Index

_

__add__() (cil.optimisation.functions.Function method) (cil.optimisation.functions.SumFunction method) __call__() (cil.optimisation.functions.BlockFunction method) (cil.optimisation.functions.ConstantFunction method) (cil.optimisation.functions.Function method) (cil.optimisation.functions.IndicatorBox method) (cil.optimisation.functions.L1Norm method) (cil.optimisation.functions.L2NormSquared method) (cil.optimisation.functions.LeastSquares method) (cil.optimisation.functions.MixedL11Norm method) (cil.optimisation.functions.MixedL21Norm method) (cil.optimisation.functions.OperatorCompositionFunction method) (cil.optimisation.functions.Rosenbrock method) (cil.optimisation.functions.ScaledFunction method) (cil.optimisation.functions.SmoothMixedL21Norm method) (cil.optimisation.functions.SumFunction method) (cil.optimisation.functions.TotalVariation method) (cil.optimisation.functions.TranslateFunction method) (cil.optimisation.functions.WeightedL2NormSquared method) (cil.plugins.ccpi_regularisation.functions.FGP_dTV method) (cil.plugins.ccpi_regularisation.functions.TGV method) (cil.plugins.ccpi_regularisation.functions.TNV method) __delattr__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __dir__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __eq__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __format__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __ge__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __getattribute__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __getitem__() (cil.optimisation.operators.BlockOperator method) __gt__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __hash__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __iadd__() (cil.framework.BlockDataContainer method) __idiv__() (cil.framework.BlockDataContainer method) __imul__() (cil.framework.BlockDataContainer method) __init__() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.functions.BlockFunction method) (cil.optimisation.functions.ConstantFunction method) (cil.optimisation.functions.Function method) (cil.optimisation.functions.IndicatorBox method) (cil.optimisation.functions.KullbackLeibler method) (cil.optimisation.functions.L1Norm method) (cil.optimisation.functions.L2NormSquared method) (cil.optimisation.functions.LeastSquares method) (cil.optimisation.functions.MixedL11Norm method) (cil.optimisation.functions.MixedL21Norm method) (cil.optimisation.functions.OperatorCompositionFunction method) (cil.optimisation.functions.Rosenbrock method) (cil.optimisation.functions.ScaledFunction method) (cil.optimisation.functions.SmoothMixedL21Norm method) (cil.optimisation.functions.SumFunction method) (cil.optimisation.functions.SumScalarFunction method) (cil.optimisation.functions.TotalVariation method) (cil.optimisation.functions.TranslateFunction method) (cil.optimisation.functions.WeightedL2NormSquared method) (cil.optimisation.functions.ZeroFunction method) (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.ChannelwiseOperator method) (cil.optimisation.operators.CompositionOperator method) (cil.optimisation.operators.DiagonalOperator method) (cil.optimisation.operators.IdentityOperator method) (cil.optimisation.operators.LinearOperator method) (cil.optimisation.operators.MaskOperator method) (cil.optimisation.operators.MatrixOperator method) (cil.optimisation.operators.Operator method) (cil.optimisation.operators.ScaledOperator method) (cil.optimisation.operators.ZeroOperator method) (cil.plugins.ccpi_regularisation.functions.FGP_dTV method) (cil.plugins.ccpi_regularisation.functions.TGV method) (cil.plugins.ccpi_regularisation.functions.TNV method)

