tomoto 0.1.0

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Files changed (420) hide show
  1. checksums.yaml +7 -0
  2. data/CHANGELOG.md +3 -0
  3. data/LICENSE.txt +22 -0
  4. data/README.md +123 -0
  5. data/ext/tomoto/ext.cpp +245 -0
  6. data/ext/tomoto/extconf.rb +28 -0
  7. data/lib/tomoto.rb +12 -0
  8. data/lib/tomoto/ct.rb +11 -0
  9. data/lib/tomoto/hdp.rb +11 -0
  10. data/lib/tomoto/lda.rb +67 -0
  11. data/lib/tomoto/version.rb +3 -0
  12. data/vendor/EigenRand/EigenRand/Core.h +1139 -0
  13. data/vendor/EigenRand/EigenRand/Dists/Basic.h +111 -0
  14. data/vendor/EigenRand/EigenRand/Dists/Discrete.h +877 -0
  15. data/vendor/EigenRand/EigenRand/Dists/GammaPoisson.h +108 -0
  16. data/vendor/EigenRand/EigenRand/Dists/NormalExp.h +626 -0
  17. data/vendor/EigenRand/EigenRand/EigenRand +19 -0
  18. data/vendor/EigenRand/EigenRand/Macro.h +24 -0
  19. data/vendor/EigenRand/EigenRand/MorePacketMath.h +978 -0
  20. data/vendor/EigenRand/EigenRand/PacketFilter.h +286 -0
  21. data/vendor/EigenRand/EigenRand/PacketRandomEngine.h +624 -0
  22. data/vendor/EigenRand/EigenRand/RandUtils.h +413 -0
  23. data/vendor/EigenRand/EigenRand/doc.h +220 -0
  24. data/vendor/EigenRand/LICENSE +21 -0
  25. data/vendor/EigenRand/README.md +288 -0
  26. data/vendor/eigen/COPYING.BSD +26 -0
  27. data/vendor/eigen/COPYING.GPL +674 -0
  28. data/vendor/eigen/COPYING.LGPL +502 -0
  29. data/vendor/eigen/COPYING.MINPACK +52 -0
  30. data/vendor/eigen/COPYING.MPL2 +373 -0
  31. data/vendor/eigen/COPYING.README +18 -0
  32. data/vendor/eigen/Eigen/CMakeLists.txt +19 -0
  33. data/vendor/eigen/Eigen/Cholesky +46 -0
  34. data/vendor/eigen/Eigen/CholmodSupport +48 -0
  35. data/vendor/eigen/Eigen/Core +537 -0
  36. data/vendor/eigen/Eigen/Dense +7 -0
  37. data/vendor/eigen/Eigen/Eigen +2 -0
  38. data/vendor/eigen/Eigen/Eigenvalues +61 -0
  39. data/vendor/eigen/Eigen/Geometry +62 -0
  40. data/vendor/eigen/Eigen/Householder +30 -0
  41. data/vendor/eigen/Eigen/IterativeLinearSolvers +48 -0
  42. data/vendor/eigen/Eigen/Jacobi +33 -0
  43. data/vendor/eigen/Eigen/LU +50 -0
  44. data/vendor/eigen/Eigen/MetisSupport +35 -0
  45. data/vendor/eigen/Eigen/OrderingMethods +73 -0
  46. data/vendor/eigen/Eigen/PaStiXSupport +48 -0
  47. data/vendor/eigen/Eigen/PardisoSupport +35 -0
  48. data/vendor/eigen/Eigen/QR +51 -0
  49. data/vendor/eigen/Eigen/QtAlignedMalloc +40 -0
  50. data/vendor/eigen/Eigen/SPQRSupport +34 -0
  51. data/vendor/eigen/Eigen/SVD +51 -0
  52. data/vendor/eigen/Eigen/Sparse +36 -0
  53. data/vendor/eigen/Eigen/SparseCholesky +45 -0
  54. data/vendor/eigen/Eigen/SparseCore +69 -0
  55. data/vendor/eigen/Eigen/SparseLU +46 -0
  56. data/vendor/eigen/Eigen/SparseQR +37 -0
  57. data/vendor/eigen/Eigen/StdDeque +27 -0
  58. data/vendor/eigen/Eigen/StdList +26 -0
  59. data/vendor/eigen/Eigen/StdVector +27 -0
  60. data/vendor/eigen/Eigen/SuperLUSupport +64 -0
  61. data/vendor/eigen/Eigen/UmfPackSupport +40 -0
  62. data/vendor/eigen/Eigen/src/Cholesky/LDLT.h +673 -0
  63. data/vendor/eigen/Eigen/src/Cholesky/LLT.h +542 -0
  64. data/vendor/eigen/Eigen/src/Cholesky/LLT_LAPACKE.h +99 -0
  65. data/vendor/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +639 -0
  66. data/vendor/eigen/Eigen/src/Core/Array.h +329 -0
  67. data/vendor/eigen/Eigen/src/Core/ArrayBase.h +226 -0
  68. data/vendor/eigen/Eigen/src/Core/ArrayWrapper.h +209 -0
  69. data/vendor/eigen/Eigen/src/Core/Assign.h +90 -0
  70. data/vendor/eigen/Eigen/src/Core/AssignEvaluator.h +935 -0
  71. data/vendor/eigen/Eigen/src/Core/Assign_MKL.h +178 -0
  72. data/vendor/eigen/Eigen/src/Core/BandMatrix.h +353 -0
  73. data/vendor/eigen/Eigen/src/Core/Block.h +452 -0
  74. data/vendor/eigen/Eigen/src/Core/BooleanRedux.h +164 -0
  75. data/vendor/eigen/Eigen/src/Core/CommaInitializer.h +160 -0
  76. data/vendor/eigen/Eigen/src/Core/ConditionEstimator.h +175 -0
  77. data/vendor/eigen/Eigen/src/Core/CoreEvaluators.h +1688 -0
  78. data/vendor/eigen/Eigen/src/Core/CoreIterators.h +127 -0
  79. data/vendor/eigen/Eigen/src/Core/CwiseBinaryOp.h +184 -0
  80. data/vendor/eigen/Eigen/src/Core/CwiseNullaryOp.h +866 -0
  81. data/vendor/eigen/Eigen/src/Core/CwiseTernaryOp.h +197 -0
  82. data/vendor/eigen/Eigen/src/Core/CwiseUnaryOp.h +103 -0
  83. data/vendor/eigen/Eigen/src/Core/CwiseUnaryView.h +128 -0
  84. data/vendor/eigen/Eigen/src/Core/DenseBase.h +611 -0
  85. data/vendor/eigen/Eigen/src/Core/DenseCoeffsBase.h +681 -0
  86. data/vendor/eigen/Eigen/src/Core/DenseStorage.h +570 -0
  87. data/vendor/eigen/Eigen/src/Core/Diagonal.h +260 -0
  88. data/vendor/eigen/Eigen/src/Core/DiagonalMatrix.h +343 -0
  89. data/vendor/eigen/Eigen/src/Core/DiagonalProduct.h +28 -0
  90. data/vendor/eigen/Eigen/src/Core/Dot.h +318 -0
  91. data/vendor/eigen/Eigen/src/Core/EigenBase.h +159 -0
  92. data/vendor/eigen/Eigen/src/Core/ForceAlignedAccess.h +146 -0
  93. data/vendor/eigen/Eigen/src/Core/Fuzzy.h +155 -0
  94. data/vendor/eigen/Eigen/src/Core/GeneralProduct.h +455 -0
  95. data/vendor/eigen/Eigen/src/Core/GenericPacketMath.h +593 -0
  96. data/vendor/eigen/Eigen/src/Core/GlobalFunctions.h +187 -0
  97. data/vendor/eigen/Eigen/src/Core/IO.h +225 -0
  98. data/vendor/eigen/Eigen/src/Core/Inverse.h +118 -0
  99. data/vendor/eigen/Eigen/src/Core/Map.h +171 -0
  100. data/vendor/eigen/Eigen/src/Core/MapBase.h +303 -0
  101. data/vendor/eigen/Eigen/src/Core/MathFunctions.h +1415 -0
  102. data/vendor/eigen/Eigen/src/Core/MathFunctionsImpl.h +101 -0
