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
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  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 +1,97 @@
1
+ /*
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+ Copyright (c) 2011, Intel Corporation. All rights reserved.
3
+
4
+ Redistribution and use in source and binary forms, with or without modification,
5
+ are permitted provided that the following conditions are met:
6
+
7
+ * Redistributions of source code must retain the above copyright notice, this
8
+ list of conditions and the following disclaimer.
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+ * Redistributions in binary form must reproduce the above copyright notice,
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+ this list of conditions and the following disclaimer in the documentation
11
+ and/or other materials provided with the distribution.
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+ * Neither the name of Intel Corporation nor the names of its contributors may
13
+ be used to endorse or promote products derived from this software without
14
+ specific prior written permission.
15
+
16
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
17
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
18
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
19
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
20
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
21
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
22
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
23
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
24
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
25
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
26
+
27
+ ********************************************************************************
28
+ * Content : Eigen bindings to LAPACKe
29
+ * Householder QR decomposition of a matrix with column pivoting based on
30
+ * LAPACKE_?geqp3 function.
31
+ ********************************************************************************
32
+ */
33
+
34
+ #ifndef EIGEN_COLPIVOTINGHOUSEHOLDERQR_LAPACKE_H
35
+ #define EIGEN_COLPIVOTINGHOUSEHOLDERQR_LAPACKE_H
36
+
37
+ namespace Eigen {
38
+
39
+ /** \internal Specialization for the data types supported by LAPACKe */
40
+
41
+ #define EIGEN_LAPACKE_QR_COLPIV(EIGTYPE, LAPACKE_TYPE, LAPACKE_PREFIX, EIGCOLROW, LAPACKE_COLROW) \
42
+ template<> template<typename InputType> inline \
43
+ ColPivHouseholderQR<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic> >& \
44
+ ColPivHouseholderQR<Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic> >::compute( \
45
+ const EigenBase<InputType>& matrix) \
46
+ \
47
+ { \
48
+ using std::abs; \
49
+ typedef Matrix<EIGTYPE, Dynamic, Dynamic, EIGCOLROW, Dynamic, Dynamic> MatrixType; \
50
+ typedef MatrixType::RealScalar RealScalar; \
51
+ Index rows = matrix.rows();\
52
+ Index cols = matrix.cols();\
53
+ \
54
+ m_qr = matrix;\
55
+ Index size = m_qr.diagonalSize();\
56
+ m_hCoeffs.resize(size);\
57
+ \
58
+ m_colsTranspositions.resize(cols);\
59
+ /*Index number_of_transpositions = 0;*/ \
60
+ \
61
+ m_nonzero_pivots = 0; \
62
+ m_maxpivot = RealScalar(0);\
63
+ m_colsPermutation.resize(cols); \
64
+ m_colsPermutation.indices().setZero(); \
65
