sequenzo 0.1.18__cp310-cp310-win_amd64.whl → 0.1.19__cp310-cp310-win_amd64.whl

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  1. sequenzo/__init__.py +39 -7
  2. sequenzo/big_data/clara/utils/get_weighted_diss.c +154 -154
  3. sequenzo/big_data/clara/utils/get_weighted_diss.cp310-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp310-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +107 -5
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp310-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +1 -2
  10. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp310-win_amd64.pyd +0 -0
  12. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  13. sequenzo/dissimilarity_measures/utils/seqconc.cp310-win_amd64.pyd +0 -0
  14. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  15. sequenzo/dissimilarity_measures/utils/seqdss.cp310-win_amd64.pyd +0 -0
  16. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  17. sequenzo/dissimilarity_measures/utils/seqdur.cp310-win_amd64.pyd +0 -0
  18. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  19. sequenzo/dissimilarity_measures/utils/seqlength.cp310-win_amd64.pyd +0 -0
  20. sequenzo/multidomain/cat.py +0 -53
  21. sequenzo/multidomain/idcd.py +0 -1
  22. sequenzo/openmp_setup.py +233 -0
  23. sequenzo/visualization/plot_transition_matrix.py +21 -22
  24. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/METADATA +43 -10
  25. sequenzo-0.1.19.dist-info/RECORD +272 -0
  26. sequenzo/dissimilarity_measures/setup.py +0 -35
  27. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  28. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  29. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  169. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  170. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  171. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  172. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  173. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  174. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  175. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  176. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  177. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  178. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  179. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  180. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  181. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  182. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  183. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  184. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  185. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  186. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  187. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  188. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  189. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  190. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  191. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  192. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  197. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  198. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  199. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  200. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  201. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  202. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  203. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  206. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  207. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  208. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  209. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  210. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  211. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
  212. sequenzo/dissimilarity_measures/src/eigen/test/evaluator_common.h +0 -0
  213. sequenzo/dissimilarity_measures/src/eigen/test/gpu_common.h +0 -176
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  395. {sequenzo-0.1.18.dist-info → sequenzo-0.1.19.dist-info}/licenses/LICENSE +0 -0