__init_subclass__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __isub__() (cil.framework.BlockDataContainer method) __iter__() (cil.framework.BlockDataContainer method) (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __itruediv__() (cil.framework.BlockDataContainer method) __le__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __lt__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __ne__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __neg__() (cil.framework.BlockDataContainer method) (cil.optimisation.operators.Operator method) __new__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.functions.IndicatorBox static method) (cil.optimisation.functions.KullbackLeibler static method) __next__() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __radd__() (cil.framework.BlockDataContainer method) (cil.optimisation.functions.Function method) __rdiv__() (cil.framework.BlockDataContainer method) __reduce__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __reduce_ex__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __repr__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __rmul__() (cil.framework.BlockDataContainer method) (cil.optimisation.functions.BlockFunction method) (cil.optimisation.functions.ConstantFunction method) (cil.optimisation.functions.Function method) (cil.optimisation.functions.LeastSquares method) (cil.optimisation.functions.TotalVariation method) (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.Operator method) (cil.plugins.ccpi_regularisation.functions.FGP_dTV method) (cil.plugins.ccpi_regularisation.functions.TGV method) (cil.plugins.ccpi_regularisation.functions.TNV method) __rpow__() (cil.framework.BlockDataContainer method) __rsub__() (cil.framework.BlockDataContainer method) __rtruediv__() (cil.framework.BlockDataContainer method) __set_up_logger() (cil.optimisation.algorithms.Algorithm method) __setattr__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __sizeof__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __str__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __sub__() (cil.optimisation.functions.Function method) (cil.optimisation.operators.Operator method) __subclasshook__() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) __weakref__ (cil.framework.BlockDataContainer attribute) (cil.optimisation.algorithms.Algorithm attribute) (cil.optimisation.algorithms.FISTA attribute) (cil.optimisation.algorithms.ISTA attribute) (cil.optimisation.functions.Function attribute) (cil.optimisation.operators.Operator attribute) _update_previous_solution() (cil.optimisation.algorithms.Algorithm method)

A

AbsorptionTransmissionConverter (class in cil.processors) AcquisitionData (class in cil.framework) AcquisitionGeometry (class in cil.framework) add() (cil.framework.BlockDataContainer method), [1] adjoint() (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.ChannelwiseOperator method) (cil.optimisation.operators.DiagonalOperator method) (cil.optimisation.operators.FiniteDifferenceOperator method) (cil.optimisation.operators.GradientOperator method) (cil.optimisation.operators.IdentityOperator method) (cil.optimisation.operators.LinearOperator method) (cil.optimisation.operators.MatrixOperator method) (cil.optimisation.operators.ScaledOperator method) (cil.optimisation.operators.SymmetrisedGradientOperator method) (cil.optimisation.operators.ZeroOperator method)

Algorithm (class in cil.optimisation.algorithms) allocate() (cil.framework.AcquisitionGeometry method) (cil.framework.BlockGeometry method) (cil.framework.ImageGeometry method) apply_circular_mask() (cil.framework.ImageData method) armijo_rule() (cil.optimisation.algorithms.GD method) as_array() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) axpby() (cil.framework.BlockDataContainer method), [1]

B

binary_operations() (cil.framework.BlockDataContainer method), [1] Binner (class in cil.processors) BlockDataContainer (class in cil.framework), [1]

BlockFunction (class in cil.optimisation.functions) BlockGeometry (class in cil.framework) BlockOperator (class in cil.optimisation.operators)

C

calculate_Lipschitz() (cil.optimisation.functions.TotalVariation method) calculate_norm() (cil.optimisation.operators.ChannelwiseOperator method) (cil.optimisation.operators.CompositionOperator method) (cil.optimisation.operators.DiagonalOperator method) (cil.optimisation.operators.GradientOperator method) (cil.optimisation.operators.IdentityOperator method) (cil.optimisation.operators.LinearOperator method) (cil.optimisation.operators.Operator method) (cil.optimisation.operators.ZeroOperator method) centered_at() (cil.optimisation.functions.Function method) CentreOfRotationCorrector (class in cil.processors) CGLS (class in cil.optimisation.algorithms) ChannelwiseOperator (class in cil.optimisation.operators) check_convergence() (cil.optimisation.algorithms.PDHG method) check_input() (cil.framework.DataProcessor method) (cil.framework.Processor method) (cil.plugins.ccpi_regularisation.functions.TNV method) cil.utilities.quality_measures module clone() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.ImageGeometry method) (cil.framework.VectorData method) column_wise_compatible() (cil.optimisation.operators.BlockOperator method) CompositionOperator (class in cil.optimisation.operators)