+ \
66
+ lapack_int lda = internal::convert_index<lapack_int,Index>(m_qr.outerStride()); \
67
+ lapack_int matrix_order = LAPACKE_COLROW; \
68
+ LAPACKE_##LAPACKE_PREFIX##geqp3( matrix_order, internal::convert_index<lapack_int,Index>(rows), internal::convert_index<lapack_int,Index>(cols), \
69
+ (LAPACKE_TYPE*)m_qr.data(), lda, (lapack_int*)m_colsPermutation.indices().data(), (LAPACKE_TYPE*)m_hCoeffs.data()); \
70
+ m_isInitialized = true; \
71
+ m_maxpivot=m_qr.diagonal().cwiseAbs().maxCoeff(); \
72
+ m_hCoeffs.adjointInPlace(); \
73
+ RealScalar premultiplied_threshold = abs(m_maxpivot) * threshold(); \
74
+ lapack_int *perm = m_colsPermutation.indices().data(); \
75
+ for(Index i=0;i<size;i++) { \
76
+ m_nonzero_pivots += (abs(m_qr.coeff(i,i)) > premultiplied_threshold);\
77
+ } \
78
+ for(Index i=0;i<cols;i++) perm[i]--;\
79
+ \
80
+ /*m_det_pq = (number_of_transpositions%2) ? -1 : 1; // TODO: It's not needed now; fix upon availability in Eigen */ \
81
+ \
82
+ return *this; \
83
+ }
84
+
85
+ EIGEN_LAPACKE_QR_COLPIV(double, double, d, ColMajor, LAPACK_COL_MAJOR)
86
+ EIGEN_LAPACKE_QR_COLPIV(float, float, s, ColMajor, LAPACK_COL_MAJOR)
87
+ EIGEN_LAPACKE_QR_COLPIV(dcomplex, lapack_complex_double, z, ColMajor, LAPACK_COL_MAJOR)
88
+ EIGEN_LAPACKE_QR_COLPIV(scomplex, lapack_complex_float, c, ColMajor, LAPACK_COL_MAJOR)
89
+
90
+ EIGEN_LAPACKE_QR_COLPIV(double, double, d, RowMajor, LAPACK_ROW_MAJOR)
91
+ EIGEN_LAPACKE_QR_COLPIV(float, float, s, RowMajor, LAPACK_ROW_MAJOR)
92
+ EIGEN_LAPACKE_QR_COLPIV(dcomplex, lapack_complex_double, z, RowMajor, LAPACK_ROW_MAJOR)
93
+ EIGEN_LAPACKE_QR_COLPIV(scomplex, lapack_complex_float, c, RowMajor, LAPACK_ROW_MAJOR)
94
+
95
+ } // end namespace Eigen
96
+
97
+ #endif // EIGEN_COLPIVOTINGHOUSEHOLDERQR_LAPACKE_H
@@ -0,0 +1,562 @@
1
+ // This file is part of Eigen, a lightweight C++ template library
2
+ // for linear algebra.
3
+ //
4
+ // Copyright (C) 2016 Rasmus Munk Larsen <rmlarsen@google.com>
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_COMPLETEORTHOGONALDECOMPOSITION_H
11
+ #define EIGEN_COMPLETEORTHOGONALDECOMPOSITION_H
12
+
13
+ namespace Eigen {
14
+
15
+ namespace internal {
16
+ template <typename _MatrixType>
17
+ struct traits<CompleteOrthogonalDecomposition<_MatrixType> >
18
+ : traits<_MatrixType> {
19
+ enum { Flags = 0 };
20
+ };
21
+
22
+ } // end namespace internal
23
+
24
+ /** \ingroup QR_Module
25
+ *
26
+ * \class CompleteOrthogonalDecomposition
27
+ *
28
+ * \brief Complete orthogonal decomposition (COD) of a matrix.
29
+ *
30
+ * \param MatrixType the type of the matrix of which we are computing the COD.
31
+ *
32
+ * This class performs a rank-revealing complete orthogonal decomposition of a
33
+ * matrix \b A into matrices \b P, \b Q, \b T, and \b Z such that
34
+ * \f[
35
+ * \mathbf{A} \, \mathbf{P} = \mathbf{Q} \,
36
+ * \begin{bmatrix} \mathbf{T} & \mathbf{0} \\
37
+ * \mathbf{0} & \mathbf{0} \end{bmatrix} \, \mathbf{Z}
38
+ * \f]
39
+ * by using Householder transformations. Here, \b P is a permutation matrix,
40
+ * \b Q and \b Z are unitary matrices and \b T an upper triangular matrix of
41
+ * size rank-by-rank. \b A may be rank deficient.
42
+ *
43
+ * This class supports the \link InplaceDecomposition inplace decomposition \endlink mechanism.
