sequenzo 0.1.18__cp312-cp312-win_amd64.whl → 0.1.20__cp312-cp312-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.cp312-win_amd64.pyd +0 -0
  4. sequenzo/clustering/KMedoids.py +39 -0
  5. sequenzo/clustering/clustering_c_code.cp312-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.cp312-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.cp312-win_amd64.pyd +0 -0
  13. sequenzo/dissimilarity_measures/utils/seqconc.c +154 -154
  14. sequenzo/dissimilarity_measures/utils/seqconc.cp312-win_amd64.pyd +0 -0
  15. sequenzo/dissimilarity_measures/utils/seqdss.c +154 -154
  16. sequenzo/dissimilarity_measures/utils/seqdss.cp312-win_amd64.pyd +0 -0
  17. sequenzo/dissimilarity_measures/utils/seqdur.c +154 -154
  18. sequenzo/dissimilarity_measures/utils/seqdur.cp312-win_amd64.pyd +0 -0
  19. sequenzo/dissimilarity_measures/utils/seqlength.c +154 -154
  20. sequenzo/dissimilarity_measures/utils/seqlength.cp312-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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@@ -1,603 +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) 2014 Benoit Steiner <benoit.steiner.goog@gmail.com>
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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_CXX11_TENSOR_TENSOR_IMAGE_PATCH_H
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- #define EIGEN_CXX11_TENSOR_TENSOR_IMAGE_PATCH_H
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-
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- namespace Eigen {
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-
15
- /** \class TensorImagePatch
16
- * \ingroup CXX11_Tensor_Module
17
- *
18
- * \brief Patch extraction specialized for image processing.
19
- * This assumes that the input has a least 3 dimensions ordered as follow:
20
- * 1st dimension: channels (of size d)
21
- * 2nd dimension: rows (of size r)
22
- * 3rd dimension: columns (of size c)
23
- * There can be additional dimensions such as time (for video) or batch (for
24
- * bulk processing after the first 3.
25
- * Calling the image patch code with patch_rows and patch_cols is equivalent
26
- * to calling the regular patch extraction code with parameters d, patch_rows,
27
- * patch_cols, and 1 for all the additional dimensions.
28
- */
29
- namespace internal {
30
-
31
- template<DenseIndex Rows, DenseIndex Cols, typename XprType>
32
- struct traits<TensorImagePatchOp<Rows, Cols, XprType> > : public traits<XprType>
33
- {
34
- typedef typename internal::remove_const<typename XprType::Scalar>::type Scalar;
35
- typedef traits<XprType> XprTraits;
36
- typedef typename XprTraits::StorageKind StorageKind;
37
- typedef typename XprTraits::Index Index;
38
- typedef typename XprType::Nested Nested;
39
- typedef typename remove_reference<Nested>::type _Nested;
40
- static const int NumDimensions = XprTraits::NumDimensions + 1;
41
- static const int Layout = XprTraits::Layout;
42
- typedef typename XprTraits::PointerType PointerType;
43
- };
44
-
45
- template<DenseIndex Rows, DenseIndex Cols, typename XprType>
46
- struct eval<TensorImagePatchOp<Rows, Cols, XprType>, Eigen::Dense>
47
- {
48
- typedef const TensorImagePatchOp<Rows, Cols, XprType>& type;
49
- };
50
-
51
- template<DenseIndex Rows, DenseIndex Cols, typename XprType>
52
- struct nested<TensorImagePatchOp<Rows, Cols, XprType>, 1, typename eval<TensorImagePatchOp<Rows, Cols, XprType> >::type>
53
- {
54
- typedef TensorImagePatchOp<Rows, Cols, XprType> type;
