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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- // 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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- #ifndef EIGEN_CXX11_TENSOR_TENSOR_VOLUME_PATCH_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_VOLUME_PATCH_H
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-
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- namespace Eigen {
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-
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- /** \class TensorVolumePatch
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- * \ingroup CXX11_Tensor_Module
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- *
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- * \brief Patch extraction specialized for processing of volumetric data.
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- * This assumes that the input has a least 4 dimensions ordered as follows:
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- * - channels
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- * - planes
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- * - rows
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- * - columns
18
- * - (optional) additional dimensions such as time or batch size.
19
- * Calling the volume patch code with patch_planes, patch_rows, and patch_cols
20
- * is equivalent to calling the regular patch extraction code with parameters
21
- * d, patch_planes, patch_rows, patch_cols, and 1 for all the additional
22
- * dimensions.
23
- */
24
- namespace internal {
25
-
26
- template<DenseIndex Planes, DenseIndex Rows, DenseIndex Cols, typename XprType>
27
- struct traits<TensorVolumePatchOp<Planes, Rows, Cols, XprType> > : public traits<XprType>
28
- {
29
- typedef typename internal::remove_const<typename XprType::Scalar>::type Scalar;
30
- typedef traits<XprType> XprTraits;
31
- typedef typename XprTraits::StorageKind StorageKind;
32
- typedef typename XprTraits::Index Index;
33
- typedef typename XprType::Nested Nested;
34
- typedef typename remove_reference<Nested>::type _Nested;
35
- static const int NumDimensions = XprTraits::NumDimensions + 1;
36
- static const int Layout = XprTraits::Layout;
37
- typedef typename XprTraits::PointerType PointerType;
38
-
39
- };
40
-
41
- template<DenseIndex Planes, DenseIndex Rows, DenseIndex Cols, typename XprType>
42
- struct eval<TensorVolumePatchOp<Planes, Rows, Cols, XprType>, Eigen::Dense>
43
- {
44
- typedef const TensorVolumePatchOp<Planes, Rows, Cols, XprType>& type;
45
- };
46
-
47
- template<DenseIndex Planes, DenseIndex Rows, DenseIndex Cols, typename XprType>
48
- struct nested<TensorVolumePatchOp<Planes, Rows, Cols, XprType>, 1, typename eval<TensorVolumePatchOp<Planes, Rows, Cols, XprType> >::type>
49
- {
50
- typedef TensorVolumePatchOp<Planes, Rows, Cols, XprType> type;
51
- };
52
-
53
- } // end namespace internal
54
-
55
- template<DenseIndex Planes, DenseIndex Rows, DenseIndex Cols, typename XprType>
56
- class TensorVolumePatchOp : public TensorBase<TensorVolumePatchOp<Planes, Rows, Cols, XprType>, ReadOnlyAccessors>
57
- {
58
- public:
59
- typedef typename Eigen::internal::traits<TensorVolumePatchOp>::Scalar Scalar;
60
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
61
- typedef typename XprType::CoeffReturnType CoeffReturnType;
62
- typedef typename Eigen::internal::nested<TensorVolumePatchOp>::type Nested;
63
- typedef typename Eigen::internal::traits<TensorVolumePatchOp>::StorageKind StorageKind;
64
- typedef typename Eigen::internal::traits<TensorVolumePatchOp>::Index Index;
65
-
66
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorVolumePatchOp(const XprType& expr, DenseIndex patch_planes, DenseIndex patch_rows, DenseIndex patch_cols,
67
- DenseIndex plane_strides, DenseIndex row_strides, DenseIndex col_strides,
68
- DenseIndex in_plane_strides, DenseIndex in_row_strides, DenseIndex in_col_strides,
69