constant() (cil.processors.Padder static method) ConstantFunction (class in cil.optimisation.functions) convex_conjugate() (cil.optimisation.functions.BlockFunction method) (cil.optimisation.functions.ConstantFunction method) (cil.optimisation.functions.Function method) (cil.optimisation.functions.L1Norm method) (cil.optimisation.functions.L2NormSquared method) (cil.optimisation.functions.MixedL21Norm method) (cil.optimisation.functions.ScaledFunction method) (cil.optimisation.functions.SumScalarFunction method) (cil.optimisation.functions.TotalVariation method) (cil.optimisation.functions.TranslateFunction method) (cil.optimisation.functions.WeightedL2NormSquared method) (cil.plugins.ccpi_regularisation.functions.FGP_dTV method) (cil.plugins.ccpi_regularisation.functions.TGV method) (cil.plugins.ccpi_regularisation.functions.TNV method) copy() (cil.framework.AcquisitionData method) (cil.framework.BlockDataContainer method), [1] (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.ImageGeometry method) (cil.framework.VectorData method) create_Cone2D() (cil.framework.AcquisitionGeometry static method) create_Cone3D() (cil.framework.AcquisitionGeometry static method) create_Parallel2D() (cil.framework.AcquisitionGeometry static method) create_Parallel3D() (cil.framework.AcquisitionGeometry static method)

D

DataContainer (class in cil.framework) DataOrder (class in cil.framework) DataProcessor (class in cil.framework) DiagonalOperator (class in cil.optimisation.operators) direct() (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.ChannelwiseOperator method) (cil.optimisation.operators.CompositionOperator method) (cil.optimisation.operators.DiagonalOperator method) (cil.optimisation.operators.FiniteDifferenceOperator method) (cil.optimisation.operators.GradientOperator method) (cil.optimisation.operators.IdentityOperator method) (cil.optimisation.operators.MatrixOperator method) (cil.optimisation.operators.Operator method) (cil.optimisation.operators.ScaledOperator method) (cil.optimisation.operators.SparseFiniteDifferenceOperator method) (cil.optimisation.operators.SymmetrisedGradientOperator method) (cil.optimisation.operators.ZeroOperator method)

divide() (cil.framework.BlockDataContainer method), [1] domain_geometry() (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.Operator method) dot() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) dot_test() (cil.optimisation.operators.LinearOperator static method) dtype() (cil.framework.AcquisitionData property) (cil.framework.DataContainer property) (cil.framework.ImageData property) (cil.framework.VectorData property)

E

edge() (cil.processors.Padder static method) estimate_normalised_error() (cil.processors.Normaliser static method) exp() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method)

F

FBP (class in cil.plugins.astra) (class in cil.plugins.tigre) (class in cil.recon) FDK (class in cil.recon) FGP_dTV (class in cil.plugins.ccpi_regularisation.functions) FGP_TV (class in cil.plugins.ccpi_regularisation.functions) figure (cil.utilities.display.show1D attribute)

fill() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) FiniteDifferenceOperator (class in cil.optimisation.operators) FISTA (class in cil.optimisation.algorithms) flag() (cil.optimisation.algorithms.CGLS method) Function (class in cil.optimisation.functions)