55
- };
56
-
57
- template <typename Self, bool Vectorizable>
58
- struct ImagePatchCopyOp {
59
- typedef typename Self::Index Index;
60
- typedef typename Self::Scalar Scalar;
61
- typedef typename Self::Impl Impl;
62
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void Run(
63
- const Self& self, const Index num_coeff_to_copy, const Index dst_index,
64
- Scalar* dst_data, const Index src_index) {
65
- const Impl& impl = self.impl();
66
- for (Index i = 0; i < num_coeff_to_copy; ++i) {
67
- dst_data[dst_index + i] = impl.coeff(src_index + i);
68
- }
69
- }
70
- };
71
-
72
- template <typename Self>
73
- struct ImagePatchCopyOp<Self, true> {
74
- typedef typename Self::Index Index;
75
- typedef typename Self::Scalar Scalar;
76
- typedef typename Self::Impl Impl;
77
- typedef typename packet_traits<Scalar>::type Packet;
78
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void Run(
79
- const Self& self, const Index num_coeff_to_copy, const Index dst_index,
80
- Scalar* dst_data, const Index src_index) {
81
- const Impl& impl = self.impl();
82
- const Index packet_size = internal::unpacket_traits<Packet>::size;
83
- const Index vectorized_size =
84
- (num_coeff_to_copy / packet_size) * packet_size;
85
- for (Index i = 0; i < vectorized_size; i += packet_size) {
86
- Packet p = impl.template packet<Unaligned>(src_index + i);
87
- internal::pstoret<Scalar, Packet, Unaligned>(dst_data + dst_index + i, p);
88
- }
89
- for (Index i = vectorized_size; i < num_coeff_to_copy; ++i) {
90
- dst_data[dst_index + i] = impl.coeff(src_index + i);
91
- }
92
- }
93
- };
94
-
95
- template <typename Self>
96
- struct ImagePatchPaddingOp {
97
- typedef typename Self::Index Index;
98
- typedef typename Self::Scalar Scalar;
99
- typedef typename packet_traits<Scalar>::type Packet;
100
- static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void Run(
101
- const Index num_coeff_to_pad, const Scalar padding_value,
102
- const Index dst_index, Scalar* dst_data) {
103
- const Index packet_size = internal::unpacket_traits<Packet>::size;
104
- const Packet padded_packet = internal::pset1<Packet>(padding_value);
105
- const Index vectorized_size =
106
- (num_coeff_to_pad / packet_size) * packet_size;
107
- for (Index i = 0; i < vectorized_size; i += packet_size) {
108
- internal::pstoret<Scalar, Packet, Unaligned>(dst_data + dst_index + i,
109
- padded_packet);
110
- }
111
- for (Index i = vectorized_size; i < num_coeff_to_pad; ++i) {
112
- dst_data[dst_index + i] = padding_value;
113
- }
114
- }
115
- };
116
-
117
- } // end namespace internal
118
-
119
- template<DenseIndex Rows, DenseIndex Cols, typename XprType>
120
- class TensorImagePatchOp : public TensorBase<TensorImagePatchOp<Rows, Cols, XprType>, ReadOnlyAccessors>
121
- {
122
- public:
123
- typedef typename Eigen::internal::traits<TensorImagePatchOp>::Scalar Scalar;
124
- typedef typename Eigen::NumTraits<Scalar>::Real RealScalar;
125
- typedef typename XprType::CoeffReturnType CoeffReturnType;
126
- typedef typename Eigen::internal::nested<TensorImagePatchOp>::type Nested;
127
- typedef typename Eigen::internal::traits<TensorImagePatchOp>::StorageKind StorageKind;
128
- typedef typename Eigen::internal::traits<TensorImagePatchOp>::Index Index;
129
-
130
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorImagePatchOp(const XprType& expr, DenseIndex patch_rows, DenseIndex patch_cols,
131
- DenseIndex row_strides, DenseIndex col_strides,
132