- DenseIndex plane_inflate_strides, DenseIndex row_inflate_strides, DenseIndex col_inflate_strides,
70
- PaddingType padding_type, Scalar padding_value)
71
- : m_xpr(expr), m_patch_planes(patch_planes), m_patch_rows(patch_rows), m_patch_cols(patch_cols),
72
- m_plane_strides(plane_strides), m_row_strides(row_strides), m_col_strides(col_strides),
73
- m_in_plane_strides(in_plane_strides), m_in_row_strides(in_row_strides), m_in_col_strides(in_col_strides),
74
- m_plane_inflate_strides(plane_inflate_strides), m_row_inflate_strides(row_inflate_strides), m_col_inflate_strides(col_inflate_strides),
75
- m_padding_explicit(false), m_padding_top_z(0), m_padding_bottom_z(0), m_padding_top(0), m_padding_bottom(0), m_padding_left(0), m_padding_right(0),
76
- m_padding_type(padding_type), m_padding_value(padding_value) {}
77
-
78
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorVolumePatchOp(const XprType& expr, DenseIndex patch_planes, DenseIndex patch_rows, DenseIndex patch_cols,
79
- DenseIndex plane_strides, DenseIndex row_strides, DenseIndex col_strides,
80
- DenseIndex in_plane_strides, DenseIndex in_row_strides, DenseIndex in_col_strides,
81
- DenseIndex plane_inflate_strides, DenseIndex row_inflate_strides, DenseIndex col_inflate_strides,
82
- DenseIndex padding_top_z, DenseIndex padding_bottom_z,
83
- DenseIndex padding_top, DenseIndex padding_bottom,
84
- DenseIndex padding_left, DenseIndex padding_right,
85
- Scalar padding_value)
86
- : m_xpr(expr), m_patch_planes(patch_planes), m_patch_rows(patch_rows), m_patch_cols(patch_cols),
87
- m_plane_strides(plane_strides), m_row_strides(row_strides), m_col_strides(col_strides),
88
- m_in_plane_strides(in_plane_strides), m_in_row_strides(in_row_strides), m_in_col_strides(in_col_strides),
89
- m_plane_inflate_strides(plane_inflate_strides), m_row_inflate_strides(row_inflate_strides), m_col_inflate_strides(col_inflate_strides),
90
- m_padding_explicit(true), m_padding_top_z(padding_top_z), m_padding_bottom_z(padding_bottom_z), m_padding_top(padding_top), m_padding_bottom(padding_bottom),
91
- m_padding_left(padding_left), m_padding_right(padding_right),
92
- m_padding_type(PADDING_VALID), m_padding_value(padding_value) {}
93
-
94
- EIGEN_DEVICE_FUNC
95
- DenseIndex patch_planes() const { return m_patch_planes; }
96
- EIGEN_DEVICE_FUNC
97
- DenseIndex patch_rows() const { return m_patch_rows; }
98
- EIGEN_DEVICE_FUNC
99
- DenseIndex patch_cols() const { return m_patch_cols; }
100
- EIGEN_DEVICE_FUNC
101
- DenseIndex plane_strides() const { return m_plane_strides; }
102
- EIGEN_DEVICE_FUNC
103
- DenseIndex row_strides() const { return m_row_strides; }
104
- EIGEN_DEVICE_FUNC
105
- DenseIndex col_strides() const { return m_col_strides; }
106
- EIGEN_DEVICE_FUNC
107
- DenseIndex in_plane_strides() const { return m_in_plane_strides; }
108
- EIGEN_DEVICE_FUNC
109
- DenseIndex in_row_strides() const { return m_in_row_strides; }
110
- EIGEN_DEVICE_FUNC
111
- DenseIndex in_col_strides() const { return m_in_col_strides; }
112
- EIGEN_DEVICE_FUNC
113
- DenseIndex plane_inflate_strides() const { return m_plane_inflate_strides; }
114
- EIGEN_DEVICE_FUNC
115
- DenseIndex row_inflate_strides() const { return m_row_inflate_strides; }
116
- EIGEN_DEVICE_FUNC
117
- DenseIndex col_inflate_strides() const { return m_col_inflate_strides; }
118
- EIGEN_DEVICE_FUNC
119
- bool padding_explicit() const { return m_padding_explicit; }
120
- EIGEN_DEVICE_FUNC
121
- DenseIndex padding_top_z() const { return m_padding_top_z; }
122
- EIGEN_DEVICE_FUNC
123
- DenseIndex padding_bottom_z() const { return m_padding_bottom_z; }
124
- EIGEN_DEVICE_FUNC
125
- DenseIndex padding_top() const { return m_padding_top; }
126
- EIGEN_DEVICE_FUNC
127
- DenseIndex padding_bottom() const { return m_padding_bottom; }
128
- EIGEN_DEVICE_FUNC
129
- DenseIndex padding_left() const { return m_padding_left; }
130
- EIGEN_DEVICE_FUNC
131
- DenseIndex padding_right() const { return m_padding_right; }
132
- EIGEN_DEVICE_FUNC
133
- PaddingType padding_type() const { return m_padding_type; }
