[med-svn] [Git][med-team/relion][master] New upstream version 5.0.1
Yavor Doganov (@yavor-guest)
gitlab at salsa.debian.org
Wed Nov 5 07:01:48 GMT 2025
Yavor Doganov pushed to branch master at Debian Med / relion
Commits:
d983f8a3 by Yavor Doganov at 2025-11-04T14:04:17+02:00
New upstream version 5.0.1
- - - - -
1673 changed files:
- + .github/workflows/build.yml
- AUTHORS
- CMakeLists.txt
- LICENSE
- README.md
- + README_sycl.md
- − betaGuide.pdf
- cmake/BuildFFTW.cmake
- cmake/BuildTBB.cmake
- cmake/BuildTypes.cmake
- + cmake/FindCondaPython.cmake
- + cmake/TBB-GCC13.patch
- + documentation/tomography/data_types/manifold_set.html
- + documentation/tomography/data_types/optimisation_set.html
- + documentation/tomography/data_types/optimisation_set.svg
- + documentation/tomography/data_types/particle_set.html
- + documentation/tomography/data_types/subtomogram.svg
- + documentation/tomography/data_types/tomogram_set.html
- + documentation/tomography/data_types/trajectory_set.html
- + documentation/tomography/programs/align.html
- + documentation/tomography/programs/fit_blobs_3d.html
- + documentation/tomography/programs/import_particles.html
- + documentation/tomography/programs/import_tomograms.html
- + documentation/tomography/programs/local_particle_refine.html
- + documentation/tomography/programs/programs_list.html
- + documentation/tomography/programs/reconstruct_particle.html
- + documentation/tomography/programs/reconstruct_tomogram.html
- + documentation/tomography/programs/refine_ctf.html
- + documentation/tomography/programs/subtomo.html
- + documentation/tomography/style.css
- + environment.yml
- + environment_blackwell.yml
- + pyproject.toml
- relion.h
- + remove_duplicates.py
- + scripts/Schemes/prep/ctffind/job.star
- + scripts/Schemes/prep/importmovies/job.star
- + scripts/Schemes/prep/motioncorr/job.star
- + scripts/Schemes/prep/scheme.star
- + scripts/Schemes/proc/autopick/job.star
- + scripts/Schemes/proc/class2d/job.star
- + scripts/Schemes/proc/extract/job.star
- + scripts/Schemes/proc/inimodel3d/job.star
- + scripts/Schemes/proc/refine3d/job.star
- + scripts/Schemes/proc/scheme.star
- + scripts/Schemes/proc/select_mics/job.star
- + scripts/Schemes/proc/select_parts/job.star
- scripts/bfactor_plot.py
- scripts/eer_trajectory_handler.py
- + scripts/filament_selection.in
- + scripts/it.py
- + scripts/python_blush.in
- + scripts/python_classranker.in
- + scripts/python_dynamight.in
- + scripts/python_fetch_weights.in
- + scripts/python_modelangelo.in
- + scripts/python_tomo_align_tilt_series.in
- + scripts/python_tomo_denoise.in
- + scripts/python_tomo_exclude_tilt_images.in
- + scripts/python_tomo_get_particle_poses.in
- + scripts/python_tomo_import.in
- + scripts/python_tomo_pick.in
- + scripts/python_tomo_view.in
- + scripts/python_topaz.in
- − scripts/relion_it.py
- + scripts/schemegui.py
- src/CPlot2D.cpp
- src/CPlot2D.h
- + src/Eigen/Cholesky
- + src/Eigen/CholmodSupport
- + src/Eigen/Core
- + src/Eigen/Dense
- + src/Eigen/Eigen
- + src/Eigen/Eigenvalues
- + src/Eigen/Geometry
- + src/Eigen/Householder
- + src/Eigen/IterativeLinearSolvers
- + src/Eigen/Jacobi
- + src/Eigen/KLUSupport
- + src/Eigen/LU
- + src/Eigen/MetisSupport
- + src/Eigen/OrderingMethods
- + src/Eigen/PaStiXSupport
- + src/Eigen/PardisoSupport
- + src/Eigen/QR
- + src/Eigen/QtAlignedMalloc
- + src/Eigen/SPQRSupport
- + src/Eigen/SVD
- + src/Eigen/Sparse
- + src/Eigen/SparseCholesky
- + src/Eigen/SparseCore
- + src/Eigen/SparseLU
- + src/Eigen/SparseQR
- + src/Eigen/StdDeque
- + src/Eigen/StdList
- + src/Eigen/StdVector
- + src/Eigen/SuperLUSupport
- + src/Eigen/UmfPackSupport
- + src/Eigen/src/Cholesky/LDLT.h
- + src/Eigen/src/Cholesky/LLT.h
- + src/Eigen/src/Cholesky/LLT_LAPACKE.h
- + src/Eigen/src/CholmodSupport/CholmodSupport.h
- + src/Eigen/src/Core/ArithmeticSequence.h
- + src/Eigen/src/Core/Array.h
- + src/Eigen/src/Core/ArrayBase.h
- + src/Eigen/src/Core/ArrayWrapper.h
- + src/Eigen/src/Core/Assign.h
- + src/Eigen/src/Core/AssignEvaluator.h
- + src/Eigen/src/Core/Assign_MKL.h
- + src/Eigen/src/Core/BandMatrix.h
- + src/Eigen/src/Core/Block.h
- + src/Eigen/src/Core/BooleanRedux.h
- + src/Eigen/src/Core/CommaInitializer.h
- + src/Eigen/src/Core/ConditionEstimator.h
- + src/Eigen/src/Core/CoreEvaluators.h
- + src/Eigen/src/Core/CoreIterators.h
- + src/Eigen/src/Core/CwiseBinaryOp.h
- + src/Eigen/src/Core/CwiseNullaryOp.h
- + src/Eigen/src/Core/CwiseTernaryOp.h
- + src/Eigen/src/Core/CwiseUnaryOp.h
- + src/Eigen/src/Core/CwiseUnaryView.h
- + src/Eigen/src/Core/DenseBase.h
- + src/Eigen/src/Core/DenseCoeffsBase.h
- + src/Eigen/src/Core/DenseStorage.h
- + src/Eigen/src/Core/Diagonal.h
- + src/Eigen/src/Core/DiagonalMatrix.h
- + src/Eigen/src/Core/DiagonalProduct.h
- + src/Eigen/src/Core/Dot.h
- + src/Eigen/src/Core/EigenBase.h
- + src/Eigen/src/Core/ForceAlignedAccess.h
- + src/Eigen/src/Core/Fuzzy.h
- + src/Eigen/src/Core/GeneralProduct.h
- + src/Eigen/src/Core/GenericPacketMath.h
- + src/Eigen/src/Core/GlobalFunctions.h
- + src/Eigen/src/Core/IO.h
- + src/Eigen/src/Core/IndexedView.h
- + src/Eigen/src/Core/Inverse.h
- + src/Eigen/src/Core/Map.h
- + src/Eigen/src/Core/MapBase.h
- + src/Eigen/src/Core/MathFunctions.h
- + src/Eigen/src/Core/MathFunctionsImpl.h
- + src/Eigen/src/Core/Matrix.h
- + src/Eigen/src/Core/MatrixBase.h
- + src/Eigen/src/Core/NestByValue.h
- + src/Eigen/src/Core/NoAlias.h
- + src/Eigen/src/Core/NumTraits.h
- + src/Eigen/src/Core/PartialReduxEvaluator.h
- + src/Eigen/src/Core/PermutationMatrix.h
- + src/Eigen/src/Core/PlainObjectBase.h
- + src/Eigen/src/Core/Product.h
- + src/Eigen/src/Core/ProductEvaluators.h
- + src/Eigen/src/Core/Random.h
- + src/Eigen/src/Core/Redux.h
- + src/Eigen/src/Core/Ref.h
- + src/Eigen/src/Core/Replicate.h
- + src/Eigen/src/Core/Reshaped.h
- + src/Eigen/src/Core/ReturnByValue.h
- + src/Eigen/src/Core/Reverse.h
- + src/Eigen/src/Core/Select.h
- + src/Eigen/src/Core/SelfAdjointView.h
- + src/Eigen/src/Core/SelfCwiseBinaryOp.h
- + src/Eigen/src/Core/Solve.h
- + src/Eigen/src/Core/SolveTriangular.h
- + src/Eigen/src/Core/SolverBase.h
- + src/Eigen/src/Core/StableNorm.h
- + src/Eigen/src/Core/StlIterators.h
- + src/Eigen/src/Core/Stride.h
- + src/Eigen/src/Core/Swap.h
- + src/Eigen/src/Core/Transpose.h
- + src/Eigen/src/Core/Transpositions.h
- + src/Eigen/src/Core/TriangularMatrix.h
- + src/Eigen/src/Core/VectorBlock.h
- + src/Eigen/src/Core/VectorwiseOp.h
- + src/Eigen/src/Core/Visitor.h
- + src/Eigen/src/Core/arch/AVX/Complex.h
- + src/Eigen/src/Core/arch/AVX/MathFunctions.h
- + src/Eigen/src/Core/arch/AVX/PacketMath.h
- + src/Eigen/src/Core/arch/AVX/TypeCasting.h
- + src/Eigen/src/Core/arch/AVX512/Complex.h
- + src/Eigen/src/Core/arch/AVX512/MathFunctions.h
- + src/Eigen/src/Core/arch/AVX512/PacketMath.h
- + src/Eigen/src/Core/arch/AVX512/TypeCasting.h
- + src/Eigen/src/Core/arch/AltiVec/Complex.h
- + src/Eigen/src/Core/arch/AltiVec/MathFunctions.h
- + src/Eigen/src/Core/arch/AltiVec/PacketMath.h
- + src/Eigen/src/Core/arch/CUDA/Complex.h
- + src/Eigen/src/Core/arch/Default/ConjHelper.h
- + src/Eigen/src/Core/arch/Default/GenericPacketMathFunctions.h
- + src/Eigen/src/Core/arch/Default/GenericPacketMathFunctionsFwd.h
- + src/Eigen/src/Core/arch/Default/Half.h
- + src/Eigen/src/Core/arch/Default/Settings.h
- + src/Eigen/src/Core/arch/Default/TypeCasting.h
- + src/Eigen/src/Core/arch/GPU/MathFunctions.h
- + src/Eigen/src/Core/arch/GPU/PacketMath.h
- + src/Eigen/src/Core/arch/GPU/TypeCasting.h
- + src/Eigen/src/Core/arch/HIP/hcc/math_constants.h
- + src/Eigen/src/Core/arch/MSA/Complex.h
- + src/Eigen/src/Core/arch/MSA/MathFunctions.h
- + src/Eigen/src/Core/arch/MSA/PacketMath.h
- + src/Eigen/src/Core/arch/NEON/Complex.h
- + src/Eigen/src/Core/arch/NEON/MathFunctions.h
- + src/Eigen/src/Core/arch/NEON/PacketMath.h
- + src/Eigen/src/Core/arch/NEON/TypeCasting.h
- + src/Eigen/src/Core/arch/SSE/Complex.h
- + src/Eigen/src/Core/arch/SSE/MathFunctions.h
- + src/Eigen/src/Core/arch/SSE/PacketMath.h
- + src/Eigen/src/Core/arch/SSE/TypeCasting.h
- + src/Eigen/src/Core/arch/SYCL/InteropHeaders.h
- + src/Eigen/src/Core/arch/SYCL/MathFunctions.h
- + src/Eigen/src/Core/arch/SYCL/PacketMath.h
- + src/Eigen/src/Core/arch/SYCL/SyclMemoryModel.h
- + src/Eigen/src/Core/arch/SYCL/TypeCasting.h
- + src/Eigen/src/Core/arch/ZVector/Complex.h
- + src/Eigen/src/Core/arch/ZVector/MathFunctions.h
- + src/Eigen/src/Core/arch/ZVector/PacketMath.h
- + src/Eigen/src/Core/functors/AssignmentFunctors.h
- + src/Eigen/src/Core/functors/BinaryFunctors.h
- + src/Eigen/src/Core/functors/NullaryFunctors.h
- + src/Eigen/src/Core/functors/StlFunctors.h
- + src/Eigen/src/Core/functors/TernaryFunctors.h
- + src/Eigen/src/Core/functors/UnaryFunctors.h
- + src/Eigen/src/Core/products/GeneralBlockPanelKernel.h
- + src/Eigen/src/Core/products/GeneralMatrixMatrix.h
- + src/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
- + src/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h
- + src/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h
- + src/Eigen/src/Core/products/GeneralMatrixVector.h
- + src/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h
- + src/Eigen/src/Core/products/Parallelizer.h
- + src/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
- + src/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h
- + src/Eigen/src/Core/products/SelfadjointMatrixVector.h
- + src/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h
- + src/Eigen/src/Core/products/SelfadjointProduct.h
- + src/Eigen/src/Core/products/SelfadjointRank2Update.h
- + src/Eigen/src/Core/products/TriangularMatrixMatrix.h
- + src/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h
- + src/Eigen/src/Core/products/TriangularMatrixVector.h