G

GD (class in cil.optimisation.algorithms) get() (cil.utilities.dataexample.SIMULATED_CONE_BEAM_DATA class method), [1] (cil.utilities.dataexample.SIMULATED_PARALLEL_BEAM_DATA class method) (cil.utilities.dataexample.SYNCHROTRON_PARALLEL_BEAM_DATA class method) get_as_list() (cil.optimisation.operators.BlockOperator method) get_data_axes_order() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) get_data_offset() (cil.io.NEXUSDataReader method) get_data_scale() (cil.io.NEXUSDataReader method) get_dataset_metadata() (cil.io.utilities.HDF5_utilities static method) get_filter_array() (cil.recon.FBP method) (cil.recon.FDK method) get_geometry() (cil.io.NEXUSDataReader method) (cil.io.NikonDataReader method) (cil.io.ZEISSDataReader method) get_ImageData() (in module cil.plugins.TomoPhantom) get_ImageGeometry() (cil.framework.AcquisitionGeometry method) get_input() (cil.framework.DataProcessor method) (cil.framework.Processor method) get_item() (cil.framework.BlockGeometry method) (cil.optimisation.operators.BlockOperator method) get_last_loss() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method) get_last_objective() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method) get_metadata() (cil.io.ZEISSDataReader method) get_output() (cil.framework.DataProcessor method) (cil.framework.Processor method) (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method) (cil.plugins.astra.FBP method) (cil.plugins.tigre.FBP method) (cil.processors.AbsorptionTransmissionConverter method) (cil.processors.Binner method) (cil.processors.CentreOfRotationCorrector method) (cil.processors.Masker method) (cil.processors.MaskGenerator method) (cil.processors.Normaliser method) (cil.processors.Padder method) (cil.processors.RingRemover method) (cil.processors.Slicer method) (cil.processors.TransmissionAbsorptionConverter method)

get_output_shape() (cil.optimisation.operators.BlockOperator method) get_roi() (cil.io.NikonDataReader method) get_slice() (cil.framework.AcquisitionData method) (cil.framework.AcquisitionGeometry method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.ImageGeometry method) (cil.framework.VectorData method) gradient() (cil.optimisation.functions.BlockFunction method) (cil.optimisation.functions.ConstantFunction method) (cil.optimisation.functions.Function method) (cil.optimisation.functions.IndicatorBox method) (cil.optimisation.functions.L2NormSquared method) (cil.optimisation.functions.LeastSquares method) (cil.optimisation.functions.OperatorCompositionFunction method) (cil.optimisation.functions.Rosenbrock method) (cil.optimisation.functions.ScaledFunction method) (cil.optimisation.functions.SmoothMixedL21Norm method) (cil.optimisation.functions.SumFunction method) (cil.optimisation.functions.TotalVariation property) (cil.optimisation.functions.TranslateFunction method) (cil.optimisation.functions.WeightedL2NormSquared method) GradientOperator (class in cil.optimisation.operators)

H

HDF5_utilities (class in cil.io.utilities)

I

IdentityOperator (class in cil.optimisation.operators) image_sharpness() (cil.processors.CentreOfRotationCorrector static method) ImageData (class in cil.framework) ImageGeometry (class in cil.framework) IndicatorBox (class in cil.optimisation.functions) interpolate() (cil.processors.Masker static method) is_compatible() (cil.framework.BlockDataContainer method), [1] is_linear() (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.CompositionOperator method) (cil.optimisation.operators.LinearOperator method) (cil.optimisation.operators.Operator method) (cil.optimisation.operators.ScaledOperator method) is_provably_convergent() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method)

islicer (class in cil.utilities.jupyter) ISTA (class in cil.optimisation.algorithms) iterations() (cil.optimisation.algorithms.Algorithm property) (cil.optimisation.algorithms.CGLS property) (cil.optimisation.algorithms.FISTA property) (cil.optimisation.algorithms.GD property) (cil.optimisation.algorithms.ISTA property) (cil.optimisation.algorithms.LADMM property) (cil.optimisation.algorithms.PDHG property) (cil.optimisation.algorithms.SIRT property) (cil.optimisation.algorithms.SPDHG property)

K

KullbackLeibler (class in cil.optimisation.functions)