- DenseIndex in_row_strides, DenseIndex in_col_strides,
133
- DenseIndex row_inflate_strides, DenseIndex col_inflate_strides,
134
- PaddingType padding_type, Scalar padding_value)
135
- : m_xpr(expr), m_patch_rows(patch_rows), m_patch_cols(patch_cols),
136
- m_row_strides(row_strides), m_col_strides(col_strides),
137
- m_in_row_strides(in_row_strides), m_in_col_strides(in_col_strides),
138
- m_row_inflate_strides(row_inflate_strides), m_col_inflate_strides(col_inflate_strides),
139
- m_padding_explicit(false), m_padding_top(0), m_padding_bottom(0), m_padding_left(0), m_padding_right(0),
140
- m_padding_type(padding_type), m_padding_value(padding_value) {}
141
-
142
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorImagePatchOp(const XprType& expr, DenseIndex patch_rows, DenseIndex patch_cols,
143
- DenseIndex row_strides, DenseIndex col_strides,
144
- DenseIndex in_row_strides, DenseIndex in_col_strides,
145
- DenseIndex row_inflate_strides, DenseIndex col_inflate_strides,
146
- DenseIndex padding_top, DenseIndex padding_bottom,
147
- DenseIndex padding_left, DenseIndex padding_right,
148
- Scalar padding_value)
149
- : m_xpr(expr), m_patch_rows(patch_rows), m_patch_cols(patch_cols),
150
- m_row_strides(row_strides), m_col_strides(col_strides),
151
- m_in_row_strides(in_row_strides), m_in_col_strides(in_col_strides),
152
- m_row_inflate_strides(row_inflate_strides), m_col_inflate_strides(col_inflate_strides),
153
- m_padding_explicit(true), m_padding_top(padding_top), m_padding_bottom(padding_bottom),
154
- m_padding_left(padding_left), m_padding_right(padding_right),
155
- m_padding_type(PADDING_VALID), m_padding_value(padding_value) {}
156
-
157
-
158
- EIGEN_DEVICE_FUNC
159
- DenseIndex patch_rows() const { return m_patch_rows; }
160
- EIGEN_DEVICE_FUNC
161
- DenseIndex patch_cols() const { return m_patch_cols; }
162
- EIGEN_DEVICE_FUNC
163
- DenseIndex row_strides() const { return m_row_strides; }
164
- EIGEN_DEVICE_FUNC
165
- DenseIndex col_strides() const { return m_col_strides; }
166
- EIGEN_DEVICE_FUNC
167
- DenseIndex in_row_strides() const { return m_in_row_strides; }
168
- EIGEN_DEVICE_FUNC
169
- DenseIndex in_col_strides() const { return m_in_col_strides; }
170
- EIGEN_DEVICE_FUNC
171
- DenseIndex row_inflate_strides() const { return m_row_inflate_strides; }
172
- EIGEN_DEVICE_FUNC
173
- DenseIndex col_inflate_strides() const { return m_col_inflate_strides; }
174
- EIGEN_DEVICE_FUNC
175
- bool padding_explicit() const { return m_padding_explicit; }
176
- EIGEN_DEVICE_FUNC
177
- DenseIndex padding_top() const { return m_padding_top; }
178
- EIGEN_DEVICE_FUNC
179
- DenseIndex padding_bottom() const { return m_padding_bottom; }
180
- EIGEN_DEVICE_FUNC
181
- DenseIndex padding_left() const { return m_padding_left; }
182
- EIGEN_DEVICE_FUNC
183
- DenseIndex padding_right() const { return m_padding_right; }
184
- EIGEN_DEVICE_FUNC
185
- PaddingType padding_type() const { return m_padding_type; }
186
- EIGEN_DEVICE_FUNC
187
- Scalar padding_value() const { return m_padding_value; }
188
-
189
- EIGEN_DEVICE_FUNC
190
- const typename internal::remove_all<typename XprType::Nested>::type&
191
- expression() const { return m_xpr; }
192
-
193
- protected:
194
- typename XprType::Nested m_xpr;
195
- const DenseIndex m_patch_rows;
196
- const DenseIndex m_patch_cols;
197
- const DenseIndex m_row_strides;
198
- const DenseIndex m_col_strides;
199
- const DenseIndex m_in_row_strides;
200
- const DenseIndex m_in_col_strides;
201