- + src/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h
- + src/Eigen/src/Core/products/TriangularSolverMatrix.h
- + src/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h
- + src/Eigen/src/Core/products/TriangularSolverVector.h
- + src/Eigen/src/Core/util/BlasUtil.h
- + src/Eigen/src/Core/util/ConfigureVectorization.h
- + src/Eigen/src/Core/util/Constants.h
- + src/Eigen/src/Core/util/DisableStupidWarnings.h
- + src/Eigen/src/Core/util/ForwardDeclarations.h
- + src/Eigen/src/Core/util/IndexedViewHelper.h
- + src/Eigen/src/Core/util/IntegralConstant.h
- + src/Eigen/src/Core/util/MKL_support.h
- + src/Eigen/src/Core/util/Macros.h
- + src/Eigen/src/Core/util/Memory.h
- + src/Eigen/src/Core/util/Meta.h
- + src/Eigen/src/Core/util/NonMPL2.h
- + src/Eigen/src/Core/util/ReenableStupidWarnings.h
- + src/Eigen/src/Core/util/ReshapedHelper.h
- + src/Eigen/src/Core/util/StaticAssert.h
- + src/Eigen/src/Core/util/SymbolicIndex.h
- + src/Eigen/src/Core/util/XprHelper.h
- + src/Eigen/src/Eigenvalues/ComplexEigenSolver.h
- + src/Eigen/src/Eigenvalues/ComplexSchur.h
- + src/Eigen/src/Eigenvalues/ComplexSchur_LAPACKE.h
- + src/Eigen/src/Eigenvalues/EigenSolver.h
- + src/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h
- + src/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
- + src/Eigen/src/Eigenvalues/HessenbergDecomposition.h
- + src/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
- + src/Eigen/src/Eigenvalues/RealQZ.h
- + src/Eigen/src/Eigenvalues/RealSchur.h
- + src/Eigen/src/Eigenvalues/RealSchur_LAPACKE.h
- + src/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
- + src/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h
- + src/Eigen/src/Eigenvalues/Tridiagonalization.h
- + src/Eigen/src/Geometry/AlignedBox.h
- + src/Eigen/src/Geometry/AngleAxis.h
- + src/Eigen/src/Geometry/EulerAngles.h
- + src/Eigen/src/Geometry/Homogeneous.h
- + src/Eigen/src/Geometry/Hyperplane.h
- + src/Eigen/src/Geometry/OrthoMethods.h
- + src/Eigen/src/Geometry/ParametrizedLine.h
- + src/Eigen/src/Geometry/Quaternion.h
- + src/Eigen/src/Geometry/Rotation2D.h
- + src/Eigen/src/Geometry/RotationBase.h
- + src/Eigen/src/Geometry/Scaling.h
- + src/Eigen/src/Geometry/Transform.h
- + src/Eigen/src/Geometry/Translation.h
- + src/Eigen/src/Geometry/Umeyama.h
- + src/Eigen/src/Geometry/arch/Geometry_SSE.h
- + src/Eigen/src/Householder/BlockHouseholder.h
- + src/Eigen/src/Householder/Householder.h
- + src/Eigen/src/Householder/HouseholderSequence.h
- + src/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
- + src/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
- + src/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
- + src/Eigen/src/IterativeLinearSolvers/IncompleteCholesky.h
- + src/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
- + src/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
- + src/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h
- + src/Eigen/src/IterativeLinearSolvers/SolveWithGuess.h
- + src/Eigen/src/Jacobi/Jacobi.h
- + src/Eigen/src/KLUSupport/KLUSupport.h
- + src/Eigen/src/LU/Determinant.h
- + src/Eigen/src/LU/FullPivLU.h
- + src/Eigen/src/LU/InverseImpl.h
- + src/Eigen/src/LU/PartialPivLU.h
- + src/Eigen/src/LU/PartialPivLU_LAPACKE.h
- + src/Eigen/src/LU/arch/Inverse_SSE.h
- + src/Eigen/src/MetisSupport/MetisSupport.h
- + src/Eigen/src/OrderingMethods/Amd.h
- + src/Eigen/src/OrderingMethods/Eigen_Colamd.h
- + src/Eigen/src/OrderingMethods/Ordering.h
- + src/Eigen/src/PaStiXSupport/PaStiXSupport.h
- + src/Eigen/src/PardisoSupport/PardisoSupport.h
- + src/Eigen/src/QR/ColPivHouseholderQR.h
- + src/Eigen/src/QR/ColPivHouseholderQR_LAPACKE.h
- + src/Eigen/src/QR/CompleteOrthogonalDecomposition.h
- + src/Eigen/src/QR/FullPivHouseholderQR.h
- + src/Eigen/src/QR/HouseholderQR.h
- + src/Eigen/src/QR/HouseholderQR_LAPACKE.h
- + src/Eigen/src/SPQRSupport/SuiteSparseQRSupport.h
- + src/Eigen/src/SVD/BDCSVD.h
- + src/Eigen/src/SVD/JacobiSVD.h
- + src/Eigen/src/SVD/JacobiSVD_LAPACKE.h
- + src/Eigen/src/SVD/SVDBase.h
- + src/Eigen/src/SVD/UpperBidiagonalization.h
- + src/Eigen/src/SparseCholesky/SimplicialCholesky.h
- + src/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h
- + src/Eigen/src/SparseCore/AmbiVector.h
- + src/Eigen/src/SparseCore/CompressedStorage.h
- + src/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
- + src/Eigen/src/SparseCore/MappedSparseMatrix.h
- + src/Eigen/src/SparseCore/SparseAssign.h
- + src/Eigen/src/SparseCore/SparseBlock.h
- + src/Eigen/src/SparseCore/SparseColEtree.h
- + src/Eigen/src/SparseCore/SparseCompressedBase.h
- + src/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
- + src/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
- + src/Eigen/src/SparseCore/SparseDenseProduct.h
- + src/Eigen/src/SparseCore/SparseDiagonalProduct.h
- + src/Eigen/src/SparseCore/SparseDot.h
- + src/Eigen/src/SparseCore/SparseFuzzy.h
- + src/Eigen/src/SparseCore/SparseMap.h
- + src/Eigen/src/SparseCore/SparseMatrix.h
- + src/Eigen/src/SparseCore/SparseMatrixBase.h
- + src/Eigen/src/SparseCore/SparsePermutation.h
- + src/Eigen/src/SparseCore/SparseProduct.h
- + src/Eigen/src/SparseCore/SparseRedux.h
- + src/Eigen/src/SparseCore/SparseRef.h
- + src/Eigen/src/SparseCore/SparseSelfAdjointView.h
- + src/Eigen/src/SparseCore/SparseSolverBase.h
- + src/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
- + src/Eigen/src/SparseCore/SparseTranspose.h
- + src/Eigen/src/SparseCore/SparseTriangularView.h
- + src/Eigen/src/SparseCore/SparseUtil.h
- + src/Eigen/src/SparseCore/SparseVector.h
- + src/Eigen/src/SparseCore/SparseView.h
- + src/Eigen/src/SparseCore/TriangularSolver.h
- + src/Eigen/src/SparseLU/SparseLU.h
- + src/Eigen/src/SparseLU/SparseLUImpl.h
- + src/Eigen/src/SparseLU/SparseLU_Memory.h
- + src/Eigen/src/SparseLU/SparseLU_Structs.h
- + src/Eigen/src/SparseLU/SparseLU_SupernodalMatrix.h
- + src/Eigen/src/SparseLU/SparseLU_Utils.h
- + src/Eigen/src/SparseLU/SparseLU_column_bmod.h
- + src/Eigen/src/SparseLU/SparseLU_column_dfs.h
- + src/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h
- + src/Eigen/src/SparseLU/SparseLU_gemm_kernel.h
- + src/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h
- + src/Eigen/src/SparseLU/SparseLU_kernel_bmod.h
- + src/Eigen/src/SparseLU/SparseLU_panel_bmod.h
- + src/Eigen/src/SparseLU/SparseLU_panel_dfs.h
- + src/Eigen/src/SparseLU/SparseLU_pivotL.h
- + src/Eigen/src/SparseLU/SparseLU_pruneL.h
- + src/Eigen/src/SparseLU/SparseLU_relax_snode.h
- + src/Eigen/src/SparseQR/SparseQR.h
- + src/Eigen/src/StlSupport/StdDeque.h
- + src/Eigen/src/StlSupport/StdList.h
- + src/Eigen/src/StlSupport/StdVector.h
- + src/Eigen/src/StlSupport/details.h
- + src/Eigen/src/SuperLUSupport/SuperLUSupport.h
- + src/Eigen/src/UmfPackSupport/UmfPackSupport.h
- + src/Eigen/src/misc/Image.h
- + src/Eigen/src/misc/Kernel.h
- + src/Eigen/src/misc/RealSvd2x2.h
- + src/Eigen/src/misc/blas.h
- + src/Eigen/src/misc/lapack.h
- + src/Eigen/src/misc/lapacke.h
- + src/Eigen/src/misc/lapacke_mangling.h
- + src/Eigen/src/plugins/ArrayCwiseBinaryOps.h
- + src/Eigen/src/plugins/ArrayCwiseUnaryOps.h
- + src/Eigen/src/plugins/BlockMethods.h
- + src/Eigen/src/plugins/CommonCwiseBinaryOps.h
- + src/Eigen/src/plugins/CommonCwiseUnaryOps.h
- + src/Eigen/src/plugins/IndexedViewMethods.h
- + src/Eigen/src/plugins/MatrixCwiseBinaryOps.h
- + src/Eigen/src/plugins/MatrixCwiseUnaryOps.h
- + src/Eigen/src/plugins/ReshapedMethods.h
- src/acc/acc_backprojector.h
- src/acc/acc_backprojector_impl.h
- src/acc/acc_helper_functions.h
- src/acc/acc_helper_functions_impl.h
- src/acc/acc_ml_optimiser.h
- src/acc/acc_ml_optimiser_impl.h
- src/acc/acc_projector.h
- src/acc/acc_projector_impl.h
- src/acc/acc_projector_plan.h
- src/acc/acc_projector_plan_impl.h
- src/acc/acc_projectorkernel_impl.h
- src/acc/acc_ptr.h
- src/acc/cpu/cpu_backprojector.cpp
- src/acc/cpu/cpu_helper_functions.cpp
- src/acc/cpu/cpu_helper_functions.h
- src/acc/cpu/cpu_kernels/BP.h
- src/acc/cpu/cpu_kernels/cpu_utils.h
- src/acc/cpu/cpu_kernels/diff2.h
- src/acc/cpu/cpu_kernels/helper.cpp
- src/acc/cpu/cpu_kernels/helper.h
- src/acc/cpu/cpu_kernels/wavg.h
- src/acc/cpu/cpu_ml_optimiser.cpp
- src/acc/cpu/cpu_ml_optimiser.h
- src/acc/cpu/cpu_projector.cpp
- src/acc/cpu/cpu_projector_plan.cpp
- src/acc/cpu/cpu_settings.h
- src/acc/cpu/cuda_stubs.h → src/acc/cpu/device_stubs.h
- − src/acc/cuda/cub/agent/agent_histogram.cuh
- − src/acc/cuda/cub/agent/agent_radix_sort_downsweep.cuh
- − src/acc/cuda/cub/agent/agent_radix_sort_upsweep.cuh
- − src/acc/cuda/cub/agent/agent_reduce.cuh
- − src/acc/cuda/cub/agent/agent_reduce_by_key.cuh
- − src/acc/cuda/cub/agent/agent_rle.cuh
- − src/acc/cuda/cub/agent/agent_scan.cuh
- − src/acc/cuda/cub/agent/agent_segment_fixup.cuh
- − src/acc/cuda/cub/agent/agent_select_if.cuh
- − src/acc/cuda/cub/agent/agent_spmv_csrt.cuh
- − src/acc/cuda/cub/agent/agent_spmv_orig.cuh
- − src/acc/cuda/cub/agent/agent_spmv_row_based.cuh
- − src/acc/cuda/cub/agent/single_pass_scan_operators.cuh
- − src/acc/cuda/cub/block/block_adjacent_difference.cuh
- − src/acc/cuda/cub/block/block_discontinuity.cuh
- − src/acc/cuda/cub/block/block_exchange.cuh
- − src/acc/cuda/cub/block/block_histogram.cuh
- − src/acc/cuda/cub/block/block_load.cuh
- − src/acc/cuda/cub/block/block_radix_rank.cuh
- − src/acc/cuda/cub/block/block_radix_sort.cuh
- − src/acc/cuda/cub/block/block_raking_layout.cuh
- − src/acc/cuda/cub/block/block_reduce.cuh
- − src/acc/cuda/cub/block/block_scan.cuh
- − src/acc/cuda/cub/block/block_shuffle.cuh
- − src/acc/cuda/cub/block/block_store.cuh
- − src/acc/cuda/cub/block/specializations/block_histogram_atomic.cuh
- − src/acc/cuda/cub/block/specializations/block_histogram_sort.cuh