L

L() (cil.optimisation.functions.BlockFunction property) (cil.optimisation.functions.ConstantFunction property) (cil.optimisation.functions.Function property) (cil.optimisation.functions.LeastSquares property) (cil.optimisation.functions.OperatorCompositionFunction property) (cil.optimisation.functions.ScaledFunction property) (cil.optimisation.functions.SumFunction property) (cil.optimisation.functions.SumScalarFunction property) L1Norm (class in cil.optimisation.functions) L2NormSquared (class in cil.optimisation.functions) LADMM (class in cil.optimisation.algorithms) LeastSquares (class in cil.optimisation.functions) linear_ramp() (cil.processors.Padder static method) LinearOperator (class in cil.optimisation.operators) link_islicer (class in cil.utilities.jupyter) Lmax() (cil.optimisation.functions.SumFunction property)

load() (cil.utilities.dataexample.TestData method) load_data() (cil.io.NEXUSDataReader method) load_projections() (cil.io.NikonDataReader method) log() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) loss() (cil.optimisation.algorithms.Algorithm property) (cil.optimisation.algorithms.CGLS property) (cil.optimisation.algorithms.FISTA property) (cil.optimisation.algorithms.GD property) (cil.optimisation.algorithms.ISTA property) (cil.optimisation.algorithms.LADMM property) (cil.optimisation.algorithms.PDHG property) (cil.optimisation.algorithms.SIRT property) (cil.optimisation.algorithms.SPDHG property)

M

mae() (in module cil.utilities.quality_measures) Masker (class in cil.processors) MaskGenerator (class in cil.processors) MaskOperator (class in cil.optimisation.operators) MatrixOperator (class in cil.optimisation.operators) max() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) max_iteration() (cil.optimisation.algorithms.Algorithm property) (cil.optimisation.algorithms.CGLS property) (cil.optimisation.algorithms.FISTA property) (cil.optimisation.algorithms.GD property) (cil.optimisation.algorithms.ISTA property) (cil.optimisation.algorithms.LADMM property) (cil.optimisation.algorithms.PDHG property) (cil.optimisation.algorithms.SIRT property) (cil.optimisation.algorithms.SPDHG property) max_iteration_stop_criterion() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method)

maximum() (cil.framework.BlockDataContainer method), [1] mean() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) (cil.processors.Masker static method) (cil.processors.MaskGenerator static method) median() (cil.processors.Masker static method) (cil.processors.MaskGenerator static method) min() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) minimum() (cil.framework.BlockDataContainer method), [1] MixedL11Norm (class in cil.optimisation.functions) MixedL21Norm (class in cil.optimisation.functions) module cil.utilities.quality_measures mse() (in module cil.utilities.quality_measures) multiply() (cil.framework.BlockDataContainer method), [1]

N

ndim() (cil.framework.AcquisitionData property) (cil.framework.DataContainer property) (cil.framework.ImageData property) (cil.framework.VectorData property) next() (cil.framework.BlockDataContainer method), [1] (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method) NEXUSDataReader (class in cil.io)

NEXUSDataWriter (class in cil.io) NikonDataReader (class in cil.io) norm() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.Operator method) (cil.optimisation.operators.ScaledOperator method) Normaliser (class in cil.processors) num_threads() (cil.optimisation.functions.IndicatorBox property) number_of_dimensions() (cil.framework.AcquisitionData property) (cil.framework.DataContainer property) (cil.framework.ImageData property) (cil.framework.VectorData property)

O

objective() (cil.optimisation.algorithms.Algorithm property) (cil.optimisation.algorithms.CGLS property) (cil.optimisation.algorithms.FISTA property) (cil.optimisation.algorithms.GD property) (cil.optimisation.algorithms.ISTA property) (cil.optimisation.algorithms.LADMM property) (cil.optimisation.algorithms.PDHG property) (cil.optimisation.algorithms.SIRT property) (cil.optimisation.algorithms.SPDHG property)

Operator (class in cil.optimisation.operators) OperatorCompositionFunction (class in cil.optimisation.functions)