44
+ *
45
+ * \sa MatrixBase::completeOrthogonalDecomposition()
46
+ */
47
+ template <typename _MatrixType>
48
+ class CompleteOrthogonalDecomposition {
49
+ public:
50
+ typedef _MatrixType MatrixType;
51
+ enum {
52
+ RowsAtCompileTime = MatrixType::RowsAtCompileTime,
53
+ ColsAtCompileTime = MatrixType::ColsAtCompileTime,
54
+ MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
55
+ MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
56
+ };
57
+ typedef typename MatrixType::Scalar Scalar;
58
+ typedef typename MatrixType::RealScalar RealScalar;
59
+ typedef typename MatrixType::StorageIndex StorageIndex;
60
+ typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
61
+ typedef PermutationMatrix<ColsAtCompileTime, MaxColsAtCompileTime>
62
+ PermutationType;
63
+ typedef typename internal::plain_row_type<MatrixType, Index>::type
64
+ IntRowVectorType;
65
+ typedef typename internal::plain_row_type<MatrixType>::type RowVectorType;
66
+ typedef typename internal::plain_row_type<MatrixType, RealScalar>::type
67
+ RealRowVectorType;
68
+ typedef HouseholderSequence<
69
+ MatrixType, typename internal::remove_all<
70
+ typename HCoeffsType::ConjugateReturnType>::type>
71
+ HouseholderSequenceType;
72
+ typedef typename MatrixType::PlainObject PlainObject;
73
+
74
+ private:
75
+ typedef typename PermutationType::Index PermIndexType;
76
+
77
+ public:
78
+ /**
79
+ * \brief Default Constructor.
80
+ *
81
+ * The default constructor is useful in cases in which the user intends to
82
+ * perform decompositions via
83
+ * \c CompleteOrthogonalDecomposition::compute(const* MatrixType&).
84
+ */
85
+ CompleteOrthogonalDecomposition() : m_cpqr(), m_zCoeffs(), m_temp() {}
86
+
87
+ /** \brief Default Constructor with memory preallocation
88
+ *
89
+ * Like the default constructor but with preallocation of the internal data
90
+ * according to the specified problem \a size.
91
+ * \sa CompleteOrthogonalDecomposition()
92
+ */
93
+ CompleteOrthogonalDecomposition(Index rows, Index cols)
94
+ : m_cpqr(rows, cols), m_zCoeffs((std::min)(rows, cols)), m_temp(cols) {}
95
+
96
+ /** \brief Constructs a complete orthogonal decomposition from a given
97
+ * matrix.
98
+ *
99
+ * This constructor computes the complete orthogonal decomposition of the
100
+ * matrix \a matrix by calling the method compute(). The default
101
+ * threshold for rank determination will be used. It is a short cut for:
102
+ *
103
+ * \code
104
+ * CompleteOrthogonalDecomposition<MatrixType> cod(matrix.rows(),
105
+ * matrix.cols());
106
+ * cod.setThreshold(Default);
107
+ * cod.compute(matrix);
108
+ * \endcode
109
+ *
110
+ * \sa compute()
111
+ */
112
+ template <typename InputType>
113
+ explicit CompleteOrthogonalDecomposition(const EigenBase<InputType>& matrix)
114
+ : m_cpqr(matrix.rows(), matrix.cols()),
115
+ m_zCoeffs((std::min)(matrix.rows(), matrix.cols())),
116
+ m_temp(matrix.cols())
117
+ {
118
+ compute(matrix.derived());
119
+ }
120
+
121
+ /** \brief Constructs a complete orthogonal decomposition from a given matrix
122
+ *
123
+ * This overloaded constructor is provided for \link InplaceDecomposition inplace decomposition \endlink when \c MatrixType is a Eigen::Ref.
124
+ *
125
+ * \sa CompleteOrthogonalDecomposition(const EigenBase&)
126
+ */
127
+ template<typename InputType>
128
+ explicit CompleteOrthogonalDecomposition(EigenBase<InputType>& matrix)
129
+ : m_cpqr(matrix.derived()),
130
+ m_zCoeffs((std::min)(matrix.rows(), matrix.cols())),
131
+ m_temp(matrix.cols())
132
+ {
133
+ computeInPlace();
134
+ }
135
+
136
+
137
+ /** This method computes the minimum-norm solution X to a least squares
138
+ * problem \f[\mathrm{minimize} \|A X - B\|, \f] where \b A is the matrix of
139
+ * which \c *this is the complete orthogonal decomposition.