- const DenseIndex m_row_inflate_strides;
202
- const DenseIndex m_col_inflate_strides;
203
- const bool m_padding_explicit;
204
- const DenseIndex m_padding_top;
205
- const DenseIndex m_padding_bottom;
206
- const DenseIndex m_padding_left;
207
- const DenseIndex m_padding_right;
208
- const PaddingType m_padding_type;
209
- const Scalar m_padding_value;
210
- };
211
-
212
- // Eval as rvalue
213
- template<DenseIndex Rows, DenseIndex Cols, typename ArgType, typename Device>
214
- struct TensorEvaluator<const TensorImagePatchOp<Rows, Cols, ArgType>, Device>
215
- {
216
- typedef TensorImagePatchOp<Rows, Cols, ArgType> XprType;
217
- typedef typename XprType::Index Index;
218
- static const int NumInputDims = internal::array_size<typename TensorEvaluator<ArgType, Device>::Dimensions>::value;
219
- static const int NumDims = NumInputDims + 1;
220
- typedef DSizes<Index, NumDims> Dimensions;
221
- typedef typename internal::remove_const<typename XprType::Scalar>::type Scalar;
222
- typedef TensorEvaluator<const TensorImagePatchOp<Rows, Cols, ArgType>,
223
- Device> Self;
224
- typedef TensorEvaluator<ArgType, Device> Impl;
225
- typedef typename XprType::CoeffReturnType CoeffReturnType;
226
- typedef typename PacketType<CoeffReturnType, Device>::type PacketReturnType;
227
- static const int PacketSize = PacketType<CoeffReturnType, Device>::size;
228
- typedef StorageMemory<CoeffReturnType, Device> Storage;
229
- typedef typename Storage::Type EvaluatorPointerType;
230
-
231
- enum {
232
- IsAligned = false,
233
- PacketAccess = TensorEvaluator<ArgType, Device>::PacketAccess,
234
- BlockAccess = false,
235
- PreferBlockAccess = true,
236
- Layout = TensorEvaluator<ArgType, Device>::Layout,
237
- CoordAccess = false,
238
- RawAccess = false
239
- };
240
-
241
- //===- Tensor block evaluation strategy (see TensorBlock.h) -------------===//
242
- typedef internal::TensorBlockNotImplemented TensorBlock;
243
- //===--------------------------------------------------------------------===//
244
-
245
- EIGEN_STRONG_INLINE TensorEvaluator( const XprType& op, const Device& device)
246
- : m_device(device), m_impl(op.expression(), device)
247
- {
248
- EIGEN_STATIC_ASSERT((NumDims >= 4), YOU_MADE_A_PROGRAMMING_MISTAKE);
249
-
250
- m_paddingValue = op.padding_value();
251
-
252
- const typename TensorEvaluator<ArgType, Device>::Dimensions& input_dims = m_impl.dimensions();
253
-
254
- // Caches a few variables.
255
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
256
- m_inputDepth = input_dims[0];
257
- m_inputRows = input_dims[1];
258
- m_inputCols = input_dims[2];
259
- } else {
260
- m_inputDepth = input_dims[NumInputDims-1];
261
- m_inputRows = input_dims[NumInputDims-2];
262
- m_inputCols = input_dims[NumInputDims-3];
263
- }
264
-
265
- m_row_strides = op.row_strides();
266
- m_col_strides = op.col_strides();
267
-
268
- // Input strides and effective input/patch size
269
- m_in_row_strides = op.in_row_strides();
270
- m_in_col_strides = op.in_col_strides();
271
- m_row_inflate_strides = op.row_inflate_strides();
272
- m_col_inflate_strides = op.col_inflate_strides();
273
- // The "effective" input rows and input cols are the input rows and cols
274
- // after inflating them with zeros.
275
- // For examples, a 2x3 matrix with row_inflate_strides and
276
- // col_inflate_strides of 2 comes from:
277
- // A B C
278
- // D E F
279
- //
280
- // to a matrix is 3 x 5:
281
- //
282
- // A . B . C
283
- // . . . . .