134
- EIGEN_DEVICE_FUNC
135
- Scalar padding_value() const { return m_padding_value; }
136
-
137
- EIGEN_DEVICE_FUNC
138
- const typename internal::remove_all<typename XprType::Nested>::type&
139
- expression() const { return m_xpr; }
140
-
141
- protected:
142
- typename XprType::Nested m_xpr;
143
- const DenseIndex m_patch_planes;
144
- const DenseIndex m_patch_rows;
145
- const DenseIndex m_patch_cols;
146
- const DenseIndex m_plane_strides;
147
- const DenseIndex m_row_strides;
148
- const DenseIndex m_col_strides;
149
- const DenseIndex m_in_plane_strides;
150
- const DenseIndex m_in_row_strides;
151
- const DenseIndex m_in_col_strides;
152
- const DenseIndex m_plane_inflate_strides;
153
- const DenseIndex m_row_inflate_strides;
154
- const DenseIndex m_col_inflate_strides;
155
- const bool m_padding_explicit;
156
- const DenseIndex m_padding_top_z;
157
- const DenseIndex m_padding_bottom_z;
158
- const DenseIndex m_padding_top;
159
- const DenseIndex m_padding_bottom;
160
- const DenseIndex m_padding_left;
161
- const DenseIndex m_padding_right;
162
- const PaddingType m_padding_type;
163
- const Scalar m_padding_value;
164
- };
165
-
166
-
167
- // Eval as rvalue
168
- template<DenseIndex Planes, DenseIndex Rows, DenseIndex Cols, typename ArgType, typename Device>
169
- struct TensorEvaluator<const TensorVolumePatchOp<Planes, Rows, Cols, ArgType>, Device>
170
- {
171
- typedef TensorVolumePatchOp<Planes, Rows, Cols, ArgType> XprType;
172
- typedef typename XprType::Index Index;
173
- static const int NumInputDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
174
- static const int NumDims = NumInputDims + 1;
175
- typedef DSizes<Index, NumDims> Dimensions;
176
- typedef typename internal::remove_const<typename XprType::Scalar>::type Scalar;
177
- typedef typename XprType::CoeffReturnType CoeffReturnType;
178
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
179
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
180
- typedef StorageMemory<CoeffReturnType, Device> Storage;
181
- typedef typename Storage::Type EvaluatorPointerType;
182
-
183
- enum {
184
- IsAligned = false,
185
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
186
- BlockAccess = false,
187
- PreferBlockAccess = TensorEvaluator<ArgType, Device>::PreferBlockAccess,
188
- Layout = TensorEvaluator<ArgType, Device>::Layout,
189
- CoordAccess = false,
190
- RawAccess = false
191
- };
192
-
193
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
194
- typedef internal::TensorBlockNotImplemented TensorBlock;
195
- //===--------------------------------------------------------------------===//
196
-
197
- EIGEN_STRONG_INLINE TensorEvaluator(const XprType& op, const Device& device) :
198
- m_impl(op.expression(), device)
199
- {
200
- EIGEN_STATIC_ASSERT((NumDims >= 5), YOU_MADE_A_PROGRAMMING_MISTAKE);
201
-
202
- m_paddingValue = op.padding_value();
203
-
204
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
205
-
206
- // Cache a few variables.
207
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
208
- m_inputDepth = input_dims[0];
209
- m_inputPlanes = input_dims[1];
210
- m_inputRows = input_dims[2];
211
- m_inputCols = input_dims[3];
212
- } else {
213
- m_inputDepth = input_dims[NumInputDims-1];
214
- m_inputPlanes = input_dims[NumInputDims-2];
215
- m_inputRows = input_dims[NumInputDims-3];
216
- m_inputCols = input_dims[NumInputDims-4];
217
- }
218
-
219
- m_plane_strides = op.plane_strides();
220
- m_row_strides = op.row_strides();
221
- m_col_strides = op.col_strides();
222
-
223
- // Input strides and effective input/patch size
224
- m_in_plane_strides = op.in_plane_strides();
225
- m_in_row_strides = op.in_row_strides();
226
- m_in_col_strides = op.in_col_strides();
227
- m_plane_inflate_strides = op.plane_inflate_strides();
228
- m_row_inflate_strides = op.row_inflate_strides();
229
- m_col_inflate_strides = op.col_inflate_strides();
230
-
231
- // The "effective" spatial size after inflating data with zeros.