- − src/acc/cuda/cub/block/specializations/block_reduce_raking.cuh
- − src/acc/cuda/cub/block/specializations/block_reduce_raking_commutative_only.cuh
- − src/acc/cuda/cub/block/specializations/block_reduce_warp_reductions.cuh
- − src/acc/cuda/cub/block/specializations/block_scan_raking.cuh
- − src/acc/cuda/cub/block/specializations/block_scan_warp_scans.cuh
- − src/acc/cuda/cub/block/specializations/block_scan_warp_scans2.cuh
- − src/acc/cuda/cub/block/specializations/block_scan_warp_scans3.cuh
- − src/acc/cuda/cub/cub.cuh
- − src/acc/cuda/cub/device/device_histogram.cuh
- − src/acc/cuda/cub/device/device_partition.cuh
- − src/acc/cuda/cub/device/device_radix_sort.cuh
- − src/acc/cuda/cub/device/device_reduce.cuh
- − src/acc/cuda/cub/device/device_run_length_encode.cuh
- − src/acc/cuda/cub/device/device_scan.cuh
- − src/acc/cuda/cub/device/device_segmented_radix_sort.cuh
- − src/acc/cuda/cub/device/device_segmented_reduce.cuh
- − src/acc/cuda/cub/device/device_select.cuh
- − src/acc/cuda/cub/device/device_spmv.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_histogram.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_radix_sort.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_reduce.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_reduce_by_key.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_rle.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_scan.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_select_if.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_spmv_csrt.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_spmv_orig.cuh
- − src/acc/cuda/cub/device/dispatch/dispatch_spmv_row_based.cuh
- − src/acc/cuda/cub/grid/grid_barrier.cuh
- − src/acc/cuda/cub/grid/grid_even_share.cuh
- − src/acc/cuda/cub/grid/grid_mapping.cuh
- − src/acc/cuda/cub/grid/grid_queue.cuh
- − src/acc/cuda/cub/host/mutex.cuh
- − src/acc/cuda/cub/iterator/arg_index_input_iterator.cuh
- − src/acc/cuda/cub/iterator/cache_modified_input_iterator.cuh
- − src/acc/cuda/cub/iterator/cache_modified_output_iterator.cuh
- − src/acc/cuda/cub/iterator/constant_input_iterator.cuh
- − src/acc/cuda/cub/iterator/counting_input_iterator.cuh
- − src/acc/cuda/cub/iterator/discard_output_iterator.cuh
- − src/acc/cuda/cub/iterator/tex_obj_input_iterator.cuh
- − src/acc/cuda/cub/iterator/tex_ref_input_iterator.cuh
- − src/acc/cuda/cub/iterator/transform_input_iterator.cuh
- − src/acc/cuda/cub/thread/thread_load.cuh
- − src/acc/cuda/cub/thread/thread_operators.cuh
- − src/acc/cuda/cub/thread/thread_reduce.cuh
- − src/acc/cuda/cub/thread/thread_scan.cuh
- − src/acc/cuda/cub/thread/thread_search.cuh
- − src/acc/cuda/cub/thread/thread_store.cuh
- − src/acc/cuda/cub/util_allocator.cuh
- − src/acc/cuda/cub/util_arch.cuh
- − src/acc/cuda/cub/util_debug.cuh
- − src/acc/cuda/cub/util_device.cuh
- − src/acc/cuda/cub/util_macro.cuh
- − src/acc/cuda/cub/util_namespace.cuh
- − src/acc/cuda/cub/util_ptx.cuh
- − src/acc/cuda/cub/util_type.cuh
- − src/acc/cuda/cub/warp/specializations/warp_reduce_shfl.cuh
- − src/acc/cuda/cub/warp/specializations/warp_reduce_smem.cuh
- − src/acc/cuda/cub/warp/specializations/warp_scan_shfl.cuh
- − src/acc/cuda/cub/warp/specializations/warp_scan_smem.cuh
- − src/acc/cuda/cub/warp/warp_reduce.cuh
- − src/acc/cuda/cub/warp/warp_scan.cuh
- src/acc/cuda/cuda_autopicker.cu
- src/acc/cuda/cuda_autopicker.h
- src/acc/cuda/cuda_benchmark_utils.h
- src/acc/cuda/cuda_fft.h
- src/acc/cuda/cuda_kernels/BP.cuh
- src/acc/cuda/cuda_kernels/diff2.cuh
- src/acc/cuda/cuda_kernels/helper.cu
- src/acc/cuda/cuda_kernels/helper.cuh
- src/acc/cuda/cuda_kernels/wavg.cuh
- src/acc/cuda/cuda_mem_utils.h
- src/acc/cuda/cuda_ml_optimiser.cu
- src/acc/cuda/cuda_ml_optimiser.h
- src/acc/cuda/cuda_projector_plan.cu
- src/acc/cuda/cuda_settings.h
- src/acc/cuda/cuda_utils_cub.cuh
- src/acc/cuda/custom_allocator.cuh
- src/gpu_utils/cuda_mem_utils.h → src/acc/hip/custom_allocator.h
- src/gpu_utils/cuda_autopicker.h → src/acc/hip/hip_autopicker.h
- src/gpu_utils/cuda_autopicker.cu → src/acc/hip/hip_autopicker.hip.cpp
- + src/acc/hip/hip_backprojector.hip.cpp
- src/gpu_utils/cuda_benchmark_utils.h → src/acc/hip/hip_benchmark_utils.h
- + src/acc/hip/hip_benchmark_utils.hip.cpp
- src/gpu_utils/cuda_fft.h → src/acc/hip/hip_fft.h
- + src/acc/hip/hip_helper_functions.hip.cpp
- src/gpu_utils/cuda_kernels/BP.cuh → src/acc/hip/hip_kernels/BP.h
- src/gpu_utils/cuda_kernels/diff2.cuh → src/acc/hip/hip_kernels/diff2.h
- src/gpu_utils/cuda_kernels/helper.cuh → src/acc/hip/hip_kernels/helper.h
- src/gpu_utils/cuda_kernels/helper.cu → src/acc/hip/hip_kernels/helper.hip.cpp
- src/gpu_utils/cuda_device_utils.cuh → src/acc/hip/hip_kernels/hip_device_utils.h
- src/gpu_utils/cuda_kernels/wavg.cuh → src/acc/hip/hip_kernels/wavg.h
- + src/acc/hip/hip_mem_utils.h
- + src/acc/hip/hip_ml_optimiser.h
- + src/acc/hip/hip_ml_optimiser.hip.cpp
- + src/acc/hip/hip_projector.hip.cpp
- + src/acc/hip/hip_projector_plan.hip.cpp
- + src/acc/hip/hip_settings.h
- src/gpu_utils/cuda_utils_cub.cuh → src/acc/hip/hip_utils_cub.h
- + src/acc/hip/shortcuts.h
- src/acc/settings.h
- + src/acc/sycl/device_stubs.h
- + src/acc/sycl/mkl_fft.h
- + src/acc/sycl/sycl_backprojector.cpp
- + src/acc/sycl/sycl_benchmark_utils.h
- + src/acc/sycl/sycl_dev.cpp
- + src/acc/sycl/sycl_dev.h
- + src/acc/sycl/sycl_helper_functions.cpp
- + src/acc/sycl/sycl_helper_functions.h
- + src/acc/sycl/sycl_kernels/BP.h
- + src/acc/sycl/sycl_kernels/BP_gpu.h
- + src/acc/sycl/sycl_kernels/BP_impl.h
- + src/acc/sycl/sycl_kernels/diff2.h
- + src/acc/sycl/sycl_kernels/diff2_gpu.h
- + src/acc/sycl/sycl_kernels/diff2_impl.h
- + src/acc/sycl/sycl_kernels/helper.cpp
- + src/acc/sycl/sycl_kernels/helper.h
- + src/acc/sycl/sycl_kernels/helper_gpu.h
- + src/acc/sycl/sycl_kernels/sycl_utils.h
- + src/acc/sycl/sycl_kernels/wavg.h
- + src/acc/sycl/sycl_kernels/wavg_gpu.h
- + src/acc/sycl/sycl_kernels/wavg_impl.h
- + src/acc/sycl/sycl_memory_pool.cpp
- + src/acc/sycl/sycl_memory_pool.h
- + src/acc/sycl/sycl_ml_optimiser.cpp
- + src/acc/sycl/sycl_ml_optimiser.h
- + src/acc/sycl/sycl_projector.cpp
- + src/acc/sycl/sycl_projector_plan.cpp
- src/gpu_utils/cuda_settings.h → src/acc/sycl/sycl_settings.h
- + src/acc/sycl/sycl_virtual_dev.h
- src/acc/utilities.h
- src/acc/utilities_impl.h
- + src/align_tiltseries_runner.cpp
- + src/align_tiltseries_runner.h
- + src/align_tiltseries_runner_mpi.cpp
- + src/align_tiltseries_runner_mpi.h
- src/apps/CMakeLists.txt
- src/apps/Zernike_test.cpp
- src/apps/align_symmetry.cpp
- + src/apps/align_tiltseries.cpp
- + src/apps/align_tiltseries_mpi.cpp
- src/apps/autopick.cpp
- src/apps/autopick_mpi.cpp
- + src/apps/batchrun.cpp
- + src/apps/batchrun_mpi.cpp
- + src/apps/class_ranker.cpp
- src/apps/convert_star.cpp
- src/apps/ctf_mask_test.cpp
- src/apps/ctf_nyquist_test.cpp
- src/apps/ctf_refine.cpp
- src/apps/ctf_refine_mpi.cpp
- src/apps/ctf_toolbox.cpp
- src/apps/defocus_stats.cpp
- src/apps/demodulate.cpp
- src/apps/double_bfac_fit.cpp
- src/apps/double_reconstruct_openmp.cpp
- src/apps/estimate_gain.cpp
- src/apps/external_reconstruct.cpp
- src/apps/helix_toolbox.cpp
- + src/apps/helix_vote_classes.cpp
- src/apps/image_handler.cpp
- src/apps/import.cpp
- src/apps/interpolation_test.cpp
- src/apps/maingui.cpp
- src/apps/merge_particles.cpp
- src/apps/motion_refine.cpp
- src/apps/motion_refine_mpi.cpp
- src/apps/movie_reconstruct.cpp
- + src/apps/mpi_tester.cpp
- src/apps/mrc2vtk.cpp
- src/apps/paper_data_synth.cpp
- − src/apps/particle_FCC.cpp
- src/apps/particle_reposition.cpp
- src/apps/particle_select.cpp
- src/apps/particle_symmetry_expand.cpp
- src/apps/pipeliner.cpp
- src/apps/plot_delocalisation.cpp
- src/apps/project.cpp
- + src/apps/pseudotomo_expansion.cpp
- − src/apps/reposition.cpp
- + src/apps/run_align_tiltseries.cpp
- + src/apps/run_align_tiltseries_mpi.cpp
- src/apps/run_ctffind_mpi.cpp
- src/apps/scheduler.cpp → src/apps/schemer.cpp
- src/apps/split_stack.cpp
- src/apps/stack_create.cpp
- src/apps/star_handler.cpp
- + src/apps/suggest_tvalue.cpp
- src/apps/tomo_test.cpp
- src/apps/vis_Ewald_weight.cpp
- src/apps/vis_delocalisation.cpp
- src/args.cpp
- src/args.h
- src/assembly.cpp
- src/assembly.h
- src/autopicker.cpp
- src/autopicker.h
- src/autopicker_mpi.cpp
- src/autopicker_mpi.h
- src/backprojector.cpp
- src/backprojector.h
- + src/batchrunner.cpp
- + src/batchrunner.h
- + src/batchrunner_mpi.cpp
- + src/batchrunner_mpi.h
- + src/class_ranker.cpp
- + src/class_ranker.h
- src/complex.h
- src/ctf.cpp
- src/ctf.h
- src/ctffind_runner.cpp
- src/ctffind_runner.h
- src/ctffind_runner_mpi.cpp
- src/ctffind_runner_mpi.h
- src/displayer.cpp
- src/displayer.h
- src/error.h
- src/exp_model.cpp
- src/exp_model.h
- src/fftw.cpp
- src/fftw.h
- src/filename.cpp
- src/filename.h
- src/flex_analyser.cpp
- + src/float16.h
- − src/gpu_utils/cub/agent/agent_histogram.cuh
- − src/gpu_utils/cub/agent/agent_radix_sort_downsweep.cuh
- − src/gpu_utils/cub/agent/agent_radix_sort_upsweep.cuh
- − src/gpu_utils/cub/agent/agent_reduce.cuh
- − src/gpu_utils/cub/agent/agent_reduce_by_key.cuh
- − src/gpu_utils/cub/agent/agent_rle.cuh
- − src/gpu_utils/cub/agent/agent_scan.cuh
- − src/gpu_utils/cub/agent/agent_segment_fixup.cuh
- − src/gpu_utils/cub/agent/agent_select_if.cuh
- − src/gpu_utils/cub/agent/agent_spmv_orig.cuh
- − src/gpu_utils/cub/agent/single_pass_scan_operators.cuh
- − src/gpu_utils/cub/block/block_adjacent_difference.cuh
- − src/gpu_utils/cub/block/block_discontinuity.cuh
- − src/gpu_utils/cub/block/block_exchange.cuh
- − src/gpu_utils/cub/block/block_histogram.cuh
- − src/gpu_utils/cub/block/block_load.cuh
- − src/gpu_utils/cub/block/block_radix_rank.cuh
- − src/gpu_utils/cub/block/block_radix_sort.cuh
