArrayAPI.h +0 -167
  456. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsBFloat16.h +0 -58
  457. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsFunctors.h +0 -330
  458. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsHalf.h +0 -58
  459. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsImpl.h +0 -2045
  460. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/SpecialFunctionsPacketMath.h +0 -79
  461. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/BesselFunctions.h +0 -46
  462. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX/SpecialFunctions.h +0 -16
  463. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/BesselFunctions.h +0 -46
  464. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/AVX512/SpecialFunctions.h +0 -16
  465. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/GPU/SpecialFunctions.h +0 -369
  466. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/BesselFunctions.h +0 -54
  467. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SpecialFunctions/arch/NEON/SpecialFunctions.h +0 -34
  468. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/Spline.h +0 -507
  469. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFitting.h +0 -431
  470. sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Splines/SplineFwd.h +0 -93
  471. sequenzo/dissimilarity_measures/src/eigen/unsupported/test/matrix_functions.h +0 -67
  472. sequenzo-0.1.17.dist-info/RECORD +0 -631
  473. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/WHEEL +0 -0
  474. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
  475. {sequenzo-0.1.17.dist-info → sequenzo-0.1.19.dist-info}/top_level.txt +0 -0
@@ -1,124 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 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_SPARSESOLVERBASE_H
11
- #define EIGEN_SPARSESOLVERBASE_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
- /** \internal
18
- * Helper functions to solve with a sparse right-hand-side and result.
19
- * The rhs is decomposed into small vertical panels which are solved through dense temporaries.
20
- */
21
- template<typename Decomposition, typename Rhs, typename Dest>
22
- typename enable_if<Rhs::ColsAtCompileTime!=1 && Dest::ColsAtCompileTime!=1>::type
23
- solve_sparse_through_dense_panels(const Decomposition &dec, const Rhs& rhs, Dest &dest)
24
- {
25
- EIGEN_STATIC_ASSERT((Dest::Flags&RowMajorBit)==0,THIS_METHOD_IS_ONLY_FOR_COLUMN_MAJOR_MATRICES);
26
- typedef typename Dest::Scalar DestScalar;
27
- // we process the sparse rhs per block of NbColsAtOnce columns temporarily stored into a dense matrix.
28
- static const Index NbColsAtOnce = 4;
29
- Index rhsCols = rhs.cols();
30
- Index size = rhs.rows();
31
- // the temporary matrices do not need more columns than NbColsAtOnce:
32
- Index tmpCols = (std::min)(rhsCols, NbColsAtOnce);
33
- Eigen::Matrix<DestScalar,Dynamic,Dynamic> tmp(size,tmpCols);
34
- Eigen::Matrix<DestScalar,Dynamic,Dynamic> tmpX(size,tmpCols);
35
- for(Index k=0; k<rhsCols; k+=NbColsAtOnce)
36
- {
37
- Index actualCols = std::min<Index>(rhsCols-k, NbColsAtOnce);
38
- tmp.leftCols(actualCols) = rhs.middleCols(k,actualCols);
39
- tmpX.leftCols(actualCols) = dec.solve(tmp.leftCols(actualCols));
40
- dest.middleCols(k,actualCols) = tmpX.leftCols(actualCols).sparseView();
41
- }
42
- }
43
-
44
- // Overload for vector as rhs
45
- template<typename Decomposition, typename Rhs, typename Dest>
46
- typename enable_if<Rhs::ColsAtCompileTime==1 || Dest::ColsAtCompileTime==1>::type
47
- solve_sparse_through_dense_panels(const Decomposition &dec, const Rhs& rhs, Dest &dest)
48
- {
49
- typedef typename Dest::Scalar DestScalar;
50
- Index size = rhs.rows();
51
- Eigen::Matrix<DestScalar,Dynamic,1> rhs_dense(rhs);
52
- Eigen::Matrix<DestScalar,Dynamic,1> dest_dense(size);
53
- dest_dense = dec.solve(rhs_dense);
54
- dest = dest_dense.sparseView();
55
- }
56
-
57
- } // end namespace internal
58
-
59
- /** \class SparseSolverBase
60
- * \ingroup SparseCore_Module
61
- * \brief A base class for sparse solvers
62
- *
63
- * \tparam Derived the actual type of the solver.