284
- // D . E . F
285
-
286
- m_input_rows_eff = (m_inputRows - 1) * m_row_inflate_strides + 1;
287
- m_input_cols_eff = (m_inputCols - 1) * m_col_inflate_strides + 1;
288
- m_patch_rows_eff = op.patch_rows() + (op.patch_rows() - 1) * (m_in_row_strides - 1);
289
- m_patch_cols_eff = op.patch_cols() + (op.patch_cols() - 1) * (m_in_col_strides - 1);
290
-
291
- if (op.padding_explicit()) {
292
- 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));
293
- 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));
294
- m_rowPaddingTop = op.padding_top();
295
- m_colPaddingLeft = op.padding_left();
296
- } else {
297
- // Computing padding from the type
298
- switch (op.padding_type()) {
299
- case PADDING_VALID:
300
- m_outputRows = numext::ceil((m_input_rows_eff - m_patch_rows_eff + 1.f) / static_cast<float>(m_row_strides));
301
- m_outputCols = numext::ceil((m_input_cols_eff - m_patch_cols_eff + 1.f) / static_cast<float>(m_col_strides));
302
- // Calculate the padding
303
- m_rowPaddingTop = numext::maxi<Index>(0, ((m_outputRows - 1) * m_row_strides + m_patch_rows_eff - m_input_rows_eff) / 2);
304
- m_colPaddingLeft = numext::maxi<Index>(0, ((m_outputCols - 1) * m_col_strides + m_patch_cols_eff - m_input_cols_eff) / 2);
305
- break;
306
- case PADDING_SAME:
307
- m_outputRows = numext::ceil(m_input_rows_eff / static_cast<float>(m_row_strides));
308
- m_outputCols = numext::ceil(m_input_cols_eff / static_cast<float>(m_col_strides));
309
- // Calculate the padding
310
- m_rowPaddingTop = ((m_outputRows - 1) * m_row_strides + m_patch_rows_eff - m_input_rows_eff) / 2;
311
- m_colPaddingLeft = ((m_outputCols - 1) * m_col_strides + m_patch_cols_eff - m_input_cols_eff) / 2;
312
- // The padding size calculation for PADDING_SAME has been updated to
313
- // be consistent with how TensorFlow extracts its paddings.
314
- m_rowPaddingTop = numext::maxi<Index>(0, m_rowPaddingTop);
315
- m_colPaddingLeft = numext::maxi<Index>(0, m_colPaddingLeft);
316
- break;
317
- default:
318
- eigen_assert(false && "unexpected padding");
319
- m_outputCols=0; // silence the uninitialised warning;
320
- m_outputRows=0; //// silence the uninitialised warning;
321
- }
322
- }
323
- eigen_assert(m_outputRows > 0);
324
- eigen_assert(m_outputCols > 0);
325
-
326
- // Dimensions for result of extraction.
327
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
328
- // ColMajor
329
- // 0: depth
330
- // 1: patch_rows
331
- // 2: patch_cols
332
- // 3: number of patches
333
- // 4 and beyond: anything else (such as batch).
334
- m_dimensions[0] = input_dims[0];
335
- m_dimensions[1] = op.patch_rows();
336
- m_dimensions[2] = op.patch_cols();
337
- m_dimensions[3] = m_outputRows * m_outputCols;
338
- for (int i = 4; i < NumDims; ++i) {
339
- m_dimensions[i] = input_dims[i-1];
340
- }
341
- } else {
342
- // RowMajor
343
- // NumDims-1: depth
344
- // NumDims-2: patch_rows
345
- // NumDims-3: patch_cols
346
- // NumDims-4: number of patches
347
- // NumDims-5 and beyond: anything else (such as batch).
348
- m_dimensions[NumDims-1] = input_dims[NumInputDims-1];
349
- m_dimensions[NumDims-2] = op.patch_rows();
350
- m_dimensions[NumDims-3] = op.patch_cols();
351
- m_dimensions[NumDims-4] = m_outputRows * m_outputCols;
352
- for (int i = NumDims-5; i >= 0; --i) {
353
- m_dimensions[i] = input_dims[i];
354
- }
355
- }
356
-
357
- // Strides for moving the patch in various dimensions.
358
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
359
- m_colStride = m_dimensions[1];
360
- m_patchStride = m_colStride * m_dimensions[2] * m_dimensions[0];
361
- m_otherStride = m_patchStride * m_dimensions[3];
362
- } else {
363
- m_colStride = m_dimensions[NumDims-2];
364
- m_patchStride = m_colStride * m_dimensions[NumDims-3] * m_dimensions[NumDims-1];
365
- m_otherStride = m_patchStride * m_dimensions[NumDims-4];
366
- }
367
-
368
- // Strides for navigating through the input tensor.
369
- m_rowInputStride = m_inputDepth;
370
- m_colInputStride = m_inputDepth * m_inputRows;
371
- m_patchInputStride = m_inputDepth * m_inputRows * m_inputCols;
372
-
373
- // Fast representations of different variables.
