sequenzo 0.1.18__cp311-cp311-win_amd64.whl → 0.1.20__cp311-cp311-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.cp311-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp311-win_amd64.pyd +0 -0
  6. sequenzo/clustering/hierarchical_clustering.py +108 -6
  7. sequenzo/define_sequence_data.py +10 -1
  8. sequenzo/dissimilarity_measures/c_code.cp311-win_amd64.pyd +0 -0
  9. sequenzo/dissimilarity_measures/get_distance_matrix.py +2 -3
  10. sequenzo/dissimilarity_measures/get_substitution_cost_matrix.py +1 -1
  11. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.c +154 -154
  12. sequenzo/dissimilarity_measures/utils/get_sm_trate_substitution_cost_matrix.cp311-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp311-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp311-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp311-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp311-win_amd64.pyd +0 -0
  21. sequenzo/multidomain/cat.py +0 -53
  22. sequenzo/multidomain/dat.py +11 -3
  23. sequenzo/multidomain/idcd.py +0 -3
  24. sequenzo/multidomain/linked_polyad.py +0 -1
  25. sequenzo/openmp_setup.py +233 -0
  26. sequenzo/visualization/plot_transition_matrix.py +21 -22
  27. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/METADATA +71 -10
  28. sequenzo-0.1.20.dist-info/RECORD +272 -0
  29. sequenzo/dissimilarity_measures/setup.py +0 -35
  30. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LDLT.h +0 -688
  31. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT.h +0 -558
  32. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +0 -99
  33. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +0 -682
  34. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +0 -346
  35. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +0 -462
  36. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +0 -91
  37. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/EigenSolver.h +0 -622
  38. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +0 -418
  39. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +0 -226
  40. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +0 -374
  41. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +0 -158
  42. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealQZ.h +0 -657
  43. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur.h +0 -558
  44. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +0 -77
  45. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +0 -904
  46. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +0 -87
  47. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +0 -561
  48. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AlignedBox.h +0 -486
  49. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/AngleAxis.h +0 -247
  50. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/EulerAngles.h +0 -114
  51. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Homogeneous.h +0 -501
  52. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Hyperplane.h +0 -282
  53. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/OrthoMethods.h +0 -235
  54. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/ParametrizedLine.h +0 -232
  55. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Quaternion.h +0 -870
  56. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Rotation2D.h +0 -199
  57. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/RotationBase.h +0 -206
  58. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Scaling.h +0 -188
  59. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Transform.h +0 -1563
  60. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Translation.h +0 -202
  61. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/Umeyama.h +0 -166
  62. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Geometry/arch/Geometry_SIMD.h +0 -168
  63. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/BlockHouseholder.h +0 -110
  64. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/Householder.h +0 -176
  65. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Householder/HouseholderSequence.h +0 -545
  66. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +0 -226
  67. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +0 -212
  68. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +0 -229
  69. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +0 -394
  70. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +0 -453
  71. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +0 -444
  72. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +0 -198
  73. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +0 -117
  74. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/Jacobi/Jacobi.h +0 -483
  75. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/KLUSupport/KLUSupport.h +0 -358
  76. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/Determinant.h +0 -117
  77. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/FullPivLU.h +0 -877
  78. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/InverseImpl.h +0 -432
  79. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU.h +0 -624
  80. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +0 -83
  81. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/LU/arch/InverseSize4.h +0 -351
  82. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/MetisSupport/MetisSupport.h +0 -137
  83. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h +0 -435
  84. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +0 -1863
  85. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Ordering.h +0 -153
  86. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +0 -678
  87. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +0 -545
  88. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR.h +0 -674
  89. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +0 -97
  90. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +0 -635
  91. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/FullPivHouseholderQR.h +0 -713
  92. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h +0 -434
  93. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +0 -68
  94. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +0 -335
  95. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/BDCSVD.h +0 -1366
  96. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD.h +0 -812
  97. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +0 -91
  98. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/SVDBase.h +0 -376
  99. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SVD/UpperBidiagonalization.h +0 -414
  100. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +0 -697
  101. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +0 -174
  102. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/AmbiVector.h +0 -378
  103. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/CompressedStorage.h +0 -274
  104. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +0 -352
  105. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +0 -67
  106. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseAssign.h +0 -270
  107. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseBlock.h +0 -571
  108. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseColEtree.h +0 -206
  109. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +0 -370
  110. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +0 -722
  111. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +0 -150
  112. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +0 -342
  113. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +0 -138
  114. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseDot.h +0 -98
  115. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseFuzzy.h +0 -29
  116. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMap.h +0 -305
  117. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrix.h +0 -1518
  118. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +0 -398
  119. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparsePermutation.h +0 -178
  120. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseProduct.h +0 -181
  121. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRedux.h +0 -49