- − src/gpu_utils/cub/block/block_raking_layout.cuh
- − src/gpu_utils/cub/block/block_reduce.cuh
- − src/gpu_utils/cub/block/block_scan.cuh
- − src/gpu_utils/cub/block/block_shuffle.cuh
- − src/gpu_utils/cub/block/block_store.cuh
- − src/gpu_utils/cub/block/specializations/block_histogram_atomic.cuh
- − src/gpu_utils/cub/block/specializations/block_histogram_sort.cuh
- − src/gpu_utils/cub/block/specializations/block_reduce_raking.cuh
- − src/gpu_utils/cub/block/specializations/block_reduce_raking_commutative_only.cuh
- − src/gpu_utils/cub/block/specializations/block_reduce_warp_reductions.cuh
- − src/gpu_utils/cub/block/specializations/block_scan_raking.cuh
- − src/gpu_utils/cub/block/specializations/block_scan_warp_scans.cuh
- − src/gpu_utils/cub/block/specializations/block_scan_warp_scans2.cuh
- − src/gpu_utils/cub/block/specializations/block_scan_warp_scans3.cuh
- − src/gpu_utils/cub/cub.cuh
- − src/gpu_utils/cub/device/device_histogram.cuh
- − src/gpu_utils/cub/device/device_partition.cuh
- − src/gpu_utils/cub/device/device_radix_sort.cuh
- − src/gpu_utils/cub/device/device_reduce.cuh
- − src/gpu_utils/cub/device/device_run_length_encode.cuh
- − src/gpu_utils/cub/device/device_scan.cuh
- − src/gpu_utils/cub/device/device_segmented_radix_sort.cuh
- − src/gpu_utils/cub/device/device_segmented_reduce.cuh
- − src/gpu_utils/cub/device/device_select.cuh
- − src/gpu_utils/cub/device/device_spmv.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_histogram.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_radix_sort.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_reduce.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_reduce_by_key.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_rle.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_scan.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_select_if.cuh
- − src/gpu_utils/cub/device/dispatch/dispatch_spmv_orig.cuh
- − src/gpu_utils/cub/grid/grid_barrier.cuh
- − src/gpu_utils/cub/grid/grid_even_share.cuh
- − src/gpu_utils/cub/grid/grid_mapping.cuh
- − src/gpu_utils/cub/grid/grid_queue.cuh
- − src/gpu_utils/cub/host/mutex.cuh
- − src/gpu_utils/cub/iterator/arg_index_input_iterator.cuh
- − src/gpu_utils/cub/iterator/cache_modified_input_iterator.cuh
- − src/gpu_utils/cub/iterator/cache_modified_output_iterator.cuh
- − src/gpu_utils/cub/iterator/constant_input_iterator.cuh
- − src/gpu_utils/cub/iterator/counting_input_iterator.cuh
- − src/gpu_utils/cub/iterator/discard_output_iterator.cuh
- − src/gpu_utils/cub/iterator/tex_obj_input_iterator.cuh
- − src/gpu_utils/cub/iterator/tex_ref_input_iterator.cuh
- − src/gpu_utils/cub/iterator/transform_input_iterator.cuh
- − src/gpu_utils/cub/thread/thread_load.cuh
- − src/gpu_utils/cub/thread/thread_operators.cuh
- − src/gpu_utils/cub/thread/thread_reduce.cuh
- − src/gpu_utils/cub/thread/thread_scan.cuh
- − src/gpu_utils/cub/thread/thread_search.cuh
- − src/gpu_utils/cub/thread/thread_store.cuh
- − src/gpu_utils/cub/util_allocator.cuh
- − src/gpu_utils/cub/util_arch.cuh
- − src/gpu_utils/cub/util_debug.cuh
- − src/gpu_utils/cub/util_device.cuh
- − src/gpu_utils/cub/util_macro.cuh
- − src/gpu_utils/cub/util_namespace.cuh
- − src/gpu_utils/cub/util_ptx.cuh
- − src/gpu_utils/cub/util_type.cuh
- − src/gpu_utils/cub/warp/specializations/warp_reduce_shfl.cuh
- − src/gpu_utils/cub/warp/specializations/warp_reduce_smem.cuh
- − src/gpu_utils/cub/warp/specializations/warp_scan_shfl.cuh
- − src/gpu_utils/cub/warp/specializations/warp_scan_smem.cuh
- − src/gpu_utils/cub/warp/warp_reduce.cuh
- − src/gpu_utils/cub/warp/warp_scan.cuh
- − src/gpu_utils/cuda_backprojector.cu
- − src/gpu_utils/cuda_backprojector.h
- − src/gpu_utils/cuda_benchmark_utils.cu
- − src/gpu_utils/cuda_helper_functions.cu
- − src/gpu_utils/cuda_helper_functions.cuh
- − src/gpu_utils/cuda_ml_optimiser.cu
- − src/gpu_utils/cuda_ml_optimiser.h
- − src/gpu_utils/cuda_projector.cu
- − src/gpu_utils/cuda_projector.cuh
- − src/gpu_utils/cuda_projector.h
- − src/gpu_utils/cuda_projector_plan.cu
- − src/gpu_utils/cuda_projector_plan.h
- − src/gpu_utils/cuda_skunks.cuh
- − src/gpu_utils/cuda_utils_stl.cuh
- − src/gpu_utils/cuda_utils_thrust.cuh_temp
- + src/gradient_optimisation.h
- src/gui_background.xpm
- src/gui_entries.cpp
- src/gui_entries.h
- src/gui_jobwindow.cpp
- src/gui_jobwindow.h
- src/gui_mainwindow.cpp
- src/gui_mainwindow.h
- src/healpix_sampling.cpp
- src/helix.cpp
- src/helix.h
- src/helix_inimodel2d.cpp
- src/image.cpp
- src/image.h
- − src/jaz/aberration_fit.cpp
- + src/jaz/archive/apps/add_tomo.cpp
- + src/jaz/archive/apps/align_frames.cpp
- + src/jaz/archive/apps/fit_aberrations.cpp
- + src/jaz/archive/apps/polish.cpp
- + src/jaz/archive/apps/refine_defocus.cpp
- + src/jaz/archive/apps/substack.cpp
- + src/jaz/archive/programs/aberration_fit.cpp
- + src/jaz/archive/programs/aberration_fit.h
- + src/jaz/archive/programs/defocus_refinement.cpp
- + src/jaz/archive/programs/defocus_refinement.h
- + src/jaz/archive/programs/frame_alignment_program.cpp
- + src/jaz/archive/programs/frame_alignment_program.h
- + src/jaz/archive/programs/polish.cpp
- + src/jaz/archive/programs/polish.h
- + src/jaz/atomic/pdb_helper.cpp
- + src/jaz/atomic/pdb_helper.h
- + src/jaz/cuda/kernels/add.cu
- + src/jaz/cuda/test00.cu
- + src/jaz/cuda/test00.h
- src/jaz/d3x3/copyright.txt
- src/jaz/d3x3/dsyev2.c
- src/jaz/d3x3/dsyevc3.c
- src/jaz/d3x3/dsyevd3.c
- src/jaz/d3x3/dsyevh3.c
- src/jaz/d3x3/dsyevj3.c
- src/jaz/d3x3/dsyevq3.c
- src/jaz/d3x3/dsyevv3.c
- src/jaz/d3x3/dsytrd3.c
- src/jaz/d3x3/slvsec3.c
- − src/jaz/gravis/.svn/all-wcprops
- − src/jaz/gravis/.svn/entries
- − src/jaz/gravis/.svn/text-base/CMakeLists.txt.svn-base
- − src/jaz/gravis/.svn/text-base/Exception.h.svn-base
- − src/jaz/gravis/.svn/text-base/Mesh.h.svn-base
- − src/jaz/gravis/.svn/text-base/NMesh.h.svn-base
- − src/jaz/gravis/.svn/text-base/NTuple.h.svn-base
- − src/jaz/gravis/.svn/text-base/OBJReader.h.svn-base
- − src/jaz/gravis/.svn/text-base/OBJWriter.h.svn-base
- − src/jaz/gravis/.svn/text-base/PushPull.h.svn-base
- − src/jaz/gravis/.svn/text-base/StringFormat.h.svn-base
- − src/jaz/gravis/.svn/text-base/Timer.hpp.svn-base
- − src/jaz/gravis/.svn/text-base/Tuple.h.svn-base
- − src/jaz/gravis/.svn/text-base/lapack.h.svn-base
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- − src/jaz/gravis/.svn/text-base/t2Vector.h.svn-base
- − src/jaz/gravis/.svn/text-base/t3Matrix.h.svn-base
- − src/jaz/gravis/.svn/text-base/t3Vector.h.svn-base
- − src/jaz/gravis/.svn/text-base/t4Matrix.h.svn-base
- − src/jaz/gravis/.svn/text-base/t4Vector.h.svn-base
- − src/jaz/gravis/.svn/text-base/tArray.h.svn-base
- − src/jaz/gravis/.svn/text-base/tBGR.h.svn-base
- − src/jaz/gravis/.svn/text-base/tDefaultVector.h.svn-base
- − src/jaz/gravis/.svn/text-base/tGray_A.h.svn-base
- − src/jaz/gravis/.svn/text-base/tImage.h.svn-base
- − src/jaz/gravis/.svn/text-base/tImageAlgorithm.h.svn-base
- − src/jaz/gravis/.svn/text-base/tLab.h.svn-base
- − src/jaz/gravis/.svn/text-base/tMM.h.svn-base
- − src/jaz/gravis/.svn/text-base/tMatrix.h.svn-base
- − src/jaz/gravis/.svn/text-base/tMesh.h.svn-base
- − src/jaz/gravis/.svn/text-base/tQuaternion.h.svn-base
- − src/jaz/gravis/.svn/text-base/tRGB.h.svn-base
- − src/jaz/gravis/.svn/text-base/tRGBA.h.svn-base
- − src/jaz/gravis/.svn/text-base/tRGB_A.h.svn-base
- − src/jaz/gravis/.svn/text-base/tVarMatrix.h.svn-base
- − src/jaz/gravis/.svn/text-base/tVarMatrix_blas.h.svn-base
- − src/jaz/gravis/.svn/text-base/tVarMatrix_blas.hxx.svn-base
- − src/jaz/gravis/.svn/text-base/tYCbCr.h.svn-base
- src/jaz/gravis/CMakeLists.txt
- src/jaz/gravis/StringFormat.h
- src/jaz/gravis/Timer.hpp
- − src/jaz/gravis/colour/.svn/all-wcprops
- − src/jaz/gravis/colour/.svn/entries
- − src/jaz/gravis/colour/.svn/text-base/CMakeLists.txt.svn-base
- − src/jaz/gravis/colour/.svn/text-base/rgb_hsv.h.svn-base
- src/jaz/gravis/colour/CMakeLists.txt
- − src/jaz/gravis/gravis/.svn/all-wcprops
- − src/jaz/gravis/gravis/.svn/entries
- − src/jaz/gravis/io/.svn/all-wcprops
- − src/jaz/gravis/io/.svn/entries
- − src/jaz/gravis/io/.svn/text-base/CMakeLists.txt.svn-base
- − src/jaz/gravis/io/.svn/text-base/array.h.svn-base
- − src/jaz/gravis/io/.svn/text-base/mesh.h.svn-base
- src/jaz/gravis/io/CMakeLists.txt
- src/jaz/gravis/io/array/.svn/all-wcprops
- src/jaz/gravis/io/array/.svn/entries
- src/jaz/gravis/io/array/.svn/text-base/ArrayStreamIO.h.svn-base
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- src/jaz/gravis/io/array/.svn/text-base/le.h.svn-base
- src/jaz/gravis/io/array/.svn/text-base/matlab.h.svn-base
- src/jaz/gravis/io/array/.svn/text-base/networkByteOrder.h.svn-base
- src/jaz/gravis/io/array/.svn/text-base/raw.h.svn-base
- src/jaz/gravis/io/array/CMakeLists.txt
- src/jaz/gravis/io/array/le.h
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- src/jaz/gravis/io/array/networkByteOrder.h
- src/jaz/gravis/io/image/.svn/all-wcprops
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- src/jaz/gravis/io/mesh/.svn/text-base/OBJWriter.h.svn-base
- src/jaz/gravis/io/mesh/.svn/text-base/absolute_paths.h.svn-base
- src/jaz/gravis/io/mesh/.svn/text-base/msh.h.svn-base
- src/jaz/gravis/io/mesh/.svn/text-base/obj.h.svn-base
- src/jaz/gravis/io/mesh/CMakeLists.txt
- − src/jaz/gravis/private/.svn/all-wcprops
- − src/jaz/gravis/private/.svn/entries
- − src/jaz/gravis/private/.svn/text-base/CMakeLists.txt.svn-base
- − src/jaz/gravis/private/.svn/text-base/OBJReader.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/OBJWriter.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/tDeterminants.h.svn-base