140
+ *
141
+ * \param b the right-hand sides of the problem to solve.
142
+ *
143
+ * \returns a solution.
144
+ *
145
+ */
146
+ template <typename Rhs>
147
+ inline const Solve<CompleteOrthogonalDecomposition, Rhs> solve(
148
+ const MatrixBase<Rhs>& b) const {
149
+ eigen_assert(m_cpqr.m_isInitialized &&
150
+ "CompleteOrthogonalDecomposition is not initialized.");
151
+ return Solve<CompleteOrthogonalDecomposition, Rhs>(*this, b.derived());
152
+ }
153
+
154
+ HouseholderSequenceType householderQ(void) const;
155
+ HouseholderSequenceType matrixQ(void) const { return m_cpqr.householderQ(); }
156
+
157
+ /** \returns the matrix \b Z.
158
+ */
159
+ MatrixType matrixZ() const {
160
+ MatrixType Z = MatrixType::Identity(m_cpqr.cols(), m_cpqr.cols());
161
+ applyZAdjointOnTheLeftInPlace(Z);
162
+ return Z.adjoint();
163
+ }
164
+
165
+ /** \returns a reference to the matrix where the complete orthogonal
166
+ * decomposition is stored
167
+ */
168
+ const MatrixType& matrixQTZ() const { return m_cpqr.matrixQR(); }
169
+
170
+ /** \returns a reference to the matrix where the complete orthogonal
171
+ * decomposition is stored.
172
+ * \warning The strict lower part and \code cols() - rank() \endcode right
173
+ * columns of this matrix contains internal values.
174
+ * Only the upper triangular part should be referenced. To get it, use
175
+ * \code matrixT().template triangularView<Upper>() \endcode
176
+ * For rank-deficient matrices, use
177
+ * \code
178
+ * matrixR().topLeftCorner(rank(), rank()).template triangularView<Upper>()
179
+ * \endcode
180
+ */
181
+ const MatrixType& matrixT() const { return m_cpqr.matrixQR(); }
182
+
183
+ template <typename InputType>
184
+ CompleteOrthogonalDecomposition& compute(const EigenBase<InputType>& matrix) {
185
+ // Compute the column pivoted QR factorization A P = Q R.
186
+ m_cpqr.compute(matrix);
187
+ computeInPlace();
188
+ return *this;
189
+ }
190
+
191
+ /** \returns a const reference to the column permutation matrix */
192
+ const PermutationType& colsPermutation() const {
193
+ return m_cpqr.colsPermutation();
194
+ }
195
+
196
+ /** \returns the absolute value of the determinant of the matrix of which
197
+ * *this is the complete orthogonal decomposition. It has only linear
198
+ * complexity (that is, O(n) where n is the dimension of the square matrix)
199
+ * as the complete orthogonal decomposition has already been computed.
200
+ *
201
+ * \note This is only for square matrices.
202
+ *
203
+ * \warning a determinant can be very big or small, so for matrices
204
+ * of large enough dimension, there is a risk of overflow/underflow.
205
+ * One way to work around that is to use logAbsDeterminant() instead.
206
+ *
207
+ * \sa logAbsDeterminant(), MatrixBase::determinant()
208
+ */
209
+ typename MatrixType::RealScalar absDeterminant() const;
210
+
211
+ /** \returns the natural log of the absolute value of the determinant of the
212
+ * matrix of which *this is the complete orthogonal decomposition. It has
213
+ * only linear complexity (that is, O(n) where n is the dimension of the
214
+ * square matrix) as the complete orthogonal decomposition has already been
215
+ * computed.
216
+ *
217
+ * \note This is only for square matrices.
218
+ *
219
+ * \note This method is useful to work around the risk of overflow/underflow
220
+ * that's inherent to determinant computation.
221
+ *
222
+ * \sa absDeterminant(), MatrixBase::determinant()
223
+ */
224
+ typename MatrixType::RealScalar logAbsDeterminant() const;
225
+
226
+ /** \returns the rank of the matrix of which *this is the complete orthogonal
227
+ * decomposition.
