tomoto 0.1.0
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- checksums.yaml +7 -0
- data/CHANGELOG.md +3 -0
- data/LICENSE.txt +22 -0
- data/README.md +123 -0
- data/ext/tomoto/ext.cpp +245 -0
- data/ext/tomoto/extconf.rb +28 -0
- data/lib/tomoto.rb +12 -0
- data/lib/tomoto/ct.rb +11 -0
- data/lib/tomoto/hdp.rb +11 -0
- data/lib/tomoto/lda.rb +67 -0
- data/lib/tomoto/version.rb +3 -0
- data/vendor/EigenRand/EigenRand/Core.h +1139 -0
- data/vendor/EigenRand/EigenRand/Dists/Basic.h +111 -0
- data/vendor/EigenRand/EigenRand/Dists/Discrete.h +877 -0
- data/vendor/EigenRand/EigenRand/Dists/GammaPoisson.h +108 -0
- data/vendor/EigenRand/EigenRand/Dists/NormalExp.h +626 -0
- data/vendor/EigenRand/EigenRand/EigenRand +19 -0
- data/vendor/EigenRand/EigenRand/Macro.h +24 -0
- data/vendor/EigenRand/EigenRand/MorePacketMath.h +978 -0
- data/vendor/EigenRand/EigenRand/PacketFilter.h +286 -0
- data/vendor/EigenRand/EigenRand/PacketRandomEngine.h +624 -0
- data/vendor/EigenRand/EigenRand/RandUtils.h +413 -0
- data/vendor/EigenRand/EigenRand/doc.h +220 -0
- data/vendor/EigenRand/LICENSE +21 -0
- data/vendor/EigenRand/README.md +288 -0
- data/vendor/eigen/COPYING.BSD +26 -0
- data/vendor/eigen/COPYING.GPL +674 -0
- data/vendor/eigen/COPYING.LGPL +502 -0
- data/vendor/eigen/COPYING.MINPACK +52 -0
- data/vendor/eigen/COPYING.MPL2 +373 -0
- data/vendor/eigen/COPYING.README +18 -0
- data/vendor/eigen/Eigen/CMakeLists.txt +19 -0
- data/vendor/eigen/Eigen/Cholesky +46 -0
- data/vendor/eigen/Eigen/CholmodSupport +48 -0
- data/vendor/eigen/Eigen/Core +537 -0
- data/vendor/eigen/Eigen/Dense +7 -0
- data/vendor/eigen/Eigen/Eigen +2 -0
- data/vendor/eigen/Eigen/Eigenvalues +61 -0
- data/vendor/eigen/Eigen/Geometry +62 -0
- data/vendor/eigen/Eigen/Householder +30 -0
- data/vendor/eigen/Eigen/IterativeLinearSolvers +48 -0
- data/vendor/eigen/Eigen/Jacobi +33 -0
- data/vendor/eigen/Eigen/LU +50 -0
- data/vendor/eigen/Eigen/MetisSupport +35 -0
- data/vendor/eigen/Eigen/OrderingMethods +73 -0
- data/vendor/eigen/Eigen/PaStiXSupport +48 -0
- data/vendor/eigen/Eigen/PardisoSupport +35 -0
- data/vendor/eigen/Eigen/QR +51 -0
- data/vendor/eigen/Eigen/QtAlignedMalloc +40 -0
- data/vendor/eigen/Eigen/SPQRSupport +34 -0
- data/vendor/eigen/Eigen/SVD +51 -0
- data/vendor/eigen/Eigen/Sparse +36 -0
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- data/vendor/eigen/Eigen/SparseCore +69 -0
- data/vendor/eigen/Eigen/SparseLU +46 -0
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- data/vendor/eigen/Eigen/SuperLUSupport +64 -0
- data/vendor/eigen/Eigen/UmfPackSupport +40 -0
- data/vendor/eigen/Eigen/src/Cholesky/LDLT.h +673 -0
- data/vendor/eigen/Eigen/src/Cholesky/LLT.h +542 -0
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- data/vendor/eigen/Eigen/src/CholmodSupport/CholmodSupport.h +639 -0
- data/vendor/eigen/Eigen/src/Core/Array.h +329 -0
- data/vendor/eigen/Eigen/src/Core/ArrayBase.h +226 -0
- data/vendor/eigen/Eigen/src/Core/ArrayWrapper.h +209 -0
- data/vendor/eigen/Eigen/src/Core/Assign.h +90 -0
- data/vendor/eigen/Eigen/src/Core/AssignEvaluator.h +935 -0
- data/vendor/eigen/Eigen/src/Core/Assign_MKL.h +178 -0
- data/vendor/eigen/Eigen/src/Core/BandMatrix.h +353 -0
- data/vendor/eigen/Eigen/src/Core/Block.h +452 -0
