template<typename TFixedImage, typename TMovingImage, typename TOutputTransform = DisplacementFieldTransform<double, TFixedImage::ImageDimension>, typename TVirtualImage = TFixedImage, typename TPointSet = PointSet<unsigned int, TFixedImage::ImageDimension>>
class itk::SyNImageRegistrationMethod< TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet >
Interface method for the performing greedy SyN image registration.
For greedy SyN we use m_Transform to map the time-parameterized middle image to the fixed image (and vice versa using m_Transform->GetInverseDisplacementField() ). We employ another ivar, m_InverseTransform, to map the time-parameterized middle image to the moving image.
Output: The output is the updated transform which has been added to the composite transform.
This implementation is based on the source code in Advanced Normalization Tools (ANTs)
Avants, B. B.; Tustison, N. J.; Song, G.; Cook, P. A.; Klein, A. & Gee, J. C. A reproducible evaluation of ANTs similarity metric performance in brain image registration. Neuroimage, Penn Image Computing and Science Laboratory, University of Pennsylvania, 2011, 54, 2033-2044
The original paper discussing the method is here:
Avants, B. B.; Epstein, C. L.; Grossman, M. & Gee, J. C. Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain. Med Image Anal, Department of Radiology, University of Pennsylvania, 2008, 12, 26-41
The method evolved since that time with crucial contributions from Gang Song and Nick Tustison. Though similar in spirit, this implementation is not identical.
- Todo:
- Need to allow the fixed image to have a composite transform.
- Author
- Nick Tustison
-
Brian Avants
Definition at line 71 of file itkSyNImageRegistrationMethod.h.
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| using | ConstPointer = SmartPointer< const Self > |
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| using | DecoratedOutputTransformPointer = typename DecoratedOutputTransformType::Pointer |
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| using | DerivativeType = typename OutputTransformType::DerivativeType |
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| using | DerivativeValueType = typename DerivativeType::ValueType |
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| using | DisplacementFieldPointer = typename DisplacementFieldType::Pointer |
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| using | DisplacementFieldTransformPointer = typename DisplacementFieldTransformType::Pointer |
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| using | DisplacementFieldTransformType = DisplacementFieldTransform< RealType, ImageDimension > |
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| using | DisplacementFieldType = typename OutputTransformType::DisplacementFieldType |
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| using | DisplacementVectorType = typename DisplacementFieldType::PixelType |
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| using | FixedImagePointer = typename FixedImageType::Pointer |
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| using | FixedImageType = TFixedImage |
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| using | FixedMaskImageType = typename ImageMaskSpatialObjectType::ImageType |
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| using | ImageMaskSpatialObjectType = ImageMaskSpatialObject< ImageDimension > |
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| using | ImageMetricPointer = typename ImageMetricType::Pointer |
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| using | MeasureType = typename ImageMetricType::MeasureType |
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| using | MetricPointer = typename MetricType::Pointer |
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| using | MovingImagePointer = typename MovingImageType::Pointer |
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| using | MovingImageType = TMovingImage |
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| using | MovingMaskImageType = typename ImageMaskSpatialObjectType::ImageType |
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| using | NumberOfIterationsArrayType = Array< SizeValueType > |
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| using | OutputTransformPointer = typename OutputTransformType::Pointer |
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| using | OutputTransformType = TOutputTransform |
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| using | Pointer = SmartPointer< Self > |
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| using | PointSetPointer = typename PointSetType::Pointer |
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| using | RealType = typename OutputTransformType::ScalarType |
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| using | Self = SyNImageRegistrationMethod |
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| using | Superclass = ImageRegistrationMethodv4< TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet > |
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| using | TransformBaseType = typename CompositeTransformType::TransformType |
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| using | VirtualImageType = typename Superclass::VirtualImageType |
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| using | CompositeTransformPointer = typename CompositeTransformType::Pointer |
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| using | CompositeTransformType = CompositeTransform< RealType, ImageDimension > |
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| using | ConstPointer = SmartPointer< const Self > |
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| using | DataObjectPointerArraySizeType = ProcessObject::DataObjectPointerArraySizeType |
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| using | DecoratedInitialTransformPointer = typename DecoratedInitialTransformType::Pointer |
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| using | DecoratedInitialTransformType = DataObjectDecorator< InitialTransformType > |
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| using | DecoratedOutputTransformPointer = typename DecoratedOutputTransformType::Pointer |
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| using | DecoratedOutputTransformType = DataObjectDecorator< OutputTransformType > |
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| using | DerivativeType = typename OutputTransformType::DerivativeType |
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| using | DerivativeValueType = typename DerivativeType::ValueType |