- − src/jaz/gravis/private/.svn/text-base/tImageConverter.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/tImageConvolution.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/tImageIO.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/tImageIO_JPG.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/tImageIO_PNG.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/tImageIO_PNM.hxx.svn-base
- − src/jaz/gravis/private/.svn/text-base/tRefCPtr.h.svn-base
- − src/jaz/gravis/private/.svn/tmp/OBJWriter.hxx.tmp
- src/jaz/gravis/private/CMakeLists.txt
- src/jaz/gravis/private/OBJReader.hxx
- src/jaz/gravis/private/OBJWriter.hxx
- src/jaz/gravis/private/tImageConverter.hxx
- src/jaz/gravis/private/tImageConvolution.hxx
- src/jaz/gravis/private/tImageIO.hxx
- src/jaz/gravis/private/tImageIO_JPG.hxx
- src/jaz/gravis/private/tImageIO_PNG.hxx
- src/jaz/gravis/private/tImageIO_PNM.hxx
- src/jaz/gravis/t3Matrix.h
- src/jaz/gravis/t3Vector.h
- src/jaz/gravis/t4Matrix.h
- src/jaz/gravis/t4Vector.h
- src/jaz/gravis/tImage.h
- − src/jaz/gravis/tImage/.svn/all-wcprops
- − src/jaz/gravis/tImage/.svn/entries
- − src/jaz/gravis/tImage/.svn/text-base/CMakeLists.txt.svn-base
- − src/jaz/gravis/tImage/.svn/text-base/access.hxx.svn-base
- − src/jaz/gravis/tImage/.svn/text-base/distance_transform.h.svn-base
- − src/jaz/gravis/tImage/.svn/text-base/draw.h.svn-base
- − src/jaz/gravis/tImage/.svn/text-base/interpolation.hxx.svn-base
- − src/jaz/gravis/tImage/.svn/text-base/normalization.h.svn-base
- − src/jaz/gravis/tImage/.svn/text-base/operators.h.svn-base
- − src/jaz/gravis/tImage/.svn/text-base/traits.h.svn-base
- src/jaz/gravis/tImage/CMakeLists.txt
- src/jaz/gravis/tImage/access.hxx
- src/jaz/gravis/tImage/interpolation.hxx
- src/jaz/gravis/tImage/normalization.h
- src/jaz/gravis/tImage/operators.h
- src/jaz/gravis/tQuaternion.h
- src/jaz/gravis/tVarMatrix_blas.hxx
- + src/jaz/hip/kernels/add.h
- + src/jaz/hip/test00.h
- + src/jaz/hip/test00.hip.cpp
- + src/jaz/image/buffered_image.h
- + src/jaz/image/centering.h
- src/jaz/img_proc/color_helper.cpp → src/jaz/image/color_helper.cpp
- src/jaz/img_proc/color_helper.h → src/jaz/image/color_helper.h
- + src/jaz/image/conversion.h
- + src/jaz/image/cutting.h
- + src/jaz/image/detection.h
- + src/jaz/image/divergence.h
- + src/jaz/image/filter.h
- + src/jaz/image/gradient.h
- + src/jaz/image/interpolation.h
- + src/jaz/image/local_extrema.h
- + src/jaz/image/noise.h
- + src/jaz/image/normalization.h
- + src/jaz/image/padding.h
- + src/jaz/image/power_spectrum.h
- + src/jaz/image/radial_avg.cpp
- + src/jaz/image/radial_avg.h
- + src/jaz/image/raw_image.h
- + src/jaz/image/resampling.cpp
- + src/jaz/image/resampling.h
- + src/jaz/image/similarity.h
- + src/jaz/image/stack_helper.cpp
- + src/jaz/image/stack_helper.h
- + src/jaz/image/structure_tensor.cpp
- + src/jaz/image/structure_tensor.h
- + src/jaz/image/symmetry.cpp
- + src/jaz/image/symmetry.h
- + src/jaz/image/tapering.h
- + src/jaz/image/translation.h
- + src/jaz/math/Euler_angles_dynamo.h
- + src/jaz/math/Euler_angles_relion.h
- + src/jaz/math/Gaussian_process.cpp
- + src/jaz/math/Gaussian_process.h
- + src/jaz/math/Tait_Bryan_angles.h
- src/jaz/math/Zernike.cpp
- + src/jaz/math/Zernike_helper.cpp
- + src/jaz/math/Zernike_helper.h
- + src/jaz/math/ellipse.h
- src/jaz/ctf/equation2x2.h → src/jaz/math/equation2x2.h
- + src/jaz/math/fcc.cpp
- + src/jaz/math/fcc.h
- + src/jaz/math/fft.cpp
- + src/jaz/math/fft.h
- + src/jaz/math/fft_buffer.cpp
- + src/jaz/math/fft_buffer.h
- + src/jaz/math/rigid_alignment.cpp
- + src/jaz/math/rigid_alignment.h
- + src/jaz/math/spherical_coordinates.cpp
- + src/jaz/math/spherical_coordinates.h
- + src/jaz/math/spline.h
- src/jaz/t_complex.cpp → src/jaz/math/t_complex.cpp
- + src/jaz/math/t_complex.h
- src/jaz/tensor2x2.h → src/jaz/math/tensor2x2.h
- src/jaz/tensor3x3.h → src/jaz/math/tensor3x3.h
- + src/jaz/membrane/area_point_blob_fit.cpp
- + src/jaz/membrane/area_point_blob_fit.h
- + src/jaz/membrane/blob_2d.cpp
- + src/jaz/membrane/blob_2d.h
- + src/jaz/membrane/blob_3d.cpp
- + src/jaz/membrane/blob_3d.h
- + src/jaz/membrane/blob_fit_2d.cpp
- + src/jaz/membrane/blob_fit_2d.h
- + src/jaz/membrane/blob_fit_3d.cpp
- + src/jaz/membrane/blob_fit_3d.h
- + src/jaz/membrane/cell_blob_fit.cpp
- + src/jaz/membrane/cell_blob_fit.h
- + src/jaz/membrane/cells.cpp
- + src/jaz/membrane/cells.h
- + src/jaz/membrane/global_blob_fit.cpp
- + src/jaz/membrane/global_blob_fit.h
- + src/jaz/membrane/membrane_fit.cpp
- + src/jaz/membrane/membrane_fit.h
- + src/jaz/membrane/membrane_segmentation.cpp
- + src/jaz/membrane/membrane_segmentation.h
- + src/jaz/membrane/multi_blob_fit.cpp
- + src/jaz/membrane/multi_blob_fit.h
- + src/jaz/membrane/phaseline_average.cpp
- + src/jaz/membrane/phaseline_average.h
- + src/jaz/membrane/point_blob_fit_2d.cpp
- + src/jaz/membrane/point_blob_fit_2d.h
- + src/jaz/membrane/quadric_disc_fit.cpp
- + src/jaz/membrane/quadric_disc_fit.h
- + src/jaz/membrane/tilt_space_blob_fit.cpp
- + src/jaz/membrane/tilt_space_blob_fit.h
- + src/jaz/mesh/mesh.cpp
- + src/jaz/mesh/mesh.h
- + src/jaz/mesh/mesh_builder.cpp
- + src/jaz/mesh/mesh_builder.h
- + src/jaz/mesh/triangle.cpp
- + src/jaz/mesh/triangle.h
- − src/jaz/motion/gp_motion_fit.cpp
- − src/jaz/motion/motion_helper.cpp
- − src/jaz/motion/motion_refiner_mpi.cpp
- + src/jaz/optics/aberration_fit.cpp
- + src/jaz/optics/aberration_fit.h
- + src/jaz/optics/aberrations_cache.cpp
- + src/jaz/optics/aberrations_cache.h
- + src/jaz/optics/astigmatism_fit.cpp
- + src/jaz/optics/astigmatism_fit.h
- + src/jaz/optics/ctf_equiphase_fit.cpp
- + src/jaz/optics/ctf_equiphase_fit.h
- src/jaz/ctf/equation2x2.cpp → src/jaz/optics/ctf_helper.cpp
- src/jaz/aberration_fit.h → src/jaz/optics/ctf_helper.h
- + src/jaz/optics/damage.cpp
- + src/jaz/optics/damage.h
- + src/jaz/optics/damage_model.h
- + src/jaz/optics/dual_contrast/dual_contrast_solution.h
- + src/jaz/optics/dual_contrast/dual_contrast_voxel.h
- + src/jaz/optics/dual_contrast/dual_contrast_writer.h
- src/jaz/ctf/magnification_helper.cpp → src/jaz/optics/magnification_helper.cpp
- src/jaz/ctf/magnification_helper.h → src/jaz/optics/magnification_helper.h
- + src/jaz/optics/optics_data.cpp
- + src/jaz/optics/optics_data.h
- + src/jaz/optics/spectral_ctf_cost.cpp
- + src/jaz/optics/spectral_ctf_cost.h
- + src/jaz/optics/spectral_ctf_fit.bak
- + src/jaz/optics/tile_ctf_cost.cpp
- + src/jaz/optics/tile_ctf_cost.h
- + src/jaz/optics/tomo_mag_fit.cpp
- + src/jaz/optics/tomo_mag_fit.h
- src/jaz/optimization/gradient_descent.cpp
- src/jaz/optimization/lbfgs.cpp
- src/jaz/optimization/lbfgs.h
- src/jaz/optimization/nelder_mead.cpp
- src/jaz/optimization/optimization.cpp
- src/jaz/optimization/optimization.h
- + src/jaz/optimization/random_walk.cpp
- + src/jaz/optimization/random_walk.h
- + src/jaz/optimization/recursive_line_search.cpp
- + src/jaz/optimization/recursive_line_search.h
- + src/jaz/scripts/BP_test.cpp
- + src/jaz/scripts/CMakeLists.txt
- + src/jaz/scripts/CTFPQ_test.cpp
- + src/jaz/scripts/add_subset.cpp
- + src/jaz/scripts/add_tomogram_name.cpp
- + src/jaz/scripts/align_2d_classes.cpp
- + src/jaz/scripts/analyse_dual_contrast.cpp
- + src/jaz/scripts/blobs_from_points.cpp
- + src/jaz/scripts/box_PCA.cpp
- + src/jaz/scripts/conversion_test.cpp
- + src/jaz/scripts/cuda_test.cpp
- + src/jaz/scripts/defilament.cpp
- + src/jaz/scripts/deramp.cpp
- + src/jaz/scripts/dose_convert.cpp
- + src/jaz/scripts/enumerate_micrographs.cpp
- + src/jaz/scripts/extract_blob_points.cpp
- + src/jaz/scripts/find_blobs_2d.cpp
- + src/jaz/scripts/fit_class_blobs.cpp
- + src/jaz/scripts/img_test.cpp
- + src/jaz/scripts/imod_test.cpp
- + src/jaz/scripts/make_split_tilts_star.cpp
- + src/jaz/scripts/measure_noise.cpp
- + src/jaz/scripts/measure_scale.cpp
- + src/jaz/scripts/membrane_dist.cpp
- + src/jaz/scripts/membrane_erase_2D.cpp
- + src/jaz/scripts/membrane_erase_3D.cpp
- + src/jaz/scripts/membrane_segment.cpp
- + src/jaz/scripts/plot_2d_classes.cpp
- + src/jaz/scripts/plot_DC_analysis.cpp
- + src/jaz/scripts/plot_dose_weight.cpp
- + src/jaz/scripts/plot_particles.cpp
- + src/jaz/scripts/plot_pdb.cpp
- + src/jaz/scripts/plot_tomo_defoci.cpp
- + src/jaz/scripts/plot_topaz_points.cpp
- + src/jaz/scripts/predict_tomo_view.cpp
- + src/jaz/scripts/print_coords.cpp
- + src/jaz/scripts/process_image.cpp
- + src/jaz/scripts/ramp.cpp
- + src/jaz/scripts/ref_delete_3d.cpp
- + src/jaz/scripts/rotate_subtomograms.cpp
- + src/jaz/scripts/sample_blob_points.cpp
- + src/jaz/scripts/scale_test.cpp
- + src/jaz/scripts/scratch.cpp
- + src/jaz/scripts/set_defocus_slope.cpp
- + src/jaz/scripts/shift_plot.cpp
- + src/jaz/scripts/sort_2d_classes.cpp
- src/jaz/svd_helper.cpp → src/jaz/scripts/spa_backproject.cpp
- + src/jaz/scripts/split_tilts.cpp
- + src/jaz/scripts/suppress_cone.cpp
- + src/jaz/scripts/test_extraction.cpp
- + src/jaz/scripts/test_logger.cpp
- + src/jaz/scripts/test_splines.cpp
- + src/jaz/scripts/update_tomogram_set.cpp
- + src/jaz/segmentation/diffusion.h
- + src/jaz/segmentation/diffusion_tensors.cpp
- + src/jaz/segmentation/diffusion_tensors.h
- + src/jaz/segmentation/primal_dual_TV.cpp
- + src/jaz/segmentation/primal_dual_TV.h
- + src/jaz/segmentation/skeletonization.cpp
- + src/jaz/segmentation/skeletonization.h
- src/jaz/Fourier_helper.cpp → src/jaz/single_particle/Fourier_helper.cpp
- src/jaz/Fourier_helper.h → src/jaz/single_particle/Fourier_helper.h
- src/jaz/Gaussian_pyramid.cpp → src/jaz/single_particle/Gaussian_pyramid.cpp
- src/jaz/Gaussian_pyramid.h → src/jaz/single_particle/Gaussian_pyramid.h
- src/jaz/Gaussian_pyramid.h.bak → src/jaz/single_particle/Gaussian_pyramid.h.bak
- src/jaz/svd_helper.h → src/jaz/single_particle/apps/backproject_2d.cpp
- + src/jaz/single_particle/apps/delete_blobs_2d.cpp
- src/jaz/archive/apps/em_motion.cpp → src/jaz/single_particle/archive/apps/em_motion.cpp
