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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@@ -1,730 +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) 2009 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_AUTODIFF_SCALAR_H
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- #define EIGEN_AUTODIFF_SCALAR_H
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-
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- namespace Eigen {
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-
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- namespace internal {
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-
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- template<typename A, typename B>
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- struct make_coherent_impl {
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- static void run(A&, B&) {}
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- };
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-
22
- // resize a to match b is a.size()==0, and conversely.
23
- template<typename A, typename B>
24
- void make_coherent(const A& a, const B&b)
25
- {
26
- make_coherent_impl<A,B>::run(a.const_cast_derived(), b.const_cast_derived());
27
- }
28
-
29
- template<typename DerivativeType, bool Enable> struct auto_diff_special_op;
30
-
31
- } // end namespace internal
32
-
33
- template<typename DerivativeType> class AutoDiffScalar;
34
-
35
- template<typename NewDerType>
36
- inline AutoDiffScalar<NewDerType> MakeAutoDiffScalar(const typename NewDerType::Scalar& value, const NewDerType &der) {
37
- return AutoDiffScalar<NewDerType>(value,der);
38
- }
39
-
40
- /** \class AutoDiffScalar
41
- * \brief A scalar type replacement with automatic differentiation capability
42
- *
43
- * \param DerivativeType the vector type used to store/represent the derivatives. The base scalar type
44
- * as well as the number of derivatives to compute are determined from this type.
45
- * Typical choices include, e.g., \c Vector4f for 4 derivatives, or \c VectorXf
46
- * if the number of derivatives is not known at compile time, and/or, the number
47
- * of derivatives is large.
48
- * Note that DerivativeType can also be a reference (e.g., \c VectorXf&) to wrap a
49
- * existing vector into an AutoDiffScalar.
50
- * Finally, DerivativeType can also be any Eigen compatible expression.
51
- *
52
- * This class represents a scalar value while tracking its respective derivatives using Eigen's expression
53
- * template mechanism.
54
- *
55
- * It supports the following list of global math function:
56
- * - std::abs, std::sqrt, std::pow, std::exp, std::log, std::sin, std::cos,
57
- * - internal::abs, internal::sqrt, numext::pow, internal::exp, internal::log, internal::sin, internal::cos,
58
- * - internal::conj, internal::real, internal::imag, numext::abs2.
59
- *
60
- * AutoDiffScalar can be used as the scalar type of an Eigen::Matrix object. However,
61
- * in that case, the expression template mechanism only occurs at the top Matrix level,
62
- * while derivatives are computed right away.
63
- *
64
- */
65
-
66
- template<typename DerivativeType>
67
- class AutoDiffScalar
68
- : public internal::auto_diff_special_op
69
- <DerivativeType, !internal::is_same<typename internal::traits<typename internal::remove_all<DerivativeType>::type>::Scalar,
70
- typename NumTraits<typename internal::traits<typename internal::remove_all<DerivativeType>::type>::Scalar>::Real>::value>
71
- {
72
- public:
73
- typedef internal::auto_diff_special_op
74
- <DerivativeType, !internal::is_same<typename internal::traits<typename internal::remove_all<DerivativeType>::type>::Scalar,
75
- typename NumTraits<typename internal::traits<typename internal::remove_all<DerivativeType>::type>::Scalar>::Real>::value> Base;
76
- typedef typename internal::remove_all<DerivativeType>::type DerType;
77
- typedef typename internal::traits<DerType>::Scalar Scalar;
78
- typedef typename NumTraits<Scalar>::Real Real;
79
-
80
- using Base::operator+;
81
- using Base::operator*;
82
-
83
- /** Default constructor without any initialization. */
84
- AutoDiffScalar() {}
85
-
86
- /** Constructs an active scalar from its \a value,
87
- and initializes the \a nbDer derivatives such that it corresponds to the \a derNumber -th variable */
88
- AutoDiffScalar(const Scalar& value, int nbDer, int derNumber)
89
- : m_value(value), m_derivatives(DerType::Zero(nbDer))
90
- {
91
- m_derivatives.coeffRef(derNumber) = Scalar(1);
92
- }
93
-
94
- /** Conversion from a scalar constant to an active scalar.