  122. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseRef.h +0 -397
  123. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +0 -659
  124. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSolverBase.h +0 -124
  125. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +0 -198
  126. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTranspose.h +0 -92
  127. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseTriangularView.h +0 -189
  128. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseUtil.h +0 -186
  129. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseVector.h +0 -478
  130. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/SparseView.h +0 -254
  131. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseCore/TriangularSolver.h +0 -315
  132. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU.h +0 -923
  133. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLUImpl.h +0 -66
  134. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +0 -226
  135. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +0 -110
  136. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +0 -375
  137. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +0 -80
  138. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +0 -181
  139. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +0 -179
  140. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +0 -107
  141. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +0 -280
  142. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +0 -126
  143. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +0 -130
  144. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +0 -223
  145. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +0 -258
  146. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +0 -137
  147. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +0 -136
  148. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +0 -83
  149. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseQR/SparseQR.h +0 -758
  150. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdDeque.h +0 -116
  151. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdList.h +0 -106
  152. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/StdVector.h +0 -131
  153. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/StlSupport/details.h +0 -84
  154. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +0 -1025
  155. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +0 -642
  156. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Image.h +0 -82
  157. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/Kernel.h +0 -79
  158. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/RealSvd2x2.h +0 -55
  159. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/blas.h +0 -440
  160. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapack.h +0 -152
  161. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke.h +0 -16292
  162. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/misc/lapacke_mangling.h +0 -17
  163. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +0 -358
  164. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +0 -696
  165. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/BlockMethods.h +0 -1442
  166. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +0 -115
  167. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +0 -177
  168. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/IndexedViewMethods.h +0 -262
  169. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +0 -152
  170. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +0 -95
  171. sequenzo/dissimilarity_measures/src/eigen/Eigen/src/plugins/ReshapedMethods.h +0 -149
  172. sequenzo/dissimilarity_measures/src/eigen/bench/BenchSparseUtil.h +0 -149
  173. sequenzo/dissimilarity_measures/src/eigen/bench/BenchTimer.h +0 -199
  174. sequenzo/dissimilarity_measures/src/eigen/bench/BenchUtil.h +0 -92
  175. sequenzo/dissimilarity_measures/src/eigen/bench/basicbenchmark.h +0 -63
  176. sequenzo/dissimilarity_measures/src/eigen/bench/btl/generic_bench/utils/utilities.h +0 -90
  177. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/blas.h +0 -675
  178. sequenzo/dissimilarity_measures/src/eigen/bench/btl/libs/BLAS/c_interface_base.h +0 -73
  179. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemm_common.h +0 -67
  180. sequenzo/dissimilarity_measures/src/eigen/bench/perf_monitoring/gemv_common.h +0 -69
  181. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchsolver.h +0 -573
  182. sequenzo/dissimilarity_measures/src/eigen/bench/spbench/spbenchstyle.h +0 -95
  183. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/benchmark.h +0 -49
  184. sequenzo/dissimilarity_measures/src/eigen/bench/tensors/tensor_benchmarks.h +0 -597
  185. sequenzo/dissimilarity_measures/src/eigen/blas/BandTriangularSolver.h +0 -97
  186. sequenzo/dissimilarity_measures/src/eigen/blas/GeneralRank1Update.h +0 -44
  187. sequenzo/dissimilarity_measures/src/eigen/blas/PackedSelfadjointProduct.h +0 -53
  188. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularMatrixVector.h +0 -79
  189. sequenzo/dissimilarity_measures/src/eigen/blas/PackedTriangularSolverVector.h +0 -88
  190. sequenzo/dissimilarity_measures/src/eigen/blas/Rank2Update.h +0 -57
  191. sequenzo/dissimilarity_measures/src/eigen/blas/common.h +0 -175
  192. sequenzo/dissimilarity_measures/src/eigen/blas/f2c/datatypes.h +0 -24
  193. sequenzo/dissimilarity_measures/src/eigen/blas/level1_cplx_impl.h +0 -155
  194. sequenzo/dissimilarity_measures/src/eigen/blas/level1_impl.h +0 -144
  195. sequenzo/dissimilarity_measures/src/eigen/blas/level1_real_impl.h +0 -122
  196. sequenzo/dissimilarity_measures/src/eigen/blas/level2_cplx_impl.h +0 -360
  197. sequenzo/dissimilarity_measures/src/eigen/blas/level2_impl.h +0 -553
  198. sequenzo/dissimilarity_measures/src/eigen/blas/level2_real_impl.h +0 -306
  199. sequenzo/dissimilarity_measures/src/eigen/blas/level3_impl.h +0 -702
  200. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/__init__.py +0 -1
  201. sequenzo/dissimilarity_measures/src/eigen/debug/gdb/printers.py +0 -314
  202. sequenzo/dissimilarity_measures/src/eigen/demos/mandelbrot/mandelbrot.h +0 -71
  203. sequenzo/dissimilarity_measures/src/eigen/demos/mix_eigen_and_c/binary_library.h +0 -71
  204. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/camera.h +0 -118
  205. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/gpuhelper.h +0 -207
  206. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/icosphere.h +0 -30
  207. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/quaternion_demo.h +0 -114
  208. sequenzo/dissimilarity_measures/src/eigen/demos/opengl/trackball.h +0 -42
  209. sequenzo/dissimilarity_measures/src/eigen/lapack/lapack_common.h +0 -29
  210. sequenzo/dissimilarity_measures/src/eigen/scripts/relicense.py +0 -69
  211. sequenzo/dissimilarity_measures/src/eigen/test/AnnoyingScalar.h +0 -165
  212. sequenzo/dissimilarity_measures/src/eigen/test/MovableScalar.h +0 -35
  213. sequenzo/dissimilarity_measures/src/eigen/test/SafeScalar.h +0 -30
  214. sequenzo/dissimilarity_measures/src/eigen/test/bug1213.h +0 -8
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  398. {sequenzo-0.1.18.dist-info → sequenzo-0.1.20.dist-info}/licenses/LICENSE +0 -0
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@@ -1,870 +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) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr>
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- // Copyright (C) 2009 Mathieu Gautier <mathieu.gautier@cea.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_QUATERNION_H
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- #define EIGEN_QUATERNION_H
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- namespace Eigen {
14
-
15
-
16
- /***************************************************************************
17
- * Definition of QuaternionBase<Derived>
18
- * The implementation is at the end of the file
19
- ***************************************************************************/
20
-
21
- namespace internal {