228
+ *
229
+ * \note This method has to determine which pivots should be considered
230
+ * nonzero. For that, it uses the threshold value that you can control by
231
+ * calling setThreshold(const RealScalar&).
232
+ */
233
+ inline Index rank() const { return m_cpqr.rank(); }
234
+
235
+ /** \returns the dimension of the kernel of the matrix of which *this is the
236
+ * complete orthogonal decomposition.
237
+ *
238
+ * \note This method has to determine which pivots should be considered
239
+ * nonzero. For that, it uses the threshold value that you can control by
240
+ * calling setThreshold(const RealScalar&).
241
+ */
242
+ inline Index dimensionOfKernel() const { return m_cpqr.dimensionOfKernel(); }
243
+
244
+ /** \returns true if the matrix of which *this is the decomposition represents
245
+ * an injective linear map, i.e. has trivial kernel; false otherwise.
246
+ *
247
+ * \note This method has to determine which pivots should be considered
248
+ * nonzero. For that, it uses the threshold value that you can control by
249
+ * calling setThreshold(const RealScalar&).
250
+ */
251
+ inline bool isInjective() const { return m_cpqr.isInjective(); }
252
+
253
+ /** \returns true if the matrix of which *this is the decomposition represents
254
+ * a surjective linear map; false otherwise.
255
+ *
256
+ * \note This method has to determine which pivots should be considered
257
+ * nonzero. For that, it uses the threshold value that you can control by
258
+ * calling setThreshold(const RealScalar&).
259
+ */
260
+ inline bool isSurjective() const { return m_cpqr.isSurjective(); }
261
+
262
+ /** \returns true if the matrix of which *this is the complete orthogonal
263
+ * decomposition is invertible.
264
+ *
265
+ * \note This method has to determine which pivots should be considered
266
+ * nonzero. For that, it uses the threshold value that you can control by
267
+ * calling setThreshold(const RealScalar&).
268
+ */
269
+ inline bool isInvertible() const { return m_cpqr.isInvertible(); }
270
+
271
+ /** \returns the pseudo-inverse of the matrix of which *this is the complete
272
+ * orthogonal decomposition.
273
+ * \warning: Do not compute \c this->pseudoInverse()*rhs to solve a linear systems.
274
+ * It is more efficient and numerically stable to call \c this->solve(rhs).
275
+ */
276
+ inline const Inverse<CompleteOrthogonalDecomposition> pseudoInverse() const
277
+ {
278
+ return Inverse<CompleteOrthogonalDecomposition>(*this);
279
+ }
280
+
281
+ inline Index rows() const { return m_cpqr.rows(); }
282
+ inline Index cols() const { return m_cpqr.cols(); }
283
+
284
+ /** \returns a const reference to the vector of Householder coefficients used
285
+ * to represent the factor \c Q.
286
+ *
287
+ * For advanced uses only.
288
+ */
289
+ inline const HCoeffsType& hCoeffs() const { return m_cpqr.hCoeffs(); }
290
+
291
+ /** \returns a const reference to the vector of Householder coefficients
292
+ * used to represent the factor \c Z.
293
+ *
294
+ * For advanced uses only.
295
+ */
296
+ const HCoeffsType& zCoeffs() const { return m_zCoeffs; }
297
+
298
+ /** Allows to prescribe a threshold to be used by certain methods, such as
299
+ * rank(), who need to determine when pivots are to be considered nonzero.
300
+ * Most be called before calling compute().
301
+ *
302
+ * When it needs to get the threshold value, Eigen calls threshold(). By
303
+ * default, this uses a formula to automatically determine a reasonable
304
+ * threshold. Once you have called the present method
305
+ * setThreshold(const RealScalar&), your value is used instead.
306
+ *
307
+ * \param threshold The new value to use as the threshold.
308
+ *
309
+ * A pivot will be considered nonzero if its absolute value is strictly
310
+ * greater than
311
+ * \f$ \vert pivot \vert \leqslant threshold \times \vert maxpivot \vert \f$
312
+ * where maxpivot is the biggest pivot.