232
- m_input_planes_eff = (m_inputPlanes - 1) * m_plane_inflate_strides + 1;
233
- m_input_rows_eff = (m_inputRows - 1) * m_row_inflate_strides + 1;
234
- m_input_cols_eff = (m_inputCols - 1) * m_col_inflate_strides + 1;
235
- m_patch_planes_eff = op.patch_planes() + (op.patch_planes() - 1) * (m_in_plane_strides - 1);
236
- m_patch_rows_eff = op.patch_rows() + (op.patch_rows() - 1) * (m_in_row_strides - 1);
237
- m_patch_cols_eff = op.patch_cols() + (op.patch_cols() - 1) * (m_in_col_strides - 1);
238
-
239
- if (op.padding_explicit()) {
240
- m_outputPlanes = numext::ceil((m_input_planes_eff + op.padding_top_z() + op.padding_bottom_z() - m_patch_planes_eff + 1.f) / static_cast<float>(m_plane_strides));
241
- m_outputRows = numext::ceil((m_input_rows_eff + op.padding_top() + op.padding_bottom() - m_patch_rows_eff + 1.f) / static_cast<float>(m_row_strides));
242
- m_outputCols = numext::ceil((m_input_cols_eff + op.padding_left() + op.padding_right() - m_patch_cols_eff + 1.f) / static_cast<float>(m_col_strides));
243
- m_planePaddingTop = op.padding_top_z();
244
- m_rowPaddingTop = op.padding_top();
245
- m_colPaddingLeft = op.padding_left();
246
- } else {
247
- // Computing padding from the type
248
- switch (op.padding_type()) {
249
- case PADDING_VALID:
250
- m_outputPlanes = numext::ceil((m_input_planes_eff - m_patch_planes_eff + 1.f) / static_cast<float>(m_plane_strides));
251
- m_outputRows = numext::ceil((m_input_rows_eff - m_patch_rows_eff + 1.f) / static_cast<float>(m_row_strides));
252
- m_outputCols = numext::ceil((m_input_cols_eff - m_patch_cols_eff + 1.f) / static_cast<float>(m_col_strides));
253
- m_planePaddingTop = 0;
254
- m_rowPaddingTop = 0;
255
- m_colPaddingLeft = 0;
256
- break;
257
- case PADDING_SAME: {
258
- m_outputPlanes = numext::ceil(m_input_planes_eff / static_cast<float>(m_plane_strides));
259
- m_outputRows = numext::ceil(m_input_rows_eff / static_cast<float>(m_row_strides));
260
- m_outputCols = numext::ceil(m_input_cols_eff / static_cast<float>(m_col_strides));
261
- const Index dz = (m_outputPlanes - 1) * m_plane_strides + m_patch_planes_eff - m_input_planes_eff;
262
- const Index dy = (m_outputRows - 1) * m_row_strides + m_patch_rows_eff - m_input_rows_eff;
263
- const Index dx = (m_outputCols - 1) * m_col_strides + m_patch_cols_eff - m_input_cols_eff;
264
- m_planePaddingTop = dz / 2;
265
- m_rowPaddingTop = dy / 2;
266
- m_colPaddingLeft = dx / 2;
267
- break;
268
- }
269
- default:
270
- eigen_assert(false && "unexpected padding");
271
- }
272
- }
273
- eigen_assert(m_outputRows > 0);
274
- eigen_assert(m_outputCols > 0);
275
- eigen_assert(m_outputPlanes > 0);
276
-
277
- // Dimensions for result of extraction.
278
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
279
- // ColMajor
280
- // 0: depth
281
- // 1: patch_planes
282
- // 2: patch_rows
283
- // 3: patch_cols
284
- // 4: number of patches
285
- // 5 and beyond: anything else (such as batch).