95
- * The derivatives are set to zero. */
96
- /*explicit*/ AutoDiffScalar(const Real& value)
97
- : m_value(value)
98
- {
99
- if(m_derivatives.size()>0)
100
- m_derivatives.setZero();
101
- }
102
-
103
- /** Constructs an active scalar from its \a value and derivatives \a der */
104
- AutoDiffScalar(const Scalar& value, const DerType& der)
105
- : m_value(value), m_derivatives(der)
106
- {}
107
-
108
- template<typename OtherDerType>
109
- AutoDiffScalar(const AutoDiffScalar<OtherDerType>& other
110
- #ifndef EIGEN_PARSED_BY_DOXYGEN
111
- , typename internal::enable_if<
112
- internal::is_same<Scalar, typename internal::traits<typename internal::remove_all<OtherDerType>::type>::Scalar>::value
113
- && internal::is_convertible<OtherDerType,DerType>::value , void*>::type = 0
114
- #endif
115
- )
116
- : m_value(other.value()), m_derivatives(other.derivatives())
117
- {}
118
-
119
- friend std::ostream & operator << (std::ostream & s, const AutoDiffScalar& a)
120
- {
121
- return s << a.value();
122
- }
123
-
124
- AutoDiffScalar(const AutoDiffScalar& other)
125
- : m_value(other.value()), m_derivatives(other.derivatives())
126
- {}
127
-
128
- template<typename OtherDerType>
129
- inline AutoDiffScalar& operator=(const AutoDiffScalar<OtherDerType>& other)
130
- {
131
- m_value = other.value();
132
- m_derivatives = other.derivatives();
133
- return *this;
134
- }
135
-
136
- inline AutoDiffScalar& operator=(const AutoDiffScalar& other)
137
- {
138
- m_value = other.value();
139
- m_derivatives = other.derivatives();
140
- return *this;
141
- }
142
-
143
- inline AutoDiffScalar& operator=(const Scalar& other)
144
- {
145
- m_value = other;
146
- if(m_derivatives.size()>0)
147
- m_derivatives.setZero();
148
- return *this;
149
- }
150
-
151
- // inline operator const Scalar& () const { return m_value; }
152
- // inline operator Scalar& () { return m_value; }
153
-
154
- inline const Scalar& value() const { return m_value; }
155
- inline Scalar& value() { return m_value; }
156
-
157
- inline const DerType& derivatives() const { return m_derivatives; }
158
- inline DerType& derivatives() { return m_derivatives; }
159
-
160
- inline bool operator< (const Scalar& other) const { return m_value < other; }
161
- inline bool operator<=(const Scalar& other) const { return m_value <= other; }
162
- inline bool operator> (const Scalar& other) const { return m_value > other; }
163
- inline bool operator>=(const Scalar& other) const { return m_value >= other; }
164
- inline bool operator==(const Scalar& other) const { return m_value == other; }
165
- inline bool operator!=(const Scalar& other) const { return m_value != other; }
166
-
167
- friend inline bool operator< (const Scalar& a, const AutoDiffScalar& b) { return a < b.value(); }
168
- friend inline bool operator<=(const Scalar& a, const AutoDiffScalar& b) { return a <= b.value(); }
169
- friend inline bool operator> (const Scalar& a, const AutoDiffScalar& b) { return a > b.value(); }
170
- friend inline bool operator>=(const Scalar& a, const AutoDiffScalar& b) { return a >= b.value(); }
171
- friend inline bool operator==(const Scalar& a, const AutoDiffScalar& b) { return a == b.value(); }
172
- friend inline bool operator!=(const Scalar& a, const AutoDiffScalar& b) { return a != b.value(); }
173
-
174
- template<typename OtherDerType> inline bool operator< (const AutoDiffScalar<OtherDerType>& b) const { return m_value < b.value(); }
175
- template<typename OtherDerType> inline bool operator<=(const AutoDiffScalar<OtherDerType>& b) const { return m_value <= b.value(); }
176
- template<typename OtherDerType> inline bool operator> (const AutoDiffScalar<OtherDerType>& b) const { return m_value > b.value(); }
177
- template<typename OtherDerType> inline bool operator>=(const AutoDiffScalar<OtherDerType>& b) const { return m_value >= b.value(); }
178