313
+ *
314
+ * If you want to come back to the default behavior, call
315
+ * setThreshold(Default_t)
316
+ */
317
+ CompleteOrthogonalDecomposition& setThreshold(const RealScalar& threshold) {
318
+ m_cpqr.setThreshold(threshold);
319
+ return *this;
320
+ }
321
+
322
+ /** Allows to come back to the default behavior, letting Eigen use its default
323
+ * formula for determining the threshold.
324
+ *
325
+ * You should pass the special object Eigen::Default as parameter here.
326
+ * \code qr.setThreshold(Eigen::Default); \endcode
327
+ *
328
+ * See the documentation of setThreshold(const RealScalar&).
329
+ */
330
+ CompleteOrthogonalDecomposition& setThreshold(Default_t) {
331
+ m_cpqr.setThreshold(Default);
332
+ return *this;
333
+ }
334
+
335
+ /** Returns the threshold that will be used by certain methods such as rank().
336
+ *
337
+ * See the documentation of setThreshold(const RealScalar&).
338
+ */
339
+ RealScalar threshold() const { return m_cpqr.threshold(); }
340
+
341
+ /** \returns the number of nonzero pivots in the complete orthogonal
342
+ * decomposition. Here nonzero is meant in the exact sense, not in a
343
+ * fuzzy sense. So that notion isn't really intrinsically interesting,
344
+ * but it is still useful when implementing algorithms.
345
+ *
346
+ * \sa rank()
347
+ */
348
+ inline Index nonzeroPivots() const { return m_cpqr.nonzeroPivots(); }
349
+
350
+ /** \returns the absolute value of the biggest pivot, i.e. the biggest
351
+ * diagonal coefficient of R.
352
+ */
353
+ inline RealScalar maxPivot() const { return m_cpqr.maxPivot(); }
354
+
355
+ /** \brief Reports whether the complete orthogonal decomposition was
356
+ * succesful.
357
+ *
358
+ * \note This function always returns \c Success. It is provided for
359
+ * compatibility
360
+ * with other factorization routines.
361
+ * \returns \c Success
362
+ */
363
+ ComputationInfo info() const {
364
+ eigen_assert(m_cpqr.m_isInitialized && "Decomposition is not initialized.");
365
+ return Success;
366
+ }
367
+
368
+ #ifndef EIGEN_PARSED_BY_DOXYGEN
369
+ template <typename RhsType, typename DstType>
370
+ EIGEN_DEVICE_FUNC void _solve_impl(const RhsType& rhs, DstType& dst) const;
371
+ #endif
372
+
373
+ protected:
374
+ static void check_template_parameters() {
375
+ EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
376
+ }
377
+
378
+ void computeInPlace();
379
+
380
+ /** Overwrites \b rhs with \f$ \mathbf{Z}^* * \mathbf{rhs} \f$.
381
+ */
382
+ template <typename Rhs>
383
+ void applyZAdjointOnTheLeftInPlace(Rhs& rhs) const;
384
+
385
+ ColPivHouseholderQR<MatrixType> m_cpqr;
386
+ HCoeffsType m_zCoeffs;
387
+ RowVectorType m_temp;
388
+ };
389
+
390
+ template <typename MatrixType>
391
+ typename MatrixType::RealScalar
392
+ CompleteOrthogonalDecomposition<MatrixType>::absDeterminant() const {
393
+ return m_cpqr.absDeterminant();
394
+ }
395
+
396
+ template <typename MatrixType>
397
+ typename MatrixType::RealScalar
398
+ CompleteOrthogonalDecomposition<MatrixType>::logAbsDeterminant() const {
399
+ return m_cpqr.logAbsDeterminant();
400
+ }
401
+
402
+ /** Performs the complete orthogonal decomposition of the given matrix \a
403
+ * matrix. The result of the factorization is stored into \c *this, and a
404
+ * reference to \c *this is returned.