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| using | FixedImageConstPointer = typename FixedImageType::ConstPointer |
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| using | FixedImageMaskConstPointer = typename FixedImageMaskType::ConstPointer |
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| using | FixedImageMasksContainerType = std::vector< FixedImageMaskConstPointer > |
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| using | FixedImageMaskType = typename ImageMetricType::FixedImageMaskType |
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| using | FixedImagePointer = typename FixedImageType::Pointer |
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| using | FixedImagesContainerType = std::vector< FixedImageConstPointer > |
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| using | FixedImageType = TFixedImage |
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| using | ImageMetricType = ImageToImageMetricv4< FixedImageType, MovingImageType, VirtualImageType, RealType > |
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| using | InitialTransformPointer = typename InitialTransformType::Pointer |
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| using | InitialTransformType = Transform< RealType, ImageDimension, ImageDimension > |
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| using | MetricPointer = typename MetricType::Pointer |
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| using | MetricSamplePointSetType = typename ImageMetricType::FixedSampledPointSetType |
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| using | MetricSamplingPercentageArrayType = Array< RealType > |
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| using | MetricSamplingStrategyEnum = ImageRegistrationMethodv4Enums::MetricSamplingStrategy |
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| using | MetricType = ObjectToObjectMetricBaseTemplate< RealType > |
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| using | MovingImageConstPointer = typename MovingImageType::ConstPointer |
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| using | MovingImageMaskConstPointer = typename MovingImageMaskType::ConstPointer |
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| using | MovingImageMasksContainerType = std::vector< MovingImageMaskConstPointer > |
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| using | MovingImageMaskType = typename ImageMetricType::MovingImageMaskType |
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| using | MovingImagePointer = typename MovingImageType::Pointer |
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| using | MovingImagesContainerType = std::vector< MovingImageConstPointer > |
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| using | MovingImageType = TMovingImage |
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| using | MultiMetricType = ObjectToObjectMultiMetricv4< ImageDimension, ImageDimension, VirtualImageType, RealType > |
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| using | OptimizerPointer = typename OptimizerType::Pointer |
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| using | OptimizerType = ObjectToObjectOptimizerBaseTemplate< RealType > |
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| using | OptimizerWeightsType = typename OptimizerType::ScalesType |
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| using | OutputTransformPointer = typename OutputTransformType::Pointer |
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| using | OutputTransformType = DisplacementFieldTransform< double, TFixedImage::ImageDimension > |
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| using | Pointer = SmartPointer< Self > |
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| using | PointSetConstPointer = typename PointSetType::ConstPointer |
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| using | PointSetMetricType = PointSetToPointSetMetricWithIndexv4< PointSetType, PointSetType, RealType > |
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| using | PointSetsContainerType = std::vector< PointSetConstPointer > |
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| using | PointSetType = PointSet< unsigned int, TFixedImage::ImageDimension > |
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| using | RealType = typename OutputTransformType::ScalarType |
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| using | Self = ImageRegistrationMethodv4 |
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| using | ShrinkFactorsArrayType = Array< SizeValueType > |
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| using | ShrinkFactorsPerDimensionContainerType = typename ShrinkFilterType::ShrinkFactorsType |
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| using | ShrinkFilterType = ShrinkImageFilter< FixedImageType, VirtualImageType > |
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| using | SmoothingSigmasArrayType = Array< RealType > |
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| using | Superclass = ProcessObject |
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| using | TransformParametersAdaptorPointer = typename TransformParametersAdaptorType::Pointer |
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| using | TransformParametersAdaptorsContainerType = std::vector< TransformParametersAdaptorPointer > |
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| using | TransformParametersAdaptorType = TransformParametersAdaptorBase< InitialTransformType > |
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| using | VectorType = Vector< RealType, ImageDimension > |
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| using | VirtualImageBaseConstPointer = typename VirtualImageBaseType::ConstPointer |
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| using | VirtualImageBaseType = ImageBase< ImageDimension > |
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| using | VirtualImagePointer = typename VirtualImageType::Pointer |
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| using | VirtualImageType = TFixedImage |
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| using | ConstPointer = SmartPointer< const Self > |
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| using | DataObjectIdentifierType = DataObject::DataObjectIdentifierType |
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| using | DataObjectPointer = DataObject::Pointer |