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@@ -1,642 +0,0 @@
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- // This file is part of Eigen, a lightweight C++ template library
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- // for linear algebra.
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- //
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- // Copyright (C) 2008-2011 Gael Guennebaud <gael.guennebaud@inria.fr>
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- //
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- // This Source Code Form is subject to the terms of the Mozilla
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- // Public License v. 2.0. If a copy of the MPL was not distributed
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- // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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-
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- #ifndef EIGEN_UMFPACKSUPPORT_H
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- #define EIGEN_UMFPACKSUPPORT_H
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-
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- // for compatibility with super old version of umfpack,
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- // not sure this is really needed, but this is harmless.
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- #ifndef SuiteSparse_long
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- #ifdef UF_long
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- #define SuiteSparse_long UF_long
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- #else
19
- #error neither SuiteSparse_long nor UF_long are defined
20
- #endif
21
- #endif
22
-
23
- namespace Eigen {
24
-
25
- /* TODO extract L, extract U, compute det, etc... */
26
-
27
- // generic double/complex<double> wrapper functions:
28
-
29
-
30
- // Defaults
31
- inline void umfpack_defaults(double control[UMFPACK_CONTROL], double, int)
32
- { umfpack_di_defaults(control); }
33
-
34
- inline void umfpack_defaults(double control[UMFPACK_CONTROL], std::complex<double>, int)
35
- { umfpack_zi_defaults(control); }
36
-
37
- inline void umfpack_defaults(double control[UMFPACK_CONTROL], double, SuiteSparse_long)
38
- { umfpack_dl_defaults(control); }
39
-
40
- inline void umfpack_defaults(double control[UMFPACK_CONTROL], std::complex<double>, SuiteSparse_long)
41
- { umfpack_zl_defaults(control); }
42
-
43
- // Report info
44
- inline void umfpack_report_info(double control[UMFPACK_CONTROL], double info[UMFPACK_INFO], double, int)
45
- { umfpack_di_report_info(control, info);}
46
-
47
- inline void umfpack_report_info(double control[UMFPACK_CONTROL], double info[UMFPACK_INFO], std::complex<double>, int)
48
- { umfpack_zi_report_info(control, info);}
49
-
50
- inline void umfpack_report_info(double control[UMFPACK_CONTROL], double info[UMFPACK_INFO], double, SuiteSparse_long)
51
- { umfpack_dl_report_info(control, info);}
52
-
53
- inline void umfpack_report_info(double control[UMFPACK_CONTROL], double info[UMFPACK_INFO], std::complex<double>, SuiteSparse_long)
54
- { umfpack_zl_report_info(control, info);}
55
-
56
- // Report status
57
- inline void umfpack_report_status(double control[UMFPACK_CONTROL], int status, double, int)
58
- { umfpack_di_report_status(control, status);}
59
-
60
- inline void umfpack_report_status(double control[UMFPACK_CONTROL], int status, std::complex<double>, int)
61
- { umfpack_zi_report_status(control, status);}
62
-
63
- inline void umfpack_report_status(double control[UMFPACK_CONTROL], int status, double, SuiteSparse_long)
64
- { umfpack_dl_report_status(control, status);}
65
-
66
- inline void umfpack_report_status(double control[UMFPACK_CONTROL], int status, std::complex<double>, SuiteSparse_long)
67
- { umfpack_zl_report_status(control, status);}
68
-
69
- // report control
70
- inline void umfpack_report_control(double control[UMFPACK_CONTROL], double, int)
71
- { umfpack_di_report_control(control);}
72
-
73
- inline void umfpack_report_control(double control[UMFPACK_CONTROL], std::complex<double>, int)
74