- src/jaz/archive/apps/ref_aberration_plot.cpp → src/jaz/single_particle/archive/apps/ref_aberration_plot.cpp
- src/jaz/archive/apps/update_angles.cpp → src/jaz/single_particle/archive/apps/update_angles.cpp
- src/jaz/archive/frame_merge.cpp → src/jaz/single_particle/archive/frame_merge.cpp
- src/jaz/archive/frame_merge.h → src/jaz/single_particle/archive/frame_merge.h
- src/jaz/archive/motion_em.cpp → src/jaz/single_particle/archive/motion_em.cpp
- src/jaz/archive/motion_em.h → src/jaz/single_particle/archive/motion_em.h
- src/jaz/archive/motion_refinement.cpp → src/jaz/single_particle/archive/motion_refinement.cpp
- src/jaz/archive/motion_refinement.h → src/jaz/single_particle/archive/motion_refinement.h
- src/jaz/archive/refinement_program.cpp → src/jaz/single_particle/archive/refinement_program.cpp
- src/jaz/archive/refinement_program.h → src/jaz/single_particle/archive/refinement_program.h
- + src/jaz/single_particle/class_helper.cpp
- + src/jaz/single_particle/class_helper.h
- src/jaz/complex_io.cpp → src/jaz/single_particle/complex_io.cpp
- src/jaz/complex_io.h → src/jaz/single_particle/complex_io.h
- src/jaz/config.h → src/jaz/single_particle/config.h
- src/jaz/convolution_helper.cpp → src/jaz/single_particle/convolution_helper.cpp
- src/jaz/convolution_helper.h → src/jaz/single_particle/convolution_helper.h
- src/jaz/ctf/aberration_estimator.cpp → src/jaz/single_particle/ctf/aberration_estimator.cpp
- src/jaz/ctf/aberration_estimator.h → src/jaz/single_particle/ctf/aberration_estimator.h
- src/jaz/ctf/bfactor_refiner.cpp → src/jaz/single_particle/ctf/bfactor_refiner.cpp
- src/jaz/ctf/bfactor_refiner.h → src/jaz/single_particle/ctf/bfactor_refiner.h
- src/jaz/ctf/ctf_refiner.cpp → src/jaz/single_particle/ctf/ctf_refiner.cpp
- src/jaz/ctf/ctf_refiner.h → src/jaz/single_particle/ctf/ctf_refiner.h
- src/jaz/ctf/ctf_refiner_mpi.cpp → src/jaz/single_particle/ctf/ctf_refiner_mpi.cpp
- src/jaz/ctf/ctf_refiner_mpi.h → src/jaz/single_particle/ctf/ctf_refiner_mpi.h
- src/jaz/ctf/defocus_estimator.cpp → src/jaz/single_particle/ctf/defocus_estimator.cpp
- src/jaz/ctf/defocus_estimator.h → src/jaz/single_particle/ctf/defocus_estimator.h
- src/jaz/ctf/defocus_helper.cpp → src/jaz/single_particle/ctf/defocus_helper.cpp
- src/jaz/ctf/defocus_helper.h → src/jaz/single_particle/ctf/defocus_helper.h
- src/jaz/ctf/delocalisation_helper.cpp → src/jaz/single_particle/ctf/delocalisation_helper.cpp
- src/jaz/ctf/delocalisation_helper.h → src/jaz/single_particle/ctf/delocalisation_helper.h
- src/jaz/ctf/magnification_estimator.cpp → src/jaz/single_particle/ctf/magnification_estimator.cpp
- src/jaz/ctf/magnification_estimator.h → src/jaz/single_particle/ctf/magnification_estimator.h
- src/jaz/ctf/modular_ctf_optimisation.cpp → src/jaz/single_particle/ctf/modular_ctf_optimisation.cpp
- src/jaz/ctf/modular_ctf_optimisation.h → src/jaz/single_particle/ctf/modular_ctf_optimisation.h
- src/jaz/ctf/tilt_estimator.cpp → src/jaz/single_particle/ctf/tilt_estimator.cpp
- src/jaz/ctf/tilt_estimator.h → src/jaz/single_particle/ctf/tilt_estimator.h
- src/jaz/ctf/tilt_helper.cpp → src/jaz/single_particle/ctf/tilt_helper.cpp
- src/jaz/ctf/tilt_helper.h → src/jaz/single_particle/ctf/tilt_helper.h
- src/jaz/ctf_helper.cpp → src/jaz/single_particle/ctf_helper.cpp
- src/jaz/ctf_helper.h → src/jaz/single_particle/ctf_helper.h
- + src/jaz/single_particle/d3x3/copyright.txt
- + src/jaz/single_particle/d3x3/dsyev2.c
- + src/jaz/single_particle/d3x3/dsyev2.h
- + src/jaz/single_particle/d3x3/dsyevc3.c
- + src/jaz/single_particle/d3x3/dsyevc3.h
- + src/jaz/single_particle/d3x3/dsyevd3.c
- + src/jaz/single_particle/d3x3/dsyevd3.h
- + src/jaz/single_particle/d3x3/dsyevh3.c
- + src/jaz/single_particle/d3x3/dsyevh3.h
- + src/jaz/single_particle/d3x3/dsyevj3.c
- + src/jaz/single_particle/d3x3/dsyevj3.h
- + src/jaz/single_particle/d3x3/dsyevq3.c
- + src/jaz/single_particle/d3x3/dsyevq3.h
- + src/jaz/single_particle/d3x3/dsyevv3.c
- + src/jaz/single_particle/d3x3/dsyevv3.h
- + src/jaz/single_particle/d3x3/dsytrd3.c
- + src/jaz/single_particle/d3x3/dsytrd3.h
- + src/jaz/single_particle/d3x3/slvsec3.c
- + src/jaz/single_particle/d3x3/slvsec3.h
- src/jaz/damage_helper.cpp → src/jaz/single_particle/damage_helper.cpp
- src/jaz/damage_helper.h → src/jaz/single_particle/damage_helper.h
- src/jaz/distribution_helper.cpp → src/jaz/single_particle/distribution_helper.cpp
- src/jaz/distribution_helper.h → src/jaz/single_particle/distribution_helper.h
- src/jaz/fftw_helper.cpp → src/jaz/single_particle/fftw_helper.cpp
- src/jaz/fftw_helper.h → src/jaz/single_particle/fftw_helper.h
- src/jaz/fsc_helper.cpp → src/jaz/single_particle/fsc_helper.cpp
- src/jaz/fsc_helper.h → src/jaz/single_particle/fsc_helper.h
- src/jaz/image_log.cpp → src/jaz/single_particle/image_log.cpp
- src/jaz/image_log.h → src/jaz/single_particle/image_log.h
- src/jaz/img_proc/filter_helper.cpp → src/jaz/single_particle/img_proc/filter_helper.cpp
- src/jaz/img_proc/filter_helper.h → src/jaz/single_particle/img_proc/filter_helper.h
- src/jaz/img_proc/image_op.cpp → src/jaz/single_particle/img_proc/image_op.cpp
- src/jaz/img_proc/image_op.h → src/jaz/single_particle/img_proc/image_op.h
- src/jaz/img_proc/radial_avg.h → src/jaz/single_particle/img_proc/radial_avg.h
- + src/jaz/single_particle/index_sort.h
- src/jaz/interpolation.cpp → src/jaz/single_particle/interpolation.cpp
- src/jaz/interpolation.h → src/jaz/single_particle/interpolation.h
- src/jaz/io/star_converter.cpp → src/jaz/single_particle/io/star_converter.cpp
- src/jaz/io/star_converter.h → src/jaz/single_particle/io/star_converter.h
- src/jaz/jaz_config.cpp → src/jaz/single_particle/jaz_config.cpp
- src/jaz/jaz_config.h → src/jaz/single_particle/jaz_config.h
- src/jaz/lbfgs/arithmetic_ansi.h → src/jaz/single_particle/lbfgs/arithmetic_ansi.h
- src/jaz/lbfgs/arithmetic_sse_double.h → src/jaz/single_particle/lbfgs/arithmetic_sse_double.h
- src/jaz/lbfgs/arithmetic_sse_float.h → src/jaz/single_particle/lbfgs/arithmetic_sse_float.h
- src/jaz/lbfgs/copyright.txt → src/jaz/single_particle/lbfgs/copyright.txt
- src/jaz/lbfgs/lbfgs.c → src/jaz/single_particle/lbfgs/lbfgs.c
- src/jaz/lbfgs/lbfgs.h → src/jaz/single_particle/lbfgs/lbfgs.h
- src/jaz/legacy_obs_model.cpp → src/jaz/single_particle/legacy_obs_model.cpp
- src/jaz/legacy_obs_model.h → src/jaz/single_particle/legacy_obs_model.h
- src/jaz/local_motion_fit.cpp → src/jaz/single_particle/local_motion_fit.cpp
- src/jaz/local_motion_fit.h → src/jaz/single_particle/local_motion_fit.h
- src/jaz/micrograph_handler.cpp → src/jaz/single_particle/micrograph_handler.cpp
- src/jaz/micrograph_handler.h → src/jaz/single_particle/micrograph_handler.h
- src/jaz/motion/alignment_set.cpp → src/jaz/single_particle/motion/alignment_set.cpp
- src/jaz/motion/alignment_set.h → src/jaz/single_particle/motion/alignment_set.h
- src/jaz/motion/frame_recombiner.cpp → src/jaz/single_particle/motion/frame_recombiner.cpp
- src/jaz/motion/frame_recombiner.h → src/jaz/single_particle/motion/frame_recombiner.h
- + src/jaz/single_particle/motion/gp_motion_fit.cpp
- src/jaz/motion/gp_motion_fit.h → src/jaz/single_particle/motion/gp_motion_fit.h
- src/jaz/motion/motion_estimator.cpp → src/jaz/single_particle/motion/motion_estimator.cpp
- src/jaz/motion/motion_estimator.h → src/jaz/single_particle/motion/motion_estimator.h
- + src/jaz/single_particle/motion/motion_helper.cpp
- src/jaz/motion/motion_helper.h → src/jaz/single_particle/motion/motion_helper.h
- src/jaz/motion/motion_param_estimator.cpp → src/jaz/single_particle/motion/motion_param_estimator.cpp
- src/jaz/motion/motion_param_estimator.h → src/jaz/single_particle/motion/motion_param_estimator.h
- src/jaz/motion/motion_refiner.cpp → src/jaz/single_particle/motion/motion_refiner.cpp
- src/jaz/motion/motion_refiner.h → src/jaz/single_particle/motion/motion_refiner.h
- + src/jaz/single_particle/motion/motion_refiner_mpi.cpp
- src/jaz/motion/motion_refiner_mpi.h → src/jaz/single_particle/motion/motion_refiner_mpi.h
- src/jaz/motion/three_hyperparameter_fit.cpp → src/jaz/single_particle/motion/three_hyperparameter_fit.cpp
- src/jaz/motion/three_hyperparameter_fit.h → src/jaz/single_particle/motion/three_hyperparameter_fit.h
- src/jaz/motion/two_hyperparameter_fit.cpp → src/jaz/single_particle/motion/two_hyperparameter_fit.cpp
- src/jaz/motion/two_hyperparameter_fit.h → src/jaz/single_particle/motion/two_hyperparameter_fit.h
- + src/jaz/single_particle/movie_loader.h
- src/jaz/new_ft.cpp → src/jaz/single_particle/new_ft.cpp
- src/jaz/new_ft.h → src/jaz/single_particle/new_ft.h
- + src/jaz/single_particle/new_reference_map.cpp
- + src/jaz/single_particle/new_reference_map.h
- src/jaz/noise_helper.cpp → src/jaz/single_particle/noise_helper.cpp
- src/jaz/noise_helper.h → src/jaz/single_particle/noise_helper.h
- src/jaz/obs_model.cpp → src/jaz/single_particle/obs_model.cpp
- src/jaz/obs_model.h → src/jaz/single_particle/obs_model.h
- src/jaz/parallel_ft.cpp → src/jaz/single_particle/parallel_ft.cpp
- src/jaz/parallel_ft.h → src/jaz/single_particle/parallel_ft.h
- + src/jaz/single_particle/programs/backproject_2d.cpp
- + src/jaz/single_particle/programs/backproject_2d.h
- + src/jaz/single_particle/programs/delete_blobs_2d.cpp
- + src/jaz/single_particle/programs/delete_blobs_2d.h
- + src/jaz/single_particle/programs/spa_backproject.cpp
- + src/jaz/single_particle/programs/spa_backproject.h
- src/jaz/reference_map.cpp → src/jaz/single_particle/reference_map.cpp
- src/jaz/reference_map.h → src/jaz/single_particle/reference_map.h
- src/jaz/refinement_helper.cpp → src/jaz/single_particle/refinement_helper.cpp
- src/jaz/refinement_helper.h → src/jaz/single_particle/refinement_helper.h