- template<typename OtherDerType> inline bool operator==(const AutoDiffScalar<OtherDerType>& b) const { return m_value == b.value(); }
179
- template<typename OtherDerType> inline bool operator!=(const AutoDiffScalar<OtherDerType>& b) const { return m_value != b.value(); }
180
-
181
- inline const AutoDiffScalar<DerType&> operator+(const Scalar& other) const
182
- {
183
- return AutoDiffScalar<DerType&>(m_value + other, m_derivatives);
184
- }
185
-
186
- friend inline const AutoDiffScalar<DerType&> operator+(const Scalar& a, const AutoDiffScalar& b)
187
- {
188
- return AutoDiffScalar<DerType&>(a + b.value(), b.derivatives());
189
- }
190
-
191
- // inline const AutoDiffScalar<DerType&> operator+(const Real& other) const
192
- // {
193
- // return AutoDiffScalar<DerType&>(m_value + other, m_derivatives);
194
- // }
195
-
196
- // friend inline const AutoDiffScalar<DerType&> operator+(const Real& a, const AutoDiffScalar& b)
197
- // {
198
- // return AutoDiffScalar<DerType&>(a + b.value(), b.derivatives());
199
- // }
200
-
201
- inline AutoDiffScalar& operator+=(const Scalar& other)
202
- {
203
- value() += other;
204
- return *this;
205
- }
206
-
207
- template<typename OtherDerType>
208
- inline const AutoDiffScalar<CwiseBinaryOp<internal::scalar_sum_op<Scalar>,const DerType,const typename internal::remove_all<OtherDerType>::type> >
209
- operator+(const AutoDiffScalar<OtherDerType>& other) const
210
- {
211
- internal::make_coherent(m_derivatives, other.derivatives());
212
- return AutoDiffScalar<CwiseBinaryOp<internal::scalar_sum_op<Scalar>,const DerType,const typename internal::remove_all<OtherDerType>::type> >(
213
- m_value + other.value(),
214
- m_derivatives + other.derivatives());
215
- }
216
-
217
- template<typename OtherDerType>
218
- inline AutoDiffScalar&
219
- operator+=(const AutoDiffScalar<OtherDerType>& other)
220
- {
221
- (*this) = (*this) + other;
222
- return *this;
223
- }
224
-
225
- inline const AutoDiffScalar<DerType&> operator-(const Scalar& b) const
226
- {
227
- return AutoDiffScalar<DerType&>(m_value - b, m_derivatives);
228
- }
229
-
230
- friend inline const AutoDiffScalar<CwiseUnaryOp<internal::scalar_opposite_op<Scalar>, const DerType> >
231
- operator-(const Scalar& a, const AutoDiffScalar& b)
232
- {
233
- return AutoDiffScalar<CwiseUnaryOp<internal::scalar_opposite_op<Scalar>, const DerType> >
234
- (a - b.value(), -b.derivatives());
235
- }
236
-
237
- inline AutoDiffScalar& operator-=(const Scalar& other)
238
- {
239
- value() -= other;
240
- return *this;
241
- }
242
-
243
- template<typename OtherDerType>
244
- inline const AutoDiffScalar<CwiseBinaryOp<internal::scalar_difference_op<Scalar>, const DerType,const typename internal::remove_all<OtherDerType>::type> >
245
- operator-(const AutoDiffScalar<OtherDerType>& other) const
246
- {
247
- internal::make_coherent(m_derivatives, other.derivatives());
248
- return AutoDiffScalar<CwiseBinaryOp<internal::scalar_difference_op<Scalar>, const DerType,const typename internal::remove_all<OtherDerType>::type> >(
249
- m_value - other.value(),
250
- m_derivatives - other.derivatives());
251
- }
252
-
253
- template<typename OtherDerType>
254
- inline AutoDiffScalar&
255
- operator-=(const AutoDiffScalar<OtherDerType>& other)
256
- {
257
- *this = *this - other;
258
- return *this;
259
- }
260
-
261
- inline const AutoDiffScalar<CwiseUnaryOp<internal::scalar_opposite_op<Scalar>, const DerType> >
262
- operator-() const
263
- {
264
- return AutoDiffScalar<CwiseUnaryOp<internal::scalar_opposite_op<Scalar>, const DerType> >(
265
- -m_value,
266
- -m_derivatives);
267
- }
268
-
269
- inline const AutoDiffScalar<EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(DerType,Scalar,product) >
270
- operator*(const Scalar& other) const
271
- {
272
- return MakeAutoDiffScalar(m_value * other, m_derivatives * other);