- { umfpack_zi_report_control(control);}
75
-
76
- inline void umfpack_report_control(double control[UMFPACK_CONTROL], double, SuiteSparse_long)
77
- { umfpack_dl_report_control(control);}
78
-
79
- inline void umfpack_report_control(double control[UMFPACK_CONTROL], std::complex<double>, SuiteSparse_long)
80
- { umfpack_zl_report_control(control);}
81
-
82
- // Free numeric
83
- inline void umfpack_free_numeric(void **Numeric, double, int)
84
- { umfpack_di_free_numeric(Numeric); *Numeric = 0; }
85
-
86
- inline void umfpack_free_numeric(void **Numeric, std::complex<double>, int)
87
- { umfpack_zi_free_numeric(Numeric); *Numeric = 0; }
88
-
89
- inline void umfpack_free_numeric(void **Numeric, double, SuiteSparse_long)
90
- { umfpack_dl_free_numeric(Numeric); *Numeric = 0; }
91
-
92
- inline void umfpack_free_numeric(void **Numeric, std::complex<double>, SuiteSparse_long)
93
- { umfpack_zl_free_numeric(Numeric); *Numeric = 0; }
94
-
95
- // Free symbolic
96
- inline void umfpack_free_symbolic(void **Symbolic, double, int)
97
- { umfpack_di_free_symbolic(Symbolic); *Symbolic = 0; }
98
-
99
- inline void umfpack_free_symbolic(void **Symbolic, std::complex<double>, int)
100
- { umfpack_zi_free_symbolic(Symbolic); *Symbolic = 0; }
101
-
102
- inline void umfpack_free_symbolic(void **Symbolic, double, SuiteSparse_long)
103
- { umfpack_dl_free_symbolic(Symbolic); *Symbolic = 0; }
104
-
105
- inline void umfpack_free_symbolic(void **Symbolic, std::complex<double>, SuiteSparse_long)
106
- { umfpack_zl_free_symbolic(Symbolic); *Symbolic = 0; }
107
-
108
- // Symbolic
109
- inline int umfpack_symbolic(int n_row,int n_col,
110
- const int Ap[], const int Ai[], const double Ax[], void **Symbolic,
111
- const double Control [UMFPACK_CONTROL], double Info [UMFPACK_INFO])
112
- {
113
- return umfpack_di_symbolic(n_row,n_col,Ap,Ai,Ax,Symbolic,Control,Info);
114
- }
115
-
116
- inline int umfpack_symbolic(int n_row,int n_col,
117
- const int Ap[], const int Ai[], const std::complex<double> Ax[], void **Symbolic,
118
- const double Control [UMFPACK_CONTROL], double Info [UMFPACK_INFO])
119
- {
120
- return umfpack_zi_symbolic(n_row,n_col,Ap,Ai,&numext::real_ref(Ax[0]),0,Symbolic,Control,Info);
121
- }
122
- inline SuiteSparse_long umfpack_symbolic( SuiteSparse_long n_row,SuiteSparse_long n_col,
123
- const SuiteSparse_long Ap[], const SuiteSparse_long Ai[], const double Ax[], void **Symbolic,
124
- const double Control [UMFPACK_CONTROL], double Info [UMFPACK_INFO])
125
- {
126
- return umfpack_dl_symbolic(n_row,n_col,Ap,Ai,Ax,Symbolic,Control,Info);
127
- }
128
-
129
- inline SuiteSparse_long umfpack_symbolic( SuiteSparse_long n_row,SuiteSparse_long n_col,
130
- const SuiteSparse_long Ap[], const SuiteSparse_long Ai[], const std::complex<double> Ax[], void **Symbolic,
131
- const double Control [UMFPACK_CONTROL], double Info [UMFPACK_INFO])
132
- {
133
- return umfpack_zl_symbolic(n_row,n_col,Ap,Ai,&numext::real_ref(Ax[0]),0,Symbolic,Control,Info);
134
- }
135
-
136
- // Numeric
137
- inline int umfpack_numeric( const int Ap[], const int Ai[], const double Ax[],
138
- void *Symbolic, void **Numeric,
139
- const double Control[UMFPACK_CONTROL],double Info [UMFPACK_INFO])
140
- {
141
- return umfpack_di_numeric(Ap,Ai,Ax,Symbolic,Numeric,Control,Info);
142
- }
143
-
144
- inline int umfpack_numeric( const int Ap[], const int Ai[], const std::complex<double> Ax[],
145
- void *Symbolic, void **Numeric,
146
- const double Control[UMFPACK_CONTROL],double Info [UMFPACK_INFO])
147
- {
148
- return umfpack_zi_numeric(Ap,Ai,&numext::real_ref(Ax[0]),0,Symbolic,Numeric,Control,Info);
149
- }
150
- inline SuiteSparse_long umfpack_numeric(const SuiteSparse_long Ap[], const SuiteSparse_long Ai[], const double Ax[],
151
- void *Symbolic, void **Numeric,
152
- const double Control[UMFPACK_CONTROL],double Info [UMFPACK_INFO])
153
- {
154
- return umfpack_dl_numeric(Ap,Ai,Ax,Symbolic,Numeric,Control,Info);
155
- }
156
-
157
- inline SuiteSparse_long umfpack_numeric(const SuiteSparse_long Ap[], const SuiteSparse_long Ai[], const std::complex<double> Ax[],
158
- void *Symbolic, void **Numeric,
159
- const double Control[UMFPACK_CONTROL],double Info [UMFPACK_INFO])