- src/jaz/resampling_helper.cpp → src/jaz/single_particle/resampling_helper.cpp
- src/jaz/resampling_helper.h → src/jaz/single_particle/resampling_helper.h
- src/jaz/slice_helper.cpp → src/jaz/single_particle/slice_helper.cpp
- src/jaz/slice_helper.h → src/jaz/single_particle/slice_helper.h
- + src/jaz/single_particle/spa_extraction.h
- src/jaz/spectral_helper.cpp → src/jaz/single_particle/spectral_helper.cpp
- src/jaz/spectral_helper.h → src/jaz/single_particle/spectral_helper.h
- src/jaz/stack_helper.cpp → src/jaz/single_particle/stack_helper.cpp
- src/jaz/stack_helper.h → src/jaz/single_particle/stack_helper.h
- src/jaz/structure_tensor.cpp → src/jaz/single_particle/structure_tensor.cpp
- src/jaz/structure_tensor.h → src/jaz/single_particle/structure_tensor.h
- + src/jaz/single_particle/t_complex.cpp
- src/jaz/t_complex.h → src/jaz/single_particle/t_complex.h
- src/jaz/tomo/backprojection_helper.cpp → src/jaz/single_particle/tomo/backprojection_helper.cpp
- src/jaz/tomo/backprojection_helper.h → src/jaz/single_particle/tomo/backprojection_helper.h
- src/jaz/tomo/projection_helper.cpp → src/jaz/single_particle/tomo/projection_helper.cpp
- src/jaz/tomo/projection_helper.h → src/jaz/single_particle/tomo/projection_helper.h
- src/jaz/tomo/tomo_stack.cpp → src/jaz/single_particle/tomo/tomo_stack.cpp
- src/jaz/tomo/tomo_stack.h → src/jaz/single_particle/tomo/tomo_stack.h
- src/jaz/volume.h → src/jaz/single_particle/volume.h
- src/jaz/volume_converter.cpp → src/jaz/single_particle/volume_converter.cpp
- src/jaz/volume_converter.h → src/jaz/single_particle/volume_converter.h
- src/jaz/volume_integration.cpp → src/jaz/single_particle/volume_integration.cpp
- src/jaz/volume_integration.h → src/jaz/single_particle/volume_integration.h
- src/jaz/vtk_helper.cpp → src/jaz/single_particle/vtk_helper.cpp
- src/jaz/vtk_helper.h → src/jaz/single_particle/vtk_helper.h
- + src/jaz/tomography/apps/Wiener_divide.cpp
- + src/jaz/tomography/apps/add_spheres.cpp
- + src/jaz/tomography/apps/align.cpp
- + src/jaz/tomography/apps/align_mpi.cpp
- + src/jaz/tomography/apps/bin_stack.cpp
- + src/jaz/tomography/apps/catalogue_tomos.cpp
- + src/jaz/tomography/apps/compute_FCC.cpp
- + src/jaz/tomography/apps/convert_projections.cpp
- + src/jaz/tomography/apps/dark_erase.cpp
- + src/jaz/tomography/apps/delete_blobs.cpp
- + src/jaz/tomography/apps/discover_motif.cpp
- + src/jaz/tomography/apps/find_fiducials.cpp
- + src/jaz/tomography/apps/find_lattice.cpp
- + src/jaz/tomography/apps/fit_bfactors.cpp
- + src/jaz/tomography/apps/fit_blobs_3d.cpp
- + src/jaz/tomography/apps/import_coordinates.cpp
- + src/jaz/tomography/apps/local_particle_refine.cpp
- + src/jaz/tomography/apps/make_optimisation_set.cpp
- + src/jaz/tomography/apps/powspec.cpp
- + src/jaz/tomography/apps/predict_tilt_series.cpp
- + src/jaz/tomography/apps/reconstruct_particle.cpp
- + src/jaz/tomography/apps/reconstruct_particle_mpi.cpp
- + src/jaz/tomography/apps/reconstruct_tomogram.cpp
- + src/jaz/tomography/apps/reconstruct_tomogram_mpi.cpp
- + src/jaz/tomography/apps/refine_ctf.cpp
- + src/jaz/tomography/apps/refine_ctf_mpi.cpp
- + src/jaz/tomography/apps/refine_mag.cpp
- + src/jaz/tomography/apps/sample_manifold.cpp
- + src/jaz/tomography/apps/split_optics.cpp
- + src/jaz/tomography/apps/subtomo.cpp
- + src/jaz/tomography/apps/subtomo_mpi.cpp
- + src/jaz/tomography/apps/taper.cpp
- + src/jaz/tomography/apps/template_pick.cpp
- + src/jaz/tomography/apps/tomo_ctf.cpp
- + src/jaz/tomography/dynamo/catalogue.cpp
- + src/jaz/tomography/dynamo/catalogue.h
- + src/jaz/tomography/dynamo/dynamo_particle.cpp
- + src/jaz/tomography/dynamo/dynamo_particle.h
- + src/jaz/tomography/dynamo_data_set.cpp
- + src/jaz/tomography/dynamo_data_set.h
- + src/jaz/tomography/extraction.h
- + src/jaz/tomography/fiducials.cpp
- + src/jaz/tomography/fiducials.h
- + src/jaz/tomography/filament/circular_Fourier_filament_model.cpp
- + src/jaz/tomography/filament/circular_Fourier_filament_model.h
- + src/jaz/tomography/filament/closest_spline_point_problem.cpp
- + src/jaz/tomography/filament/closest_spline_point_problem.h
- + src/jaz/tomography/filament/coordinate_conventions.h
- + src/jaz/tomography/filament/filament.cpp
- + src/jaz/tomography/filament/filament.h
- + src/jaz/tomography/filament/filament_fit.cpp
- + src/jaz/tomography/filament/filament_fit.h
- + src/jaz/tomography/filament/filament_mapping.cpp
- + src/jaz/tomography/filament/filament_mapping.h
- + src/jaz/tomography/filament/filament_model.cpp
- + src/jaz/tomography/filament/filament_model.h
- + src/jaz/tomography/filament/membrane_template.cpp
- + src/jaz/tomography/filament/membrane_template.h
- + src/jaz/tomography/filament/multi_filament_fit.cpp
- + src/jaz/tomography/filament/multi_filament_fit.h
- + src/jaz/tomography/filament/pixel_set.h
- src/jaz/tomo/imod_helper.cpp → src/jaz/tomography/imod_helper.cpp
- src/jaz/tomo/imod_helper.h → src/jaz/tomography/imod_helper.h
- + src/jaz/tomography/imod_import.cpp
- + src/jaz/tomography/imod_import.h
- + src/jaz/tomography/lattice/motif.cpp
- + src/jaz/tomography/lattice/motif.h
- + src/jaz/tomography/lattice/motif_alignment.cpp
- + src/jaz/tomography/lattice/motif_alignment.h
- + src/jaz/tomography/lattice/motif_detection.cpp
- + src/jaz/tomography/lattice/motif_detection.h
- + src/jaz/tomography/lattice/motif_refinement.cpp
- + src/jaz/tomography/lattice/motif_refinement.h
- + src/jaz/tomography/lattice/point_cloud.cpp
- + src/jaz/tomography/lattice/point_cloud.h
- + src/jaz/tomography/local_particle_refinement.cpp
- + src/jaz/tomography/local_particle_refinement.h
- + src/jaz/tomography/manifold/CMM_loader.cpp
- + src/jaz/tomography/manifold/CMM_loader.h
- + src/jaz/tomography/manifold/manifold.h
- + src/jaz/tomography/manifold/manifold_loader.cpp
- + src/jaz/tomography/manifold/manifold_loader.h
- + src/jaz/tomography/manifold/manifold_set.cpp
- + src/jaz/tomography/manifold/manifold_set.h
- + src/jaz/tomography/manifold/sphere.cpp
- + src/jaz/tomography/manifold/sphere.h
- + src/jaz/tomography/manifold/spheroid.cpp
- + src/jaz/tomography/manifold/spheroid.h
- + src/jaz/tomography/motion/2D_deformation.h
- + src/jaz/tomography/motion/Fourier_2D_deformation.cpp
- + src/jaz/tomography/motion/Fourier_2D_deformation.h
- + src/jaz/tomography/motion/linear_2D_deformation.cpp
- + src/jaz/tomography/motion/linear_2D_deformation.h
- + src/jaz/tomography/motion/modular_alignment/Fourier_2D_deformation_model.cpp
- + src/jaz/tomography/motion/modular_alignment/Fourier_2D_deformation_model.h
- + src/jaz/tomography/motion/modular_alignment/GP_motion_model.cpp
- + src/jaz/tomography/motion/modular_alignment/GP_motion_model.h
- + src/jaz/tomography/motion/modular_alignment/linear_2D_deformation_model.cpp
- + src/jaz/tomography/motion/modular_alignment/linear_2D_deformation_model.h
- + src/jaz/tomography/motion/modular_alignment/modular_alignment.cpp
- + src/jaz/tomography/motion/modular_alignment/modular_alignment.h
- + src/jaz/tomography/motion/modular_alignment/no_2D_deformation_model.cpp
- + src/jaz/tomography/motion/modular_alignment/no_2D_deformation_model.h
- + src/jaz/tomography/motion/modular_alignment/no_motion_model.cpp
- + src/jaz/tomography/motion/modular_alignment/no_motion_model.h
- + src/jaz/tomography/motion/modular_alignment/spline_2D_deformation_model.cpp
- + src/jaz/tomography/motion/modular_alignment/spline_2D_deformation_model.h
- + src/jaz/tomography/motion/motion_fit.cpp
- + src/jaz/tomography/motion/motion_fit.h
- + src/jaz/tomography/motion/proto_alignment.cpp
- + src/jaz/tomography/motion/proto_alignment.h
- + src/jaz/tomography/motion/shift_alignment.cpp
- + src/jaz/tomography/motion/shift_alignment.h
- + src/jaz/tomography/motion/spectral_alignment.cpp
- + src/jaz/tomography/motion/spectral_alignment.h
- + src/jaz/tomography/motion/spline_2D_deformation.cpp
- + src/jaz/tomography/motion/spline_2D_deformation.h
- + src/jaz/tomography/motion/trajectory.cpp
- + src/jaz/tomography/motion/trajectory.h
- + src/jaz/tomography/motion/trajectory_set.cpp
- + src/jaz/tomography/motion/trajectory_set.h
- + src/jaz/tomography/optimisation_set.cpp
- + src/jaz/tomography/optimisation_set.h
- + src/jaz/tomography/particle_set.cpp
- + src/jaz/tomography/particle_set.h
- + src/jaz/tomography/prediction.cpp
- + src/jaz/tomography/prediction.h
- + src/jaz/tomography/programs/align.cpp
- + src/jaz/tomography/programs/align.h
- + src/jaz/tomography/programs/align_mpi.cpp
- + src/jaz/tomography/programs/align_mpi.h
- + src/jaz/tomography/programs/bfactor_fit.cpp
- + src/jaz/tomography/programs/bfactor_fit.h
- + src/jaz/tomography/programs/convert_projections.cpp
- + src/jaz/tomography/programs/convert_projections.h
- + src/jaz/tomography/programs/ctf_refinement.cpp
- + src/jaz/tomography/programs/ctf_refinement.h
- + src/jaz/tomography/programs/ctf_refinement_mpi.cpp
- + src/jaz/tomography/programs/ctf_refinement_mpi.h
- + src/jaz/tomography/programs/dark_erase.cpp
- + src/jaz/tomography/programs/dark_erase.h
- + src/jaz/tomography/programs/delete_blobs.cpp
- + src/jaz/tomography/programs/delete_blobs.h
- + src/jaz/tomography/programs/discover_motif.cpp
- + src/jaz/tomography/programs/discover_motif.h
- + src/jaz/tomography/programs/fcc_computation.cpp
- + src/jaz/tomography/programs/fcc_computation.h
- + src/jaz/tomography/programs/find_fiducials.cpp
- + src/jaz/tomography/programs/find_fiducials.h
- + src/jaz/tomography/programs/find_lattice.cpp
- + src/jaz/tomography/programs/find_lattice.h
- + src/jaz/tomography/programs/fit_blobs_3d.cpp
- + src/jaz/tomography/programs/fit_blobs_3d.h
- + src/jaz/tomography/programs/local_particle_refine.cpp
- + src/jaz/tomography/programs/local_particle_refine.h