64
- *
65
- */
66
- template<typename Derived>
67
- class SparseSolverBase : internal::noncopyable
68
- {
69
- public:
70
-
71
- /** Default constructor */
72
- SparseSolverBase()
73
- : m_isInitialized(false)
74
- {}
75
-
76
- ~SparseSolverBase()
77
- {}
78
-
79
- Derived& derived() { return *static_cast<Derived*>(this); }
80
- const Derived& derived() const { return *static_cast<const Derived*>(this); }
81
-
82
- /** \returns an expression of the solution x of \f$ A x = b \f$ using the current decomposition of A.
83
- *
84
- * \sa compute()
85
- */
86
- template<typename Rhs>
87
- inline const Solve<Derived, Rhs>
88
- solve(const MatrixBase<Rhs>& b) const
89
- {
90
- eigen_assert(m_isInitialized && "Solver is not initialized.");
91
- eigen_assert(derived().rows()==b.rows() && "solve(): invalid number of rows of the right hand side matrix b");
92
- return Solve<Derived, Rhs>(derived(), b.derived());
93
- }
94
-
95
- /** \returns an expression of the solution x of \f$ A x = b \f$ using the current decomposition of A.
96
- *
97
- * \sa compute()
98
- */
99
- template<typename Rhs>
100
- inline const Solve<Derived, Rhs>
101
- solve(const SparseMatrixBase<Rhs>& b) const
102
- {
103
- eigen_assert(m_isInitialized && "Solver is not initialized.");
104
- eigen_assert(derived().rows()==b.rows() && "solve(): invalid number of rows of the right hand side matrix b");
105
- return Solve<Derived, Rhs>(derived(), b.derived());
106
- }
107
-
108
- #ifndef EIGEN_PARSED_BY_DOXYGEN
109
- /** \internal default implementation of solving with a sparse rhs */
110
- template<typename Rhs,typename Dest>
111
- void _solve_impl(const SparseMatrixBase<Rhs> &b, SparseMatrixBase<Dest> &dest) const
112
- {
113
- internal::solve_sparse_through_dense_panels(derived(), b.derived(), dest.derived());
114
- }
115
- #endif // EIGEN_PARSED_BY_DOXYGEN
116
-
117
- protected:
118
-
119
- mutable bool m_isInitialized;
120
- };
121
-
122
- } // end namespace Eigen
123
-
124
- #endif // EIGEN_SPARSESOLVERBASE_H
@@ -1,198 +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_SPARSESPARSEPRODUCTWITHPRUNING_H
11
- #define EIGEN_SPARSESPARSEPRODUCTWITHPRUNING_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
-
17
-
18
- // perform a pseudo in-place sparse * sparse product assuming all matrices are col major
19
- template<typename Lhs, typename Rhs, typename ResultType>
20
- static void sparse_sparse_product_with_pruning_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, const typename ResultType::RealScalar& tolerance)
21
- {
22
- // return sparse_sparse_product_with_pruning_impl2(lhs,rhs,res);
23
-
24
- typedef typename remove_all<Rhs>::type::Scalar RhsScalar;
25
- typedef typename remove_all<ResultType>::type::Scalar ResScalar;
26
- typedef typename remove_all<Lhs>::type::StorageIndex StorageIndex;
27
-
28
- // make sure to call innerSize/outerSize since we fake the storage order.