  103. data/vendor/eigen/Eigen/src/Core/Matrix.h +459 -0
  104. data/vendor/eigen/Eigen/src/Core/MatrixBase.h +529 -0
  105. data/vendor/eigen/Eigen/src/Core/NestByValue.h +110 -0
  106. data/vendor/eigen/Eigen/src/Core/NoAlias.h +108 -0
  107. data/vendor/eigen/Eigen/src/Core/NumTraits.h +248 -0
  108. data/vendor/eigen/Eigen/src/Core/PermutationMatrix.h +633 -0
  109. data/vendor/eigen/Eigen/src/Core/PlainObjectBase.h +1035 -0
  110. data/vendor/eigen/Eigen/src/Core/Product.h +186 -0
  111. data/vendor/eigen/Eigen/src/Core/ProductEvaluators.h +1112 -0
  112. data/vendor/eigen/Eigen/src/Core/Random.h +182 -0
  113. data/vendor/eigen/Eigen/src/Core/Redux.h +505 -0
  114. data/vendor/eigen/Eigen/src/Core/Ref.h +283 -0
  115. data/vendor/eigen/Eigen/src/Core/Replicate.h +142 -0
  116. data/vendor/eigen/Eigen/src/Core/ReturnByValue.h +117 -0
  117. data/vendor/eigen/Eigen/src/Core/Reverse.h +211 -0
  118. data/vendor/eigen/Eigen/src/Core/Select.h +162 -0
  119. data/vendor/eigen/Eigen/src/Core/SelfAdjointView.h +352 -0
  120. data/vendor/eigen/Eigen/src/Core/SelfCwiseBinaryOp.h +47 -0
  121. data/vendor/eigen/Eigen/src/Core/Solve.h +188 -0
  122. data/vendor/eigen/Eigen/src/Core/SolveTriangular.h +235 -0
  123. data/vendor/eigen/Eigen/src/Core/SolverBase.h +130 -0
  124. data/vendor/eigen/Eigen/src/Core/StableNorm.h +221 -0
  125. data/vendor/eigen/Eigen/src/Core/Stride.h +111 -0
  126. data/vendor/eigen/Eigen/src/Core/Swap.h +67 -0
  127. data/vendor/eigen/Eigen/src/Core/Transpose.h +403 -0
  128. data/vendor/eigen/Eigen/src/Core/Transpositions.h +407 -0
  129. data/vendor/eigen/Eigen/src/Core/TriangularMatrix.h +983 -0
  130. data/vendor/eigen/Eigen/src/Core/VectorBlock.h +96 -0
  131. data/vendor/eigen/Eigen/src/Core/VectorwiseOp.h +695 -0
  132. data/vendor/eigen/Eigen/src/Core/Visitor.h +273 -0
  133. data/vendor/eigen/Eigen/src/Core/arch/AVX/Complex.h +451 -0
  134. data/vendor/eigen/Eigen/src/Core/arch/AVX/MathFunctions.h +439 -0
  135. data/vendor/eigen/Eigen/src/Core/arch/AVX/PacketMath.h +637 -0
  136. data/vendor/eigen/Eigen/src/Core/arch/AVX/TypeCasting.h +51 -0
  137. data/vendor/eigen/Eigen/src/Core/arch/AVX512/MathFunctions.h +391 -0
  138. data/vendor/eigen/Eigen/src/Core/arch/AVX512/PacketMath.h +1316 -0
  139. data/vendor/eigen/Eigen/src/Core/arch/AltiVec/Complex.h +430 -0
  140. data/vendor/eigen/Eigen/src/Core/arch/AltiVec/MathFunctions.h +322 -0
  141. data/vendor/eigen/Eigen/src/Core/arch/AltiVec/PacketMath.h +1061 -0
  142. data/vendor/eigen/Eigen/src/Core/arch/CUDA/Complex.h +103 -0
  143. data/vendor/eigen/Eigen/src/Core/arch/CUDA/Half.h +674 -0
  144. data/vendor/eigen/Eigen/src/Core/arch/CUDA/MathFunctions.h +91 -0
  145. data/vendor/eigen/Eigen/src/Core/arch/CUDA/PacketMath.h +333 -0
  146. data/vendor/eigen/Eigen/src/Core/arch/CUDA/PacketMathHalf.h +1124 -0
  147. data/vendor/eigen/Eigen/src/Core/arch/CUDA/TypeCasting.h +212 -0
  148. data/vendor/eigen/Eigen/src/Core/arch/Default/ConjHelper.h +29 -0
  149. data/vendor/eigen/Eigen/src/Core/arch/Default/Settings.h +49 -0
  150. data/vendor/eigen/Eigen/src/Core/arch/NEON/Complex.h +490 -0
  151. data/vendor/eigen/Eigen/src/Core/arch/NEON/MathFunctions.h +91 -0
  152. data/vendor/eigen/Eigen/src/Core/arch/NEON/PacketMath.h +760 -0
  153. data/vendor/eigen/Eigen/src/Core/arch/SSE/Complex.h +471 -0
  154. data/vendor/eigen/Eigen/src/Core/arch/SSE/MathFunctions.h +562 -0
  155. data/vendor/eigen/Eigen/src/Core/arch/SSE/PacketMath.h +895 -0
  156. data/vendor/eigen/Eigen/src/Core/arch/SSE/TypeCasting.h +77 -0
  157. data/vendor/eigen/Eigen/src/Core/arch/ZVector/Complex.h +397 -0
  158. data/vendor/eigen/Eigen/src/Core/arch/ZVector/MathFunctions.h +137 -0
  159. data/vendor/eigen/Eigen/src/Core/arch/ZVector/PacketMath.h +945 -0
  160. data/vendor/eigen/Eigen/src/Core/functors/AssignmentFunctors.h +168 -0
  161. data/vendor/eigen/Eigen/src/Core/functors/BinaryFunctors.h +475 -0
  162. data/vendor/eigen/Eigen/src/Core/functors/NullaryFunctors.h +188 -0
  163. data/vendor/eigen/Eigen/src/Core/functors/StlFunctors.h +136 -0
  164. data/vendor/eigen/Eigen/src/Core/functors/TernaryFunctors.h +25 -0
  165. data/vendor/eigen/Eigen/src/Core/functors/UnaryFunctors.h +792 -0
  166. data/vendor/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h +2156 -0
  167. data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrix.h +492 -0
  168. data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h +311 -0
  169. data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h +145 -0
  170. data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h +122 -0
  171. data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixVector.h +619 -0
  172. data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h +136 -0
  173. data/vendor/eigen/Eigen/src/Core/products/Parallelizer.h +163 -0
  174. data/vendor/eigen/Eigen/src/Core/products/SelfadjointMatrixMatrix.h +521 -0
  175. data/vendor/eigen/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h +287 -0
  176. data/vendor/eigen/Eigen/src/Core/products/SelfadjointMatrixVector.h +260 -0
  177. data/vendor/eigen/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h +118 -0
  178. data/vendor/eigen/Eigen/src/Core/products/SelfadjointProduct.h +133 -0
  179. data/vendor/eigen/Eigen/src/Core/products/SelfadjointRank2Update.h +93 -0
  180. data/vendor/eigen/Eigen/src/Core/products/TriangularMatrixMatrix.h +466 -0
  181. data/vendor/eigen/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h +315 -0
  182. data/vendor/eigen/Eigen/src/Core/products/TriangularMatrixVector.h +350 -0