160
- {
161
- return umfpack_zl_numeric(Ap,Ai,&numext::real_ref(Ax[0]),0,Symbolic,Numeric,Control,Info);
162
- }
163
-
164
- // solve
165
- inline int umfpack_solve( int sys, const int Ap[], const int Ai[], const double Ax[],
166
- double X[], const double B[], void *Numeric,
167
- const double Control[UMFPACK_CONTROL], double Info[UMFPACK_INFO])
168
- {
169
- return umfpack_di_solve(sys,Ap,Ai,Ax,X,B,Numeric,Control,Info);
170
- }
171
-
172
- inline int umfpack_solve( int sys, const int Ap[], const int Ai[], const std::complex<double> Ax[],
173
- std::complex<double> X[], const std::complex<double> B[], void *Numeric,
174
- const double Control[UMFPACK_CONTROL], double Info[UMFPACK_INFO])
175
- {
176
- return umfpack_zi_solve(sys,Ap,Ai,&numext::real_ref(Ax[0]),0,&numext::real_ref(X[0]),0,&numext::real_ref(B[0]),0,Numeric,Control,Info);
177
- }
178
-
179
- inline SuiteSparse_long umfpack_solve(int sys, const SuiteSparse_long Ap[], const SuiteSparse_long Ai[], const double Ax[],
180
- double X[], const double B[], void *Numeric,
181
- const double Control[UMFPACK_CONTROL], double Info[UMFPACK_INFO])
182
- {
183
- return umfpack_dl_solve(sys,Ap,Ai,Ax,X,B,Numeric,Control,Info);
184
- }
185
-
186
- inline SuiteSparse_long umfpack_solve(int sys, const SuiteSparse_long Ap[], const SuiteSparse_long Ai[], const std::complex<double> Ax[],
187
- std::complex<double> X[], const std::complex<double> B[], void *Numeric,
188
- const double Control[UMFPACK_CONTROL], double Info[UMFPACK_INFO])
189
- {
190
- return umfpack_zl_solve(sys,Ap,Ai,&numext::real_ref(Ax[0]),0,&numext::real_ref(X[0]),0,&numext::real_ref(B[0]),0,Numeric,Control,Info);
191
- }
192
-
193
- // Get Lunz
194
- inline int umfpack_get_lunz(int *lnz, int *unz, int *n_row, int *n_col, int *nz_udiag, void *Numeric, double)
195
- {
196
- return umfpack_di_get_lunz(lnz,unz,n_row,n_col,nz_udiag,Numeric);
197
- }
198
-
199
- inline int umfpack_get_lunz(int *lnz, int *unz, int *n_row, int *n_col, int *nz_udiag, void *Numeric, std::complex<double>)
200
- {
201
- return umfpack_zi_get_lunz(lnz,unz,n_row,n_col,nz_udiag,Numeric);
202
- }
203
-
204
- inline SuiteSparse_long umfpack_get_lunz( SuiteSparse_long *lnz, SuiteSparse_long *unz, SuiteSparse_long *n_row, SuiteSparse_long *n_col,
205
- SuiteSparse_long *nz_udiag, void *Numeric, double)
206
- {
207
- return umfpack_dl_get_lunz(lnz,unz,n_row,n_col,nz_udiag,Numeric);
208
- }
209
-
210
- inline SuiteSparse_long umfpack_get_lunz( SuiteSparse_long *lnz, SuiteSparse_long *unz, SuiteSparse_long *n_row, SuiteSparse_long *n_col,
211
- SuiteSparse_long *nz_udiag, void *Numeric, std::complex<double>)
212
- {
213
- return umfpack_zl_get_lunz(lnz,unz,n_row,n_col,nz_udiag,Numeric);
214
- }
215
-
216
- // Get Numeric
217
- inline int umfpack_get_numeric(int Lp[], int Lj[], double Lx[], int Up[], int Ui[], double Ux[],
218
- int P[], int Q[], double Dx[], int *do_recip, double Rs[], void *Numeric)
219
- {
220
- return umfpack_di_get_numeric(Lp,Lj,Lx,Up,Ui,Ux,P,Q,Dx,do_recip,Rs,Numeric);
221
- }
222
-
223
- inline int umfpack_get_numeric(int Lp[], int Lj[], std::complex<double> Lx[], int Up[], int Ui[], std::complex<double> Ux[],
224
- int P[], int Q[], std::complex<double> Dx[], int *do_recip, double Rs[], void *Numeric)
225
- {
226
- double& lx0_real = numext::real_ref(Lx[0]);
227
- double& ux0_real = numext::real_ref(Ux[0]);
228
- double& dx0_real = numext::real_ref(Dx[0]);
229
- return umfpack_zi_get_numeric(Lp,Lj,Lx?&lx0_real:0,0,Up,Ui,Ux?&ux0_real:0,0,P,Q,
230
- Dx?&dx0_real:0,0,do_recip,Rs,Numeric);
231
- }
232
- inline SuiteSparse_long umfpack_get_numeric(SuiteSparse_long Lp[], SuiteSparse_long Lj[], double Lx[], SuiteSparse_long Up[], SuiteSparse_long Ui[], double Ux[],
233
- SuiteSparse_long P[], SuiteSparse_long Q[], double Dx[], SuiteSparse_long *do_recip, double Rs[], void *Numeric)
234
- {
235
- return umfpack_dl_get_numeric(Lp,Lj,Lx,Up,Ui,Ux,P,Q,Dx,do_recip,Rs,Numeric);
236
- }
237
-
238
- inline SuiteSparse_long umfpack_get_numeric(SuiteSparse_long Lp[], SuiteSparse_long Lj[], std::complex<double> Lx[], SuiteSparse_long Up[], SuiteSparse_long Ui[], std::complex<double> Ux[],
239
