sequenzo 0.1.17__cp311-cp311-win_amd64.whl → 0.1.19__cp311-cp311-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 +154 -154
  4. sequenzo/big_data/clara/utils/get_weighted_diss.cp311-win_amd64.pyd +0 -0
  5. sequenzo/clustering/KMedoids.py +39 -0
  6. sequenzo/clustering/clustering_c_code.cp311-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.cp311-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 +154 -154
  76. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  77. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  78. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  79. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  80. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  81. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  82. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  83. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  84. sequenzo/dissimilarity_measures/utils/seqlength.cp311-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
@@ -1,398 +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