286
- m_dimensions[0] = input_dims[0];
287
- m_dimensions[1] = op.patch_planes();
288
- m_dimensions[2] = op.patch_rows();
289
- m_dimensions[3] = op.patch_cols();
290
- m_dimensions[4] = m_outputPlanes * m_outputRows * m_outputCols;
291
- for (int i = 5; i < NumDims; ++i) {
292
- m_dimensions[i] = input_dims[i-1];
293
- }
294
- } else {
295
- // RowMajor
296
- // NumDims-1: depth
297
- // NumDims-2: patch_planes
298
- // NumDims-3: patch_rows
299
- // NumDims-4: patch_cols
300
- // NumDims-5: number of patches
301
- // NumDims-6 and beyond: anything else (such as batch).
302
- m_dimensions[NumDims-1] = input_dims[NumInputDims-1];
303
- m_dimensions[NumDims-2] = op.patch_planes();
304
- m_dimensions[NumDims-3] = op.patch_rows();
305
- m_dimensions[NumDims-4] = op.patch_cols();
306
- m_dimensions[NumDims-5] = m_outputPlanes * m_outputRows * m_outputCols;
307
- for (int i = NumDims-6; i >= 0; --i) {
308
- m_dimensions[i] = input_dims[i];
309
- }
310
- }
311
-
312
- // Strides for the output tensor.
313
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
314
- m_rowStride = m_dimensions[1];
315
- m_colStride = m_dimensions[2] * m_rowStride;
316
- m_patchStride = m_colStride * m_dimensions[3] * m_dimensions[0];
317
- m_otherStride = m_patchStride * m_dimensions[4];
318
- } else {
319
- m_rowStride = m_dimensions[NumDims-2];
320
- m_colStride = m_dimensions[NumDims-3] * m_rowStride;
321
- m_patchStride = m_colStride * m_dimensions[NumDims-4] * m_dimensions[NumDims-1];
322
- m_otherStride = m_patchStride * m_dimensions[NumDims-5];
323
- }
324
-
325
- // Strides for navigating through the input tensor.
326
- m_planeInputStride = m_inputDepth;
327
- m_rowInputStride = m_inputDepth * m_inputPlanes;
328
- m_colInputStride = m_inputDepth * m_inputRows * m_inputPlanes;
329
- m_otherInputStride = m_inputDepth * m_inputRows * m_inputCols * m_inputPlanes;
330
-
331
- m_outputPlanesRows = m_outputPlanes * m_outputRows;
332
-
333
- // Fast representations of different variables.
334
- m_fastOtherStride = internal::TensorIntDivisor<Index>(m_otherStride);
335
-
336
- m_fastPatchStride = internal::TensorIntDivisor<Index>(m_patchStride);
337
- m_fastColStride = internal::TensorIntDivisor<Index>(m_colStride);
338
- m_fastRowStride = internal::TensorIntDivisor<Index>(m_rowStride);
339
- m_fastInputRowStride = internal::TensorIntDivisor<Index>(m_row_inflate_strides);
340
- m_fastInputColStride = internal::TensorIntDivisor<Index>(m_col_inflate_strides);
341
- m_fastInputPlaneStride = internal::TensorIntDivisor<Index>(m_plane_inflate_strides);
342
- m_fastInputColsEff = internal::TensorIntDivisor<Index>(m_input_cols_eff);
343
- m_fastOutputPlanes = internal::TensorIntDivisor<Index>(m_outputPlanes);
344
- m_fastOutputPlanesRows = internal::TensorIntDivisor<Index>(m_outputPlanesRows);
345
-
346
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
347
- m_fastOutputDepth = internal::TensorIntDivisor<Index>(m_dimensions[0]);
348
- } else {
349
- m_fastOutputDepth = internal::TensorIntDivisor<Index>(m_dimensions[NumDims-1]);
350
- }
351
- }
352
-
353
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
354
-
355
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType /*data*/) {
356
- m_impl.evalSubExprsIfNeeded(NULL);
357
- return true;
358
- }
359
-
360
- EIGEN_STRONG_INLINE void cleanup() {
361
- m_impl.cleanup();
362
- }
363
-
364
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
365
- {
366
- // Patch index corresponding to the passed in index.
367
- const Index patchIndex = index / m_fastPatchStride;
368
-
369
- // Spatial offset within the patch. This has to be translated into 3D
370
- // coordinates within the patch.
371
- const Index patchOffset = (index - patchIndex * m_patchStride) / m_fastOutputDepth;
372
-
373
- // Batch, etc.