273
- }
274
-
275
- friend inline const AutoDiffScalar<EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(DerType,Scalar,product) >
276
- operator*(const Scalar& other, const AutoDiffScalar& a)
277
- {
278
- return MakeAutoDiffScalar(a.value() * other, a.derivatives() * other);
279
- }
280
-
281
- // inline const AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >
282
- // operator*(const Real& other) const
283
- // {
284
- // return AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >(
285
- // m_value * other,
286
- // (m_derivatives * other));
287
- // }
288
- //
289
- // friend inline const AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >
290
- // operator*(const Real& other, const AutoDiffScalar& a)
291
- // {
292
- // return AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >(
293
- // a.value() * other,
294
- // a.derivatives() * other);
295
- // }
296
-
297
- inline const AutoDiffScalar<EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(DerType,Scalar,product) >
298
- operator/(const Scalar& other) const
299
- {
300
- return MakeAutoDiffScalar(m_value / other, (m_derivatives * (Scalar(1)/other)));
301
- }
302
-
303
- friend inline const AutoDiffScalar<EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(DerType,Scalar,product) >
304
- operator/(const Scalar& other, const AutoDiffScalar& a)
305
- {
306
- return MakeAutoDiffScalar(other / a.value(), a.derivatives() * (Scalar(-other) / (a.value()*a.value())));
307
- }
308
-
309
- // inline const AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >
310
- // operator/(const Real& other) const
311
- // {
312
- // return AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >(
313
- // m_value / other,
314
- // (m_derivatives * (Real(1)/other)));
315
- // }
316
- //
317
- // friend inline const AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >
318
- // operator/(const Real& other, const AutoDiffScalar& a)
319
- // {
320
- // return AutoDiffScalar<typename CwiseUnaryOp<internal::scalar_multiple_op<Real>, DerType>::Type >(
321
- // other / a.value(),
322
- // a.derivatives() * (-Real(1)/other));
323
- // }
324
-
325
- template<typename OtherDerType>
326
- inline const AutoDiffScalar<EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(
327
- CwiseBinaryOp<internal::scalar_difference_op<Scalar> EIGEN_COMMA
328
- const EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(DerType,Scalar,product) EIGEN_COMMA
329
- const EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(typename internal::remove_all<OtherDerType>::type,Scalar,product) >,Scalar,product) >
330
- operator/(const AutoDiffScalar<OtherDerType>& other) const
331
- {
332
- internal::make_coherent(m_derivatives, other.derivatives());
333
- return MakeAutoDiffScalar(
334
- m_value / other.value(),
335
- ((m_derivatives * other.value()) - (other.derivatives() * m_value))
336
- * (Scalar(1)/(other.value()*other.value())));
337
- }
338
-
339
- template<typename OtherDerType>
340
- inline const AutoDiffScalar<CwiseBinaryOp<internal::scalar_sum_op<Scalar>,
341
- const EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(DerType,Scalar,product),
342
- const EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(typename internal::remove_all<OtherDerType>::type,Scalar,product) > >
343
- operator*(const AutoDiffScalar<OtherDerType>& other) const
344
- {
345
- internal::make_coherent(m_derivatives, other.derivatives());
346
- return MakeAutoDiffScalar(
347
- m_value * other.value(),
348
- (m_derivatives * other.value()) + (other.derivatives() * m_value));
349
- }
350
-
351
- inline AutoDiffScalar& operator*=(const Scalar& other)
352
- {
353
- *this = *this * other;
354
- return *this;
355
- }
356
-
357
- template<typename OtherDerType>
358
- inline AutoDiffScalar& operator*=(const AutoDiffScalar<OtherDerType>& other)
359
- {
360
- *this = *this * other;