P

Padder (class in cil.processors) partition() (cil.framework.AcquisitionData method) PDHG (class in cil.optimisation.algorithms) power() (cil.framework.BlockDataContainer method), [1] PowerMethod() (cil.optimisation.operators.LinearOperator static method) print_metadata() (cil.io.utilities.HDF5_utilities static method) process() (cil.processors.Binner method) (cil.processors.Slicer method) Processor (class in cil.framework) ProjectionOperator (class in cil.plugins.astra) (class in cil.plugins.tigre) proximal() (cil.optimisation.functions.BlockFunction method) (cil.optimisation.functions.ConstantFunction method) (cil.optimisation.functions.Function method) (cil.optimisation.functions.IndicatorBox method) (cil.optimisation.functions.L1Norm method) (cil.optimisation.functions.L2NormSquared method) (cil.optimisation.functions.MixedL11Norm method) (cil.optimisation.functions.MixedL21Norm method) (cil.optimisation.functions.ScaledFunction method) (cil.optimisation.functions.SumScalarFunction method) (cil.optimisation.functions.TotalVariation method) (cil.optimisation.functions.TranslateFunction method) (cil.optimisation.functions.WeightedL2NormSquared method)

proximal_conjugate() (cil.optimisation.functions.BlockFunction method) (cil.optimisation.functions.Function method) (cil.optimisation.functions.ScaledFunction method) psnr() (in module cil.utilities.quality_measures)

Q

quantile() (cil.processors.MaskGenerator static method)

R

random_noise() (cil.utilities.dataexample.TestData static method) range_geometry() (cil.optimisation.operators.BlockOperator method) (cil.optimisation.operators.Operator method) RAWFileWriter (class in cil.io) read() (cil.io.NEXUSDataReader method) (cil.io.NikonDataReader method) (cil.io.TIFFStackReader method) (cil.io.utilities.HDF5_utilities static method) (cil.io.ZEISSDataReader method) read_as_AcquisitionData() (cil.io.TIFFStackReader method) read_as_ImageData() (cil.io.TIFFStackReader method) read_as_original() (cil.io.NEXUSDataReader method) read_rescaled() (cil.io.TIFFStackReader method) read_scale_offset() (cil.io.TIFFStackReader method) read_to() (cil.io.utilities.HDF5_utilities static method) reflect() (cil.processors.Padder static method) reorder() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method)

reset() (cil.recon.FBP method) (cil.recon.FDK method) RingRemover (class in cil.processors) Rosenbrock (class in cil.optimisation.functions) row_wise_compatible() (cil.optimisation.operators.BlockOperator method) run() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method) (cil.recon.FBP method) (cil.recon.FBP.FBP method) (cil.recon.FDK method)

S

sapyb() (cil.framework.AcquisitionData method) (cil.framework.BlockDataContainer method), [1] (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) save() (cil.utilities.display.show1D method) (cil.utilities.display.show2D method) (cil.utilities.display.show_geometry method) ScaledFunction (class in cil.optimisation.functions) ScaledOperator (class in cil.optimisation.operators) scikit_random_noise() (cil.utilities.dataexample.TestData static method) set_angles() (cil.framework.AcquisitionGeometry method) set_channels() (cil.framework.AcquisitionGeometry method) set_fft_order() (cil.recon.FBP method) (cil.recon.FDK method) set_filter() (cil.recon.FBP method) (cil.recon.FDK method) set_filter_inplace() (cil.recon.FBP method) (cil.recon.FDK method) set_gamma_fconj() (cil.optimisation.algorithms.PDHG method) set_gamma_g() (cil.optimisation.algorithms.PDHG method) set_image_geometry() (cil.recon.FBP method) (cil.recon.FDK method) set_input() (cil.framework.DataProcessor method) (cil.framework.Processor method) (cil.plugins.astra.FBP method) (cil.plugins.tigre.FBP method) (cil.processors.AbsorptionTransmissionConverter method) (cil.processors.Binner method) (cil.processors.CentreOfRotationCorrector method) (cil.processors.Masker method) (cil.processors.MaskGenerator method) (cil.processors.Normaliser method) (cil.processors.Padder method) (cil.processors.RingRemover method) (cil.processors.Slicer method) (cil.processors.TransmissionAbsorptionConverter method) (cil.recon.FBP method) (cil.recon.FDK method) set_labels() (cil.framework.AcquisitionGeometry method) set_norm() (cil.optimisation.operators.Operator method) set_num_threads() (cil.optimisation.functions.IndicatorBox method) set_panel() (cil.framework.AcquisitionGeometry method) set_relaxation_parameter() (cil.optimisation.algorithms.SIRT method) set_split_processing() (cil.recon.FBP method) set_step_size() (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.ISTA method) set_step_sizes() (cil.optimisation.algorithms.PDHG method) set_suppress_evaluation() (cil.optimisation.functions.IndicatorBox method) set_up() (cil.io.NEXUSDataReader method) (cil.io.NEXUSDataWriter method) (cil.io.ZEISSDataReader method) (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method)