- data/vendor/eigen/Eigen/src/Core/BooleanRedux.h +164 -0
- data/vendor/eigen/Eigen/src/Core/CommaInitializer.h +160 -0
- data/vendor/eigen/Eigen/src/Core/ConditionEstimator.h +175 -0
- data/vendor/eigen/Eigen/src/Core/CoreEvaluators.h +1688 -0
- data/vendor/eigen/Eigen/src/Core/CoreIterators.h +127 -0
- data/vendor/eigen/Eigen/src/Core/CwiseBinaryOp.h +184 -0
- data/vendor/eigen/Eigen/src/Core/CwiseNullaryOp.h +866 -0
- data/vendor/eigen/Eigen/src/Core/CwiseTernaryOp.h +197 -0
- data/vendor/eigen/Eigen/src/Core/CwiseUnaryOp.h +103 -0
- data/vendor/eigen/Eigen/src/Core/CwiseUnaryView.h +128 -0
- data/vendor/eigen/Eigen/src/Core/DenseBase.h +611 -0
- data/vendor/eigen/Eigen/src/Core/DenseCoeffsBase.h +681 -0
- data/vendor/eigen/Eigen/src/Core/DenseStorage.h +570 -0
- data/vendor/eigen/Eigen/src/Core/Diagonal.h +260 -0
- data/vendor/eigen/Eigen/src/Core/DiagonalMatrix.h +343 -0
- data/vendor/eigen/Eigen/src/Core/DiagonalProduct.h +28 -0
- data/vendor/eigen/Eigen/src/Core/Dot.h +318 -0
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- data/vendor/eigen/Eigen/src/Core/GeneralProduct.h +455 -0
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- data/vendor/eigen/Eigen/src/Core/Random.h +182 -0
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- data/vendor/eigen/Eigen/src/Core/Select.h +162 -0
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- data/vendor/eigen/Eigen/src/Core/Stride.h +111 -0
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- data/vendor/eigen/Eigen/src/Core/Transpose.h +403 -0
- data/vendor/eigen/Eigen/src/Core/Transpositions.h +407 -0
- data/vendor/eigen/Eigen/src/Core/TriangularMatrix.h +983 -0
- data/vendor/eigen/Eigen/src/Core/VectorBlock.h +96 -0
- data/vendor/eigen/Eigen/src/Core/VectorwiseOp.h +695 -0
- data/vendor/eigen/Eigen/src/Core/Visitor.h +273 -0
- data/vendor/eigen/Eigen/src/Core/arch/AVX/Complex.h +451 -0
- data/vendor/eigen/Eigen/src/Core/arch/AVX/MathFunctions.h +439 -0
- data/vendor/eigen/Eigen/src/Core/arch/AVX/PacketMath.h +637 -0
- data/vendor/eigen/Eigen/src/Core/arch/AVX/TypeCasting.h +51 -0
- data/vendor/eigen/Eigen/src/Core/arch/AVX512/MathFunctions.h +391 -0
- data/vendor/eigen/Eigen/src/Core/arch/AVX512/PacketMath.h +1316 -0
- data/vendor/eigen/Eigen/src/Core/arch/AltiVec/Complex.h +430 -0
- data/vendor/eigen/Eigen/src/Core/arch/AltiVec/MathFunctions.h +322 -0
- data/vendor/eigen/Eigen/src/Core/arch/AltiVec/PacketMath.h +1061 -0
- data/vendor/eigen/Eigen/src/Core/arch/CUDA/Complex.h +103 -0
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- data/vendor/eigen/Eigen/src/Core/arch/CUDA/MathFunctions.h +91 -0
- data/vendor/eigen/Eigen/src/Core/arch/CUDA/PacketMath.h +333 -0
- data/vendor/eigen/Eigen/src/Core/arch/CUDA/PacketMathHalf.h +1124 -0
- data/vendor/eigen/Eigen/src/Core/arch/CUDA/TypeCasting.h +212 -0
- data/vendor/eigen/Eigen/src/Core/arch/Default/ConjHelper.h +29 -0
- data/vendor/eigen/Eigen/src/Core/arch/Default/Settings.h +49 -0
- data/vendor/eigen/Eigen/src/Core/arch/NEON/Complex.h +490 -0
- data/vendor/eigen/Eigen/src/Core/arch/NEON/MathFunctions.h +91 -0
- data/vendor/eigen/Eigen/src/Core/arch/NEON/PacketMath.h +760 -0
- data/vendor/eigen/Eigen/src/Core/arch/SSE/Complex.h +471 -0
- data/vendor/eigen/Eigen/src/Core/arch/SSE/MathFunctions.h +562 -0