  183. data/vendor/eigen/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h +255 -0
  184. data/vendor/eigen/Eigen/src/Core/products/TriangularSolverMatrix.h +335 -0
  185. data/vendor/eigen/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h +163 -0
  186. data/vendor/eigen/Eigen/src/Core/products/TriangularSolverVector.h +145 -0
  187. data/vendor/eigen/Eigen/src/Core/util/BlasUtil.h +398 -0
  188. data/vendor/eigen/Eigen/src/Core/util/Constants.h +547 -0
  189. data/vendor/eigen/Eigen/src/Core/util/DisableStupidWarnings.h +83 -0
  190. data/vendor/eigen/Eigen/src/Core/util/ForwardDeclarations.h +302 -0
  191. data/vendor/eigen/Eigen/src/Core/util/MKL_support.h +130 -0
  192. data/vendor/eigen/Eigen/src/Core/util/Macros.h +1001 -0
  193. data/vendor/eigen/Eigen/src/Core/util/Memory.h +993 -0
  194. data/vendor/eigen/Eigen/src/Core/util/Meta.h +534 -0
  195. data/vendor/eigen/Eigen/src/Core/util/NonMPL2.h +3 -0
  196. data/vendor/eigen/Eigen/src/Core/util/ReenableStupidWarnings.h +27 -0
  197. data/vendor/eigen/Eigen/src/Core/util/StaticAssert.h +218 -0
  198. data/vendor/eigen/Eigen/src/Core/util/XprHelper.h +821 -0
  199. data/vendor/eigen/Eigen/src/Eigenvalues/ComplexEigenSolver.h +346 -0
  200. data/vendor/eigen/Eigen/src/Eigenvalues/ComplexSchur.h +459 -0
  201. data/vendor/eigen/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h +91 -0
  202. data/vendor/eigen/Eigen/src/Eigenvalues/EigenSolver.h +622 -0
  203. data/vendor/eigen/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h +418 -0
  204. data/vendor/eigen/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h +226 -0
  205. data/vendor/eigen/Eigen/src/Eigenvalues/HessenbergDecomposition.h +374 -0
  206. data/vendor/eigen/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h +158 -0
  207. data/vendor/eigen/Eigen/src/Eigenvalues/RealQZ.h +654 -0
  208. data/vendor/eigen/Eigen/src/Eigenvalues/RealSchur.h +546 -0
  209. data/vendor/eigen/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h +77 -0
  210. data/vendor/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h +870 -0
  211. data/vendor/eigen/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h +87 -0
  212. data/vendor/eigen/Eigen/src/Eigenvalues/Tridiagonalization.h +556 -0
  213. data/vendor/eigen/Eigen/src/Geometry/AlignedBox.h +392 -0
  214. data/vendor/eigen/Eigen/src/Geometry/AngleAxis.h +247 -0
  215. data/vendor/eigen/Eigen/src/Geometry/EulerAngles.h +114 -0
  216. data/vendor/eigen/Eigen/src/Geometry/Homogeneous.h +497 -0
  217. data/vendor/eigen/Eigen/src/Geometry/Hyperplane.h +282 -0
  218. data/vendor/eigen/Eigen/src/Geometry/OrthoMethods.h +234 -0
  219. data/vendor/eigen/Eigen/src/Geometry/ParametrizedLine.h +195 -0
  220. data/vendor/eigen/Eigen/src/Geometry/Quaternion.h +814 -0
  221. data/vendor/eigen/Eigen/src/Geometry/Rotation2D.h +199 -0
  222. data/vendor/eigen/Eigen/src/Geometry/RotationBase.h +206 -0
  223. data/vendor/eigen/Eigen/src/Geometry/Scaling.h +170 -0
  224. data/vendor/eigen/Eigen/src/Geometry/Transform.h +1542 -0
  225. data/vendor/eigen/Eigen/src/Geometry/Translation.h +208 -0
  226. data/vendor/eigen/Eigen/src/Geometry/Umeyama.h +166 -0
  227. data/vendor/eigen/Eigen/src/Geometry/arch/Geometry_SSE.h +161 -0
  228. data/vendor/eigen/Eigen/src/Householder/BlockHouseholder.h +103 -0
  229. data/vendor/eigen/Eigen/src/Householder/Householder.h +172 -0
  230. data/vendor/eigen/Eigen/src/Householder/HouseholderSequence.h +470 -0
  231. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h +226 -0
  232. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h +228 -0
  233. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h +246 -0
  234. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h +400 -0
  235. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h +462 -0
  236. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h +394 -0
  237. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h +216 -0
  238. data/vendor/eigen/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h +115 -0
  239. data/vendor/eigen/Eigen/src/Jacobi/Jacobi.h +462 -0
  240. data/vendor/eigen/Eigen/src/LU/Determinant.h +101 -0
  241. data/vendor/eigen/Eigen/src/LU/FullPivLU.h +891 -0
  242. data/vendor/eigen/Eigen/src/LU/InverseImpl.h +415 -0
  243. data/vendor/eigen/Eigen/src/LU/PartialPivLU.h +611 -0
  244. data/vendor/eigen/Eigen/src/LU/PartialPivLU_LAPACKE.h +83 -0
  245. data/vendor/eigen/Eigen/src/LU/arch/Inverse_SSE.h +338 -0
  246. data/vendor/eigen/Eigen/src/MetisSupport/MetisSupport.h +137 -0
  247. data/vendor/eigen/Eigen/src/OrderingMethods/Amd.h +445 -0
  248. data/vendor/eigen/Eigen/src/OrderingMethods/Eigen_Colamd.h +1843 -0
  249. data/vendor/eigen/Eigen/src/OrderingMethods/Ordering.h +157 -0
  250. data/vendor/eigen/Eigen/src/PaStiXSupport/PaStiXSupport.h +678 -0
  251. data/vendor/eigen/Eigen/src/PardisoSupport/PardisoSupport.h +543 -0
  252. data/vendor/eigen/Eigen/src/QR/ColPivHouseholderQR.h +653 -0
  253. data/vendor/eigen/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h +97 -0
  254. data/vendor/eigen/Eigen/src/QR/CompleteOrthogonalDecomposition.h +562 -0
  255. data/vendor/eigen/Eigen/src/QR/FullPivHouseholderQR.h +676 -0
  256. data/vendor/eigen/Eigen/src/QR/HouseholderQR.h +409 -0
  257. data/vendor/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h +68 -0
  258. data/vendor/eigen/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h +313 -0
  259. data/vendor/eigen/Eigen/src/SVD/BDCSVD.h +1246 -0