374
- const Index otherIndex = (NumDims == 5) ? 0 : index / m_fastOtherStride;
375
- const Index patch3DIndex = (NumDims == 5) ? patchIndex : (index - otherIndex * m_otherStride) / m_fastPatchStride;
376
-
377
- // Calculate column index in the input original tensor.
378
- const Index colIndex = patch3DIndex / m_fastOutputPlanesRows;
379
- const Index colOffset = patchOffset / m_fastColStride;
380
- const Index inputCol = colIndex * m_col_strides + colOffset * m_in_col_strides - m_colPaddingLeft;
381
- const Index origInputCol = (m_col_inflate_strides == 1) ? inputCol : ((inputCol >= 0) ? (inputCol / m_fastInputColStride) : 0);
382
- if (inputCol < 0 || inputCol >= m_input_cols_eff ||
383
- ((m_col_inflate_strides != 1) && (inputCol != origInputCol * m_col_inflate_strides))) {
384
- return Scalar(m_paddingValue);
385
- }
386
-
387
- // Calculate row index in the original input tensor.
388
- const Index rowIndex = (patch3DIndex - colIndex * m_outputPlanesRows) / m_fastOutputPlanes;
389
- const Index rowOffset = (patchOffset - colOffset * m_colStride) / m_fastRowStride;
390
- const Index inputRow = rowIndex * m_row_strides + rowOffset * m_in_row_strides - m_rowPaddingTop;
391
- const Index origInputRow = (m_row_inflate_strides == 1) ? inputRow : ((inputRow >= 0) ? (inputRow / m_fastInputRowStride) : 0);
392
- if (inputRow < 0 || inputRow >= m_input_rows_eff ||
393
- ((m_row_inflate_strides != 1) && (inputRow != origInputRow * m_row_inflate_strides))) {
394
- return Scalar(m_paddingValue);
395
- }
396
-
397
- // Calculate plane index in the original input tensor.
398
- const Index planeIndex = (patch3DIndex - m_outputPlanes * (colIndex * m_outputRows + rowIndex));
399
- const Index planeOffset = patchOffset - colOffset * m_colStride - rowOffset * m_rowStride;
400
- const Index inputPlane = planeIndex * m_plane_strides + planeOffset * m_in_plane_strides - m_planePaddingTop;
401
- const Index origInputPlane = (m_plane_inflate_strides == 1) ? inputPlane : ((inputPlane >= 0) ? (inputPlane / m_fastInputPlaneStride) : 0);
402
- if (inputPlane < 0 || inputPlane >= m_input_planes_eff ||
403
- ((m_plane_inflate_strides != 1) && (inputPlane != origInputPlane * m_plane_inflate_strides))) {
404
- return Scalar(m_paddingValue);
405
- }
406
-
407
- const int depth_index = static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 0 : NumDims - 1;
408
- const Index depth = index - (index / m_fastOutputDepth) * m_dimensions[depth_index];
409
-
410
- const Index inputIndex = depth +
411
- origInputRow * m_rowInputStride +
412
- origInputCol * m_colInputStride +
413
- origInputPlane * m_planeInputStride +
414
- otherIndex * m_otherInputStride;
415
-
416
- return m_impl.coeff(inputIndex);
417
- }
418
-
419
- template<int LoadMode>
420
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
421
- {
422
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
423
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
424
-
425
- if (m_in_row_strides != 1 || m_in_col_strides != 1 || m_row_inflate_strides != 1 || m_col_inflate_strides != 1 ||
426
- m_in_plane_strides != 1 || m_plane_inflate_strides != 1) {
427
- return packetWithPossibleZero(index);
428
- }
429
-
430
- const Index indices[2] = {index, index + PacketSize - 1};
431
- const Index patchIndex = indices[0] / m_fastPatchStride;
432
- if (patchIndex != indices[1] / m_fastPatchStride) {
433
- return packetWithPossibleZero(index);
434
- }
435
- const Index otherIndex = (NumDims == 5) ? 0 : indices[0] / m_fastOtherStride;
436
- eigen_assert(otherIndex == indices[1] / m_fastOtherStride);
437
-
438
- // Find the offset of the element wrt the location of the first element.