- data/vendor/eigen/Eigen/src/Core/arch/SSE/PacketMath.h +895 -0
- data/vendor/eigen/Eigen/src/Core/arch/SSE/TypeCasting.h +77 -0
- data/vendor/eigen/Eigen/src/Core/arch/ZVector/Complex.h +397 -0
- data/vendor/eigen/Eigen/src/Core/arch/ZVector/MathFunctions.h +137 -0
- data/vendor/eigen/Eigen/src/Core/arch/ZVector/PacketMath.h +945 -0
- data/vendor/eigen/Eigen/src/Core/functors/AssignmentFunctors.h +168 -0
- data/vendor/eigen/Eigen/src/Core/functors/BinaryFunctors.h +475 -0
- data/vendor/eigen/Eigen/src/Core/functors/NullaryFunctors.h +188 -0
- data/vendor/eigen/Eigen/src/Core/functors/StlFunctors.h +136 -0
- data/vendor/eigen/Eigen/src/Core/functors/TernaryFunctors.h +25 -0
- data/vendor/eigen/Eigen/src/Core/functors/UnaryFunctors.h +792 -0
- data/vendor/eigen/Eigen/src/Core/products/GeneralBlockPanelKernel.h +2156 -0
- data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrix.h +492 -0
- data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h +311 -0
- data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h +145 -0
- data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h +122 -0
- data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixVector.h +619 -0
- data/vendor/eigen/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h +136 -0
- data/vendor/eigen/Eigen/src/Core/products/Parallelizer.h +163 -0
- data/vendor/eigen/Eigen/src/Core/products/SelfadjointMatrixMatrix.h +521 -0
- data/vendor/eigen/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h +287 -0
- data/vendor/eigen/Eigen/src/Core/products/SelfadjointMatrixVector.h +260 -0
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- data/vendor/eigen/Eigen/src/Core/products/SelfadjointProduct.h +133 -0
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- data/vendor/eigen/Eigen/src/Core/products/TriangularMatrixMatrix.h +466 -0
- data/vendor/eigen/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h +315 -0
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- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h +107 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h +280 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h +126 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_kernel_bmod.h +130 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_panel_bmod.h +223 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_panel_dfs.h +258 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_pivotL.h +137 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_pruneL.h +136 -0
- data/vendor/eigen/Eigen/src/SparseLU/SparseLU_relax_snode.h +83 -0
- data/vendor/eigen/Eigen/src/SparseQR/SparseQR.h +745 -0
- data/vendor/eigen/Eigen/src/StlSupport/StdDeque.h +126 -0
- data/vendor/eigen/Eigen/src/StlSupport/StdList.h +106 -0
- data/vendor/eigen/Eigen/src/StlSupport/StdVector.h +131 -0
- data/vendor/eigen/Eigen/src/StlSupport/details.h +84 -0
- data/vendor/eigen/Eigen/src/SuperLUSupport/SuperLUSupport.h +1027 -0
- data/vendor/eigen/Eigen/src/UmfPackSupport/UmfPackSupport.h +506 -0
- data/vendor/eigen/Eigen/src/misc/Image.h +82 -0
- data/vendor/eigen/Eigen/src/misc/Kernel.h +79 -0
- data/vendor/eigen/Eigen/src/misc/RealSvd2x2.h +55 -0
- data/vendor/eigen/Eigen/src/misc/blas.h +440 -0
- data/vendor/eigen/Eigen/src/misc/lapack.h +152 -0
- data/vendor/eigen/Eigen/src/misc/lapacke.h +16291 -0