29
- Index rows = lhs.innerSize();
30
- Index cols = rhs.outerSize();
31
- //Index size = lhs.outerSize();
32
- eigen_assert(lhs.outerSize() == rhs.innerSize());
33
-
34
- // allocate a temporary buffer
35
- AmbiVector<ResScalar,StorageIndex> tempVector(rows);
36
-
37
- // mimics a resizeByInnerOuter:
38
- if(ResultType::IsRowMajor)
39
- res.resize(cols, rows);
40
- else
41
- res.resize(rows, cols);
42
-
43
- evaluator<Lhs> lhsEval(lhs);
44
- evaluator<Rhs> rhsEval(rhs);
45
-
46
- // estimate the number of non zero entries
47
- // given a rhs column containing Y non zeros, we assume that the respective Y columns
48
- // of the lhs differs in average of one non zeros, thus the number of non zeros for
49
- // the product of a rhs column with the lhs is X+Y where X is the average number of non zero
50
- // per column of the lhs.
51
- // Therefore, we have nnz(lhs*rhs) = nnz(lhs) + nnz(rhs)
52
- Index estimated_nnz_prod = lhsEval.nonZerosEstimate() + rhsEval.nonZerosEstimate();
53
-
54
- res.reserve(estimated_nnz_prod);
55
- double ratioColRes = double(estimated_nnz_prod)/(double(lhs.rows())*double(rhs.cols()));
56
- for (Index j=0; j<cols; ++j)
57
- {
58
- // FIXME:
59
- //double ratioColRes = (double(rhs.innerVector(j).nonZeros()) + double(lhs.nonZeros())/double(lhs.cols()))/double(lhs.rows());
60
- // let's do a more accurate determination of the nnz ratio for the current column j of res
61
- tempVector.init(ratioColRes);
62
- tempVector.setZero();
63
- for (typename evaluator<Rhs>::InnerIterator rhsIt(rhsEval, j); rhsIt; ++rhsIt)
64
- {
65
- // FIXME should be written like this: tmp += rhsIt.value() * lhs.col(rhsIt.index())
66
- tempVector.restart();
67
- RhsScalar x = rhsIt.value();
68
- for (typename evaluator<Lhs>::InnerIterator lhsIt(lhsEval, rhsIt.index()); lhsIt; ++lhsIt)
69
- {
70
- tempVector.coeffRef(lhsIt.index()) += lhsIt.value() * x;
71
- }
72
- }
73
- res.startVec(j);
74
- for (typename AmbiVector<ResScalar,StorageIndex>::Iterator it(tempVector,tolerance); it; ++it)
75
- res.insertBackByOuterInner(j,it.index()) = it.value();
76
- }
77
- res.finalize();
78
- }
79
-
80
- template<typename Lhs, typename Rhs, typename ResultType,
81
- int LhsStorageOrder = traits<Lhs>::Flags&RowMajorBit,
82
- int RhsStorageOrder = traits<Rhs>::Flags&RowMajorBit,
83
- int ResStorageOrder = traits<ResultType>::Flags&RowMajorBit>
84
- struct sparse_sparse_product_with_pruning_selector;
85
-
86
- template<typename Lhs, typename Rhs, typename ResultType>
87
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,ColMajor>
88
- {
89
- typedef typename ResultType::RealScalar RealScalar;
90
-
91
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
92
- {
93
- typename remove_all<ResultType>::type _res(res.rows(), res.cols());
94
- internal::sparse_sparse_product_with_pruning_impl<Lhs,Rhs,ResultType>(lhs, rhs, _res, tolerance);
95
- res.swap(_res);
96
- }
97
- };
98
-
99
- template<typename Lhs, typename Rhs, typename ResultType>
100
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,RowMajor>
101
- {
102
- typedef typename ResultType::RealScalar RealScalar;
103
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
104
- {
105
- // we need a col-major matrix to hold the result
106
- typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> SparseTemporaryType;
107
- SparseTemporaryType _res(res.rows(), res.cols());
108
- internal::sparse_sparse_product_with_pruning_impl<Lhs,Rhs,SparseTemporaryType>(lhs, rhs, _res, tolerance);
109
- res = _res;
110
- }
111
- };
112
-
113