361
- return *this;
362
- }
363
-
364
- inline AutoDiffScalar& operator/=(const Scalar& other)
365
- {
366
- *this = *this / other;
367
- return *this;
368
- }
369
-
370
- template<typename OtherDerType>
371
- inline AutoDiffScalar& operator/=(const AutoDiffScalar<OtherDerType>& other)
372
- {
373
- *this = *this / other;
374
- return *this;
375
- }
376
-
377
- protected:
378
- Scalar m_value;
379
- DerType m_derivatives;
380
-
381
- };
382
-
383
- namespace internal {
384
-
385
- template<typename DerivativeType>
386
- struct auto_diff_special_op<DerivativeType, true>
387
- // : auto_diff_scalar_op<DerivativeType, typename NumTraits<Scalar>::Real,
388
- // is_same<Scalar,typename NumTraits<Scalar>::Real>::value>
389
- {
390
- typedef typename remove_all<DerivativeType>::type DerType;
391
- typedef typename traits<DerType>::Scalar Scalar;
392
- typedef typename NumTraits<Scalar>::Real Real;
393
-
394
- // typedef auto_diff_scalar_op<DerivativeType, typename NumTraits<Scalar>::Real,
395
- // is_same<Scalar,typename NumTraits<Scalar>::Real>::value> Base;
396
-
397
- // using Base::operator+;
398
- // using Base::operator+=;
399
- // using Base::operator-;
400
- // using Base::operator-=;
401
- // using Base::operator*;
402
- // using Base::operator*=;
403
-
404
- const AutoDiffScalar<DerivativeType>& derived() const { return *static_cast<const AutoDiffScalar<DerivativeType>*>(this); }
405
- AutoDiffScalar<DerivativeType>& derived() { return *static_cast<AutoDiffScalar<DerivativeType>*>(this); }
406
-
407
-
408
- inline const AutoDiffScalar<DerType&> operator+(const Real& other) const
409
- {
410
- return AutoDiffScalar<DerType&>(derived().value() + other, derived().derivatives());
411
- }
412
-
413
- friend inline const AutoDiffScalar<DerType&> operator+(const Real& a, const AutoDiffScalar<DerivativeType>& b)
414
- {
415
- return AutoDiffScalar<DerType&>(a + b.value(), b.derivatives());
416
- }
417
-
418
- inline AutoDiffScalar<DerivativeType>& operator+=(const Real& other)
419
- {
420
- derived().value() += other;
421
- return derived();
422
- }
423
-
424
-
425
- inline const AutoDiffScalar<typename CwiseUnaryOp<bind2nd_op<scalar_product_op<Scalar,Real> >, DerType>::Type >
426
- operator*(const Real& other) const
427
- {
428
- return AutoDiffScalar<typename CwiseUnaryOp<bind2nd_op<scalar_product_op<Scalar,Real> >, DerType>::Type >(
429
- derived().value() * other,
430
- derived().derivatives() * other);
431
- }
432
-
433
- friend inline const AutoDiffScalar<typename CwiseUnaryOp<bind1st_op<scalar_product_op<Real,Scalar> >, DerType>::Type >
434
- operator*(const Real& other, const AutoDiffScalar<DerivativeType>& a)
435
- {
436
- return AutoDiffScalar<typename CwiseUnaryOp<bind1st_op<scalar_product_op<Real,Scalar> >, DerType>::Type >(
437
- a.value() * other,
438
- a.derivatives() * other);
439
- }
440
-
441
- inline AutoDiffScalar<DerivativeType>& operator*=(const Scalar& other)
442
- {
443
- *this = *this * other;
444
- return derived();
445
- }
446
- };
447
-
448
- template<typename DerivativeType>
449
- struct auto_diff_special_op<DerivativeType, false>
450
- {
451
- void operator*() const;
452
- void operator-() const;
453
- void operator+() const;
454
- };
455
-
456
- template<typename BinOp, typename A, typename B, typename RefType>
457
- void make_coherent_expression(CwiseBinaryOp<BinOp,A,B> xpr, const RefType &ref)
458
- {
459
- make_coherent(xpr.const_cast_derived().lhs(), ref);
460
- make_coherent(xpr.const_cast_derived().rhs(), ref);
461
- }
462
-
463
- template<typename UnaryOp, typename A, typename RefType>
464
- void make_coherent_expression(const CwiseUnaryOp<UnaryOp,A> &xpr, const RefType &ref)
465
- {
466
- make_coherent(xpr.nestedExpression().const_cast_derived(), ref);
467
- }
468
-
469
- // needed for compilation only
470
- template<typename UnaryOp, typename A, typename RefType>