- data/vendor/eigen/Eigen/src/misc/lapacke_mangling.h +17 -0
- data/vendor/eigen/Eigen/src/plugins/ArrayCwiseBinaryOps.h +332 -0
- data/vendor/eigen/Eigen/src/plugins/ArrayCwiseUnaryOps.h +552 -0
- data/vendor/eigen/Eigen/src/plugins/BlockMethods.h +1058 -0
- data/vendor/eigen/Eigen/src/plugins/CommonCwiseBinaryOps.h +115 -0
- data/vendor/eigen/Eigen/src/plugins/CommonCwiseUnaryOps.h +163 -0
- data/vendor/eigen/Eigen/src/plugins/MatrixCwiseBinaryOps.h +152 -0
- data/vendor/eigen/Eigen/src/plugins/MatrixCwiseUnaryOps.h +85 -0
- data/vendor/eigen/README.md +3 -0
- data/vendor/eigen/bench/README.txt +55 -0
- data/vendor/eigen/bench/btl/COPYING +340 -0
- data/vendor/eigen/bench/btl/README +154 -0
- data/vendor/eigen/bench/tensors/README +21 -0
- data/vendor/eigen/blas/README.txt +6 -0
- data/vendor/eigen/demos/mandelbrot/README +10 -0
- data/vendor/eigen/demos/mix_eigen_and_c/README +9 -0
- data/vendor/eigen/demos/opengl/README +13 -0
- data/vendor/eigen/unsupported/Eigen/CXX11/src/Tensor/README.md +1760 -0
- data/vendor/eigen/unsupported/README.txt +50 -0
- data/vendor/tomotopy/LICENSE +21 -0
- data/vendor/tomotopy/README.kr.rst +375 -0
- data/vendor/tomotopy/README.rst +382 -0
- data/vendor/tomotopy/src/Labeling/FoRelevance.cpp +362 -0
- data/vendor/tomotopy/src/Labeling/FoRelevance.h +88 -0
- data/vendor/tomotopy/src/Labeling/Labeler.h +50 -0
- data/vendor/tomotopy/src/TopicModel/CT.h +37 -0
- data/vendor/tomotopy/src/TopicModel/CTModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/CTModel.hpp +293 -0
- data/vendor/tomotopy/src/TopicModel/DMR.h +51 -0
- data/vendor/tomotopy/src/TopicModel/DMRModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/DMRModel.hpp +374 -0
- data/vendor/tomotopy/src/TopicModel/DT.h +65 -0
- data/vendor/tomotopy/src/TopicModel/DTM.h +22 -0
- data/vendor/tomotopy/src/TopicModel/DTModel.cpp +15 -0
- data/vendor/tomotopy/src/TopicModel/DTModel.hpp +572 -0
- data/vendor/tomotopy/src/TopicModel/GDMR.h +37 -0
- data/vendor/tomotopy/src/TopicModel/GDMRModel.cpp +14 -0
- data/vendor/tomotopy/src/TopicModel/GDMRModel.hpp +485 -0
- data/vendor/tomotopy/src/TopicModel/HDP.h +74 -0
- data/vendor/tomotopy/src/TopicModel/HDPModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/HDPModel.hpp +592 -0
- data/vendor/tomotopy/src/TopicModel/HLDA.h +40 -0
- data/vendor/tomotopy/src/TopicModel/HLDAModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/HLDAModel.hpp +681 -0
- data/vendor/tomotopy/src/TopicModel/HPA.h +27 -0
- data/vendor/tomotopy/src/TopicModel/HPAModel.cpp +21 -0
- data/vendor/tomotopy/src/TopicModel/HPAModel.hpp +588 -0
- data/vendor/tomotopy/src/TopicModel/LDA.h +144 -0
- data/vendor/tomotopy/src/TopicModel/LDACVB0Model.hpp +442 -0
- data/vendor/tomotopy/src/TopicModel/LDAModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/LDAModel.hpp +1058 -0
- data/vendor/tomotopy/src/TopicModel/LLDA.h +45 -0
- data/vendor/tomotopy/src/TopicModel/LLDAModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/LLDAModel.hpp +203 -0
- data/vendor/tomotopy/src/TopicModel/MGLDA.h +63 -0
- data/vendor/tomotopy/src/TopicModel/MGLDAModel.cpp +17 -0
- data/vendor/tomotopy/src/TopicModel/MGLDAModel.hpp +558 -0
- data/vendor/tomotopy/src/TopicModel/PA.h +43 -0