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| using | DataObjectPointerArray = std::vector< DataObjectPointer > |
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| using | DataObjectPointerArraySizeType = DataObjectPointerArray::size_type |
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| using | MultiThreaderType = MultiThreaderBase |
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| using | NameArray = std::vector< DataObjectIdentifierType > |
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| using | Pointer = SmartPointer< Self > |
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| using | Self = ProcessObject |
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| using | Superclass = Object |
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| using | ConstPointer = SmartPointer< const Self > |
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| using | Pointer = SmartPointer< Self > |
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| using | Self = Object |
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| using | Superclass = LightObject |
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| using | ConstPointer = SmartPointer< const Self > |
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| using | Pointer = SmartPointer< Self > |
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| using | Self = LightObject |
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| virtual DisplacementFieldPointer | ComputeMetricGradientField (const FixedImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const MovingImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const FixedImageMasksContainerType, const MovingImageMasksContainerType, MeasureType &) |
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| virtual DisplacementFieldPointer | ComputeUpdateField (const FixedImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const MovingImagesContainerType, const PointSetsContainerType, const TransformBaseType *, const FixedImageMasksContainerType, const MovingImageMasksContainerType, MeasureType &) |
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| virtual DisplacementFieldPointer | GaussianSmoothDisplacementField (const DisplacementFieldType *, const RealType) |
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| void | GenerateData () override |
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| void | InitializeRegistrationAtEachLevel (const SizeValueType) override |
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| virtual DisplacementFieldPointer | InvertDisplacementField (const DisplacementFieldType *, const DisplacementFieldType *=nullptr) |
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| void | PrintSelf (std::ostream &os, Indent indent) const override |
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| virtual DisplacementFieldPointer | ScaleUpdateField (const DisplacementFieldType *) |
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| virtual void | StartOptimization () |
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| | SyNImageRegistrationMethod () |
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| | ~SyNImageRegistrationMethod () override=default |
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| virtual void | AllocateOutputs () |
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| void | GenerateData () override |
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| virtual VirtualImageBaseConstPointer | GetCurrentLevelVirtualDomainImage () |
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| | ImageRegistrationMethodv4 () |
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| virtual void | InitializeRegistrationAtEachLevel (const SizeValueType) |
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| void | PrintSelf (std::ostream &os, Indent indent) const override |
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| virtual void | SetMetricSamplePoints () |
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| | ~ImageRegistrationMethodv4 () override=default |
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| virtual void | AddInput (DataObject *input) |
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| void | AddOptionalInputName (const DataObjectIdentifierType &) |
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| void | AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx) |
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| virtual void | AddOutput (DataObject *output) |
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| bool | AddRequiredInputName (const DataObjectIdentifierType &) |
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| bool | AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx) |
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| virtual void | CacheInputReleaseDataFlags () |
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| virtual void | GenerateData () |
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| virtual void | GenerateInputRequestedRegion () |
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| virtual void | GenerateOutputInformation () |
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| virtual void | GenerateOutputRequestedRegion (DataObject *output) |
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| DataObject * | GetInput (const DataObjectIdentifierType &key) |
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| const DataObject * | GetInput (const DataObjectIdentifierType &key) const |
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| virtual const DataObjectPointerArraySizeType & | GetNumberOfRequiredInputs () const |
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| virtual const DataObjectPointerArraySizeType & | GetNumberOfRequiredOutputs () const |
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| bool | IsIndexedInputName (const DataObjectIdentifierType &) const |
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| bool | IsIndexedOutputName (const DataObjectIdentifierType &) const |
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| bool | IsRequiredInputName (const DataObjectIdentifierType &) const |
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| DataObjectPointerArraySizeType | MakeIndexFromInputName (const DataObjectIdentifierType &name) const |
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| DataObjectPointerArraySizeType | MakeIndexFromOutputName (const DataObjectIdentifierType &name) const |
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| DataObjectIdentifierType | MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const |