  260. data/vendor/eigen/Eigen/src/SVD/JacobiSVD.h +804 -0
  261. data/vendor/eigen/Eigen/src/SVD/JacobiSVD_LAPACKE.h +91 -0
  262. data/vendor/eigen/Eigen/src/SVD/SVDBase.h +315 -0
  263. data/vendor/eigen/Eigen/src/SVD/UpperBidiagonalization.h +414 -0
  264. data/vendor/eigen/Eigen/src/SparseCholesky/SimplicialCholesky.h +689 -0
  265. data/vendor/eigen/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h +199 -0
  266. data/vendor/eigen/Eigen/src/SparseCore/AmbiVector.h +377 -0
  267. data/vendor/eigen/Eigen/src/SparseCore/CompressedStorage.h +258 -0
  268. data/vendor/eigen/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h +352 -0
  269. data/vendor/eigen/Eigen/src/SparseCore/MappedSparseMatrix.h +67 -0
  270. data/vendor/eigen/Eigen/src/SparseCore/SparseAssign.h +216 -0
  271. data/vendor/eigen/Eigen/src/SparseCore/SparseBlock.h +603 -0
  272. data/vendor/eigen/Eigen/src/SparseCore/SparseColEtree.h +206 -0
  273. data/vendor/eigen/Eigen/src/SparseCore/SparseCompressedBase.h +341 -0
  274. data/vendor/eigen/Eigen/src/SparseCore/SparseCwiseBinaryOp.h +726 -0
  275. data/vendor/eigen/Eigen/src/SparseCore/SparseCwiseUnaryOp.h +148 -0
  276. data/vendor/eigen/Eigen/src/SparseCore/SparseDenseProduct.h +320 -0
  277. data/vendor/eigen/Eigen/src/SparseCore/SparseDiagonalProduct.h +138 -0
  278. data/vendor/eigen/Eigen/src/SparseCore/SparseDot.h +98 -0
  279. data/vendor/eigen/Eigen/src/SparseCore/SparseFuzzy.h +29 -0
  280. data/vendor/eigen/Eigen/src/SparseCore/SparseMap.h +305 -0
  281. data/vendor/eigen/Eigen/src/SparseCore/SparseMatrix.h +1403 -0
  282. data/vendor/eigen/Eigen/src/SparseCore/SparseMatrixBase.h +405 -0
  283. data/vendor/eigen/Eigen/src/SparseCore/SparsePermutation.h +178 -0
  284. data/vendor/eigen/Eigen/src/SparseCore/SparseProduct.h +169 -0
  285. data/vendor/eigen/Eigen/src/SparseCore/SparseRedux.h +49 -0
  286. data/vendor/eigen/Eigen/src/SparseCore/SparseRef.h +397 -0
  287. data/vendor/eigen/Eigen/src/SparseCore/SparseSelfAdjointView.h +656 -0
  288. data/vendor/eigen/Eigen/src/SparseCore/SparseSolverBase.h +124 -0
  289. data/vendor/eigen/Eigen/src/SparseCore/SparseSparseProductWithPruning.h +198 -0
  290. data/vendor/eigen/Eigen/src/SparseCore/SparseTranspose.h +92 -0
  291. data/vendor/eigen/Eigen/src/SparseCore/SparseTriangularView.h +189 -0
  292. data/vendor/eigen/Eigen/src/SparseCore/SparseUtil.h +178 -0
  293. data/vendor/eigen/Eigen/src/SparseCore/SparseVector.h +478 -0
  294. data/vendor/eigen/Eigen/src/SparseCore/SparseView.h +253 -0
  295. data/vendor/eigen/Eigen/src/SparseCore/TriangularSolver.h +315 -0
  296. data/vendor/eigen/Eigen/src/SparseLU/SparseLU.h +773 -0
  297. data/vendor/eigen/Eigen/src/SparseLU/SparseLUImpl.h +66 -0
  298. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_Memory.h +226 -0
  299. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_Structs.h +110 -0
  300. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h +301 -0
  301. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_Utils.h +80 -0
  302. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_column_bmod.h +181 -0
  303. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h +179 -0
  304. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +107 -0
  305. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +280 -0
  306. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +126 -0
  307. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +130 -0
  308. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +223 -0
  309. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +258 -0
  310. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +137 -0
  311. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +136 -0
  312. data/vendor/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +83 -0
  313. data/vendor/eigen/Eigen/src/SparseQR/SparseQR.h +745 -0
  314. data/vendor/eigen/Eigen/src/StlSupport/StdDeque.h +126 -0
  315. data/vendor/eigen/Eigen/src/StlSupport/StdList.h +106 -0
  316. data/vendor/eigen/Eigen/src/StlSupport/StdVector.h +131 -0
  317. data/vendor/eigen/Eigen/src/StlSupport/details.h +84 -0
  318. data/vendor/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +1027 -0
  319. data/vendor/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +506 -0
  320. data/vendor/eigen/Eigen/src/misc/Image.h +82 -0
  321. data/vendor/eigen/Eigen/src/misc/Kernel.h +79 -0
  322. data/vendor/eigen/Eigen/src/misc/RealSvd2x2.h +55 -0
  323. data/vendor/eigen/Eigen/src/misc/blas.h +440 -0
  324. data/vendor/eigen/Eigen/src/misc/lapack.h +152 -0
  325. data/vendor/eigen/Eigen/src/misc/lapacke.h +16291 -0
  326. data/vendor/eigen/Eigen/src/misc/lapacke_mangling.h +17 -0
  327. data/vendor/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +332 -0
  328. data/vendor/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +552 -0
  329. data/vendor/eigen/Eigen/src/plugins/BlockMethods.h +1058 -0
  330. data/vendor/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +115 -0
  331. data/vendor/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +163 -0
  332. data/vendor/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +152 -0
  333. data/vendor/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +85 -0
  334. data/vendor/eigen/README.md +3 -0
  335. data/vendor/eigen/bench/README.txt +55 -0
  336. data/vendor/eigen/bench/btl/COPYING +340 -0
  337. data/vendor/eigen/bench/btl/README +154 -0
  338. data/vendor/eigen/bench/tensors/README +21 -0
  339. data/vendor/eigen/blas/README.txt +6 -0