- data/vendor/tomotopy/src/TopicModel/PAModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/PAModel.hpp +467 -0
- data/vendor/tomotopy/src/TopicModel/PLDA.h +17 -0
- data/vendor/tomotopy/src/TopicModel/PLDAModel.cpp +13 -0
- data/vendor/tomotopy/src/TopicModel/PLDAModel.hpp +214 -0
- data/vendor/tomotopy/src/TopicModel/SLDA.h +54 -0
- data/vendor/tomotopy/src/TopicModel/SLDAModel.cpp +17 -0
- data/vendor/tomotopy/src/TopicModel/SLDAModel.hpp +456 -0
- data/vendor/tomotopy/src/TopicModel/TopicModel.hpp +692 -0
- data/vendor/tomotopy/src/Utils/AliasMethod.hpp +169 -0
- data/vendor/tomotopy/src/Utils/Dictionary.h +80 -0
- data/vendor/tomotopy/src/Utils/EigenAddonOps.hpp +181 -0
- data/vendor/tomotopy/src/Utils/LBFGS.h +202 -0
- data/vendor/tomotopy/src/Utils/LBFGS/LineSearchBacktracking.h +120 -0
- data/vendor/tomotopy/src/Utils/LBFGS/LineSearchBracketing.h +122 -0
- data/vendor/tomotopy/src/Utils/LBFGS/Param.h +213 -0
- data/vendor/tomotopy/src/Utils/LUT.hpp +82 -0
- data/vendor/tomotopy/src/Utils/MultiNormalDistribution.hpp +69 -0
- data/vendor/tomotopy/src/Utils/PolyaGamma.hpp +200 -0
- data/vendor/tomotopy/src/Utils/PolyaGammaHybrid.hpp +672 -0
- data/vendor/tomotopy/src/Utils/ThreadPool.hpp +150 -0
- data/vendor/tomotopy/src/Utils/Trie.hpp +220 -0
- data/vendor/tomotopy/src/Utils/TruncMultiNormal.hpp +94 -0
- data/vendor/tomotopy/src/Utils/Utils.hpp +337 -0
- data/vendor/tomotopy/src/Utils/avx_gamma.h +46 -0
- data/vendor/tomotopy/src/Utils/avx_mathfun.h +736 -0
- data/vendor/tomotopy/src/Utils/exception.h +28 -0
- data/vendor/tomotopy/src/Utils/math.h +281 -0
- data/vendor/tomotopy/src/Utils/rtnorm.hpp +2690 -0
- data/vendor/tomotopy/src/Utils/sample.hpp +192 -0
- data/vendor/tomotopy/src/Utils/serializer.hpp +695 -0
- data/vendor/tomotopy/src/Utils/slp.hpp +131 -0
- data/vendor/tomotopy/src/Utils/sse_gamma.h +48 -0
- data/vendor/tomotopy/src/Utils/sse_mathfun.h +710 -0
- data/vendor/tomotopy/src/Utils/text.hpp +49 -0
- data/vendor/tomotopy/src/Utils/tvector.hpp +543 -0
- metadata +531 -0
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// This file is part of Eigen, a lightweight C++ template library
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// for linear algebra.
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//
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// Copyright (C) 2008-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
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//
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// This Source Code Form is subject to the terms of the Mozilla
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// Public License v. 2.0. If a copy of the MPL was not distributed
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// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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#ifndef EIGEN_COMPRESSED_STORAGE_H
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#define EIGEN_COMPRESSED_STORAGE_H
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namespace Eigen {
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namespace internal {
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/** \internal
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* Stores a sparse set of values as a list of values and a list of indices.