shape() (cil.framework.AcquisitionData property) (cil.framework.DataContainer property) (cil.framework.ImageData property) (cil.framework.VectorData property) should_stop() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method) show1D (class in cil.utilities.display) show2D (class in cil.utilities.display) show_geometry (class in cil.utilities.display) SIMULATED_CONE_BEAM_DATA (class in cil.utilities.dataexample), [1] SIMULATED_PARALLEL_BEAM_DATA (class in cil.utilities.dataexample) SIRT (class in cil.optimisation.algorithms) size() (cil.framework.AcquisitionData property) (cil.framework.DataContainer property) (cil.framework.ImageData property) (cil.framework.VectorData property) slice_metadata() (cil.io.ZEISSDataReader method) Slicer (class in cil.processors) SmoothMixedL21Norm (class in cil.optimisation.functions) SparseFiniteDifferenceOperator (class in cil.optimisation.operators) SPDHG (class in cil.optimisation.algorithms) special_values() (cil.processors.MaskGenerator static method) squared_norm() (cil.framework.AcquisitionData method) (cil.framework.DataContainer method) (cil.framework.ImageData method) (cil.framework.VectorData method) subtract() (cil.framework.BlockDataContainer method), [1] SumFunction (class in cil.optimisation.functions) SumScalarFunction (class in cil.optimisation.functions) symmetric() (cil.processors.Padder static method) SymmetrisedGradientOperator (class in cil.optimisation.operators) SYNCHROTRON_PARALLEL_BEAM_DATA (class in cil.utilities.dataexample)

T

T() (cil.optimisation.operators.BlockOperator property) TestData (class in cil.utilities.dataexample) TGV (class in cil.plugins.ccpi_regularisation.functions) threshold() (cil.processors.MaskGenerator static method) TIFFStackReader (class in cil.io)

TIFFWriter (class in cil.io) TNV (class in cil.plugins.ccpi_regularisation.functions) TotalVariation (class in cil.optimisation.functions) TranslateFunction (class in cil.optimisation.functions) TransmissionAbsorptionConverter (class in cil.processors)

U

unary_operations() (cil.framework.BlockDataContainer method), [1] update() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method)

update_objective() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method) update_step_sizes() (cil.optimisation.algorithms.PDHG method)

V

value() (cil.processors.Masker static method) VectorData (class in cil.framework) verbose_output() (cil.optimisation.algorithms.Algorithm method) (cil.optimisation.algorithms.CGLS method) (cil.optimisation.algorithms.FISTA method) (cil.optimisation.algorithms.GD method) (cil.optimisation.algorithms.ISTA method) (cil.optimisation.algorithms.LADMM method) (cil.optimisation.algorithms.PDHG method) (cil.optimisation.algorithms.SIRT method) (cil.optimisation.algorithms.SPDHG method)

W

WeightedL2NormSquared (class in cil.optimisation.functions) wrap() (cil.processors.Padder static method)

write() (cil.io.NEXUSDataWriter method) (cil.io.RAWFileWriter method) (cil.io.TIFFWriter method)

X

xcorrelation() (cil.processors.CentreOfRotationCorrector static method)

xRemoveStripesVertical() (cil.processors.RingRemover method)

Z

ZEISSDataReader (class in cil.io)

ZeroFunction (class in cil.optimisation.functions) ZeroOperator (class in cil.optimisation.operators)