  340. data/vendor/eigen/demos/mandelbrot/README +10 -0
  341. data/vendor/eigen/demos/mix_eigen_and_c/README +9 -0
  342. data/vendor/eigen/demos/opengl/README +13 -0
  343. data/vendor/eigen/unsupported/Eigen/CXX11/src/Tensor/README.md +1760 -0
  344. data/vendor/eigen/unsupported/README.txt +50 -0
  345. data/vendor/tomotopy/LICENSE +21 -0
  346. data/vendor/tomotopy/README.kr.rst +375 -0
  347. data/vendor/tomotopy/README.rst +382 -0
  348. data/vendor/tomotopy/src/Labeling/FoRelevance.cpp +362 -0
  349. data/vendor/tomotopy/src/Labeling/FoRelevance.h +88 -0
  350. data/vendor/tomotopy/src/Labeling/Labeler.h +50 -0
  351. data/vendor/tomotopy/src/TopicModel/CT.h +37 -0
  352. data/vendor/tomotopy/src/TopicModel/CTModel.cpp +13 -0
  353. data/vendor/tomotopy/src/TopicModel/CTModel.hpp +293 -0
  354. data/vendor/tomotopy/src/TopicModel/DMR.h +51 -0
  355. data/vendor/tomotopy/src/TopicModel/DMRModel.cpp +13 -0
  356. data/vendor/tomotopy/src/TopicModel/DMRModel.hpp +374 -0
  357. data/vendor/tomotopy/src/TopicModel/DT.h +65 -0
  358. data/vendor/tomotopy/src/TopicModel/DTM.h +22 -0
  359. data/vendor/tomotopy/src/TopicModel/DTModel.cpp +15 -0
  360. data/vendor/tomotopy/src/TopicModel/DTModel.hpp +572 -0
  361. data/vendor/tomotopy/src/TopicModel/GDMR.h +37 -0
  362. data/vendor/tomotopy/src/TopicModel/GDMRModel.cpp +14 -0
  363. data/vendor/tomotopy/src/TopicModel/GDMRModel.hpp +485 -0
  364. data/vendor/tomotopy/src/TopicModel/HDP.h +74 -0
  365. data/vendor/tomotopy/src/TopicModel/HDPModel.cpp +13 -0
  366. data/vendor/tomotopy/src/TopicModel/HDPModel.hpp +592 -0
  367. data/vendor/tomotopy/src/TopicModel/HLDA.h +40 -0
  368. data/vendor/tomotopy/src/TopicModel/HLDAModel.cpp +13 -0
  369. data/vendor/tomotopy/src/TopicModel/HLDAModel.hpp +681 -0
  370. data/vendor/tomotopy/src/TopicModel/HPA.h +27 -0
  371. data/vendor/tomotopy/src/TopicModel/HPAModel.cpp +21 -0
  372. data/vendor/tomotopy/src/TopicModel/HPAModel.hpp +588 -0
  373. data/vendor/tomotopy/src/TopicModel/LDA.h +144 -0
  374. data/vendor/tomotopy/src/TopicModel/LDACVB0Model.hpp +442 -0
  375. data/vendor/tomotopy/src/TopicModel/LDAModel.cpp +13 -0
  376. data/vendor/tomotopy/src/TopicModel/LDAModel.hpp +1058 -0
  377. data/vendor/tomotopy/src/TopicModel/LLDA.h +45 -0
  378. data/vendor/tomotopy/src/TopicModel/LLDAModel.cpp +13 -0
  379. data/vendor/tomotopy/src/TopicModel/LLDAModel.hpp +203 -0
  380. data/vendor/tomotopy/src/TopicModel/MGLDA.h +63 -0
  381. data/vendor/tomotopy/src/TopicModel/MGLDAModel.cpp +17 -0
  382. data/vendor/tomotopy/src/TopicModel/MGLDAModel.hpp +558 -0
  383. data/vendor/tomotopy/src/TopicModel/PA.h +43 -0
  384. data/vendor/tomotopy/src/TopicModel/PAModel.cpp +13 -0
  385. data/vendor/tomotopy/src/TopicModel/PAModel.hpp +467 -0
  386. data/vendor/tomotopy/src/TopicModel/PLDA.h +17 -0
  387. data/vendor/tomotopy/src/TopicModel/PLDAModel.cpp +13 -0
  388. data/vendor/tomotopy/src/TopicModel/PLDAModel.hpp +214 -0
  389. data/vendor/tomotopy/src/TopicModel/SLDA.h +54 -0
  390. data/vendor/tomotopy/src/TopicModel/SLDAModel.cpp +17 -0
  391. data/vendor/tomotopy/src/TopicModel/SLDAModel.hpp +456 -0
  392. data/vendor/tomotopy/src/TopicModel/TopicModel.hpp +692 -0
  393. data/vendor/tomotopy/src/Utils/AliasMethod.hpp +169 -0
  394. data/vendor/tomotopy/src/Utils/Dictionary.h +80 -0
  395. data/vendor/tomotopy/src/Utils/EigenAddonOps.hpp +181 -0
  396. data/vendor/tomotopy/src/Utils/LBFGS.h +202 -0
  397. data/vendor/tomotopy/src/Utils/LBFGS/LineSearchBacktracking.h +120 -0
  398. data/vendor/tomotopy/src/Utils/LBFGS/LineSearchBracketing.h +122 -0
  399. data/vendor/tomotopy/src/Utils/LBFGS/Param.h +213 -0
  400. data/vendor/tomotopy/src/Utils/LUT.hpp +82 -0
  401. data/vendor/tomotopy/src/Utils/MultiNormalDistribution.hpp +69 -0
  402. data/vendor/tomotopy/src/Utils/PolyaGamma.hpp +200 -0
  403. data/vendor/tomotopy/src/Utils/PolyaGammaHybrid.hpp +672 -0
  404. data/vendor/tomotopy/src/Utils/ThreadPool.hpp +150 -0
  405. data/vendor/tomotopy/src/Utils/Trie.hpp +220 -0
  406. data/vendor/tomotopy/src/Utils/TruncMultiNormal.hpp +94 -0
  407. data/vendor/tomotopy/src/Utils/Utils.hpp +337 -0
  408. data/vendor/tomotopy/src/Utils/avx_gamma.h +46 -0
  409. data/vendor/tomotopy/src/Utils/avx_mathfun.h +736 -0
  410. data/vendor/tomotopy/src/Utils/exception.h +28 -0
  411. data/vendor/tomotopy/src/Utils/math.h +281 -0
  412. data/vendor/tomotopy/src/Utils/rtnorm.hpp +2690 -0
  413. data/vendor/tomotopy/src/Utils/sample.hpp +192 -0
  414. data/vendor/tomotopy/src/Utils/serializer.hpp +695 -0
  415. data/vendor/tomotopy/src/Utils/slp.hpp +131 -0
  416. data/vendor/tomotopy/src/Utils/sse_gamma.h +48 -0
  417. data/vendor/tomotopy/src/Utils/sse_mathfun.h +710 -0
  418. data/vendor/tomotopy/src/Utils/text.hpp +49 -0
  419. data/vendor/tomotopy/src/Utils/tvector.hpp +543 -0
  420. metadata +531 -0
@@ -0,0 +1,258 @@
1
+ // This file is part of Eigen, a lightweight C++ template library
2
+ // for linear algebra.
3
+ //
4
+ // Copyright (C) 2008-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
5
+ //
6
+ // This Source Code Form is subject to the terms of the Mozilla
7
+ // Public License v. 2.0. If a copy of the MPL was not distributed
8
+ // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
+
10
+ #ifndef EIGEN_COMPRESSED_STORAGE_H
11
+ #define EIGEN_COMPRESSED_STORAGE_H
12
+
13
+ namespace Eigen {
14
+
15
+ namespace internal {
16
+
17
+ /** \internal
18
+ * Stores a sparse set of values as a list of values and a list of indices.