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*
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*/
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template<typename _Scalar,typename _StorageIndex>
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class CompressedStorage
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{
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public:
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typedef _Scalar Scalar;
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typedef _StorageIndex StorageIndex;
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protected:
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typedef typename NumTraits<Scalar>::Real RealScalar;
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public:
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CompressedStorage()
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: m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
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{}
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explicit CompressedStorage(Index size)
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: m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
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{
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resize(size);
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}
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CompressedStorage(const CompressedStorage& other)
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: m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
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{
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*this = other;
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}
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CompressedStorage& operator=(const CompressedStorage& other)
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{
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resize(other.size());
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if(other.size()>0)
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{
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internal::smart_copy(other.m_values, other.m_values + m_size, m_values);
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internal::smart_copy(other.m_indices, other.m_indices + m_size, m_indices);
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}
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return *this;
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}
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void swap(CompressedStorage& other)
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{
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std::swap(m_values, other.m_values);
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std::swap(m_indices, other.m_indices);
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std::swap(m_size, other.m_size);
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std::swap(m_allocatedSize, other.m_allocatedSize);
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}
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~CompressedStorage()
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{
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delete[] m_values;
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delete[] m_indices;
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}
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void reserve(Index size)
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{
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Index newAllocatedSize = m_size + size;
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if (newAllocatedSize > m_allocatedSize)
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reallocate(newAllocatedSize);
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}
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void squeeze()
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{
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if (m_allocatedSize>m_size)
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reallocate(m_size);
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}
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void resize(Index size, double reserveSizeFactor = 0)
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{
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if (m_allocatedSize<size)
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{
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Index realloc_size = (std::min<Index>)(NumTraits<StorageIndex>::highest(), size + Index(reserveSizeFactor*double(size)));
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if(realloc_size<size)
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internal::throw_std_bad_alloc();
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reallocate(realloc_size);
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}
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m_size = size;
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}
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void append(const Scalar& v, Index i)
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{
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Index id = m_size;
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resize(m_size+1, 1);
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m_values[id] = v;
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m_indices[id] = internal::convert_index<StorageIndex>(i);
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}
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inline Index size() const { return m_size; }
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inline Index allocatedSize() const { return m_allocatedSize; }
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inline void clear() { m_size = 0; }
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const Scalar* valuePtr() const { return m_values; }
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Scalar* valuePtr() { return m_values; }
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const StorageIndex* indexPtr() const { return m_indices; }
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StorageIndex* indexPtr() { return m_indices; }
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inline Scalar& value(Index i) { eigen_internal_assert(m_values!=0); return m_values[i]; }
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inline const Scalar& value(Index i) const { eigen_internal_assert(m_values!=0); return m_values[i]; }
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inline StorageIndex& index(Index i) { eigen_internal_assert(m_indices!=0); return m_indices[i]; }
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inline const StorageIndex& index(Index i) const { eigen_internal_assert(m_indices!=0); return m_indices[i]; }
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/** \returns the largest \c k such that for all \c j in [0,k) index[\c j]\<\a key */
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inline Index searchLowerIndex(Index key) const
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{
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return searchLowerIndex(0, m_size, key);
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}
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/** \returns the largest \c k in [start,end) such that for all \c j in [start,k) index[\c j]\<\a key */
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inline Index searchLowerIndex(Index start, Index end, Index key) const
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{
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while(end>start)
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{
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Index mid = (end+start)>>1;
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if (m_indices[mid]<key)
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start = mid+1;
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else
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end = mid;
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}
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return start;
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}
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/** \returns the stored value at index \a key
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* If the value does not exist, then the value \a defaultValue is returned without any insertion. */
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inline Scalar at(Index key, const Scalar& defaultValue = Scalar(0)) const
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{
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if (m_size==0)
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return defaultValue;
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else if (key==m_indices[m_size-1])
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return m_values[m_size-1];
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// ^^ optimization: let's first check if it is the last coefficient
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// (very common in high level algorithms)
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const Index id = searchLowerIndex(0,m_size-1,key);
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return ((id<m_size) && (m_indices[id]==key)) ? m_values[id] : defaultValue;