374
- m_fastOtherStride = internal::TensorIntDivisor<Index>(m_otherStride);
375
- m_fastPatchStride = internal::TensorIntDivisor<Index>(m_patchStride);
376
- m_fastColStride = internal::TensorIntDivisor<Index>(m_colStride);
377
- m_fastInflateRowStride = internal::TensorIntDivisor<Index>(m_row_inflate_strides);
378
- m_fastInflateColStride = internal::TensorIntDivisor<Index>(m_col_inflate_strides);
379
- m_fastInputColsEff = internal::TensorIntDivisor<Index>(m_input_cols_eff);
380
-
381
- // Number of patches in the width dimension.
382
- m_fastOutputRows = internal::TensorIntDivisor<Index>(m_outputRows);
383
- if (static_cast<int>(Layout) == static_cast<int>(ColMajor)) {
384
- m_fastOutputDepth = internal::TensorIntDivisor<Index>(m_dimensions[0]);
385
- } else {
386
- m_fastOutputDepth = internal::TensorIntDivisor<Index>(m_dimensions[NumDims-1]);
387
- }
388
- }
389
-
390
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const Dimensions& dimensions() const { return m_dimensions; }
391
-
392
- EIGEN_STRONG_INLINE bool evalSubExprsIfNeeded(EvaluatorPointerType /*data*/) {
393
- m_impl.evalSubExprsIfNeeded(NULL);
394
- return true;
395
- }
396
-
397
- #ifdef EIGEN_USE_THREADS
398
- template <typename EvalSubExprsCallback>
399
- EIGEN_STRONG_INLINE void evalSubExprsIfNeededAsync(
400
- EvaluatorPointerType, EvalSubExprsCallback done) {
401
- m_impl.evalSubExprsIfNeededAsync(nullptr, [done](bool) { done(true); });
402
- }
403
- #endif // EIGEN_USE_THREADS
404
-
405
- EIGEN_STRONG_INLINE void cleanup() {
406
- m_impl.cleanup();
407
- }
408
-
409
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE CoeffReturnType coeff(Index index) const
410
- {
411
- // Patch index corresponding to the passed in index.
412
- const Index patchIndex = index / m_fastPatchStride;
413
- // Find the offset of the element wrt the location of the first element.
414
- const Index patchOffset = (index - patchIndex * m_patchStride) / m_fastOutputDepth;
415
-
416
- // Other ways to index this element.
417
- const Index otherIndex = (NumDims == 4) ? 0 : index / m_fastOtherStride;
418
- const Index patch2DIndex = (NumDims == 4) ? patchIndex : (index - otherIndex * m_otherStride) / m_fastPatchStride;
419
-
420
- // Calculate col index in the input original tensor.
421
- const Index colIndex = patch2DIndex / m_fastOutputRows;
422
- const Index colOffset = patchOffset / m_fastColStride;
423
- const Index inputCol = colIndex * m_col_strides + colOffset * m_in_col_strides - m_colPaddingLeft;
424
- const Index origInputCol = (m_col_inflate_strides == 1) ? inputCol : ((inputCol >= 0) ? (inputCol / m_fastInflateColStride) : 0);
425
- if (inputCol < 0 || inputCol >= m_input_cols_eff ||
426
- ((m_col_inflate_strides != 1) && (inputCol != origInputCol * m_col_inflate_strides))) {
427
- return Scalar(m_paddingValue);
428
- }
429
-
430
- // Calculate row index in the original input tensor.