- template<typename Lhs, typename Rhs, typename ResultType>
114
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,RowMajor>
115
- {
116
- typedef typename ResultType::RealScalar RealScalar;
117
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
118
- {
119
- // let's transpose the product to get a column x column product
120
- typename remove_all<ResultType>::type _res(res.rows(), res.cols());
121
- internal::sparse_sparse_product_with_pruning_impl<Rhs,Lhs,ResultType>(rhs, lhs, _res, tolerance);
122
- res.swap(_res);
123
- }
124
- };
125
-
126
- template<typename Lhs, typename Rhs, typename ResultType>
127
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,ColMajor>
128
- {
129
- typedef typename ResultType::RealScalar RealScalar;
130
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
131
- {
132
- typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixLhs;
133
- typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixRhs;
134
- ColMajorMatrixLhs colLhs(lhs);
135
- ColMajorMatrixRhs colRhs(rhs);
136
- internal::sparse_sparse_product_with_pruning_impl<ColMajorMatrixLhs,ColMajorMatrixRhs,ResultType>(colLhs, colRhs, res, tolerance);
137
-
138
- // let's transpose the product to get a column x column product
139
- // typedef SparseMatrix<typename ResultType::Scalar> SparseTemporaryType;
140
- // SparseTemporaryType _res(res.cols(), res.rows());
141
- // sparse_sparse_product_with_pruning_impl<Rhs,Lhs,SparseTemporaryType>(rhs, lhs, _res);
142
- // res = _res.transpose();
143
- }
144
- };
145
-
146
- template<typename Lhs, typename Rhs, typename ResultType>
147
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,RowMajor>
148
- {
149
- typedef typename ResultType::RealScalar RealScalar;
150
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
151
- {
152
- typedef SparseMatrix<typename Lhs::Scalar,RowMajor,typename Lhs::StorageIndex> RowMajorMatrixLhs;
153
- RowMajorMatrixLhs rowLhs(lhs);
154
- sparse_sparse_product_with_pruning_selector<RowMajorMatrixLhs,Rhs,ResultType,RowMajor,RowMajor>(rowLhs,rhs,res,tolerance);
155
- }
156
- };
157
-
158
- template<typename Lhs, typename Rhs, typename ResultType>
159
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,RowMajor>
160
- {
161
- typedef typename ResultType::RealScalar RealScalar;
162
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
163
- {
164
- typedef SparseMatrix<typename Rhs::Scalar,RowMajor,typename Lhs::StorageIndex> RowMajorMatrixRhs;
165
- RowMajorMatrixRhs rowRhs(rhs);
166
- sparse_sparse_product_with_pruning_selector<Lhs,RowMajorMatrixRhs,ResultType,RowMajor,RowMajor,RowMajor>(lhs,rowRhs,res,tolerance);
167
- }
168
- };
169
-
170
- template<typename Lhs, typename Rhs, typename ResultType>
171
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,ColMajor>
172
- {
173
- typedef typename ResultType::RealScalar RealScalar;
174
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
175
- {
176
- typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixRhs;
177
- ColMajorMatrixRhs colRhs(rhs);
178
- internal::sparse_sparse_product_with_pruning_impl<Lhs,ColMajorMatrixRhs,ResultType>(lhs, colRhs, res, tolerance);
179
- }
180
- };
181
-
182
- template<typename Lhs, typename Rhs, typename ResultType>
183
- struct sparse_sparse_product_with_pruning_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,ColMajor>
184
- {
185
- typedef typename ResultType::RealScalar RealScalar;
186
- static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res, const RealScalar& tolerance)
187
- {
188
- typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename Lhs::StorageIndex> ColMajorMatrixLhs;