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}
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/** Like at(), but the search is performed in the range [start,end) */
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inline Scalar atInRange(Index start, Index end, Index key, const Scalar &defaultValue = Scalar(0)) const
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{
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if (start>=end)
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return defaultValue;
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else if (end>start && key==m_indices[end-1])
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return m_values[end-1];
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// ^^ optimization: let's first check if it is the last coefficient
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// (very common in high level algorithms)
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const Index id = searchLowerIndex(start,end-1,key);
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return ((id<end) && (m_indices[id]==key)) ? m_values[id] : defaultValue;
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}
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/** \returns a reference to the value at index \a key
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* If the value does not exist, then the value \a defaultValue is inserted
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* such that the keys are sorted. */
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inline Scalar& atWithInsertion(Index key, const Scalar& defaultValue = Scalar(0))
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{
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Index id = searchLowerIndex(0,m_size,key);
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if (id>=m_size || m_indices[id]!=key)
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{
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if (m_allocatedSize<m_size+1)
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{
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m_allocatedSize = 2*(m_size+1);
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internal::scoped_array<Scalar> newValues(m_allocatedSize);
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internal::scoped_array<StorageIndex> newIndices(m_allocatedSize);
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// copy first chunk
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internal::smart_copy(m_values, m_values +id, newValues.ptr());
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internal::smart_copy(m_indices, m_indices+id, newIndices.ptr());
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// copy the rest
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if(m_size>id)
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{
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internal::smart_copy(m_values +id, m_values +m_size, newValues.ptr() +id+1);
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internal::smart_copy(m_indices+id, m_indices+m_size, newIndices.ptr()+id+1);
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}
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std::swap(m_values,newValues.ptr());
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std::swap(m_indices,newIndices.ptr());
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}
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else if(m_size>id)
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{
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internal::smart_memmove(m_values +id, m_values +m_size, m_values +id+1);
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internal::smart_memmove(m_indices+id, m_indices+m_size, m_indices+id+1);
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}
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m_size++;
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m_indices[id] = internal::convert_index<StorageIndex>(key);
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m_values[id] = defaultValue;
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}
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return m_values[id];
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}
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void prune(const Scalar& reference, const RealScalar& epsilon = NumTraits<RealScalar>::dummy_precision())
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{
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Index k = 0;
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Index n = size();
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for (Index i=0; i<n; ++i)
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{
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if (!internal::isMuchSmallerThan(value(i), reference, epsilon))
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{
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value(k) = value(i);
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index(k) = index(i);
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++k;
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}
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}
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resize(k,0);
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}
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protected:
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inline void reallocate(Index size)
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{
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#ifdef EIGEN_SPARSE_COMPRESSED_STORAGE_REALLOCATE_PLUGIN
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EIGEN_SPARSE_COMPRESSED_STORAGE_REALLOCATE_PLUGIN
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#endif
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eigen_internal_assert(size!=m_allocatedSize);
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internal::scoped_array<Scalar> newValues(size);
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internal::scoped_array<StorageIndex> newIndices(size);
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Index copySize = (std::min)(size, m_size);
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if (copySize>0) {
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internal::smart_copy(m_values, m_values+copySize, newValues.ptr());
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internal::smart_copy(m_indices, m_indices+copySize, newIndices.ptr());
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}
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std::swap(m_values,newValues.ptr());
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std::swap(m_indices,newIndices.ptr());
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m_allocatedSize = size;
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}
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protected:
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Scalar* m_values;
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StorageIndex* m_indices;
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Index m_size;
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Index m_allocatedSize;
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};
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} // end namespace internal
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} // end namespace Eigen
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#endif // EIGEN_COMPRESSED_STORAGE_H
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@@ -0,0 +1,352 @@
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// This file is part of Eigen, a lightweight C++ template library
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// for linear algebra.
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//
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// Copyright (C) 2008-2015 Gael Guennebaud <gael.guennebaud@inria.fr>
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//
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// This Source Code Form is subject to the terms of the Mozilla
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// Public License v. 2.0. If a copy of the MPL was not distributed
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// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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#ifndef EIGEN_CONSERVATIVESPARSESPARSEPRODUCT_H
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#define EIGEN_CONSERVATIVESPARSESPARSEPRODUCT_H
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namespace Eigen {
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namespace internal {
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template<typename Lhs, typename Rhs, typename ResultType>
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static void conservative_sparse_sparse_product_impl(const Lhs& lhs, const Rhs& rhs, ResultType& res, bool sortedInsertion = false)
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{
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typedef typename remove_all<Lhs>::type::Scalar LhsScalar;
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typedef typename remove_all<Rhs>::type::Scalar RhsScalar;
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typedef typename remove_all<ResultType>::type::Scalar ResScalar;
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// make sure to call innerSize/outerSize since we fake the storage order.