- SuiteSparse_long P[], SuiteSparse_long Q[], std::complex<double> Dx[], SuiteSparse_long *do_recip, double Rs[], void *Numeric)
240
- {
241
- double& lx0_real = numext::real_ref(Lx[0]);
242
- double& ux0_real = numext::real_ref(Ux[0]);
243
- double& dx0_real = numext::real_ref(Dx[0]);
244
- return umfpack_zl_get_numeric(Lp,Lj,Lx?&lx0_real:0,0,Up,Ui,Ux?&ux0_real:0,0,P,Q,
245
- Dx?&dx0_real:0,0,do_recip,Rs,Numeric);
246
- }
247
-
248
- // Get Determinant
249
- inline int umfpack_get_determinant(double *Mx, double *Ex, void *NumericHandle, double User_Info [UMFPACK_INFO], int)
250
- {
251
- return umfpack_di_get_determinant(Mx,Ex,NumericHandle,User_Info);
252
- }
253
-
254
- inline int umfpack_get_determinant(std::complex<double> *Mx, double *Ex, void *NumericHandle, double User_Info [UMFPACK_INFO], int)
255
- {
256
- double& mx_real = numext::real_ref(*Mx);
257
- return umfpack_zi_get_determinant(&mx_real,0,Ex,NumericHandle,User_Info);
258
- }
259
-
260
- inline SuiteSparse_long umfpack_get_determinant(double *Mx, double *Ex, void *NumericHandle, double User_Info [UMFPACK_INFO], SuiteSparse_long)
261
- {
262
- return umfpack_dl_get_determinant(Mx,Ex,NumericHandle,User_Info);
263
- }
264
-
265
- inline SuiteSparse_long umfpack_get_determinant(std::complex<double> *Mx, double *Ex, void *NumericHandle, double User_Info [UMFPACK_INFO], SuiteSparse_long)
266
- {
267
- double& mx_real = numext::real_ref(*Mx);
268
- return umfpack_zl_get_determinant(&mx_real,0,Ex,NumericHandle,User_Info);
269
- }
270
-
271
-
272
- /** \ingroup UmfPackSupport_Module
273
- * \brief A sparse LU factorization and solver based on UmfPack
274
- *
275
- * This class allows to solve for A.X = B sparse linear problems via a LU factorization
276
- * using the UmfPack library. The sparse matrix A must be squared and full rank.
277
- * The vectors or matrices X and B can be either dense or sparse.
278
- *
279
- * \warning The input matrix A should be in a \b compressed and \b column-major form.
280
- * Otherwise an expensive copy will be made. You can call the inexpensive makeCompressed() to get a compressed matrix.
281
- * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<>
282
- *
283
- * \implsparsesolverconcept
284
- *
285
- * \sa \ref TutorialSparseSolverConcept, class SparseLU
286
- */
287
- template<typename _MatrixType>
288
- class UmfPackLU : public SparseSolverBase<UmfPackLU<_MatrixType> >
289
- {
290
- protected:
291
- typedef SparseSolverBase<UmfPackLU<_MatrixType> > Base;
292
- using Base::m_isInitialized;
293
- public:
294
- using Base::_solve_impl;
295
- typedef _MatrixType MatrixType;
296
- typedef typename MatrixType::Scalar Scalar;
297
- typedef typename MatrixType::RealScalar RealScalar;
298
- typedef typename MatrixType::StorageIndex StorageIndex;
299
- typedef Matrix<Scalar,Dynamic,1> Vector;
300
- typedef Matrix<int, 1, MatrixType::ColsAtCompileTime> IntRowVectorType;
301
- typedef Matrix<int, MatrixType::RowsAtCompileTime, 1> IntColVectorType;
302
- typedef SparseMatrix<Scalar> LUMatrixType;
303
- typedef SparseMatrix<Scalar,ColMajor,StorageIndex> UmfpackMatrixType;
304
- typedef Ref<const UmfpackMatrixType, StandardCompressedFormat> UmfpackMatrixRef;
305
- enum {
306
- ColsAtCompileTime = MatrixType::ColsAtCompileTime,
307
- MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
308
- };
309
-
310
- public:
311
-
312
- typedef Array<double, UMFPACK_CONTROL, 1> UmfpackControl;
313
- typedef Array<double, UMFPACK_INFO, 1> UmfpackInfo;
314
-
315
- UmfPackLU()
316
- : m_dummy(0,0), mp_matrix(m_dummy)
317
- {
318
- init();
319
- }
320
-
321
- template<typename InputMatrixType>
322
- explicit UmfPackLU(const InputMatrixType& matrix)
323
- : mp_matrix(matrix)
324
- {
325
- init();
326
- compute(matrix);
327
- }
328
-
329
- ~UmfPackLU()
330
- {
331
- if(m_symbolic) umfpack_free_symbolic(&m_symbolic,Scalar(), StorageIndex());
332
- if(m_numeric) umfpack_free_numeric(&m_numeric,Scalar(), StorageIndex());
333
- }
334
-
335
- inline Index rows() const { return mp_matrix.rows(); }
336
- inline Index cols() const { return mp_matrix.cols(); }
337
-
338
- /** \brief Reports whether previous computation was successful.