405
+ *
406
+ * \sa class CompleteOrthogonalDecomposition,
407
+ * CompleteOrthogonalDecomposition(const MatrixType&)
408
+ */
409
+ template <typename MatrixType>
410
+ void CompleteOrthogonalDecomposition<MatrixType>::computeInPlace()
411
+ {
412
+ check_template_parameters();
413
+
414
+ // the column permutation is stored as int indices, so just to be sure:
415
+ eigen_assert(m_cpqr.cols() <= NumTraits<int>::highest());
416
+
417
+ const Index rank = m_cpqr.rank();
418
+ const Index cols = m_cpqr.cols();
419
+ const Index rows = m_cpqr.rows();
420
+ m_zCoeffs.resize((std::min)(rows, cols));
421
+ m_temp.resize(cols);
422
+
423
+ if (rank < cols) {
424
+ // We have reduced the (permuted) matrix to the form
425
+ // [R11 R12]
426
+ // [ 0 R22]
427
+ // where R11 is r-by-r (r = rank) upper triangular, R12 is
428
+ // r-by-(n-r), and R22 is empty or the norm of R22 is negligible.
429
+ // We now compute the complete orthogonal decomposition by applying
430
+ // Householder transformations from the right to the upper trapezoidal
431
+ // matrix X = [R11 R12] to zero out R12 and obtain the factorization
432
+ // [R11 R12] = [T11 0] * Z, where T11 is r-by-r upper triangular and
433
+ // Z = Z(0) * Z(1) ... Z(r-1) is an n-by-n orthogonal matrix.
434
+ // We store the data representing Z in R12 and m_zCoeffs.
435
+ for (Index k = rank - 1; k >= 0; --k) {
436
+ if (k != rank - 1) {
437
+ // Given the API for Householder reflectors, it is more convenient if
438
+ // we swap the leading parts of columns k and r-1 (zero-based) to form
439
+ // the matrix X_k = [X(0:k, k), X(0:k, r:n)]
440
+ m_cpqr.m_qr.col(k).head(k + 1).swap(
441
+ m_cpqr.m_qr.col(rank - 1).head(k + 1));
442
+ }
443
+ // Construct Householder reflector Z(k) to zero out the last row of X_k,
444
+ // i.e. choose Z(k) such that
445
+ // [X(k, k), X(k, r:n)] * Z(k) = [beta, 0, .., 0].
446
+ RealScalar beta;
447
+ m_cpqr.m_qr.row(k)
448
+ .tail(cols - rank + 1)
449
+ .makeHouseholderInPlace(m_zCoeffs(k), beta);
450
+ m_cpqr.m_qr(k, rank - 1) = beta;
451
+ if (k > 0) {
452
+ // Apply Z(k) to the first k rows of X_k
453
+ m_cpqr.m_qr.topRightCorner(k, cols - rank + 1)
454
+ .applyHouseholderOnTheRight(
455
+ m_cpqr.m_qr.row(k).tail(cols - rank).transpose(), m_zCoeffs(k),
456
+ &m_temp(0));
457
+ }
458
+ if (k != rank - 1) {
459
+ // Swap X(0:k,k) back to its proper location.