189
- ColMajorMatrixLhs colLhs(lhs);
190
- internal::sparse_sparse_product_with_pruning_impl<ColMajorMatrixLhs,Rhs,ResultType>(colLhs, rhs, res, tolerance);
191
- }
192
- };
193
-
194
- } // end namespace internal
195
-
196
- } // end namespace Eigen
197
-
198
- #endif // EIGEN_SPARSESPARSEPRODUCTWITHPRUNING_H
@@ -1,92 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2008-2015 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_SPARSETRANSPOSE_H
11
- #define EIGEN_SPARSETRANSPOSE_H
12
-
13
- namespace Eigen {
14
-
15
- namespace internal {
16
- template<typename MatrixType,int CompressedAccess=int(MatrixType::Flags&CompressedAccessBit)>
17
- class SparseTransposeImpl
18
- : public SparseMatrixBase<Transpose<MatrixType> >
19
- {};
20
-
21
- template<typename MatrixType>
22
- class SparseTransposeImpl<MatrixType,CompressedAccessBit>
23
- : public SparseCompressedBase<Transpose<MatrixType> >
24
- {
25
- typedef SparseCompressedBase<Transpose<MatrixType> > Base;
26
- public:
27
- using Base::derived;
28
- typedef typename Base::Scalar Scalar;
29
- typedef typename Base::StorageIndex StorageIndex;
30
-
31
- inline Index nonZeros() const { return derived().nestedExpression().nonZeros(); }
32
-
33
- inline const Scalar* valuePtr() const { return derived().nestedExpression().valuePtr(); }
34
- inline const StorageIndex* innerIndexPtr() const { return derived().nestedExpression().innerIndexPtr(); }
35
- inline const StorageIndex* outerIndexPtr() const { return derived().nestedExpression().outerIndexPtr(); }
36
- inline const StorageIndex* innerNonZeroPtr() const { return derived().nestedExpression().innerNonZeroPtr(); }
37
-
38
- inline Scalar* valuePtr() { return derived().nestedExpression().valuePtr(); }
39
- inline StorageIndex* innerIndexPtr() { return derived().nestedExpression().innerIndexPtr(); }
40
- inline StorageIndex* outerIndexPtr() { return derived().nestedExpression().outerIndexPtr(); }
41
- inline StorageIndex* innerNonZeroPtr() { return derived().nestedExpression().innerNonZeroPtr(); }
42
- };
43
- }
44
-
45
- template<typename MatrixType> class TransposeImpl<MatrixType,Sparse>
46
- : public internal::SparseTransposeImpl<MatrixType>
47
- {
48
- protected:
49
- typedef internal::SparseTransposeImpl<MatrixType> Base;
50
- };
51
-
52
- namespace internal {
53
-
54
- template<typename ArgType>
55
- struct unary_evaluator<Transpose<ArgType>, IteratorBased>
56
- : public evaluator_base<Transpose<ArgType> >
57
- {
58
- typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
59
- public:
60
- typedef Transpose<ArgType> XprType;
61
-
62
- inline Index nonZerosEstimate() const {
63
- return m_argImpl.nonZerosEstimate();
64
- }
65
-
66
- class InnerIterator : public EvalIterator
67
- {
68
- public:
69
- EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& unaryOp, Index outer)
70
- : EvalIterator(unaryOp.m_argImpl,outer)
71
- {}
72
-
73
- Index row() const { return EvalIterator::col(); }
74
- Index col() const { return EvalIterator::row(); }
75
- };
76
-
77
- enum {
78
- CoeffReadCost = evaluator<ArgType>::CoeffReadCost,
79
- Flags = XprType::Flags
80
- };
81
-
82
- explicit unary_evaluator(const XprType& op) :m_argImpl(op.nestedExpression()) {}
83
-
84
- protected:
85
- evaluator<ArgType> m_argImpl;
86
- };
87
-
88
- } // end namespace internal
89
-
90
- } // end namespace Eigen
91
-
92
- #endif // EIGEN_SPARSETRANSPOSE_H
@@ -1,189 +0,0 @@
1
- // This file is part of Eigen, a lightweight C++ template library
2
- // for linear algebra.