339
- *
340
- * \returns \c Success if computation was successful,
341
- * \c NumericalIssue if the matrix.appears to be negative.
342
- */
343
- ComputationInfo info() const
344
- {
345
- eigen_assert(m_isInitialized && "Decomposition is not initialized.");
346
- return m_info;
347
- }
348
-
349
- inline const LUMatrixType& matrixL() const
350
- {
351
- if (m_extractedDataAreDirty) extractData();
352
- return m_l;
353
- }
354
-
355
- inline const LUMatrixType& matrixU() const
356
- {
357
- if (m_extractedDataAreDirty) extractData();
358
- return m_u;
359
- }
360
-
361
- inline const IntColVectorType& permutationP() const
362
- {
363
- if (m_extractedDataAreDirty) extractData();
364
- return m_p;
365
- }
366
-
367
- inline const IntRowVectorType& permutationQ() const
368
- {
369
- if (m_extractedDataAreDirty) extractData();
370
- return m_q;
371
- }
372
-
373
- /** Computes the sparse Cholesky decomposition of \a matrix
374
- * Note that the matrix should be column-major, and in compressed format for best performance.
375
- * \sa SparseMatrix::makeCompressed().
376
- */
377
- template<typename InputMatrixType>
378
- void compute(const InputMatrixType& matrix)
379
- {
380
- if(m_symbolic) umfpack_free_symbolic(&m_symbolic,Scalar(),StorageIndex());
381
- if(m_numeric) umfpack_free_numeric(&m_numeric,Scalar(),StorageIndex());
382
- grab(matrix.derived());
383
- analyzePattern_impl();
384
- factorize_impl();
385
- }
386
-
387
- /** Performs a symbolic decomposition on the sparcity of \a matrix.
388
- *
389
- * This function is particularly useful when solving for several problems having the same structure.
390
- *
391
- * \sa factorize(), compute()
392
- */
393
- template<typename InputMatrixType>
394
- void analyzePattern(const InputMatrixType& matrix)
395
- {
396
- if(m_symbolic) umfpack_free_symbolic(&m_symbolic,Scalar(),StorageIndex());
397
- if(m_numeric) umfpack_free_numeric(&m_numeric,Scalar(),StorageIndex());
398
-
399
- grab(matrix.derived());
400
-
401
- analyzePattern_impl();
402
- }
403
-
404
- /** Provides the return status code returned by UmfPack during the numeric
405
- * factorization.
406
- *
407
- * \sa factorize(), compute()
408
- */
409
- inline int umfpackFactorizeReturncode() const
410
- {
411
- eigen_assert(m_numeric && "UmfPackLU: you must first call factorize()");
412
- return m_fact_errorCode;
413
- }
414
-
415
- /** Provides access to the control settings array used by UmfPack.
416
- *
417
- * If this array contains NaN's, the default values are used.
418
- *
419
- * See UMFPACK documentation for details.
420
- */
421
- inline const UmfpackControl& umfpackControl() const
422
- {
423
- return m_control;
424
- }
425
-
426
- /** Provides access to the control settings array used by UmfPack.
427
- *
428
- * If this array contains NaN's, the default values are used.
429
- *
430
- * See UMFPACK documentation for details.