471
- void make_coherent_expression(const CwiseNullaryOp<UnaryOp,A> &, const RefType &)
472
- {}
473
-
474
- template<typename A_Scalar, int A_Rows, int A_Cols, int A_Options, int A_MaxRows, int A_MaxCols, typename B>
475
- struct make_coherent_impl<Matrix<A_Scalar, A_Rows, A_Cols, A_Options, A_MaxRows, A_MaxCols>, B> {
476
- typedef Matrix<A_Scalar, A_Rows, A_Cols, A_Options, A_MaxRows, A_MaxCols> A;
477
- static void run(A& a, B& b) {
478
- if((A_Rows==Dynamic || A_Cols==Dynamic) && (a.size()==0))
479
- {
480
- a.resize(b.size());
481
- a.setZero();
482
- }
483
- else if (B::SizeAtCompileTime==Dynamic && a.size()!=0 && b.size()==0)
484
- {
485
- make_coherent_expression(b,a);
486
- }
487
- }
488
- };
489
-
490
- template<typename A, typename B_Scalar, int B_Rows, int B_Cols, int B_Options, int B_MaxRows, int B_MaxCols>
491
- struct make_coherent_impl<A, Matrix<B_Scalar, B_Rows, B_Cols, B_Options, B_MaxRows, B_MaxCols> > {
492
- typedef Matrix<B_Scalar, B_Rows, B_Cols, B_Options, B_MaxRows, B_MaxCols> B;
493
- static void run(A& a, B& b) {
494
- if((B_Rows==Dynamic || B_Cols==Dynamic) && (b.size()==0))
495
- {
496
- b.resize(a.size());
497
- b.setZero();
498
- }
499
- else if (A::SizeAtCompileTime==Dynamic && b.size()!=0 && a.size()==0)
500
- {
501
- make_coherent_expression(a,b);
502
- }
503
- }
504
- };
505
-
506
- template<typename A_Scalar, int A_Rows, int A_Cols, int A_Options, int A_MaxRows, int A_MaxCols,
507
- typename B_Scalar, int B_Rows, int B_Cols, int B_Options, int B_MaxRows, int B_MaxCols>
508
- struct make_coherent_impl<Matrix<A_Scalar, A_Rows, A_Cols, A_Options, A_MaxRows, A_MaxCols>,
509
- Matrix<B_Scalar, B_Rows, B_Cols, B_Options, B_MaxRows, B_MaxCols> > {
510
- typedef Matrix<A_Scalar, A_Rows, A_Cols, A_Options, A_MaxRows, A_MaxCols> A;
511
- typedef Matrix<B_Scalar, B_Rows, B_Cols, B_Options, B_MaxRows, B_MaxCols> B;
512
- static void run(A& a, B& b) {
513
- if((A_Rows==Dynamic || A_Cols==Dynamic) && (a.size()==0))
514
- {
515
- a.resize(b.size());
516
- a.setZero();
517
- }
518
- else if((B_Rows==Dynamic || B_Cols==Dynamic) && (b.size()==0))
519
- {
520
- b.resize(a.size());
521
- b.setZero();
522
- }
523
- }
524
- };
525
-
526
- } // end namespace internal
527
-
528
- template<typename DerType, typename BinOp>
529
- struct ScalarBinaryOpTraits<AutoDiffScalar<DerType>,typename DerType::Scalar,BinOp>
530
- {
531
- typedef AutoDiffScalar<DerType> ReturnType;
532
- };
533
-
534
- template<typename DerType, typename BinOp>
535
- struct ScalarBinaryOpTraits<typename DerType::Scalar,AutoDiffScalar<DerType>, BinOp>
536
- {
537
- typedef AutoDiffScalar<DerType> ReturnType;
538
- };
539
-
540
-
541
- // The following is an attempt to let Eigen's known about expression template, but that's more tricky!
542
-
543
- // template<typename DerType, typename BinOp>
544
- // struct ScalarBinaryOpTraits<AutoDiffScalar<DerType>,AutoDiffScalar<DerType>, BinOp>
545
- // {
546
- // enum { Defined = 1 };
547
- // typedef AutoDiffScalar<typename DerType::PlainObject> ReturnType;
548
- // };
549
- //
550
- // template<typename DerType1,typename DerType2, typename BinOp>
551
- // struct ScalarBinaryOpTraits<AutoDiffScalar<DerType1>,AutoDiffScalar<DerType2>, BinOp>
552
- // {
553
- // enum { Defined = 1 };//internal::is_same<typename DerType1::Scalar,typename DerType2::Scalar>::value };
554
- // typedef AutoDiffScalar<typename DerType1::PlainObject> ReturnType;
555
- // };
556
-
557
- #define EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(FUNC,CODE) \
558
- template<typename DerType> \
559
- inline const Eigen::AutoDiffScalar< \
560
- EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(typename Eigen::internal::remove_all<DerType>::type, typename Eigen::internal::traits<typename Eigen::internal::remove_all<DerType>::type>::Scalar, product) > \
561