460
+ m_cpqr.m_qr.col(k).head(k + 1).swap(
461
+ m_cpqr.m_qr.col(rank - 1).head(k + 1));
462
+ }
463
+ }
464
+ }
465
+ }
466
+
467
+ template <typename MatrixType>
468
+ template <typename Rhs>
469
+ void CompleteOrthogonalDecomposition<MatrixType>::applyZAdjointOnTheLeftInPlace(
470
+ Rhs& rhs) const {
471
+ const Index cols = this->cols();
472
+ const Index nrhs = rhs.cols();
473
+ const Index rank = this->rank();
474
+ Matrix<typename MatrixType::Scalar, Dynamic, 1> temp((std::max)(cols, nrhs));
475
+ for (Index k = 0; k < rank; ++k) {
476
+ if (k != rank - 1) {
477
+ rhs.row(k).swap(rhs.row(rank - 1));
478
+ }
479
+ rhs.middleRows(rank - 1, cols - rank + 1)
480
+ .applyHouseholderOnTheLeft(
481
+ matrixQTZ().row(k).tail(cols - rank).adjoint(), zCoeffs()(k),
482
+ &temp(0));
483
+ if (k != rank - 1) {
484
+ rhs.row(k).swap(rhs.row(rank - 1));
485
+ }
486
+ }
487
+ }
488
+
489
+ #ifndef EIGEN_PARSED_BY_DOXYGEN
490
+ template <typename _MatrixType>
491
+ template <typename RhsType, typename DstType>
492
+ void CompleteOrthogonalDecomposition<_MatrixType>::_solve_impl(
493
+ const RhsType& rhs, DstType& dst) const {
494
+ eigen_assert(rhs.rows() == this->rows());
495
+
496
+ const Index rank = this->rank();
497
+ if (rank == 0) {
498
+ dst.setZero();
499
+ return;
500
+ }
501
+
502
+ // Compute c = Q^* * rhs
503
+ // Note that the matrix Q = H_0^* H_1^*... so its inverse is
504
+ // Q^* = (H_0 H_1 ...)^T
505
+ typename RhsType::PlainObject c(rhs);
506
+ c.applyOnTheLeft(
507
+ householderSequence(matrixQTZ(), hCoeffs()).setLength(rank).transpose());
508
+
509
+ // Solve T z = c(1:rank, :)
510
+ dst.topRows(rank) = matrixT()
511
+ .topLeftCorner(rank, rank)
512
+ .template triangularView<Upper>()
513
+ .solve(c.topRows(rank));
514
+
515
+ const Index cols = this->cols();
516
+ if (rank < cols) {
517
+ // Compute y = Z^* * [ z ]
518
+ // [ 0 ]
519
+ dst.bottomRows(cols - rank).setZero();
520
+ applyZAdjointOnTheLeftInPlace(dst);
521
+ }
522
+
523
+ // Undo permutation to get x = P^{-1} * y.
524
+ dst = colsPermutation() * dst;
525
+ }
526
+ #endif
527
+
528
+ namespace internal {
529
+
530
+ template<typename DstXprType, typename MatrixType>
531
+ struct Assignment<DstXprType, Inverse<CompleteOrthogonalDecomposition<MatrixType> >, internal::assign_op<typename DstXprType::Scalar,typename CompleteOrthogonalDecomposition<MatrixType>::Scalar>, Dense2Dense>
532
+ {
533
+ typedef CompleteOrthogonalDecomposition<MatrixType> CodType;
534
+ typedef Inverse<CodType> SrcXprType;
535
+ static void run(DstXprType &dst, const SrcXprType &src, const internal::assign_op<typename DstXprType::Scalar,typename CodType::Scalar> &)
536
+ {
537
+ dst = src.nestedExpression().solve(MatrixType::Identity(src.rows(), src.rows()));
538
+ }
539
+ };
540
+
541
+ } // end namespace internal
542
+
543
+ /** \returns the matrix Q as a sequence of householder transformations */
544
+ template <typename MatrixType>
545
+ typename CompleteOrthogonalDecomposition<MatrixType>::HouseholderSequenceType
546
+ CompleteOrthogonalDecomposition<MatrixType>::householderQ() const {
547
+ return m_cpqr.householderQ();
548
+ }
549
+
550
+ /** \return the complete orthogonal decomposition of \c *this.
551
+ *
552
+ * \sa class CompleteOrthogonalDecomposition
553
+ */
554
+ template <typename Derived>
555
+ const CompleteOrthogonalDecomposition<typename MatrixBase<Derived>::PlainObject>
556
+ MatrixBase<Derived>::completeOrthogonalDecomposition() const {
557
+ return CompleteOrthogonalDecomposition<PlainObject>(eval());
558
+ }
559
+
560
+ } // end namespace Eigen
561
+
562
+ #endif // EIGEN_COMPLETEORTHOGONALDECOMPOSITION_H