439
- const Index patchOffsets[2] = {(indices[0] - patchIndex * m_patchStride) / m_fastOutputDepth,
440
- (indices[1] - patchIndex * m_patchStride) / m_fastOutputDepth};
441
-
442
- const Index patch3DIndex = (NumDims == 5) ? patchIndex : (indices[0] - otherIndex * m_otherStride) / m_fastPatchStride;
443
- eigen_assert(patch3DIndex == (indices[1] - otherIndex * m_otherStride) / m_fastPatchStride);
444
-
445
- const Index colIndex = patch3DIndex / m_fastOutputPlanesRows;
446
- const Index colOffsets[2] = {
447
- patchOffsets[0] / m_fastColStride,
448
- patchOffsets[1] / m_fastColStride};
449
-
450
- // Calculate col indices in the original input tensor.
451
- const Index inputCols[2] = {
452
- colIndex * m_col_strides + colOffsets[0] - m_colPaddingLeft,
453
- colIndex * m_col_strides + colOffsets[1] - m_colPaddingLeft};
454
- if (inputCols[1] < 0 || inputCols[0] >= m_inputCols) {
455
- return internal::pset1<PacketReturnType>(Scalar(m_paddingValue));
456
- }
457
-
458
- if (inputCols[0] != inputCols[1]) {
459
- return packetWithPossibleZero(index);
460
- }
461
-
462
- const Index rowIndex = (patch3DIndex - colIndex * m_outputPlanesRows) / m_fastOutputPlanes;
463
- const Index rowOffsets[2] = {
464
- (patchOffsets[0] - colOffsets[0] * m_colStride) / m_fastRowStride,
465
- (patchOffsets[1] - colOffsets[1] * m_colStride) / m_fastRowStride};
466
- eigen_assert(rowOffsets[0] <= rowOffsets[1]);
467
- // Calculate col indices in the original input tensor.
468
- const Index inputRows[2] = {
469
- rowIndex * m_row_strides + rowOffsets[0] - m_rowPaddingTop,
470
- rowIndex * m_row_strides + rowOffsets[1] - m_rowPaddingTop};
471
-
472
- if (inputRows[1] < 0 || inputRows[0] >= m_inputRows) {
473
- return internal::pset1<PacketReturnType>(Scalar(m_paddingValue));
474
- }
475
-
476
- if (inputRows[0] != inputRows[1]) {
477
- return packetWithPossibleZero(index);
478
- }
479
-
480
- const Index planeIndex = (patch3DIndex - m_outputPlanes * (colIndex * m_outputRows + rowIndex));
481
- const Index planeOffsets[2] = {
482
- patchOffsets[0] - colOffsets[0] * m_colStride - rowOffsets[0] * m_rowStride,
483
- patchOffsets[1] - colOffsets[1] * m_colStride - rowOffsets[1] * m_rowStride};
484
- eigen_assert(planeOffsets[0] <= planeOffsets[1]);
485
- const Index inputPlanes[2] = {
486
- planeIndex * m_plane_strides + planeOffsets[0] - m_planePaddingTop,
487
- planeIndex * m_plane_strides + planeOffsets[1] - m_planePaddingTop};
488
-
489
- if (inputPlanes[1] < 0 || inputPlanes[0] >= m_inputPlanes) {
490
- return internal::pset1<PacketReturnType>(Scalar(m_paddingValue));
491
- }
492
-
493
- if (inputPlanes[0] >= 0 && inputPlanes[1] < m_inputPlanes) {
494
- // no padding
495
- const int depth_index = static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 0 : NumDims - 1;
496
- const Index depth = index - (index / m_fastOutputDepth) * m_dimensions[depth_index];
497
- const Index inputIndex = depth +
498
- inputRows[0] * m_rowInputStride +
499
- inputCols[0] * m_colInputStride +
500
- m_planeInputStride * inputPlanes[0] +
501
- otherIndex * m_otherInputStride;
502
- return m_impl.template packet<Unaligned>(inputIndex);
503
- }
504
-
505
- return packetWithPossibleZero(index);
506
- }
507
-
508
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
509
- costPerCoeff(bool vectorized) const {
510
- const double compute_cost =
511
- 10 * TensorOpCost::DivCost<Index>() + 21 * TensorOpCost::MulCost<Index>() +
512
- 8 * TensorOpCost::AddCost<Index>();
513
- return TensorOpCost(0, 0, compute_cost, vectorized, PacketSize);
514
- }
515
-
516
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return NULL; }
517
-
518
- const TensorEvaluator<ArgType, Device>& impl() const { return m_impl; }
519
-
520
-
521
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index planePaddingTop() const { return m_planePaddingTop; }
522
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index rowPaddingTop() const { return m_rowPaddingTop; }
523
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index colPaddingLeft() const { return m_colPaddingLeft; }
524