- + src/jaz/tomography/programs/mag_fit.cpp
- + src/jaz/tomography/programs/mag_fit.h
- + src/jaz/tomography/programs/powspec.cpp
- + src/jaz/tomography/programs/powspec.h
- + src/jaz/tomography/programs/reconstruct_particle.cpp
- + src/jaz/tomography/programs/reconstruct_particle.h
- + src/jaz/tomography/programs/reconstruct_particle_mpi.cpp
- + src/jaz/tomography/programs/reconstruct_particle_mpi.h
- + src/jaz/tomography/programs/reconstruct_tomogram.cpp
- + src/jaz/tomography/programs/reconstruct_tomogram.h
- + src/jaz/tomography/programs/refinement.cpp
- + src/jaz/tomography/programs/refinement.h
- + src/jaz/tomography/programs/sample_manifold.cpp
- + src/jaz/tomography/programs/sample_manifold.h
- + src/jaz/tomography/programs/subtomo.cpp
- + src/jaz/tomography/programs/subtomo.h
- + src/jaz/tomography/programs/subtomo_mpi.cpp
- + src/jaz/tomography/programs/subtomo_mpi.h
- + src/jaz/tomography/programs/template_picker.cpp
- + src/jaz/tomography/programs/template_picker.h
- + src/jaz/tomography/programs/tomo_ctf.cpp
- + src/jaz/tomography/programs/tomo_ctf.h
- + src/jaz/tomography/projection/Fourier_backprojection.h
- + src/jaz/tomography/projection/cross_projection.h
- + src/jaz/tomography/projection/fwd_projection.h
- + src/jaz/tomography/projection/point_insertion.h
- + src/jaz/tomography/projection/projection.h
- + src/jaz/tomography/projection/projection_test.h
- + src/jaz/tomography/projection/real_backprojection.h
- + src/jaz/tomography/projection_IO.cpp
- + src/jaz/tomography/projection_IO.h
- + src/jaz/tomography/reconstruction.h
- + src/jaz/tomography/reference_map.cpp
- + src/jaz/tomography/reference_map.h
- + src/jaz/tomography/tilt_geometry.cpp
- + src/jaz/tomography/tilt_geometry.h
- + src/jaz/tomography/tomo_ctf_find.cpp
- + src/jaz/tomography/tomo_ctf_find.h
- + src/jaz/tomography/tomo_ctf_helper.cpp
- + src/jaz/tomography/tomo_ctf_helper.h
- + src/jaz/tomography/tomo_stack.h
- + src/jaz/tomography/tomogram.cpp
- + src/jaz/tomography/tomogram.h
- + src/jaz/tomography/tomogram_set.cpp
- + src/jaz/tomography/tomogram_set.h
- + src/jaz/tomography/tomolist.cpp
- + src/jaz/tomography/tomolist.h
- + src/jaz/util/ansi_codes.cpp
- + src/jaz/util/ansi_codes.h
- + src/jaz/util/drawing.h
- + src/jaz/util/image_file_helper.cpp
- + src/jaz/util/image_file_helper.h
- src/jaz/index_sort.h → src/jaz/util/index_sort.h
- + src/jaz/util/log.cpp
- + src/jaz/util/log.h
- + src/jaz/util/new_vtk_helper.h
- + src/jaz/util/topaz_helper.cpp
- + src/jaz/util/topaz_helper.h
- + src/jaz/util/zio.cpp
- + src/jaz/util/zio.h
- + src/lbfgs/arithmetic_ansi.h
- + src/lbfgs/arithmetic_sse_double.h
- + src/lbfgs/arithmetic_sse_float.h
- + src/lbfgs/copyright.txt
- + src/lbfgs/lbfgs.c
- + src/lbfgs/lbfgs.h
- src/macros.h
- src/manualpicker.cpp
- src/manualpicker.h
- src/mask.cpp
- src/metadata_container.cpp
- src/metadata_container.h
- src/metadata_label.cpp
- src/metadata_label.h
- src/metadata_table.cpp
- src/metadata_table.h
- src/micrograph_model.cpp
- src/ml_model.cpp
- src/ml_model.h
- src/ml_optimiser.cpp
- src/ml_optimiser.h
- src/ml_optimiser_mpi.cpp
- src/ml_optimiser_mpi.h
- src/motioncorr_runner.cpp
- src/motioncorr_runner.h
- src/motioncorr_runner_mpi.cpp
- src/mpi.cpp
- src/mpi.h
- src/multidim_array.h
- + src/npy.hpp
- src/parallel.cpp
- src/parallel.h
- src/particle_subtractor.cpp
- src/particle_subtractor.h
- src/pipeline_control.cpp
- src/pipeline_control.h
- src/pipeline_jobs.cpp
- src/pipeline_jobs.h
- src/pipeliner.cpp
- src/pipeliner.h
- src/postprocessing.cpp
- src/postprocessing.h
- src/preprocessing.cpp
- src/preprocessing.h
- src/preprocessing_mpi.cpp
- src/projector.cpp
- src/projector.h
- src/reconstructor.cpp
- src/reconstructor.h
- src/renderEER.cpp
- src/renderEER.h
- src/rwIMAGIC.h
- src/rwMRC.h
- src/rwSPIDER.h
- src/rwTIFF.h
- src/scheduler.cpp → src/schemer.cpp
- src/scheduler.h → src/schemer.h
- + src/spherical-harmonics/Makefile
- + src/spherical-harmonics/README.md
- + src/spherical-harmonics/SphericalHarmonics.cc
- + src/spherical-harmonics/SphericalHarmonics.h
- + src/spherical-harmonics/epl-v10.html
- src/strings.cpp
- src/strings.h
- src/tiff_converter.cpp
- src/time.cpp
- + src/tomography_python_programs/__init__.py
- + src/tomography_python_programs/_metadata_models/__init__.py
- + src/tomography_python_programs/_metadata_models/gui/__init__.py
- + src/tomography_python_programs/_metadata_models/gui/lazy_tilt_series_data.py
- + src/tomography_python_programs/_metadata_models/gui/tilt_series.py
- + src/tomography_python_programs/_metadata_models/gui/tilt_series_set.py
- + src/tomography_python_programs/_metadata_models/relion/__init__.py
- + src/tomography_python_programs/_metadata_models/relion/tilt_series.py
- + src/tomography_python_programs/_metadata_models/relion/tilt_series_set.py
- + src/tomography_python_programs/_qt/__init__.py
- + src/tomography_python_programs/_qt/components/__init__.py
- + src/tomography_python_programs/_qt/components/checkable_tilt_image_list.py
- + src/tomography_python_programs/_qt/components/save_dialog.py
- + src/tomography_python_programs/_qt/components/selection_buttons.py
- + src/tomography_python_programs/_qt/components/tilt_image_selection_widget.py
- + src/tomography_python_programs/_qt/components/tilt_series_browser.py
- + src/tomography_python_programs/_qt/components/tilt_series_list.py
- + src/tomography_python_programs/_qt/components/tomogram_browser.py
- + src/tomography_python_programs/_qt/tilt_image_excluder.py
- + src/tomography_python_programs/_tests/conftest.py
- + src/tomography_python_programs/_tests/test_metadata_model.py
- + src/tomography_python_programs/_tests/test_project_directory/tilt_series_metadata/tilt_series.star
- + src/tomography_python_programs/_tests/test_project_directory/tilt_series_metadata/tilt_series/220728_TS_01.star
- + src/tomography_python_programs/_tests/test_project_directory/tilt_series_metadata/tilt_series/220728_TS_03.star
- + src/tomography_python_programs/_tests/test_project_directory/tilt_series_metadata/tilt_series/220728_TS_43.star
- + src/tomography_python_programs/_tests/test_project_directory/tilt_series_metadata/tilt_series/220728_TS_45.star
- + src/tomography_python_programs/_tests/test_project_directory/tilt_series_metadata/tilt_series/220728_TS_54.star
- + src/tomography_python_programs/_utils/__init__.py
- + src/tomography_python_programs/_utils/file.py
- + src/tomography_python_programs/_utils/image.py
- + src/tomography_python_programs/_utils/mdoc.py
- + src/tomography_python_programs/_utils/mrc.py
- + src/tomography_python_programs/_utils/relion.py
- + src/tomography_python_programs/_utils/star.py
- + src/tomography_python_programs/_utils/tests/test_file.py
- + src/tomography_python_programs/_utils/tests/test_transformations.py
- + src/tomography_python_programs/_utils/transformations.py
- + src/tomography_python_programs/align_tilt_series/__init__.py
- + src/tomography_python_programs/align_tilt_series/_cli.py
- + src/tomography_python_programs/align_tilt_series/_job_utils.py
- + src/tomography_python_programs/align_tilt_series/aretomo/__init__.py
- + src/tomography_python_programs/align_tilt_series/aretomo/align_tilt_series.py
- + src/tomography_python_programs/align_tilt_series/aretomo/cli.py
- + src/tomography_python_programs/align_tilt_series/aretomo/utils.py
- + src/tomography_python_programs/align_tilt_series/imod/__init__.py
- + src/tomography_python_programs/align_tilt_series/imod/_utils.py
- + src/tomography_python_programs/align_tilt_series/imod/align_tilt_series.py
- + src/tomography_python_programs/align_tilt_series/imod/cli_fiducials.py
- + src/tomography_python_programs/align_tilt_series/imod/cli_patch_tracking.py
- + src/tomography_python_programs/denoise/__init__.py
- + src/tomography_python_programs/denoise/_cli.py
- + src/tomography_python_programs/denoise/cryoCARE/__init__.py
- + src/tomography_python_programs/denoise/cryoCARE/_utils.py
- + src/tomography_python_programs/denoise/cryoCARE/constants.py
- + src/tomography_python_programs/denoise/cryoCARE/predict.py
- + src/tomography_python_programs/denoise/cryoCARE/train.py
- + src/tomography_python_programs/exclude_tilt_images/__init__.py
- + src/tomography_python_programs/exclude_tilt_images/_cli.py
- + src/tomography_python_programs/exclude_tilt_images/relion_tilt_image_excluder.py
- + src/tomography_python_programs/get_particle_poses/__init__.py
- + src/tomography_python_programs/get_particle_poses/_cli.py
- + src/tomography_python_programs/get_particle_poses/filaments.py
- + src/tomography_python_programs/get_particle_poses/particles.py
- + src/tomography_python_programs/get_particle_poses/spheres.py
- + src/tomography_python_programs/import_tilt_series/__init__.py
- + src/tomography_python_programs/import_tilt_series/_cli.py
- + src/tomography_python_programs/import_tilt_series/serialem.py
- + src/tomography_python_programs/import_tilt_series/stub_alternative.py
- + src/tomography_python_programs/pick/__init__.py
- + src/tomography_python_programs/pick/_cli.py
- + src/tomography_python_programs/pick/filaments.py
- + src/tomography_python_programs/pick/particles.py
- + src/tomography_python_programs/pick/spheres.py
- + src/tomography_python_programs/view/__init__.py
- + src/tomography_python_programs/view/_cli.py
- + src/tomography_python_programs/view/particles.py
- + src/tomography_python_programs/view/tilt_series.py
- + src/tomography_python_programs/view/tomograms.py
- src/transformations.cpp
- src/transformations.h
- tests/CMakeLists.txt
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/relion/-/commit/d983f8a301a6ac2e013333fc1eeebf74db361b95
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