22
- template<typename Other,
23
- int OtherRows=Other::RowsAtCompileTime,
24
- int OtherCols=Other::ColsAtCompileTime>
25
- struct quaternionbase_assign_impl;
26
- }
27
-
28
- /** \geometry_module \ingroup Geometry_Module
29
- * \class QuaternionBase
30
- * \brief Base class for quaternion expressions
31
- * \tparam Derived derived type (CRTP)
32
- * \sa class Quaternion
33
- */
34
- template<class Derived>
35
- class QuaternionBase : public RotationBase<Derived, 3>
36
- {
37
- public:
38
- typedef RotationBase<Derived, 3> Base;
39
-
40
- using Base::operator*;
41
- using Base::derived;
42
-
43
- typedef typename internal::traits<Derived>::Scalar Scalar;
44
- typedef typename NumTraits<Scalar>::Real RealScalar;
45
- typedef typename internal::traits<Derived>::Coefficients Coefficients;
46
- typedef typename Coefficients::CoeffReturnType CoeffReturnType;
47
- typedef typename internal::conditional<bool(internal::traits<Derived>::Flags&LvalueBit),
48
- Scalar&, CoeffReturnType>::type NonConstCoeffReturnType;
49
-
50
-
51
- enum {
52
- Flags = Eigen::internal::traits<Derived>::Flags
53
- };
54
-
55
- // typedef typename Matrix<Scalar,4,1> Coefficients;
56
- /** the type of a 3D vector */
57
- typedef Matrix<Scalar,3,1> Vector3;
58
- /** the equivalent rotation matrix type */
59
- typedef Matrix<Scalar,3,3> Matrix3;
60
- /** the equivalent angle-axis type */
61
- typedef AngleAxis<Scalar> AngleAxisType;
62
-
63
-
64
-
65
- /** \returns the \c x coefficient */
66
- EIGEN_DEVICE_FUNC inline CoeffReturnType x() const { return this->derived().coeffs().coeff(0); }
67
- /** \returns the \c y coefficient */
68
- EIGEN_DEVICE_FUNC inline CoeffReturnType y() const { return this->derived().coeffs().coeff(1); }
69
- /** \returns the \c z coefficient */
70
- EIGEN_DEVICE_FUNC inline CoeffReturnType z() const { return this->derived().coeffs().coeff(2); }
71
- /** \returns the \c w coefficient */
72
- EIGEN_DEVICE_FUNC inline CoeffReturnType w() const { return this->derived().coeffs().coeff(3); }
73
-
74
- /** \returns a reference to the \c x coefficient (if Derived is a non-const lvalue) */
75
- EIGEN_DEVICE_FUNC inline NonConstCoeffReturnType x() { return this->derived().coeffs().x(); }
76
- /** \returns a reference to the \c y coefficient (if Derived is a non-const lvalue) */
77
- EIGEN_DEVICE_FUNC inline NonConstCoeffReturnType y() { return this->derived().coeffs().y(); }
78
- /** \returns a reference to the \c z coefficient (if Derived is a non-const lvalue) */
79
- EIGEN_DEVICE_FUNC inline NonConstCoeffReturnType z() { return this->derived().coeffs().z(); }
80
- /** \returns a reference to the \c w coefficient (if Derived is a non-const lvalue) */
81
- EIGEN_DEVICE_FUNC inline NonConstCoeffReturnType w() { return this->derived().coeffs().w(); }
82
-
83
- /** \returns a read-only vector expression of the imaginary part (x,y,z) */
84
- EIGEN_DEVICE_FUNC inline const VectorBlock<const Coefficients,3> vec() const { return coeffs().template head<3>(); }
85
-
86
- /** \returns a vector expression of the imaginary part (x,y,z) */
87
- EIGEN_DEVICE_FUNC inline VectorBlock<Coefficients,3> vec() { return coeffs().template head<3>(); }
88
-
89
- /** \returns a read-only vector expression of the coefficients (x,y,z,w) */
90
- EIGEN_DEVICE_FUNC inline const typename internal::traits<Derived>::Coefficients& coeffs() const { return derived().coeffs(); }
91
-
92
- /** \returns a vector expression of the coefficients (x,y,z,w) */
93
- EIGEN_DEVICE_FUNC inline typename internal::traits<Derived>::Coefficients& coeffs() { return derived().coeffs(); }
94
-
95
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE QuaternionBase<Derived>& operator=(const QuaternionBase<Derived>& other);
96
- template<class OtherDerived> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator=(const QuaternionBase<OtherDerived>& other);
97
-
98
- // disabled this copy operator as it is giving very strange compilation errors when compiling
99
- // test_stdvector with GCC 4.4.2. This looks like a GCC bug though, so feel free to re-enable it if it's
100
- // useful; however notice that we already have the templated operator= above and e.g. in MatrixBase
101
- // we didn't have to add, in addition to templated operator=, such a non-templated copy operator.
102
- // Derived& operator=(const QuaternionBase& other)
103
- // { return operator=<Derived>(other); }
104
-
105
- EIGEN_DEVICE_FUNC Derived& operator=(const AngleAxisType& aa);
106
- template<class OtherDerived> EIGEN_DEVICE_FUNC Derived& operator=(const MatrixBase<OtherDerived>& m);
107
-
108
- /** \returns a quaternion representing an identity rotation
109
- * \sa MatrixBase::Identity()
110
- */
111
- EIGEN_DEVICE_FUNC static inline Quaternion<Scalar> Identity() { return Quaternion<Scalar>(Scalar(1), Scalar(0), Scalar(0), Scalar(0)); }
112
-
113
- /** \sa QuaternionBase::Identity(), MatrixBase::setIdentity()
114
- */
115
- EIGEN_DEVICE_FUNC inline QuaternionBase& setIdentity() { coeffs() << Scalar(0), Scalar(0), Scalar(0), Scalar(1); return *this; }
116
-
117
- /** \returns the squared norm of the quaternion's coefficients
118
- * \sa QuaternionBase::norm(), MatrixBase::squaredNorm()
119
- */
120
- EIGEN_DEVICE_FUNC inline Scalar squaredNorm() const { return coeffs().squaredNorm(); }
121
-
122
- /** \returns the norm of the quaternion's coefficients
123
- * \sa QuaternionBase::squaredNorm(), MatrixBase::norm()
124
- */
125
- EIGEN_DEVICE_FUNC inline Scalar norm() const { return coeffs().norm(); }
126
-
127
- /** Normalizes the quaternion \c *this
128
- * \sa normalized(), MatrixBase::normalize() */
129
- EIGEN_DEVICE_FUNC inline void normalize() { coeffs().normalize(); }
130
- /** \returns a normalized copy of \c *this
131
- * \sa normalize(), MatrixBase::normalized() */
132
- EIGEN_DEVICE_FUNC inline Quaternion<Scalar> normalized() const { return Quaternion<Scalar>(coeffs().normalized()); }
133
-
134
- /** \returns the dot product of \c *this and \a other
135
- * Geometrically speaking, the dot product of two unit quaternions
136
- * corresponds to the cosine of half the angle between the two rotations.
137
- * \sa angularDistance()
138
- */
139
- template<class OtherDerived> EIGEN_DEVICE_FUNC inline Scalar dot(const QuaternionBase<OtherDerived>& other) const { return coeffs().dot(other.coeffs()); }
140
-
141
- template<class OtherDerived> EIGEN_DEVICE_FUNC Scalar angularDistance(const QuaternionBase<OtherDerived>& other) const;
142
-
143
- /** \returns an equivalent 3x3 rotation matrix */
144
- EIGEN_DEVICE_FUNC inline Matrix3 toRotationMatrix() const;
145
-
146
- /** \returns the quaternion which transform \a a into \a b through a rotation */
147
- template<typename Derived1, typename Derived2>
148
- EIGEN_DEVICE_FUNC Derived& setFromTwoVectors(const MatrixBase<Derived1>& a, const MatrixBase<Derived2>& b);
149
-
150
- template<class OtherDerived> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Quaternion<Scalar> operator* (const QuaternionBase<OtherDerived>& q) const;
151
- template<class OtherDerived> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& operator*= (const QuaternionBase<OtherDerived>& q);
152
-
153
- /** \returns the quaternion describing the inverse rotation */
154
- EIGEN_DEVICE_FUNC Quaternion<Scalar> inverse() const;
155
-
156
- /** \returns the conjugated quaternion */
157
- EIGEN_DEVICE_FUNC Quaternion<Scalar> conjugate() const;
158
-
159
- template<class OtherDerived> EIGEN_DEVICE_FUNC Quaternion<Scalar> slerp(const Scalar& t, const QuaternionBase<OtherDerived>& other) const;
160
-
161
- /** \returns true if each coefficients of \c *this and \a other are all exactly equal.
162
- * \warning When using floating point scalar values you probably should rather use a
163
- * fuzzy comparison such as isApprox()
164
- * \sa isApprox(), operator!= */
165
- template<class OtherDerived>
166
- EIGEN_DEVICE_FUNC inline bool operator==(const QuaternionBase<OtherDerived>& other) const
167
- { return coeffs() == other.coeffs(); }
168
-
169
- /** \returns true if at least one pair of coefficients of \c *this and \a other are not exactly equal to each other.