431
- */
432
- inline UmfpackControl& umfpackControl()
433
- {
434
- return m_control;
435
- }
436
-
437
- /** Performs a numeric decomposition of \a matrix
438
- *
439
- * The given matrix must has the same sparcity than the matrix on which the pattern anylysis has been performed.
440
- *
441
- * \sa analyzePattern(), compute()
442
- */
443
- template<typename InputMatrixType>
444
- void factorize(const InputMatrixType& matrix)
445
- {
446
- eigen_assert(m_analysisIsOk && "UmfPackLU: you must first call analyzePattern()");
447
- if(m_numeric)
448
- umfpack_free_numeric(&m_numeric,Scalar(),StorageIndex());
449
-
450
- grab(matrix.derived());
451
-
452
- factorize_impl();
453
- }
454
-
455
- /** Prints the current UmfPack control settings.
456
- *
457
- * \sa umfpackControl()
458
- */
459
- void printUmfpackControl()
460
- {
461
- umfpack_report_control(m_control.data(), Scalar(),StorageIndex());
462
- }
463
-
464
- /** Prints statistics collected by UmfPack.
465
- *
466
- * \sa analyzePattern(), compute()
467
- */
468
- void printUmfpackInfo()
469
- {
470
- eigen_assert(m_analysisIsOk && "UmfPackLU: you must first call analyzePattern()");
471
- umfpack_report_info(m_control.data(), m_umfpackInfo.data(), Scalar(),StorageIndex());
472
- }
473
-
474
- /** Prints the status of the previous factorization operation performed by UmfPack (symbolic or numerical factorization).
475
- *
476
- * \sa analyzePattern(), compute()
477
- */
478
- void printUmfpackStatus() {
479
- eigen_assert(m_analysisIsOk && "UmfPackLU: you must first call analyzePattern()");
480
- umfpack_report_status(m_control.data(), m_fact_errorCode, Scalar(),StorageIndex());
481
- }
482
-
483
- /** \internal */
484
- template<typename BDerived,typename XDerived>
485
- bool _solve_impl(const MatrixBase<BDerived> &b, MatrixBase<XDerived> &x) const;
486
-
487
- Scalar determinant() const;
488
-
489
- void extractData() const;
490
-
491
- protected:
492
-
493
- void init()
494
- {
495
- m_info = InvalidInput;
496
- m_isInitialized = false;
497
- m_numeric = 0;
498
- m_symbolic = 0;
499
- m_extractedDataAreDirty = true;
500
-
501
- umfpack_defaults(m_control.data(), Scalar(),StorageIndex());
502
- }
503
-
504
- void analyzePattern_impl()
505
- {
506
- m_fact_errorCode = umfpack_symbolic(internal::convert_index<StorageIndex>(mp_matrix.rows()),
507
- internal::convert_index<StorageIndex>(mp_matrix.cols()),
508
- mp_matrix.outerIndexPtr(), mp_matrix.innerIndexPtr(), mp_matrix.valuePtr(),
509
- &m_symbolic, m_control.data(), m_umfpackInfo.data());
510
-
511
- m_isInitialized = true;
512
- m_info = m_fact_errorCode ? InvalidInput : Success;
513
- m_analysisIsOk = true;
514
- m_factorizationIsOk = false;
515
- m_extractedDataAreDirty = true;
516
- }
517
-
518
- void factorize_impl()
519
- {
520
-
521
- m_fact_errorCode = umfpack_numeric(mp_matrix.outerIndexPtr(), mp_matrix.innerIndexPtr(), mp_matrix.valuePtr(),
522
- m_symbolic, &m_numeric, m_control.data(), m_umfpackInfo.data());
523
-
524
- m_info = m_fact_errorCode == UMFPACK_OK ? Success : NumericalIssue;
525
- m_factorizationIsOk = true;
526
- m_extractedDataAreDirty = true;
527
- }
528
-
529
- template<typename MatrixDerived>
530
- void grab(const EigenBase<MatrixDerived> &A)
531
- {
532
- mp_matrix.~UmfpackMatrixRef();
533
- ::new (&mp_matrix) UmfpackMatrixRef(A.derived());
534
- }
535
-
536
- void grab(const UmfpackMatrixRef &A)
537
- {
538
- if(&(A.derived()) != &mp_matrix)
539
- {
540
- mp_matrix.~UmfpackMatrixRef();
541
- ::new (&mp_matrix) UmfpackMatrixRef(A);
542
- }
543
- }
544
-
545
- // cached data to reduce reallocation, etc.