- FUNC(const Eigen::AutoDiffScalar<DerType>& x) { \
562
- using namespace Eigen; \
563
- typedef typename Eigen::internal::traits<typename Eigen::internal::remove_all<DerType>::type>::Scalar Scalar; \
564
- EIGEN_UNUSED_VARIABLE(sizeof(Scalar)); \
565
- CODE; \
566
- }
567
-
568
- template<typename DerType>
569
- struct CleanedUpDerType {
570
- typedef AutoDiffScalar<typename Eigen::internal::remove_all<DerType>::type::PlainObject> type;
571
- };
572
-
573
- template<typename DerType>
574
- inline const AutoDiffScalar<DerType>& conj(const AutoDiffScalar<DerType>& x) { return x; }
575
- template<typename DerType>
576
- inline const AutoDiffScalar<DerType>& real(const AutoDiffScalar<DerType>& x) { return x; }
577
- template<typename DerType>
578
- inline typename DerType::Scalar imag(const AutoDiffScalar<DerType>&) { return 0.; }
579
- template<typename DerType, typename T>
580
- inline typename CleanedUpDerType<DerType>::type (min)(const AutoDiffScalar<DerType>& x, const T& y) {
581
- typedef typename CleanedUpDerType<DerType>::type ADS;
582
- return (x <= y ? ADS(x) : ADS(y));
583
- }
584
- template<typename DerType, typename T>
585
- inline typename CleanedUpDerType<DerType>::type (max)(const AutoDiffScalar<DerType>& x, const T& y) {
586
- typedef typename CleanedUpDerType<DerType>::type ADS;
587
- return (x >= y ? ADS(x) : ADS(y));
588
- }
589
- template<typename DerType, typename T>
590
- inline typename CleanedUpDerType<DerType>::type (min)(const T& x, const AutoDiffScalar<DerType>& y) {
591
- typedef typename CleanedUpDerType<DerType>::type ADS;
592
- return (x < y ? ADS(x) : ADS(y));
593
- }
594
- template<typename DerType, typename T>
595
- inline typename CleanedUpDerType<DerType>::type (max)(const T& x, const AutoDiffScalar<DerType>& y) {
596
- typedef typename CleanedUpDerType<DerType>::type ADS;
597
- return (x > y ? ADS(x) : ADS(y));
598
- }
599
- template<typename DerType>
600
- inline typename CleanedUpDerType<DerType>::type (min)(const AutoDiffScalar<DerType>& x, const AutoDiffScalar<DerType>& y) {
601
- return (x.value() < y.value() ? x : y);
602
- }
603
- template<typename DerType>
604
- inline typename CleanedUpDerType<DerType>::type (max)(const AutoDiffScalar<DerType>& x, const AutoDiffScalar<DerType>& y) {
605
- return (x.value() >= y.value() ? x : y);
606
- }
607
-
608
-
609
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(abs,
610
- using std::abs;
611
- return Eigen::MakeAutoDiffScalar(abs(x.value()), x.derivatives() * (x.value()<0 ? -1 : 1) );)
612
-
613
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(abs2,
614
- using numext::abs2;
615
- return Eigen::MakeAutoDiffScalar(abs2(x.value()), x.derivatives() * (Scalar(2)*x.value()));)
616
-
617
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(sqrt,
618
- using std::sqrt;
619
- Scalar sqrtx = sqrt(x.value());
620
- return Eigen::MakeAutoDiffScalar(sqrtx,x.derivatives() * (Scalar(0.5) / sqrtx));)
621
-
622
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(cos,
623
- using std::cos;
624
- using std::sin;
625
- return Eigen::MakeAutoDiffScalar(cos(x.value()), x.derivatives() * (-sin(x.value())));)
626
-
627
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(sin,
628
- using std::sin;
629
- using std::cos;
630
- return Eigen::MakeAutoDiffScalar(sin(x.value()),x.derivatives() * cos(x.value()));)
631
-
632
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(exp,
633
- using std::exp;
634
- Scalar expx = exp(x.value());
635
- return Eigen::MakeAutoDiffScalar(expx,x.derivatives() * expx);)
636
-
637
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(log,
638
- using std::log;
639
- return Eigen::MakeAutoDiffScalar(log(x.value()),x.derivatives() * (Scalar(1)/x.value()));)
640
-
641
- template<typename DerType>
642
- inline const Eigen::AutoDiffScalar<
643