170
- * \warning When using floating point scalar values you probably should rather use a
171
- * fuzzy comparison such as isApprox()
172
- * \sa isApprox(), operator== */
173
- template<class OtherDerived>
174
- EIGEN_DEVICE_FUNC inline bool operator!=(const QuaternionBase<OtherDerived>& other) const
175
- { return coeffs() != other.coeffs(); }
176
-
177
- /** \returns \c true if \c *this is approximately equal to \a other, within the precision
178
- * determined by \a prec.
179
- *
180
- * \sa MatrixBase::isApprox() */
181
- template<class OtherDerived>
182
- EIGEN_DEVICE_FUNC bool isApprox(const QuaternionBase<OtherDerived>& other, const RealScalar& prec = NumTraits<Scalar>::dummy_precision()) const
183
- { return coeffs().isApprox(other.coeffs(), prec); }
184
-
185
- /** return the result vector of \a v through the rotation*/
186
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Vector3 _transformVector(const Vector3& v) const;
187
-
188
- #ifdef EIGEN_PARSED_BY_DOXYGEN
189
- /** \returns \c *this with scalar type casted to \a NewScalarType
190
- *
191
- * Note that if \a NewScalarType is equal to the current scalar type of \c *this
192
- * then this function smartly returns a const reference to \c *this.
193
- */
194
- template<typename NewScalarType>
195
- EIGEN_DEVICE_FUNC inline typename internal::cast_return_type<Derived,Quaternion<NewScalarType> >::type cast() const;
196
-
197
- #else
198
-
199
- template<typename NewScalarType>
200
- EIGEN_DEVICE_FUNC inline
201
- typename internal::enable_if<internal::is_same<Scalar,NewScalarType>::value,const Derived&>::type cast() const
202
- {
203
- return derived();
204
- }
205
-
206
- template<typename NewScalarType>
207
- EIGEN_DEVICE_FUNC inline
208
- typename internal::enable_if<!internal::is_same<Scalar,NewScalarType>::value,Quaternion<NewScalarType> >::type cast() const
209
- {
210
- return Quaternion<NewScalarType>(coeffs().template cast<NewScalarType>());
211
- }
212
- #endif
213
-
214
- #ifndef EIGEN_NO_IO
215
- friend std::ostream& operator<<(std::ostream& s, const QuaternionBase<Derived>& q) {
216
- s << q.x() << "i + " << q.y() << "j + " << q.z() << "k" << " + " << q.w();
217
- return s;
218
- }
219
- #endif
220
-
221
- #ifdef EIGEN_QUATERNIONBASE_PLUGIN
222
- # include EIGEN_QUATERNIONBASE_PLUGIN
223
- #endif
224
- protected:
225
- EIGEN_DEFAULT_COPY_CONSTRUCTOR(QuaternionBase)
226
- EIGEN_DEFAULT_EMPTY_CONSTRUCTOR_AND_DESTRUCTOR(QuaternionBase)
227
- };
228
-
229
- /***************************************************************************
230
- * Definition/implementation of Quaternion<Scalar>
231
- ***************************************************************************/
232
-
233
- /** \geometry_module \ingroup Geometry_Module
234
- *
235
- * \class Quaternion
236
- *
237
- * \brief The quaternion class used to represent 3D orientations and rotations
238
- *
239
- * \tparam _Scalar the scalar type, i.e., the type of the coefficients
240
- * \tparam _Options controls the memory alignment of the coefficients. Can be \# AutoAlign or \# DontAlign. Default is AutoAlign.
241
- *
242
- * This class represents a quaternion \f$ w+xi+yj+zk \f$ that is a convenient representation of
243
- * orientations and rotations of objects in three dimensions. Compared to other representations
244
- * like Euler angles or 3x3 matrices, quaternions offer the following advantages:
245
- * \li \b compact storage (4 scalars)
246
- * \li \b efficient to compose (28 flops),
247
- * \li \b stable spherical interpolation
248
- *
249
- * The following two typedefs are provided for convenience:
250
- * \li \c Quaternionf for \c float
251
- * \li \c Quaterniond for \c double
252
- *
253
- * \warning Operations interpreting the quaternion as rotation have undefined behavior if the quaternion is not normalized.
254
- *
255
- * \sa class AngleAxis, class Transform
256
- */
257
-
258
- namespace internal {
259
- template<typename _Scalar,int _Options>
260
- struct traits<Quaternion<_Scalar,_Options> >
261
- {
262
- typedef Quaternion<_Scalar,_Options> PlainObject;
263
- typedef _Scalar Scalar;
264
- typedef Matrix<_Scalar,4,1,_Options> Coefficients;
265
- enum{
266
- Alignment = internal::traits<Coefficients>::Alignment,
267
- Flags = LvalueBit
268
- };
269
- };
270
- }
271
-
272
- template<typename _Scalar, int _Options>
273
- class Quaternion : public QuaternionBase<Quaternion<_Scalar,_Options> >
274
- {
275
- public:
276
- typedef QuaternionBase<Quaternion<_Scalar,_Options> > Base;
277
- enum { NeedsAlignment = internal::traits<Quaternion>::Alignment>0 };
278
-
279
- typedef _Scalar Scalar;
280
-
281
- EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Quaternion)
282
- using Base::operator*=;
283
-
284
- typedef typename internal::traits<Quaternion>::Coefficients Coefficients;
285
- typedef typename Base::AngleAxisType AngleAxisType;
286
-
287
- /** Default constructor leaving the quaternion uninitialized. */
288
- EIGEN_DEVICE_FUNC inline Quaternion() {}
289
-
290
- /** Constructs and initializes the quaternion \f$ w+xi+yj+zk \f$ from
291
- * its four coefficients \a w, \a x, \a y and \a z.
292
- *
293
- * \warning Note the order of the arguments: the real \a w coefficient first,
294
- * while internally the coefficients are stored in the following order:
295
- * [\c x, \c y, \c z, \c w]
296
- */
297
- EIGEN_DEVICE_FUNC inline Quaternion(const Scalar& w, const Scalar& x, const Scalar& y, const Scalar& z) : m_coeffs(x, y, z, w){}
298
-
299
- /** Constructs and initialize a quaternion from the array data */
300
- EIGEN_DEVICE_FUNC explicit inline Quaternion(const Scalar* data) : m_coeffs(data) {}
301
-
302
- /** Copy constructor */
303
- template<class Derived> EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Quaternion(const QuaternionBase<Derived>& other) { this->Base::operator=(other); }
304
-
305
- /** Constructs and initializes a quaternion from the angle-axis \a aa */
306
- EIGEN_DEVICE_FUNC explicit inline Quaternion(const AngleAxisType& aa) { *this = aa; }
307
-
308
- /** Constructs and initializes a quaternion from either:
309
- * - a rotation matrix expression,
310
- * - a 4D vector expression representing quaternion coefficients.