3
- //
4
- // Copyright (C) 2009-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
5
- // Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
6
- //
7
- // This Source Code Form is subject to the terms of the Mozilla
8
- // Public License v. 2.0. If a copy of the MPL was not distributed
9
- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
10
-
11
- #ifndef EIGEN_SPARSE_TRIANGULARVIEW_H
12
- #define EIGEN_SPARSE_TRIANGULARVIEW_H
13
-
14
- namespace Eigen {
15
-
16
- /** \ingroup SparseCore_Module
17
- *
18
- * \brief Base class for a triangular part in a \b sparse matrix
19
- *
20
- * This class is an abstract base class of class TriangularView, and objects of type TriangularViewImpl cannot be instantiated.
21
- * It extends class TriangularView with additional methods which are available for sparse expressions only.
22
- *
23
- * \sa class TriangularView, SparseMatrixBase::triangularView()
24
- */
25
- template<typename MatrixType, unsigned int Mode> class TriangularViewImpl<MatrixType,Mode,Sparse>
26
- : public SparseMatrixBase<TriangularView<MatrixType,Mode> >
27
- {
28
- enum { SkipFirst = ((Mode&Lower) && !(MatrixType::Flags&RowMajorBit))
29
- || ((Mode&Upper) && (MatrixType::Flags&RowMajorBit)),
30
- SkipLast = !SkipFirst,
31
- SkipDiag = (Mode&ZeroDiag) ? 1 : 0,
32
- HasUnitDiag = (Mode&UnitDiag) ? 1 : 0
33
- };
34
-
35
- typedef TriangularView<MatrixType,Mode> TriangularViewType;
36
-
37
- protected:
38
- // dummy solve function to make TriangularView happy.
39
- void solve() const;
40
-
41
- typedef SparseMatrixBase<TriangularViewType> Base;
42
- public:
43
-
44
- EIGEN_SPARSE_PUBLIC_INTERFACE(TriangularViewType)
45
-
46
- typedef typename MatrixType::Nested MatrixTypeNested;
47
- typedef typename internal::remove_reference<MatrixTypeNested>::type MatrixTypeNestedNonRef;
48
- typedef typename internal::remove_all<MatrixTypeNested>::type MatrixTypeNestedCleaned;
49
-
50
- template<typename RhsType, typename DstType>
51
- EIGEN_DEVICE_FUNC
52
- EIGEN_STRONG_INLINE void _solve_impl(const RhsType &rhs, DstType &dst) const {
53
- if(!(internal::is_same<RhsType,DstType>::value && internal::extract_data(dst) == internal::extract_data(rhs)))
54
- dst = rhs;
55
- this->solveInPlace(dst);
56
- }
57
-
58
- /** Applies the inverse of \c *this to the dense vector or matrix \a other, "in-place" */
59
- template<typename OtherDerived> void solveInPlace(MatrixBase<OtherDerived>& other) const;
60
-
61
- /** Applies the inverse of \c *this to the sparse vector or matrix \a other, "in-place" */
62
- template<typename OtherDerived> void solveInPlace(SparseMatrixBase<OtherDerived>& other) const;
63
-
64
- };
65
-
66
- namespace internal {
67
-
68
- template<typename ArgType, unsigned int Mode>
69
- struct unary_evaluator<TriangularView<ArgType,Mode>, IteratorBased>
70
- : evaluator_base<TriangularView<ArgType,Mode> >
71
- {
72
- typedef TriangularView<ArgType,Mode> XprType;
73
-
74
- protected:
75
-
76
- typedef typename XprType::Scalar Scalar;
77
- typedef typename XprType::StorageIndex StorageIndex;
78
- typedef typename evaluator<ArgType>::InnerIterator EvalIterator;
79
-
80
- enum { SkipFirst = ((Mode&Lower) && !(ArgType::Flags&RowMajorBit))
81