546
- mutable LUMatrixType m_l;
547
- StorageIndex m_fact_errorCode;
548
- UmfpackControl m_control;
549
- mutable UmfpackInfo m_umfpackInfo;
550
-
551
- mutable LUMatrixType m_u;
552
- mutable IntColVectorType m_p;
553
- mutable IntRowVectorType m_q;
554
-
555
- UmfpackMatrixType m_dummy;
556
- UmfpackMatrixRef mp_matrix;
557
-
558
- void* m_numeric;
559
- void* m_symbolic;
560
-
561
- mutable ComputationInfo m_info;
562
- int m_factorizationIsOk;
563
- int m_analysisIsOk;
564
- mutable bool m_extractedDataAreDirty;
565
-
566
- private:
567
- UmfPackLU(const UmfPackLU& ) { }
568
- };
569
-
570
-
571
- template<typename MatrixType>
572
- void UmfPackLU<MatrixType>::extractData() const
573
- {
574
- if (m_extractedDataAreDirty)
575
- {
576
- // get size of the data
577
- StorageIndex lnz, unz, rows, cols, nz_udiag;
578
- umfpack_get_lunz(&lnz, &unz, &rows, &cols, &nz_udiag, m_numeric, Scalar());
579
-
580
- // allocate data
581
- m_l.resize(rows,(std::min)(rows,cols));
582
- m_l.resizeNonZeros(lnz);
583
-
584
- m_u.resize((std::min)(rows,cols),cols);
585
- m_u.resizeNonZeros(unz);
586
-
587
- m_p.resize(rows);
588
- m_q.resize(cols);
589
-
590
- // extract
591
- umfpack_get_numeric(m_l.outerIndexPtr(), m_l.innerIndexPtr(), m_l.valuePtr(),
592
- m_u.outerIndexPtr(), m_u.innerIndexPtr(), m_u.valuePtr(),
593
- m_p.data(), m_q.data(), 0, 0, 0, m_numeric);
594
-
595
- m_extractedDataAreDirty = false;
596
- }
597
- }
598
-
599
- template<typename MatrixType>
600
- typename UmfPackLU<MatrixType>::Scalar UmfPackLU<MatrixType>::determinant() const
601
- {
602
- Scalar det;
603
- umfpack_get_determinant(&det, 0, m_numeric, 0, StorageIndex());
604
- return det;
605
- }
606
-
607
- template<typename MatrixType>
608
- template<typename BDerived,typename XDerived>
609
- bool UmfPackLU<MatrixType>::_solve_impl(const MatrixBase<BDerived> &b, MatrixBase<XDerived> &x) const
610
- {
611
- Index rhsCols = b.cols();
612
- eigen_assert((BDerived::Flags&RowMajorBit)==0 && "UmfPackLU backend does not support non col-major rhs yet");
613
- eigen_assert((XDerived::Flags&RowMajorBit)==0 && "UmfPackLU backend does not support non col-major result yet");
614
- eigen_assert(b.derived().data() != x.derived().data() && " Umfpack does not support inplace solve");
615
-
616
- Scalar* x_ptr = 0;
617
- Matrix<Scalar,Dynamic,1> x_tmp;
618
- if(x.innerStride()!=1)
619
- {
620
- x_tmp.resize(x.rows());
621
- x_ptr = x_tmp.data();
622
- }
623
- for (int j=0; j<rhsCols; ++j)
624
- {
625
- if(x.innerStride()==1)
626
- x_ptr = &x.col(j).coeffRef(0);
627
- StorageIndex errorCode = umfpack_solve(UMFPACK_A,
628
- mp_matrix.outerIndexPtr(), mp_matrix.innerIndexPtr(), mp_matrix.valuePtr(),
629
- x_ptr, &b.const_cast_derived().col(j).coeffRef(0),
630
- m_numeric, m_control.data(), m_umfpackInfo.data());
631
- if(x.innerStride()!=1)
632
- x.col(j) = x_tmp;
633
- if (errorCode!=0)
634
- return false;
635
- }
636
-
637
- return true;
638
- }
639
-
640
- } // end namespace Eigen
641
-
642
- #endif // EIGEN_UMFPACKSUPPORT_H