311
- */
312
- template<typename Derived>
313
- EIGEN_DEVICE_FUNC explicit inline Quaternion(const MatrixBase<Derived>& other) { *this = other; }
314
-
315
- /** Explicit copy constructor with scalar conversion */
316
- template<typename OtherScalar, int OtherOptions>
317
- EIGEN_DEVICE_FUNC explicit inline Quaternion(const Quaternion<OtherScalar, OtherOptions>& other)
318
- { m_coeffs = other.coeffs().template cast<Scalar>(); }
319
-
320
- #if EIGEN_HAS_RVALUE_REFERENCES
321
- // We define a copy constructor, which means we don't get an implicit move constructor or assignment operator.
322
- /** Default move constructor */
323
- EIGEN_DEVICE_FUNC inline Quaternion(Quaternion&& other) EIGEN_NOEXCEPT_IF(std::is_nothrow_move_constructible<Scalar>::value)
324
- : m_coeffs(std::move(other.coeffs()))
325
- {}
326
-
327
- /** Default move assignment operator */
328
- EIGEN_DEVICE_FUNC Quaternion& operator=(Quaternion&& other) EIGEN_NOEXCEPT_IF(std::is_nothrow_move_assignable<Scalar>::value)
329
- {
330
- m_coeffs = std::move(other.coeffs());
331
- return *this;
332
- }
333
- #endif
334
-
335
- EIGEN_DEVICE_FUNC static Quaternion UnitRandom();
336
-
337
- template<typename Derived1, typename Derived2>
338
- EIGEN_DEVICE_FUNC static Quaternion FromTwoVectors(const MatrixBase<Derived1>& a, const MatrixBase<Derived2>& b);
339
-
340
- EIGEN_DEVICE_FUNC inline Coefficients& coeffs() { return m_coeffs;}
341
- EIGEN_DEVICE_FUNC inline const Coefficients& coeffs() const { return m_coeffs;}
342
-
343
- EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF(bool(NeedsAlignment))
344
-
345
- #ifdef EIGEN_QUATERNION_PLUGIN
346
- # include EIGEN_QUATERNION_PLUGIN
347
- #endif
348
-
349
- protected:
350
- Coefficients m_coeffs;
351
-
352
- #ifndef EIGEN_PARSED_BY_DOXYGEN
353
- static EIGEN_STRONG_INLINE void _check_template_params()
354
- {
355
- EIGEN_STATIC_ASSERT( (_Options & DontAlign) == _Options,
356
- INVALID_MATRIX_TEMPLATE_PARAMETERS)
357
- }
358
- #endif
359
- };
360
-
361
- /** \ingroup Geometry_Module
362
- * single precision quaternion type */
363
- typedef Quaternion<float> Quaternionf;
364
- /** \ingroup Geometry_Module
365
- * double precision quaternion type */
366
- typedef Quaternion<double> Quaterniond;
367
-
368
- /***************************************************************************
369
- * Specialization of Map<Quaternion<Scalar>>
370
- ***************************************************************************/
371
-
372
- namespace internal {
373
- template<typename _Scalar, int _Options>
374
- struct traits<Map<Quaternion<_Scalar>, _Options> > : traits<Quaternion<_Scalar, (int(_Options)&Aligned)==Aligned ? AutoAlign : DontAlign> >
375
- {
376
- typedef Map<Matrix<_Scalar,4,1>, _Options> Coefficients;
377
- };
378
- }
379
-
380
- namespace internal {
381
- template<typename _Scalar, int _Options>
382
- struct traits<Map<const Quaternion<_Scalar>, _Options> > : traits<Quaternion<_Scalar, (int(_Options)&Aligned)==Aligned ? AutoAlign : DontAlign> >
383
- {
384
- typedef Map<const Matrix<_Scalar,4,1>, _Options> Coefficients;
385
- typedef traits<Quaternion<_Scalar, (int(_Options)&Aligned)==Aligned ? AutoAlign : DontAlign> > TraitsBase;
386
- enum {
387
- Flags = TraitsBase::Flags & ~LvalueBit
388
- };
389
- };
390
- }
391
-
392
- /** \ingroup Geometry_Module
393
- * \brief Quaternion expression mapping a constant memory buffer
394
- *
395
- * \tparam _Scalar the type of the Quaternion coefficients
396
- * \tparam _Options see class Map
397
- *
398
- * This is a specialization of class Map for Quaternion. This class allows to view
399
- * a 4 scalar memory buffer as an Eigen's Quaternion object.
400
- *
401
- * \sa class Map, class Quaternion, class QuaternionBase
402
- */
403
- template<typename _Scalar, int _Options>
404
- class Map<const Quaternion<_Scalar>, _Options >
405
- : public QuaternionBase<Map<const Quaternion<_Scalar>, _Options> >
406
- {
407
- public:
408
- typedef QuaternionBase<Map<const Quaternion<_Scalar>, _Options> > Base;
409
-
410
- typedef _Scalar Scalar;
411
- typedef typename internal::traits<Map>::Coefficients Coefficients;
412
- EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Map)
413
- using Base::operator*=;
414
-
415
- /** Constructs a Mapped Quaternion object from the pointer \a coeffs
416
- *
417
- * The pointer \a coeffs must reference the four coefficients of Quaternion in the following order:
418
- * \code *coeffs == {x, y, z, w} \endcode
419
- *
420
- * If the template parameter _Options is set to #Aligned, then the pointer coeffs must be aligned. */
421
- EIGEN_DEVICE_FUNC explicit EIGEN_STRONG_INLINE Map(const Scalar* coeffs) : m_coeffs(coeffs) {}
422
-
423
- EIGEN_DEVICE_FUNC inline const Coefficients& coeffs() const { return m_coeffs;}
424
-
425
- protected:
426
- const Coefficients m_coeffs;
427
- };
428
-
429
- /** \ingroup Geometry_Module
430
- * \brief Expression of a quaternion from a memory buffer
431
- *
432
- * \tparam _Scalar the type of the Quaternion coefficients
433
- * \tparam _Options see class Map
434
- *
435
- * This is a specialization of class Map for Quaternion. This class allows to view
436
- * a 4 scalar memory buffer as an Eigen's Quaternion object.