431
- const Index rowIndex = patch2DIndex - colIndex * m_outputRows;
432
- const Index rowOffset = patchOffset - colOffset * m_colStride;
433
- const Index inputRow = rowIndex * m_row_strides + rowOffset * m_in_row_strides - m_rowPaddingTop;
434
- const Index origInputRow = (m_row_inflate_strides == 1) ? inputRow : ((inputRow >= 0) ? (inputRow / m_fastInflateRowStride) : 0);
435
- if (inputRow < 0 || inputRow >= m_input_rows_eff ||
436
- ((m_row_inflate_strides != 1) && (inputRow != origInputRow * m_row_inflate_strides))) {
437
- return Scalar(m_paddingValue);
438
- }
439
-
440
- const int depth_index = static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 0 : NumDims - 1;
441
- const Index depth = index - (index / m_fastOutputDepth) * m_dimensions[depth_index];
442
-
443
- const Index inputIndex = depth + origInputRow * m_rowInputStride + origInputCol * m_colInputStride + otherIndex * m_patchInputStride;
444
- return m_impl.coeff(inputIndex);
445
- }
446
-
447
- template<int LoadMode>
448
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packet(Index index) const
449
- {
450
- EIGEN_STATIC_ASSERT((PacketSize > 1), YOU_MADE_A_PROGRAMMING_MISTAKE)
451
- eigen_assert(index+PacketSize-1 < dimensions().TotalSize());
452
-
453
- if (m_in_row_strides != 1 || m_in_col_strides != 1 || m_row_inflate_strides != 1 || m_col_inflate_strides != 1) {
454
- return packetWithPossibleZero(index);
455
- }
456
-
457
- const Index indices[2] = {index, index + PacketSize - 1};
458
- const Index patchIndex = indices[0] / m_fastPatchStride;
459
- if (patchIndex != indices[1] / m_fastPatchStride) {
460
- return packetWithPossibleZero(index);
461
- }
462
- const Index otherIndex = (NumDims == 4) ? 0 : indices[0] / m_fastOtherStride;
463
- eigen_assert(otherIndex == indices[1] / m_fastOtherStride);
464
-
465
- // Find the offset of the element wrt the location of the first element.
466
- const Index patchOffsets[2] = {(indices[0] - patchIndex * m_patchStride) / m_fastOutputDepth,
467
- (indices[1] - patchIndex * m_patchStride) / m_fastOutputDepth};
468
-
469
- const Index patch2DIndex = (NumDims == 4) ? patchIndex : (indices[0] - otherIndex * m_otherStride) / m_fastPatchStride;
470
- eigen_assert(patch2DIndex == (indices[1] - otherIndex * m_otherStride) / m_fastPatchStride);
471
-
472
- const Index colIndex = patch2DIndex / m_fastOutputRows;
473
- const Index colOffsets[2] = {patchOffsets[0] / m_fastColStride, patchOffsets[1] / m_fastColStride};
474
-
475
- // Calculate col indices in the original input tensor.
476
- const Index inputCols[2] = {colIndex * m_col_strides + colOffsets[0] -
477
- m_colPaddingLeft, colIndex * m_col_strides + colOffsets[1] - m_colPaddingLeft};
478
- if (inputCols[1] < 0 || inputCols[0] >= m_inputCols) {
479
- return internal::pset1<PacketReturnType>(Scalar(m_paddingValue));
480
- }
481
-
482
- if (inputCols[0] == inputCols[1]) {
483
- const Index rowIndex = patch2DIndex - colIndex * m_outputRows;
484
- const Index rowOffsets[2] = {patchOffsets[0] - colOffsets[0]*m_colStride, patchOffsets[1] - colOffsets[1]*m_colStride};
485
- eigen_assert(rowOffsets[0] <= rowOffsets[1]);
486
- // Calculate col indices in the original input tensor.