19
+ *
20
+ */
21
+ template<typename _Scalar,typename _StorageIndex>
22
+ class CompressedStorage
23
+ {
24
+ public:
25
+
26
+ typedef _Scalar Scalar;
27
+ typedef _StorageIndex StorageIndex;
28
+
29
+ protected:
30
+
31
+ typedef typename NumTraits<Scalar>::Real RealScalar;
32
+
33
+ public:
34
+
35
+ CompressedStorage()
36
+ : m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
37
+ {}
38
+
39
+ explicit CompressedStorage(Index size)
40
+ : m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
41
+ {
42
+ resize(size);
43
+ }
44
+
45
+ CompressedStorage(const CompressedStorage& other)
46
+ : m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
47
+ {
48
+ *this = other;
49
+ }
50
+
51
+ CompressedStorage& operator=(const CompressedStorage& other)
52
+ {
53
+ resize(other.size());
54
+ if(other.size()>0)
55
+ {
56
+ internal::smart_copy(other.m_values, other.m_values + m_size, m_values);
57
+ internal::smart_copy(other.m_indices, other.m_indices + m_size, m_indices);
58
+ }
59
+ return *this;
60
+ }
61
+
62
+ void swap(CompressedStorage& other)
63
+ {
64
+ std::swap(m_values, other.m_values);
65
+ std::swap(m_indices, other.m_indices);
66
+ std::swap(m_size, other.m_size);
67
+ std::swap(m_allocatedSize, other.m_allocatedSize);
68
+ }
69
+
70
+ ~CompressedStorage()
71
+ {
72
+ delete[] m_values;
73
+ delete[] m_indices;
74
+ }
75
+
76
+ void reserve(Index size)
77
+ {
78
+ Index newAllocatedSize = m_size + size;
79
+ if (newAllocatedSize > m_allocatedSize)
80
+ reallocate(newAllocatedSize);
81
+ }
82
+
83
+ void squeeze()
84
+ {
85
+ if (m_allocatedSize>m_size)
86
+ reallocate(m_size);
87
+ }
88
+
89
+ void resize(Index size, double reserveSizeFactor = 0)
90
+ {
91
+ if (m_allocatedSize<size)
92
+ {
93
+ Index realloc_size = (std::min<Index>)(NumTraits<StorageIndex>::highest(), size + Index(reserveSizeFactor*double(size)));
94
+ if(realloc_size<size)
95
+ internal::throw_std_bad_alloc();
96
+ reallocate(realloc_size);
97
+ }
98
+ m_size = size;
99
+ }
100
+
101
+ void append(const Scalar& v, Index i)
102
+ {
103
+ Index id = m_size;
104
+ resize(m_size+1, 1);
105
+ m_values[id] = v;
106
+ m_indices[id] = internal::convert_index<StorageIndex>(i);
107
+ }
108
+
109
+ inline Index size() const { return m_size; }
110
+ inline Index allocatedSize() const { return m_allocatedSize; }
111
+ inline void clear() { m_size = 0; }
112
+
113
+ const Scalar* valuePtr() const { return m_values; }
114
+ Scalar* valuePtr() { return m_values; }
115
+ const StorageIndex* indexPtr() const { return m_indices; }
116
+ StorageIndex* indexPtr() { return m_indices; }
117
+
118
+ inline Scalar& value(Index i) { eigen_internal_assert(m_values!=0); return m_values[i]; }
119
+ inline const Scalar& value(Index i) const { eigen_internal_assert(m_values!=0); return m_values[i]; }
120
+
121
+ inline StorageIndex& index(Index i) { eigen_internal_assert(m_indices!=0); return m_indices[i]; }
122
+ inline const StorageIndex& index(Index i) const { eigen_internal_assert(m_indices!=0); return m_indices[i]; }
123
+
124
+ /** \returns the largest \c k such that for all \c j in [0,k) index[\c j]\<\a key */
125
+ inline Index searchLowerIndex(Index key) const
126
+ {
127
+ return searchLowerIndex(0, m_size, key);
128
+ }
129
+
130
+ /** \returns the largest \c k in [start,end) such that for all \c j in [start,k) index[\c j]\<\a key */
131
+ inline Index searchLowerIndex(Index start, Index end, Index key) const
132
+ {
133
+ while(end>start)
134
+ {
135
+ Index mid = (end+start)>>1;
136
+ if (m_indices[mid]<key)
137
+ start = mid+1;
138
+ else
139
+ end = mid;
140
+ }
141
+ return start;
142
+ }
143
+
144
+ /** \returns the stored value at index \a key
145
+ * If the value does not exist, then the value \a defaultValue is returned without any insertion. */
146
+ inline Scalar at(Index key, const Scalar& defaultValue = Scalar(0)) const
147
+ {
148
+ if (m_size==0)
149
+ return defaultValue;
150
+ else if (key==m_indices[m_size-1])
151
+ return m_values[m_size-1];
152
+ // ^^ optimization: let's first check if it is the last coefficient
153
+ // (very common in high level algorithms)
154
+ const Index id = searchLowerIndex(0,m_size-1,key);
155
+ return ((id<m_size) && (m_indices[id]==key)) ? m_values[id] : defaultValue;
156
+ }
157
+
158
+ /** Like at(), but the search is performed in the range [start,end) */
159
+ inline Scalar atInRange(Index start, Index end, Index key, const Scalar &defaultValue = Scalar(0)) const
160
+ {
161
+ if (start>=end)
162
+ return defaultValue;
163
+ else if (end>start && key==m_indices[end-1])
164
+ return m_values[end-1];
165
+ // ^^ optimization: let's first check if it is the last coefficient
166
+ // (very common in high level algorithms)
167
+ const Index id = searchLowerIndex(start,end-1,key);
168
+ return ((id<end) && (m_indices[id]==key)) ? m_values[id] : defaultValue;
169
+ }
170
+
171
+ /** \returns a reference to the value at index \a key
172
+ * If the value does not exist, then the value \a defaultValue is inserted
173
+ * such that the keys are sorted. */
174
+ inline Scalar& atWithInsertion(Index key, const Scalar& defaultValue = Scalar(0))
175
+ {
176
+ Index id = searchLowerIndex(0,m_size,key);
177
+ if (id>=m_size || m_indices[id]!=key)
178
+ {
179
+ if (m_allocatedSize<m_size+1)
180
+ {
181
+ m_allocatedSize = 2*(m_size+1);
182
+ internal::scoped_array<Scalar> newValues(m_allocatedSize);
183
+ internal::scoped_array<StorageIndex> newIndices(m_allocatedSize);
184
+
185
+ // copy first chunk
186
+ internal::smart_copy(m_values, m_values +id, newValues.ptr());
187
+ internal::smart_copy(m_indices, m_indices+id, newIndices.ptr());
188
+
189
+ // copy the rest
190
+ if(m_size>id)
191
+ {
192
+ internal::smart_copy(m_values +id, m_values +m_size, newValues.ptr() +id+1);
193
+ internal::smart_copy(m_indices+id, m_indices+m_size, newIndices.ptr()+id+1);
194
+ }
195
+ std::swap(m_values,newValues.ptr());
196
+ std::swap(m_indices,newIndices.ptr());
197
+ }
198
+ else if(m_size>id)
199
+ {
200
+ internal::smart_memmove(m_values +id, m_values +m_size, m_values +id+1);
201
+ internal::smart_memmove(m_indices+id, m_indices+m_size, m_indices+id+1);
202
+ }
203
+ m_size++;
204
+ m_indices[id] = internal::convert_index<StorageIndex>(key);
205
+ m_values[id] = defaultValue;
206
+ }
207
+ return m_values[id];
208
+ }
209
+
210
+ void prune(const Scalar& reference, const RealScalar& epsilon = NumTraits<RealScalar>::dummy_precision())
211
+ {
212
+ Index k = 0;
213
+ Index n = size();
214
+ for (Index i=0; i<n; ++i)
215
+ {
216
+ if (!internal::isMuchSmallerThan(value(i), reference, epsilon))
217
+ {
218
+ value(k) = value(i);
219
+ index(k) = index(i);
220
+ ++k;
221
+ }
222
+ }
223
+ resize(k,0);
224
+ }
225
+
226
+ protected:
227
+
228
+ inline void reallocate(Index size)
229
+ {
230
+ #ifdef EIGEN_SPARSE_COMPRESSED_STORAGE_REALLOCATE_PLUGIN
231
+ EIGEN_SPARSE_COMPRESSED_STORAGE_REALLOCATE_PLUGIN
232
+ #endif
233
+ eigen_internal_assert(size!=m_allocatedSize);
234
+ internal::scoped_array<Scalar> newValues(size);
235
+ internal::scoped_array<StorageIndex> newIndices(size);
236
+ Index copySize = (std::min)(size, m_size);
237
+ if (copySize>0) {
238
+ internal::smart_copy(m_values, m_values+copySize, newValues.ptr());
239
+ internal::smart_copy(m_indices, m_indices+copySize, newIndices.ptr());
240
+ }
241
+ std::swap(m_values,newValues.ptr());
242
+ std::swap(m_indices,newIndices.ptr());
243
+ m_allocatedSize = size;
244
+ }
245
+
246
+ protected:
247
+ Scalar* m_values;
248
+ StorageIndex* m_indices;
249
+ Index m_size;
250
+ Index m_allocatedSize;
251
+
252
+ };
253
+
254
+ } // end namespace internal
255
+
256
+ } // end namespace Eigen
257
+
258
+ #endif // EIGEN_COMPRESSED_STORAGE_H
@@ -0,0 +1,352 @@
1
+ // This file is part of Eigen, a lightweight C++ template library
2
+ // for linear algebra.