437
- *
438
- * \sa class Map, class Quaternion, class QuaternionBase
439
- */
440
- template<typename _Scalar, int _Options>
441
- class Map<Quaternion<_Scalar>, _Options >
442
- : public QuaternionBase<Map<Quaternion<_Scalar>, _Options> >
443
- {
444
- public:
445
- typedef QuaternionBase<Map<Quaternion<_Scalar>, _Options> > Base;
446
-
447
- typedef _Scalar Scalar;
448
- typedef typename internal::traits<Map>::Coefficients Coefficients;
449
- EIGEN_INHERIT_ASSIGNMENT_OPERATORS(Map)
450
- using Base::operator*=;
451
-
452
- /** Constructs a Mapped Quaternion object from the pointer \a coeffs
453
- *
454
- * The pointer \a coeffs must reference the four coefficients of Quaternion in the following order:
455
- * \code *coeffs == {x, y, z, w} \endcode
456
- *
457
- * If the template parameter _Options is set to #Aligned, then the pointer coeffs must be aligned. */
458
- EIGEN_DEVICE_FUNC explicit EIGEN_STRONG_INLINE Map(Scalar* coeffs) : m_coeffs(coeffs) {}
459
-
460
- EIGEN_DEVICE_FUNC inline Coefficients& coeffs() { return m_coeffs; }
461
- EIGEN_DEVICE_FUNC inline const Coefficients& coeffs() const { return m_coeffs; }
462
-
463
- protected:
464
- Coefficients m_coeffs;
465
- };
466
-
467
- /** \ingroup Geometry_Module
468
- * Map an unaligned array of single precision scalars as a quaternion */
469
- typedef Map<Quaternion<float>, 0> QuaternionMapf;
470
- /** \ingroup Geometry_Module
471
- * Map an unaligned array of double precision scalars as a quaternion */
472
- typedef Map<Quaternion<double>, 0> QuaternionMapd;
473
- /** \ingroup Geometry_Module
474
- * Map a 16-byte aligned array of single precision scalars as a quaternion */
475
- typedef Map<Quaternion<float>, Aligned> QuaternionMapAlignedf;
476
- /** \ingroup Geometry_Module
477
- * Map a 16-byte aligned array of double precision scalars as a quaternion */
478
- typedef Map<Quaternion<double>, Aligned> QuaternionMapAlignedd;
479
-
480
- /***************************************************************************
481
- * Implementation of QuaternionBase methods
482
- ***************************************************************************/
483
-
484
- // Generic Quaternion * Quaternion product
485
- // This product can be specialized for a given architecture via the Arch template argument.
486
- namespace internal {
487
- template<int Arch, class Derived1, class Derived2, typename Scalar> struct quat_product
488
- {
489
- EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE Quaternion<Scalar> run(const QuaternionBase<Derived1>& a, const QuaternionBase<Derived2>& b){
490
- return Quaternion<Scalar>
491
- (
492
- a.w() * b.w() - a.x() * b.x() - a.y() * b.y() - a.z() * b.z(),
493
- a.w() * b.x() + a.x() * b.w() + a.y() * b.z() - a.z() * b.y(),
494
- a.w() * b.y() + a.y() * b.w() + a.z() * b.x() - a.x() * b.z(),
495
- a.w() * b.z() + a.z() * b.w() + a.x() * b.y() - a.y() * b.x()
496
- );
497
- }
498
- };
499
- }
500
-
501
- /** \returns the concatenation of two rotations as a quaternion-quaternion product */
502
- template <class Derived>
503
- template <class OtherDerived>
504
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Quaternion<typename internal::traits<Derived>::Scalar>
505
- QuaternionBase<Derived>::operator* (const QuaternionBase<OtherDerived>& other) const
506
- {
507
- EIGEN_STATIC_ASSERT((internal::is_same<typename Derived::Scalar, typename OtherDerived::Scalar>::value),
508
- YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
509
- return internal::quat_product<Architecture::Target, Derived, OtherDerived,
510
- typename internal::traits<Derived>::Scalar>::run(*this, other);
511
- }
512
-
513
- /** \sa operator*(Quaternion) */
514
- template <class Derived>
515
- template <class OtherDerived>
516
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& QuaternionBase<Derived>::operator*= (const QuaternionBase<OtherDerived>& other)
517
- {
518
- derived() = derived() * other.derived();
519
- return derived();
520
- }
521
-
522
- /** Rotation of a vector by a quaternion.
523
- * \remarks If the quaternion is used to rotate several points (>1)
524
- * then it is much more efficient to first convert it to a 3x3 Matrix.
525
- * Comparison of the operation cost for n transformations:
526
- * - Quaternion2: 30n
527
- * - Via a Matrix3: 24 + 15n
528
- */
529
- template <class Derived>
530
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE typename QuaternionBase<Derived>::Vector3
531
- QuaternionBase<Derived>::_transformVector(const Vector3& v) const
532
- {
533
- // Note that this algorithm comes from the optimization by hand
534
- // of the conversion to a Matrix followed by a Matrix/Vector product.
535
- // It appears to be much faster than the common algorithm found
536
- // in the literature (30 versus 39 flops). It also requires two
537
- // Vector3 as temporaries.
538
- Vector3 uv = this->vec().cross(v);
539
- uv += uv;
540
- return v + this->w() * uv + this->vec().cross(uv);
541
- }
542
-
543
- template<class Derived>
544
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE QuaternionBase<Derived>& QuaternionBase<Derived>::operator=(const QuaternionBase<Derived>& other)
545
- {
546
- coeffs() = other.coeffs();
547
- return derived();
548
- }
549
-
550
- template<class Derived>
551
- template<class OtherDerived>
552
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& QuaternionBase<Derived>::operator=(const QuaternionBase<OtherDerived>& other)
553
- {
554
- coeffs() = other.coeffs();
555
- return derived();
556
- }
557
-
558
- /** Set \c *this from an angle-axis \a aa and returns a reference to \c *this
559
- */
560
- template<class Derived>
561
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Derived& QuaternionBase<Derived>::operator=(const AngleAxisType& aa)
562
- {
563
- EIGEN_USING_STD(cos)
564
- EIGEN_USING_STD(sin)
565
- Scalar ha = Scalar(0.5)*aa.angle(); // Scalar(0.5) to suppress precision loss warnings
566
- this->w() = cos(ha);
567
- this->vec() = sin(ha) * aa.axis();
568
- return derived();
569
- }
570
-
571
- /** Set \c *this from the expression \a xpr:
572
- * - if \a xpr is a 4x1 vector, then \a xpr is assumed to be a quaternion
573
- * - if \a xpr is a 3x3 matrix, then \a xpr is assumed to be rotation matrix
574
- * and \a xpr is converted to a quaternion
575
- */
576
-
577
- template<class Derived>
578
- template<class MatrixDerived>
579
- EIGEN_DEVICE_FUNC inline Derived& QuaternionBase<Derived>::operator=(const MatrixBase<MatrixDerived>& xpr)
580
- {
581
- EIGEN_STATIC_ASSERT((internal::is_same<typename Derived::Scalar, typename MatrixDerived::Scalar>::value),
582
- YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
583
- internal::quaternionbase_assign_impl<MatrixDerived>::run(*this, xpr.derived());
584
- return derived();
585
- }
586
-
587
- /** Convert the quaternion to a 3x3 rotation matrix. The quaternion is required to
588
- * be normalized, otherwise the result is undefined.