- EIGEN_EXPR_BINARYOP_SCALAR_RETURN_TYPE(typename internal::remove_all<DerType>::type,typename internal::traits<typename internal::remove_all<DerType>::type>::Scalar,product) >
644
- pow(const Eigen::AutoDiffScalar<DerType> &x, const typename internal::traits<typename internal::remove_all<DerType>::type>::Scalar &y)
645
- {
646
- using namespace Eigen;
647
- using std::pow;
648
- return Eigen::MakeAutoDiffScalar(pow(x.value(),y), x.derivatives() * (y * pow(x.value(),y-1)));
649
- }
650
-
651
-
652
- template<typename DerTypeA,typename DerTypeB>
653
- inline const AutoDiffScalar<Matrix<typename internal::traits<typename internal::remove_all<DerTypeA>::type>::Scalar,Dynamic,1> >
654
- atan2(const AutoDiffScalar<DerTypeA>& a, const AutoDiffScalar<DerTypeB>& b)
655
- {
656
- using std::atan2;
657
- typedef typename internal::traits<typename internal::remove_all<DerTypeA>::type>::Scalar Scalar;
658
- typedef AutoDiffScalar<Matrix<Scalar,Dynamic,1> > PlainADS;
659
- PlainADS ret;
660
- ret.value() = atan2(a.value(), b.value());
661
-
662
- Scalar squared_hypot = a.value() * a.value() + b.value() * b.value();
663
-
664
- // if (squared_hypot==0) the derivation is undefined and the following results in a NaN:
665
- ret.derivatives() = (a.derivatives() * b.value() - a.value() * b.derivatives()) / squared_hypot;
666
-
667
- return ret;
668
- }
669
-
670
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(tan,
671
- using std::tan;
672
- using std::cos;
673
- return Eigen::MakeAutoDiffScalar(tan(x.value()),x.derivatives() * (Scalar(1)/numext::abs2(cos(x.value()))));)
674
-
675
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(asin,
676
- using std::sqrt;
677
- using std::asin;
678
- return Eigen::MakeAutoDiffScalar(asin(x.value()),x.derivatives() * (Scalar(1)/sqrt(1-numext::abs2(x.value()))));)
679
-
680
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(acos,
681
- using std::sqrt;
682
- using std::acos;
683
- return Eigen::MakeAutoDiffScalar(acos(x.value()),x.derivatives() * (Scalar(-1)/sqrt(1-numext::abs2(x.value()))));)
684
-
685
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(tanh,
686
- using std::cosh;
687
- using std::tanh;
688
- return Eigen::MakeAutoDiffScalar(tanh(x.value()),x.derivatives() * (Scalar(1)/numext::abs2(cosh(x.value()))));)
689
-
690
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(sinh,
691
- using std::sinh;
692
- using std::cosh;
693
- return Eigen::MakeAutoDiffScalar(sinh(x.value()),x.derivatives() * cosh(x.value()));)
694
-
695
- EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY(cosh,
696
- using std::sinh;
697
- using std::cosh;
698
- return Eigen::MakeAutoDiffScalar(cosh(x.value()),x.derivatives() * sinh(x.value()));)
699
-
700
- #undef EIGEN_AUTODIFF_DECLARE_GLOBAL_UNARY
701
-
702
- template<typename DerType> struct NumTraits<AutoDiffScalar<DerType> >
703
- : NumTraits< typename NumTraits<typename internal::remove_all<DerType>::type::Scalar>::Real >
704
- {
705
- typedef typename internal::remove_all<DerType>::type DerTypeCleaned;
706
- typedef AutoDiffScalar<Matrix<typename NumTraits<typename DerTypeCleaned::Scalar>::Real,DerTypeCleaned::RowsAtCompileTime,DerTypeCleaned::ColsAtCompileTime,
707
- 0, DerTypeCleaned::MaxRowsAtCompileTime, DerTypeCleaned::MaxColsAtCompileTime> > Real;
708
- typedef AutoDiffScalar<DerType> NonInteger;
709
- typedef AutoDiffScalar<DerType> Nested;
710
- typedef typename NumTraits<typename DerTypeCleaned::Scalar>::Literal Literal;
711
- enum{
712
- RequireInitialization = 1
713
- };
714
- };
715
-
716
- }
717
-
718
- namespace std {
719
-
720
- template <typename T>
721
- class numeric_limits<Eigen::AutoDiffScalar<T> >
722
- : public numeric_limits<typename T::Scalar> {};
723
-
724
- template <typename T>
725
- class numeric_limits<Eigen::AutoDiffScalar<T&> >
726
- : public numeric_limits<typename T::Scalar> {};
727
-
728
- } // namespace std
729
-
730
- #endif // EIGEN_AUTODIFF_SCALAR_H