3
+ //
4
+ // Copyright (C) 2008-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
5
+ //
6
+ // This Source Code Form is subject to the terms of the Mozilla
7
+ // Public License v. 2.0. If a copy of the MPL was not distributed
8
+ // with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
9
+
10
+ #ifndef EIGEN_CONSERVATIVESPARSESPARSEPRODUCT_H
11
+ #define EIGEN_CONSERVATIVESPARSESPARSEPRODUCT_H
12
+
13
+ namespace Eigen {
14
+
15
+ namespace internal {
16
+
17
+ template<typename Lhs, typename Rhs, typename ResultType>
18
+ static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false)
19
+ {
20
+ typedef typename remove_all<Lhs>::type::Scalar LhsScalar;
21
+ typedef typename remove_all<Rhs>::type::Scalar RhsScalar;
22
+ typedef typename remove_all<ResultType>::type::Scalar ResScalar;
23
+
24
+ // make sure to call innerSize/outerSize since we fake the storage order.
25
+ Index rows = lhs.innerSize();
26
+ Index cols = rhs.outerSize();
27
+ eigen_assert(lhs.outerSize() == rhs.innerSize());
28
+
29
+ ei_declare_aligned_stack_constructed_variable(bool, mask, rows, 0);
30
+ ei_declare_aligned_stack_constructed_variable(ResScalar, values, rows, 0);
31
+ ei_declare_aligned_stack_constructed_variable(Index, indices, rows, 0);
32
+
33
+ std::memset(mask,0,sizeof(bool)*rows);
34
+
35
+ evaluator<Lhs> lhsEval(lhs);
36
+ evaluator<Rhs> rhsEval(rhs);
37
+
38
+ // estimate the number of non zero entries
39
+ // given a rhs column containing Y non zeros, we assume that the respective Y columns
40
+ // of the lhs differs in average of one non zeros, thus the number of non zeros for
41
+ // the product of a rhs column with the lhs is X+Y where X is the average number of non zero
42
+ // per column of the lhs.
43
+ // Therefore, we have nnz(lhs*rhs) = nnz(lhs) + nnz(rhs)
44
+ Index estimated_nnz_prod = lhsEval.nonZerosEstimate() + rhsEval.nonZerosEstimate();
45
+
46
+ res.setZero();
47
+ res.reserve(Index(estimated_nnz_prod));
48
+ // we compute each column of the result, one after the other
49
+ for (Index j=0; j<cols; ++j)
50
+ {
51
+
52
+ res.startVec(j);
53
+ Index nnz = 0;
54
+ for (typename evaluator<Rhs>::InnerIterator rhsIt(rhsEval, j); rhsIt; ++rhsIt)
55
+ {
56
+ RhsScalar y = rhsIt.value();
57
+ Index k = rhsIt.index();
58
+ for (typename evaluator<Lhs>::InnerIterator lhsIt(lhsEval, k); lhsIt; ++lhsIt)
59
+ {
60
+ Index i = lhsIt.index();
61
+ LhsScalar x = lhsIt.value();
62
+ if(!mask[i])
63
+ {
64
+ mask[i] = true;
65
+ values[i] = x * y;
66
+ indices[nnz] = i;
67
+ ++nnz;
68
+ }
69
+ else
70
+ values[i] += x * y;
71
+ }
72
+ }
73
+ if(!sortedInsertion)
74
+ {
75
+ // unordered insertion
76
+ for(Index k=0; k<nnz; ++k)
77
+ {
78
+ Index i = indices[k];
79
+ res.insertBackByOuterInnerUnordered(j,i) = values[i];
80
+ mask[i] = false;
81
+ }
82
+ }
83
+ else
84
+ {
85
+ // alternative ordered insertion code:
86
+ const Index t200 = rows/11; // 11 == (log2(200)*1.39)
87
+ const Index t = (rows*100)/139;
88
+
89
+ // FIXME reserve nnz non zeros
90
+ // FIXME implement faster sorting algorithms for very small nnz
91
+ // if the result is sparse enough => use a quick sort
92
+ // otherwise => loop through the entire vector
93
+ // In order to avoid to perform an expensive log2 when the
94
+ // result is clearly very sparse we use a linear bound up to 200.
95
+ if((nnz<200 && nnz<t200) || nnz * numext::log2(int(nnz)) < t)
96
+ {
97
+ if(nnz>1) std::sort(indices,indices+nnz);
98
+ for(Index k=0; k<nnz; ++k)
99
+ {
100
+ Index i = indices[k];
101
+ res.insertBackByOuterInner(j,i) = values[i];
102
+ mask[i] = false;
103
+ }
104
+ }
105
+ else
106
+ {
107
+ // dense path
108
+ for(Index i=0; i<rows; ++i)
109
+ {
110
+ if(mask[i])
111
+ {
112
+ mask[i] = false;
113
+ res.insertBackByOuterInner(j,i) = values[i];
114
+ }
115
+ }
116
+ }
117
+ }
118
+ }
119
+ res.finalize();
120
+ }
121
+
122
+
123
+ } // end namespace internal
124
+
125
+ namespace internal {
126
+
127
+ template<typename Lhs, typename Rhs, typename ResultType,
128
+ int LhsStorageOrder = (traits<Lhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
129
+ int RhsStorageOrder = (traits<Rhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
130
+ int ResStorageOrder = (traits<ResultType>::Flags&RowMajorBit) ? RowMajor : ColMajor>
131
+ struct conservative_sparse_sparse_product_selector;
132
+
133
+ template<typename Lhs, typename Rhs, typename ResultType>
134
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,ColMajor>
135
+ {
136
+ typedef typename remove_all<Lhs>::type LhsCleaned;
137
+ typedef typename LhsCleaned::Scalar Scalar;
138
+
139
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
140
+ {
141
+ typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorMatrix;
142
+ typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorMatrixAux;
143
+ typedef typename sparse_eval<ColMajorMatrixAux,ResultType::RowsAtCompileTime,ResultType::ColsAtCompileTime,ColMajorMatrixAux::Flags>::type ColMajorMatrix;
144
+
145
+ // If the result is tall and thin (in the extreme case a column vector)
146
+ // then it is faster to sort the coefficients inplace instead of transposing twice.
147
+ // FIXME, the following heuristic is probably not very good.