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Index rows = lhs.innerSize();
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Index cols = rhs.outerSize();
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eigen_assert(lhs.outerSize() == rhs.innerSize());
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ei_declare_aligned_stack_constructed_variable(bool, mask, rows, 0);
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ei_declare_aligned_stack_constructed_variable(ResScalar, values, rows, 0);
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ei_declare_aligned_stack_constructed_variable(Index, indices, rows, 0);
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std::memset(mask,0,sizeof(bool)*rows);
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evaluator<Lhs> lhsEval(lhs);
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evaluator<Rhs> rhsEval(rhs);
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// estimate the number of non zero entries
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// given a rhs column containing Y non zeros, we assume that the respective Y columns
|
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// of the lhs differs in average of one non zeros, thus the number of non zeros for
|
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// the product of a rhs column with the lhs is X+Y where X is the average number of non zero
|
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// per column of the lhs.
|
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// Therefore, we have nnz(lhs*rhs) = nnz(lhs) + nnz(rhs)
|
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Index estimated_nnz_prod = lhsEval.nonZerosEstimate() + rhsEval.nonZerosEstimate();
|
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+
|
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res.setZero();
|
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res.reserve(Index(estimated_nnz_prod));
|
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// we compute each column of the result, one after the other
|
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for (Index j=0; j<cols; ++j)
|
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{
|
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res.startVec(j);
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Index nnz = 0;
|
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for (typename evaluator<Rhs>::InnerIterator rhsIt(rhsEval, j); rhsIt; ++rhsIt)
|
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{
|
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RhsScalar y = rhsIt.value();
|
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Index k = rhsIt.index();
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for (typename evaluator<Lhs>::InnerIterator lhsIt(lhsEval, k); lhsIt; ++lhsIt)
|
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{
|
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Index i = lhsIt.index();
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LhsScalar x = lhsIt.value();
|
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if(!mask[i])
|
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{
|
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mask[i] = true;
|
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values[i] = x * y;
|
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|
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indices[nnz] = i;
|
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++nnz;
|
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}
|
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else
|
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values[i] += x * y;
|
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}
|
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}
|
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if(!sortedInsertion)
|
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{
|
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// unordered insertion
|
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for(Index k=0; k<nnz; ++k)
|
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{
|
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Index i = indices[k];
|
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res.insertBackByOuterInnerUnordered(j,i) = values[i];
|
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mask[i] = false;
|
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}
|
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}
|
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else
|
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{
|
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// alternative ordered insertion code:
|
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const Index t200 = rows/11; // 11 == (log2(200)*1.39)
|
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const Index t = (rows*100)/139;
|
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|
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// FIXME reserve nnz non zeros
|
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// FIXME implement faster sorting algorithms for very small nnz
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// if the result is sparse enough => use a quick sort
|
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// otherwise => loop through the entire vector
|
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// In order to avoid to perform an expensive log2 when the
|
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// result is clearly very sparse we use a linear bound up to 200.
|
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|
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if((nnz<200 && nnz<t200) || nnz * numext::log2(int(nnz)) < t)
|
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|
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{
|
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if(nnz>1) std::sort(indices,indices+nnz);
|
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for(Index k=0; k<nnz; ++k)
|
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|
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{
|
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Index i = indices[k];
|
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res.insertBackByOuterInner(j,i) = values[i];
|
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mask[i] = false;
|
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}
|
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}
|
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|
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else
|
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|
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{
|
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// dense path
|
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for(Index i=0; i<rows; ++i)
|
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|
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{
|
110
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if(mask[i])
|
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{
|
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mask[i] = false;
|
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res.insertBackByOuterInner(j,i) = values[i];
|
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}
|
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}
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}
|
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}
|
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}
|
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res.finalize();
|
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}
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|
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} // end namespace internal
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namespace internal {
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|
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template<typename Lhs, typename Rhs, typename ResultType,
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int LhsStorageOrder = (traits<Lhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
|
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int RhsStorageOrder = (traits<Rhs>::Flags&RowMajorBit) ? RowMajor : ColMajor,
|
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int ResStorageOrder = (traits<ResultType>::Flags&RowMajorBit) ? RowMajor : ColMajor>
|
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|
+
struct conservative_sparse_sparse_product_selector;
|
132
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+
|
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+
template<typename Lhs, typename Rhs, typename ResultType>
|
134
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struct conservative_sparse_sparse_product_selector<Lhs,Rhs,ResultType,ColMajor,ColMajor,ColMajor>
|
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|
+
{
|
136
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+
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
|