589
- */
590
- template<class Derived>
591
- EIGEN_DEVICE_FUNC inline typename QuaternionBase<Derived>::Matrix3
592
- QuaternionBase<Derived>::toRotationMatrix(void) const
593
- {
594
- // NOTE if inlined, then gcc 4.2 and 4.4 get rid of the temporary (not gcc 4.3 !!)
595
- // if not inlined then the cost of the return by value is huge ~ +35%,
596
- // however, not inlining this function is an order of magnitude slower, so
597
- // it has to be inlined, and so the return by value is not an issue
598
- Matrix3 res;
599
-
600
- const Scalar tx = Scalar(2)*this->x();
601
- const Scalar ty = Scalar(2)*this->y();
602
- const Scalar tz = Scalar(2)*this->z();
603
- const Scalar twx = tx*this->w();
604
- const Scalar twy = ty*this->w();
605
- const Scalar twz = tz*this->w();
606
- const Scalar txx = tx*this->x();
607
- const Scalar txy = ty*this->x();
608
- const Scalar txz = tz*this->x();
609
- const Scalar tyy = ty*this->y();
610
- const Scalar tyz = tz*this->y();
611
- const Scalar tzz = tz*this->z();
612
-
613
- res.coeffRef(0,0) = Scalar(1)-(tyy+tzz);
614
- res.coeffRef(0,1) = txy-twz;
615
- res.coeffRef(0,2) = txz+twy;
616
- res.coeffRef(1,0) = txy+twz;
617
- res.coeffRef(1,1) = Scalar(1)-(txx+tzz);
618
- res.coeffRef(1,2) = tyz-twx;
619
- res.coeffRef(2,0) = txz-twy;
620
- res.coeffRef(2,1) = tyz+twx;
621
- res.coeffRef(2,2) = Scalar(1)-(txx+tyy);
622
-
623
- return res;
624
- }
625
-
626
- /** Sets \c *this to be a quaternion representing a rotation between
627
- * the two arbitrary vectors \a a and \a b. In other words, the built
628
- * rotation represent a rotation sending the line of direction \a a
629
- * to the line of direction \a b, both lines passing through the origin.
630
- *
631
- * \returns a reference to \c *this.
632
- *
633
- * Note that the two input vectors do \b not have to be normalized, and
634
- * do not need to have the same norm.
635
- */
636
- template<class Derived>
637
- template<typename Derived1, typename Derived2>
638
- EIGEN_DEVICE_FUNC inline Derived& QuaternionBase<Derived>::setFromTwoVectors(const MatrixBase<Derived1>& a, const MatrixBase<Derived2>& b)
639
- {
640
- EIGEN_USING_STD(sqrt)
641
- Vector3 v0 = a.normalized();
642
- Vector3 v1 = b.normalized();
643
- Scalar c = v1.dot(v0);
644
-
645
- // if dot == -1, vectors are nearly opposites
646
- // => accurately compute the rotation axis by computing the
647
- // intersection of the two planes. This is done by solving:
648
- // x^T v0 = 0
649
- // x^T v1 = 0
650
- // under the constraint:
651
- // ||x|| = 1
652
- // which yields a singular value problem
653
- if (c < Scalar(-1)+NumTraits<Scalar>::dummy_precision())
654
- {
655
- c = numext::maxi(c,Scalar(-1));
656
- Matrix<Scalar,2,3> m; m << v0.transpose(), v1.transpose();
657
- JacobiSVD<Matrix<Scalar,2,3> > svd(m, ComputeFullV);
658
- Vector3 axis = svd.matrixV().col(2);
659
-
660
- Scalar w2 = (Scalar(1)+c)*Scalar(0.5);
661
- this->w() = sqrt(w2);
662
- this->vec() = axis * sqrt(Scalar(1) - w2);
663
- return derived();
664
- }
665
- Vector3 axis = v0.cross(v1);
666
- Scalar s = sqrt((Scalar(1)+c)*Scalar(2));
667
- Scalar invs = Scalar(1)/s;
668
- this->vec() = axis * invs;
669
- this->w() = s * Scalar(0.5);
670
-
671
- return derived();
672
- }
673
-
674
- /** \returns a random unit quaternion following a uniform distribution law on SO(3)
675
- *
676
- * \note The implementation is based on http://planning.cs.uiuc.edu/node198.html
677
- */
678
- template<typename Scalar, int Options>
679
- EIGEN_DEVICE_FUNC Quaternion<Scalar,Options> Quaternion<Scalar,Options>::UnitRandom()
680
- {
681
- EIGEN_USING_STD(sqrt)
682
- EIGEN_USING_STD(sin)
683
- EIGEN_USING_STD(cos)
684
- const Scalar u1 = internal::random<Scalar>(0, 1),
685
- u2 = internal::random<Scalar>(0, 2*EIGEN_PI),
686
- u3 = internal::random<Scalar>(0, 2*EIGEN_PI);
687
- const Scalar a = sqrt(Scalar(1) - u1),
688
- b = sqrt(u1);
689
- return Quaternion (a * sin(u2), a * cos(u2), b * sin(u3), b * cos(u3));
690
- }
691
-
692
-
693
- /** Returns a quaternion representing a rotation between
694
- * the two arbitrary vectors \a a and \a b. In other words, the built
695
- * rotation represent a rotation sending the line of direction \a a
696
- * to the line of direction \a b, both lines passing through the origin.
697
- *
698
- * \returns resulting quaternion
699
- *
700
- * Note that the two input vectors do \b not have to be normalized, and
701
- * do not need to have the same norm.
702
- */
703
- template<typename Scalar, int Options>
704
- template<typename Derived1, typename Derived2>
705
- EIGEN_DEVICE_FUNC Quaternion<Scalar,Options> Quaternion<Scalar,Options>::FromTwoVectors(const MatrixBase<Derived1>& a, const MatrixBase<Derived2>& b)
706
- {
707
- Quaternion quat;
708
- quat.setFromTwoVectors(a, b);
709
- return quat;
710
- }
711
-
712
-
713
- /** \returns the multiplicative inverse of \c *this
714
- * Note that in most cases, i.e., if you simply want the opposite rotation,
715
- * and/or the quaternion is normalized, then it is enough to use the conjugate.