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| DataObjectIdentifierType | MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const |
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| virtual void | PopBackInput () |
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| virtual void | PopFrontInput () |
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| void | PrintSelf (std::ostream &os, Indent indent) const override |
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| | ProcessObject () |
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| virtual void | PropagateResetPipeline () |
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| virtual void | PushBackInput (const DataObject *input) |
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| virtual void | PushFrontInput (const DataObject *input) |
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| virtual void | ReleaseInputs () |
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| virtual void | RemoveInput (const DataObjectIdentifierType &key) |
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| virtual void | RemoveInput (DataObjectPointerArraySizeType) |
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| virtual void | RemoveOutput (const DataObjectIdentifierType &key) |
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| virtual void | RemoveOutput (DataObjectPointerArraySizeType idx) |
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| bool | RemoveRequiredInputName (const DataObjectIdentifierType &) |
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| virtual void | RestoreInputReleaseDataFlags () |
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| virtual void | SetInput (const DataObjectIdentifierType &key, DataObject *input) |
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| virtual void | SetNthInput (DataObjectPointerArraySizeType idx, DataObject *input) |
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| virtual void | SetNthOutput (DataObjectPointerArraySizeType idx, DataObject *output) |
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| void | SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num) |
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| void | SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num) |
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| virtual void | SetNumberOfRequiredInputs (DataObjectPointerArraySizeType) |
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| virtual void | SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg) |
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| virtual void | SetOutput (const DataObjectIdentifierType &name, DataObject *output) |
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| virtual void | SetPrimaryInput (DataObject *object) |
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| virtual void | SetPrimaryOutput (DataObject *object) |
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| void | SetRequiredInputNames (const NameArray &) |
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| virtual void | VerifyInputInformation () ITKv5_CONST |
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| virtual void | VerifyPreconditions () ITKv5_CONST |
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| | ~ProcessObject () override |
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| DataObject * | GetInput (DataObjectPointerArraySizeType idx) |
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| const DataObject * | GetInput (DataObjectPointerArraySizeType idx) const |
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| DataObject * | GetPrimaryInput () |
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| const DataObject * | GetPrimaryInput () const |
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| virtual void | SetPrimaryInputName (const DataObjectIdentifierType &key) |
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| virtual const char * | GetPrimaryInputName () const |
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| DataObject * | GetOutput (const DataObjectIdentifierType &key) |
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| const DataObject * | GetOutput (const DataObjectIdentifierType &key) const |
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| virtual void | SetPrimaryOutputName (const DataObjectIdentifierType &key) |
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| virtual const char * | GetPrimaryOutputName () const |
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| DataObject * | GetOutput (DataObjectPointerArraySizeType i) |
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| const DataObject * | GetOutput (DataObjectPointerArraySizeType i) const |
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| DataObject * | GetPrimaryOutput () |
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| const DataObject * | GetPrimaryOutput () const |
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| virtual bool | GetThreaderUpdateProgress () const |
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| virtual void | ThreaderUpdateProgressOn () |
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| virtual void | SetThreaderUpdateProgress (bool arg) |
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| | Object () |
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| bool | PrintObservers (std::ostream &os, Indent indent) const |
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| void | PrintSelf (std::ostream &os, Indent indent) const override |
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| virtual void | SetTimeStamp (const TimeStamp &timeStamp) |
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| | ~Object () override |
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| virtual LightObject::Pointer | InternalClone () const |
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| | LightObject () |
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| virtual void | PrintHeader (std::ostream &os, Indent indent) const |
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| virtual void | PrintSelf (std::ostream &os, Indent indent) const |
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| virtual void | PrintTrailer (std::ostream &os, Indent indent) const |
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| virtual | ~LightObject () |
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Inheritance diagram for itk::SyNImageRegistrationMethod< TFixedImage, TMovingImage, TOutputTransform, TVirtualImage, TPointSet >:
1.9.3