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index outputPlanes() const { return m_outputPlanes; }
525
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index outputRows() const { return m_outputRows; }
526
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index outputCols() const { return m_outputCols; }
527
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userPlaneStride() const { return m_plane_strides; }
528
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userRowStride() const { return m_row_strides; }
529
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userColStride() const { return m_col_strides; }
530
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userInPlaneStride() const { return m_in_plane_strides; }
531
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userInRowStride() const { return m_in_row_strides; }
532
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userInColStride() const { return m_in_col_strides; }
533
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index planeInflateStride() const { return m_plane_inflate_strides; }
534
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index rowInflateStride() const { return m_row_inflate_strides; }
535
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index colInflateStride() const { return m_col_inflate_strides; }
536
-
537
- #ifdef EIGEN_USE_SYCL
538
- // binding placeholder accessors to a command group handler for SYCL
539
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
540
- m_impl.bind(cgh);
541
- }
542
- #endif
543
- protected:
544
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packetWithPossibleZero(Index index) const
545
- {
546
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
547
- EIGEN_UNROLL_LOOP
548
- for (int i = 0; i < PacketSize; ++i) {
549
- values[i] = coeff(index+i);
550
- }
551
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
552
- return rslt;
553
- }
554
-
555
- Dimensions m_dimensions;
556
-
557
- // Parameters passed to the constructor.
558
- Index m_plane_strides;
559
- Index m_row_strides;
560
- Index m_col_strides;
561
-
562
- Index m_outputPlanes;
563
- Index m_outputRows;
564
- Index m_outputCols;
565
-
566
- Index m_planePaddingTop;
567
- Index m_rowPaddingTop;
568
- Index m_colPaddingLeft;
569
-
570
- Index m_in_plane_strides;
571
- Index m_in_row_strides;
572
- Index m_in_col_strides;
573
-
574
- Index m_plane_inflate_strides;
575
- Index m_row_inflate_strides;
576
- Index m_col_inflate_strides;
577
-
578
- // Cached input size.
579
- Index m_inputDepth;
580
- Index m_inputPlanes;
581
- Index m_inputRows;
582
- Index m_inputCols;
583
-
584
- // Other cached variables.
585
- Index m_outputPlanesRows;
586
-
587
- // Effective input/patch post-inflation size.
588
- Index m_input_planes_eff;
589
- Index m_input_rows_eff;
590
- Index m_input_cols_eff;
591
- Index m_patch_planes_eff;
592
- Index m_patch_rows_eff;
593
- Index m_patch_cols_eff;
594
-
595
- // Strides for the output tensor.
596
- Index m_otherStride;
597
- Index m_patchStride;
598
- Index m_rowStride;
599
- Index m_colStride;
600
-
601
- // Strides for the input tensor.
602
- Index m_planeInputStride;
603
- Index m_rowInputStride;
604
- Index m_colInputStride;
605
- Index m_otherInputStride;
606
-
607
- internal::TensorIntDivisor<Index> m_fastOtherStride;
608
- internal::TensorIntDivisor<Index> m_fastPatchStride;
609
- internal::TensorIntDivisor<Index> m_fastColStride;
610
- internal::TensorIntDivisor<Index> m_fastRowStride;
611
- internal::TensorIntDivisor<Index> m_fastInputPlaneStride;
612
- internal::TensorIntDivisor<Index> m_fastInputRowStride;
613
- internal::TensorIntDivisor<Index> m_fastInputColStride;
614
- internal::TensorIntDivisor<Index> m_fastInputColsEff;
615
- internal::TensorIntDivisor<Index> m_fastOutputPlanesRows;
616
- internal::TensorIntDivisor<Index> m_fastOutputPlanes;
617
- internal::TensorIntDivisor<Index> m_fastOutputDepth;
618
-
619
- Scalar m_paddingValue;
620
-
621
- TensorEvaluator<ArgType, Device> m_impl;
622
-
623
-
624
- };
625
-
626
-
627
- } // end namespace Eigen
628
-
629
- #endif // EIGEN_CXX11_TENSOR_TENSOR_VOLUME_PATCH_H