716
- *
717
- * \sa QuaternionBase::conjugate()
718
- */
719
- template <class Derived>
720
- EIGEN_DEVICE_FUNC inline Quaternion<typename internal::traits<Derived>::Scalar> QuaternionBase<Derived>::inverse() const
721
- {
722
- // FIXME should this function be called multiplicativeInverse and conjugate() be called inverse() or opposite() ??
723
- Scalar n2 = this->squaredNorm();
724
- if (n2 > Scalar(0))
725
- return Quaternion<Scalar>(conjugate().coeffs() / n2);
726
- else
727
- {
728
- // return an invalid result to flag the error
729
- return Quaternion<Scalar>(Coefficients::Zero());
730
- }
731
- }
732
-
733
- // Generic conjugate of a Quaternion
734
- namespace internal {
735
- template<int Arch, class Derived, typename Scalar> struct quat_conj
736
- {
737
- EIGEN_DEVICE_FUNC static EIGEN_STRONG_INLINE Quaternion<Scalar> run(const QuaternionBase<Derived>& q){
738
- return Quaternion<Scalar>(q.w(),-q.x(),-q.y(),-q.z());
739
- }
740
- };
741
- }
742
-
743
- /** \returns the conjugate of the \c *this which is equal to the multiplicative inverse
744
- * if the quaternion is normalized.
745
- * The conjugate of a quaternion represents the opposite rotation.
746
- *
747
- * \sa Quaternion2::inverse()
748
- */
749
- template <class Derived>
750
- EIGEN_DEVICE_FUNC inline Quaternion<typename internal::traits<Derived>::Scalar>
751
- QuaternionBase<Derived>::conjugate() const
752
- {
753
- return internal::quat_conj<Architecture::Target, Derived,
754
- typename internal::traits<Derived>::Scalar>::run(*this);
755
-
756
- }
757
-
758
- /** \returns the angle (in radian) between two rotations
759
- * \sa dot()
760
- */
761
- template <class Derived>
762
- template <class OtherDerived>
763
- EIGEN_DEVICE_FUNC inline typename internal::traits<Derived>::Scalar
764
- QuaternionBase<Derived>::angularDistance(const QuaternionBase<OtherDerived>& other) const
765
- {
766
- EIGEN_USING_STD(atan2)
767
- Quaternion<Scalar> d = (*this) * other.conjugate();
768
- return Scalar(2) * atan2( d.vec().norm(), numext::abs(d.w()) );
769
- }
770
-
771
-
772
-
773
- /** \returns the spherical linear interpolation between the two quaternions
774
- * \c *this and \a other at the parameter \a t in [0;1].
775
- *
776
- * This represents an interpolation for a constant motion between \c *this and \a other,
777
- * see also http://en.wikipedia.org/wiki/Slerp.
778
- */
779
- template <class Derived>
780
- template <class OtherDerived>
781
- EIGEN_DEVICE_FUNC Quaternion<typename internal::traits<Derived>::Scalar>
782
- QuaternionBase<Derived>::slerp(const Scalar& t, const QuaternionBase<OtherDerived>& other) const
783
- {
784
- EIGEN_USING_STD(acos)
785
- EIGEN_USING_STD(sin)
786
- const Scalar one = Scalar(1) - NumTraits<Scalar>::epsilon();
787
- Scalar d = this->dot(other);
788
- Scalar absD = numext::abs(d);
789
-
790
- Scalar scale0;
791
- Scalar scale1;
792
-
793
- if(absD>=one)
794
- {
795
- scale0 = Scalar(1) - t;
796
- scale1 = t;
797
- }
798
- else
799
- {
800
- // theta is the angle between the 2 quaternions
801
- Scalar theta = acos(absD);
802
- Scalar sinTheta = sin(theta);
803
-
804
- scale0 = sin( ( Scalar(1) - t ) * theta) / sinTheta;
805
- scale1 = sin( ( t * theta) ) / sinTheta;
806
- }
807
- if(d<Scalar(0)) scale1 = -scale1;
808
-
809
- return Quaternion<Scalar>(scale0 * coeffs() + scale1 * other.coeffs());
810
- }
811
-
812
- namespace internal {
813
-
814
- // set from a rotation matrix
815
- template<typename Other>
816
- struct quaternionbase_assign_impl<Other,3,3>
817
- {
818
- typedef typename Other::Scalar Scalar;
819
- template<class Derived> EIGEN_DEVICE_FUNC static inline void run(QuaternionBase<Derived>& q, const Other& a_mat)
820
- {
821
- const typename internal::nested_eval<Other,2>::type mat(a_mat);
822
- EIGEN_USING_STD(sqrt)
823
- // This algorithm comes from "Quaternion Calculus and Fast Animation",
824
- // Ken Shoemake, 1987 SIGGRAPH course notes
825
- Scalar t = mat.trace();
826
- if (t > Scalar(0))
827
- {
828
- t = sqrt(t + Scalar(1.0));
829
- q.w() = Scalar(0.5)*t;
830
- t = Scalar(0.5)/t;
831
- q.x() = (mat.coeff(2,1) - mat.coeff(1,2)) * t;
832
- q.y() = (mat.coeff(0,2) - mat.coeff(2,0)) * t;
833
- q.z() = (mat.coeff(1,0) - mat.coeff(0,1)) * t;
834
- }
835
- else
836
- {
837
- Index i = 0;
838
- if (mat.coeff(1,1) > mat.coeff(0,0))
839
- i = 1;
840
- if (mat.coeff(2,2) > mat.coeff(i,i))
841
- i = 2;
842
- Index j = (i+1)%3;
843
- Index k = (j+1)%3;
844
-
845
- t = sqrt(mat.coeff(i,i)-mat.coeff(j,j)-mat.coeff(k,k) + Scalar(1.0));
846
- q.coeffs().coeffRef(i) = Scalar(0.5) * t;
847
- t = Scalar(0.5)/t;
848
- q.w() = (mat.coeff(k,j)-mat.coeff(j,k))*t;
849
- q.coeffs().coeffRef(j) = (mat.coeff(j,i)+mat.coeff(i,j))*t;
850
- q.coeffs().coeffRef(k) = (mat.coeff(k,i)+mat.coeff(i,k))*t;
851
- }
852
- }
853
- };
854
-
855
- // set from a vector of coefficients assumed to be a quaternion
856
- template<typename Other>
857
- struct quaternionbase_assign_impl<Other,4,1>
858
- {
859
- typedef typename Other::Scalar Scalar;
860
- template<class Derived> EIGEN_DEVICE_FUNC static inline void run(QuaternionBase<Derived>& q, const Other& vec)
861
- {
862
- q.coeffs() = vec;
863
- }
864
- };
865
-
866
- } // end namespace internal
867
-
868
- } // end namespace Eigen
869
-
870
- #endif // EIGEN_QUATERNION_H