148
+ if(lhs.rows()>rhs.cols())
149
+ {
150
+ ColMajorMatrix resCol(lhs.rows(),rhs.cols());
151
+ // perform sorted insertion
152
+ internal::conservative_sparse_sparse_product_impl<Lhs,Rhs,ColMajorMatrix>(lhs, rhs, resCol, true);
153
+ res = resCol.markAsRValue();
154
+ }
155
+ else
156
+ {
157
+ ColMajorMatrixAux resCol(lhs.rows(),rhs.cols());
158
+ // ressort to transpose to sort the entries
159
+ internal::conservative_sparse_sparse_product_impl<Lhs,Rhs,ColMajorMatrixAux>(lhs, rhs, resCol, false);
160
+ RowMajorMatrix resRow(resCol);
161
+ res = resRow.markAsRValue();
162
+ }
163
+ }
164
+ };
165
+
166
+ template<typename Lhs, typename Rhs, typename ResultType>
167
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,ColMajor>
168
+ {
169
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
170
+ {
171
+ typedef SparseMatrix<typename Rhs::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorRhs;
172
+ typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorRes;
173
+ RowMajorRhs rhsRow = rhs;
174
+ RowMajorRes resRow(lhs.rows(), rhs.cols());
175
+ internal::conservative_sparse_sparse_product_impl<RowMajorRhs,Lhs,RowMajorRes>(rhsRow, lhs, resRow);
176
+ res = resRow;
177
+ }
178
+ };
179
+
180
+ template<typename Lhs, typename Rhs, typename ResultType>
181
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,ColMajor>
182
+ {
183
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
184
+ {
185
+ typedef SparseMatrix<typename Lhs::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorLhs;
186
+ typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorRes;
187
+ RowMajorLhs lhsRow = lhs;
188
+ RowMajorRes resRow(lhs.rows(), rhs.cols());
189
+ internal::conservative_sparse_sparse_product_impl<Rhs,RowMajorLhs,RowMajorRes>(rhs, lhsRow, resRow);
190
+ res = resRow;
191
+ }
192
+ };
193
+
194
+ template<typename Lhs, typename Rhs, typename ResultType>
195
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,ColMajor>
196
+ {
197
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
198
+ {
199
+ typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorMatrix;
200
+ RowMajorMatrix resRow(lhs.rows(), rhs.cols());
201
+ internal::conservative_sparse_sparse_product_impl<Rhs,Lhs,RowMajorMatrix>(rhs, lhs, resRow);
202
+ res = resRow;
203
+ }
204
+ };
205
+
206
+
207
+ template<typename Lhs, typename Rhs, typename ResultType>
208
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,RowMajor>
209
+ {
210
+ typedef typename traits<typename remove_all<Lhs>::type>::Scalar Scalar;
211
+
212
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
213
+ {
214
+ typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorMatrix;
215
+ ColMajorMatrix resCol(lhs.rows(), rhs.cols());
216
+ internal::conservative_sparse_sparse_product_impl<Lhs,Rhs,ColMajorMatrix>(lhs, rhs, resCol);
217
+ res = resCol;
218
+ }
219
+ };
220
+
221
+ template<typename Lhs, typename Rhs, typename ResultType>
222
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor,RowMajor>
223
+ {
224
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
225
+ {
226
+ typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorLhs;
227
+ typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRes;
228
+ ColMajorLhs lhsCol = lhs;
229
+ ColMajorRes resCol(lhs.rows(), rhs.cols());
230
+ internal::conservative_sparse_sparse_product_impl<ColMajorLhs,Rhs,ColMajorRes>(lhsCol, rhs, resCol);
231
+ res = resCol;
232
+ }
233
+ };
234
+
235
+ template<typename Lhs, typename Rhs, typename ResultType>
236
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor,RowMajor>
237
+ {
238
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
239
+ {
240
+ typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRhs;
241
+ typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRes;
242
+ ColMajorRhs rhsCol = rhs;
243
+ ColMajorRes resCol(lhs.rows(), rhs.cols());
244
+ internal::conservative_sparse_sparse_product_impl<Lhs,ColMajorRhs,ColMajorRes>(lhs, rhsCol, resCol);
245
+ res = resCol;
246
+ }
247
+ };
248
+
249
+ template<typename Lhs, typename Rhs, typename ResultType>
250
+ struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor,RowMajor>
251
+ {
252
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
253
+ {
254
+ typedef SparseMatrix<typename ResultType::Scalar,RowMajor,typename ResultType::StorageIndex> RowMajorMatrix;
255
+ typedef SparseMatrix<typename ResultType::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorMatrix;
256
+ RowMajorMatrix resRow(lhs.rows(),rhs.cols());
257
+ internal::conservative_sparse_sparse_product_impl<Rhs,Lhs,RowMajorMatrix>(rhs, lhs, resRow);
258
+ // sort the non zeros:
259
+ ColMajorMatrix resCol(resRow);
260
+ res = resCol;
261
+ }
262
+ };
263
+
264
+ } // end namespace internal
265
+
266
+
267
+ namespace internal {
268
+
269
+ template<typename Lhs, typename Rhs, typename ResultType>
270
+ static void sparse_sparse_to_dense_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res)
271
+ {
272
+ typedef typename remove_all<Lhs>::type::Scalar LhsScalar;
273
+ typedef typename remove_all<Rhs>::type::Scalar RhsScalar;
274
+ Index cols = rhs.outerSize();
275
+ eigen_assert(lhs.outerSize() == rhs.innerSize());
276
+
277
+ evaluator<Lhs> lhsEval(lhs);
278
+ evaluator<Rhs> rhsEval(rhs);
279
+
280
+ for (Index j=0; j<cols; ++j)
281
+ {
282
+ for (typename evaluator<Rhs>::InnerIterator rhsIt(rhsEval, j); rhsIt; ++rhsIt)
283
+ {
284
+ RhsScalar y = rhsIt.value();
285
+ Index k = rhsIt.index();
286
+ for (typename evaluator<Lhs>::InnerIterator lhsIt(lhsEval, k); lhsIt; ++lhsIt)
287
+ {
288
+ Index i = lhsIt.index();
289
+ LhsScalar x = lhsIt.value();
290
+ res.coeffRef(i,j) += x * y;
291
+ }
292
+ }
293
+ }
294
+ }
295
+
296
+
297
+ } // end namespace internal
298
+
299
+ namespace internal {
300
+
301
+ template<typename Lhs, typename Rhs, typename ResultType,
302
+ int LhsStorageOrder = (traits<Lhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
303
+ int RhsStorageOrder = (traits<Rhs>::Flags&RowMajorBit) ? RowMajor : ColMajor>
304
+ struct sparse_sparse_to_dense_product_selector;
305
+
306
+ template<typename Lhs, typename Rhs, typename ResultType>
307
+ struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor>
308
+ {
309
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
310
+ {
311
+ internal::sparse_sparse_to_dense_product_impl<Lhs,Rhs,ResultType>(lhs, rhs, res);
312
+ }
313
+ };
314
+
315
+ template<typename Lhs, typename Rhs, typename ResultType>
316
+ struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,RowMajor,ColMajor>
317
+ {
318
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
319
+ {
320
+ typedef SparseMatrix<typename Lhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorLhs;
321
+ ColMajorLhs lhsCol(lhs);
322
+ internal::sparse_sparse_to_dense_product_impl<ColMajorLhs,Rhs,ResultType>(lhsCol, rhs, res);
323
+ }
324
+ };
325
+
326
+ template<typename Lhs, typename Rhs, typename ResultType>
327
+ struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,ColMajor,RowMajor>
328
+ {
329
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
330
+ {
331
+ typedef SparseMatrix<typename Rhs::Scalar,ColMajor,typename ResultType::StorageIndex> ColMajorRhs;
332
+ ColMajorRhs rhsCol(rhs);
333
+ internal::sparse_sparse_to_dense_product_impl<Lhs,ColMajorRhs,ResultType>(lhs, rhsCol, res);
334
+ }
335
+ };
336
+
337
+ template<typename Lhs, typename Rhs, typename ResultType>
338
+ struct sparse_sparse_to_dense_product_selector<Lhs,Rhs,ResultType,RowMajor,RowMajor>
339
+ {
340
+ static void run(const Lhs& lhs, const Rhs& rhs, ResultType& res)
341
+ {
342
+ Transpose<ResultType> trRes(res);
343
+ internal::sparse_sparse_to_dense_product_impl<Rhs,Lhs,Transpose<ResultType> >(rhs, lhs, trRes);
344
+ }
345
+ };
346
+
347
+
348
+ } // end namespace internal
349
+
350
+ } // end namespace Eigen
351
+
352
+ #endif // EIGEN_CONSERVATIVESPARSESPARSEPRODUCT_H