- || ((Mode&Upper) && (ArgType::Flags&RowMajorBit)),
82
- SkipLast = !SkipFirst,
83
- SkipDiag = (Mode&ZeroDiag) ? 1 : 0,
84
- HasUnitDiag = (Mode&UnitDiag) ? 1 : 0
85
- };
86
-
87
- public:
88
-
89
- enum {
90
- CoeffReadCost = evaluator<ArgType>::CoeffReadCost,
91
- Flags = XprType::Flags
92
- };
93
-
94
- explicit unary_evaluator(const XprType &xpr) : m_argImpl(xpr.nestedExpression()), m_arg(xpr.nestedExpression()) {}
95
-
96
- inline Index nonZerosEstimate() const {
97
- return m_argImpl.nonZerosEstimate();
98
- }
99
-
100
- class InnerIterator : public EvalIterator
101
- {
102
- typedef EvalIterator Base;
103
- public:
104
-
105
- EIGEN_STRONG_INLINE InnerIterator(const unary_evaluator& xprEval, Index outer)
106
- : Base(xprEval.m_argImpl,outer), m_returnOne(false), m_containsDiag(Base::outer()<xprEval.m_arg.innerSize())
107
- {
108
- if(SkipFirst)
109
- {
110
- while((*this) && ((HasUnitDiag||SkipDiag) ? this->index()<=outer : this->index()<outer))
111
- Base::operator++();
112
- if(HasUnitDiag)
113
- m_returnOne = m_containsDiag;
114
- }
115
- else if(HasUnitDiag && ((!Base::operator bool()) || Base::index()>=Base::outer()))
116
- {
117
- if((!SkipFirst) && Base::operator bool())
118
- Base::operator++();
119
- m_returnOne = m_containsDiag;
120
- }
121
- }
122
-
123
- EIGEN_STRONG_INLINE InnerIterator& operator++()
124
- {
125
- if(HasUnitDiag && m_returnOne)
126
- m_returnOne = false;
127
- else
128
- {
129
- Base::operator++();
130
- if(HasUnitDiag && (!SkipFirst) && ((!Base::operator bool()) || Base::index()>=Base::outer()))
131
- {
132
- if((!SkipFirst) && Base::operator bool())
133
- Base::operator++();
134
- m_returnOne = m_containsDiag;
135
- }
136
- }
137
- return *this;
138
- }
139
-
140
- EIGEN_STRONG_INLINE operator bool() const
141
- {
142
- if(HasUnitDiag && m_returnOne)
143
- return true;
144
- if(SkipFirst) return Base::operator bool();
145
- else
146
- {
147
- if (SkipDiag) return (Base::operator bool() && this->index() < this->outer());
148
- else return (Base::operator bool() && this->index() <= this->outer());
149
- }
150
- }
151
-
152
- // inline Index row() const { return (ArgType::Flags&RowMajorBit ? Base::outer() : this->index()); }
153
- // inline Index col() const { return (ArgType::Flags&RowMajorBit ? this->index() : Base::outer()); }
154
- inline StorageIndex index() const
155
- {
156
- if(HasUnitDiag && m_returnOne) return internal::convert_index<StorageIndex>(Base::outer());
157
- else return Base::index();
158
- }
159
- inline Scalar value() const
160
- {
161
- if(HasUnitDiag && m_returnOne) return Scalar(1);
162
- else return Base::value();
163
- }
164
-
165
- protected:
166
- bool m_returnOne;
167
- bool m_containsDiag;
168
- private:
169
- Scalar& valueRef();
170
- };
171
-
172
- protected:
173
- evaluator<ArgType> m_argImpl;
174
- const ArgType& m_arg;
175
- };
176
-
177
- } // end namespace internal
178
-
179
- template<typename Derived>
180
- template<int Mode>
181
- inline const TriangularView<const Derived, Mode>
182
- SparseMatrixBase<Derived>::triangularView() const
183
- {
184
- return TriangularView<const Derived, Mode>(derived());
185
- }
186
-
187
- } // end namespace Eigen
188
-
189
- #endif // EIGEN_SPARSE_TRIANGULARVIEW_H