487
- const Index inputRows[2] = {rowIndex * m_row_strides + rowOffsets[0] -
488
- m_rowPaddingTop, rowIndex * m_row_strides + rowOffsets[1] - m_rowPaddingTop};
489
-
490
- if (inputRows[1] < 0 || inputRows[0] >= m_inputRows) {
491
- return internal::pset1<PacketReturnType>(Scalar(m_paddingValue));
492
- }
493
-
494
- if (inputRows[0] >= 0 && inputRows[1] < m_inputRows) {
495
- // no padding
496
- const int depth_index = static_cast<int>(Layout) == static_cast<int>(ColMajor) ? 0 : NumDims - 1;
497
- const Index depth = index - (index / m_fastOutputDepth) * m_dimensions[depth_index];
498
- const Index inputIndex = depth + inputRows[0] * m_rowInputStride + inputCols[0] * m_colInputStride + otherIndex * m_patchInputStride;
499
- return m_impl.template packet<Unaligned>(inputIndex);
500
- }
501
- }
502
-
503
- return packetWithPossibleZero(index);
504
- }
505
-
506
- EIGEN_DEVICE_FUNC EvaluatorPointerType data() const { return NULL; }
507
-
508
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE const TensorEvaluator<ArgType, Device>& impl() const { return m_impl; }
509
-
510
- #ifdef EIGEN_USE_SYCL
511
- // binding placeholder accessors to a command group handler for SYCL
512
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void bind(cl::sycl::handler &cgh) const {
513
- m_impl.bind(cgh);
514
- }
515
- #endif
516
-
517
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index rowPaddingTop() const { return m_rowPaddingTop; }
518
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index colPaddingLeft() const { return m_colPaddingLeft; }
519
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index outputRows() const { return m_outputRows; }
520
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index outputCols() const { return m_outputCols; }
521
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userRowStride() const { return m_row_strides; }
522
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userColStride() const { return m_col_strides; }
523
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userInRowStride() const { return m_in_row_strides; }
524
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index userInColStride() const { return m_in_col_strides; }
525
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index rowInflateStride() const { return m_row_inflate_strides; }
526
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE Index colInflateStride() const { return m_col_inflate_strides; }
527
-
528
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE TensorOpCost
529
- costPerCoeff(bool vectorized) const {
530
- // We conservatively estimate the cost for the code path where the computed
531
- // index is inside the original image and
532
- // TensorEvaluator<ArgType, Device>::CoordAccess is false.
533
- const double compute_cost = 3 * TensorOpCost::DivCost<Index>() +
534
- 6 * TensorOpCost::MulCost<Index>() +
535
- 8 * TensorOpCost::MulCost<Index>();
536
- return m_impl.costPerCoeff(vectorized) +
537
- TensorOpCost(0, 0, compute_cost, vectorized, PacketSize);
538
- }
539
-
540
- protected:
541
- EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE PacketReturnType packetWithPossibleZero(Index index) const
542
- {
543
- EIGEN_ALIGN_MAX typename internal::remove_const<CoeffReturnType>::type values[PacketSize];
544
- EIGEN_UNROLL_LOOP
545
- for (int i = 0; i < PacketSize; ++i) {
546
- values[i] = coeff(index+i);
547
- }
548
- PacketReturnType rslt = internal::pload<PacketReturnType>(values);
549
- return rslt;
550
- }
551
-
552
- Dimensions m_dimensions;
553
-
554
- Index m_otherStride;
555
- Index m_patchStride;
556
- Index m_colStride;
557
- Index m_row_strides;
558
- Index m_col_strides;
559
-
560
- Index m_in_row_strides;
561
- Index m_in_col_strides;
562
- Index m_row_inflate_strides;
563
- Index m_col_inflate_strides;
564
-
565
- Index m_input_rows_eff;
566
- Index m_input_cols_eff;
567
- Index m_patch_rows_eff;
568
- Index m_patch_cols_eff;
569
-
570
- internal::TensorIntDivisor<Index> m_fastOtherStride;
571
- internal::TensorIntDivisor<Index> m_fastPatchStride;
572
- internal::TensorIntDivisor<Index> m_fastColStride;
573
- internal::TensorIntDivisor<Index> m_fastInflateRowStride;
574
- internal::TensorIntDivisor<Index> m_fastInflateColStride;
575
- internal::TensorIntDivisor<Index> m_fastInputColsEff;
576
-
577
- Index m_rowInputStride;
578
- Index m_colInputStride;
579
- Index m_patchInputStride;
580
-
581
- Index m_inputDepth;
582
- Index m_inputRows;
583
- Index m_inputCols;
584
-
585
- Index m_outputRows;
586
- Index m_outputCols;
587
-
588
- Index m_rowPaddingTop;
589
- Index m_colPaddingLeft;
590
-
591
- internal::TensorIntDivisor<Index> m_fastOutputRows;
592
- internal::TensorIntDivisor<Index> m_fastOutputDepth;
593
-
594
- Scalar m_paddingValue;
595
-
596
- const Device EIGEN_DEVICE_REF m_device;
597
- TensorEvaluator<ArgType, Device> m_impl;
598
- };
599
-
600
-
601
- } // end namespace Eigen
602
-
603
- #endif // EIGEN_CXX11_TENSOR_TENSOR_IMAGE_PATCH_H