#include <elxStatisticalShapePenalty.h>
An metric based on the itk::StatisticalShapePointPenalty.
The parameters used in this class are:
Metric: Select this metric as follows:
(Metric "StatisticalShapePenalty")
ShrinkageIntensity: The mixing ratio ($\beta$) of the provided covariance matrix and an identity matrix. $\Sigma' = (1-\beta)\Sigma + \beta \sigma_0^2 I$ Can be defined for each resolution
example: (ShrinkageIntensity 0.2)
BaseVariance: The width ($\sigma_0^2$) of the non-informative prior. Can be defined for each resolution
example: (BaseVariance 1000.0)
Definition at line 58 of file elxStatisticalShapePenalty.h.
Public Types | |
using | CombinationTransformType = itk::AdvancedCombinationTransform<CoordRepType, Self::FixedImageDimension> |
using | ConstPointer = SmartPointer<const Self> |
using | CoordRepType = typename OutputPointType::CoordRepType |
using | FixedImageType |
using | ImageType = FixedImageType |
using | InitialTransformType = typename CombinationTransformType::InitialTransformType |
using | ITKBaseType = typename Superclass2::ITKBaseType |
using | MovingImageType |
using | Pointer = SmartPointer<Self> |
using | PointSetType = FixedPointSetType |
using | Self = StatisticalShapePenalty |
using | Superclass1 |
using | Superclass2 = MetricBase<TElastix> |
using | VnlVectorType = vnl_vector<CoordRepType> |
Public Types inherited from itk::StatisticalShapePointPenalty< TFixedPointSet, TMovingPointSet > | |
using | ConstPointer = SmartPointer<const Self> |
using | CoordRepType = typename OutputPointType::CoordRepType |
using | DerivativeValueType |
using | FixedPointSetConstPointer |
using | FixedPointSetType |
using | InputPointType |
using | MovingPointSetConstPointer |
using | MovingPointSetType |
using | NonZeroJacobianIndicesType |
using | OutputPointType |
using | PCACovarianceType = vnl_svd_economy<CoordRepType> |
using | PointDataIterator |
using | Pointer = SmartPointer<Self> |
using | PointIterator |
using | ProposalDerivativeType = typename std::vector<VnlVectorType *> |
using | Self = StatisticalShapePointPenalty |
using | Superclass = SingleValuedPointSetToPointSetMetric<TFixedPointSet, TMovingPointSet> |
using | TransformJacobianType |
using | TransformParametersType |
using | TransformPointer |
using | TransformType |
using | VnlMatrixType = vnl_matrix<CoordRepType> |
using | VnlVectorType = vnl_vector<CoordRepType> |
Public Types inherited from itk::SingleValuedPointSetToPointSetMetric< TFixedPointSet, TMovingPointSet > | |
using | ConstPointer = SmartPointer<const Self> |
using | CoordinateRepresentationType = Superclass::ParametersValueType |
using | DerivativeValueType = typename DerivativeType::ValueType |
using | FixedImageMaskConstPointer = typename FixedImageMaskType::ConstPointer |
using | FixedImageMaskPointer = typename FixedImageMaskType::Pointer |
using | FixedImageMaskType = ImageMaskSpatialObject<Self::FixedPointSetDimension> |
using | FixedPointSetConstPointer = typename FixedPointSetType::ConstPointer |
using | FixedPointSetPixelType = typename FixedPointSetType::PixelType |
using | FixedPointSetType = TFixedPointSet |
using | InputPointType = typename TransformType::InputPointType |
using | MovingImageMaskConstPointer = typename MovingImageMaskType::ConstPointer |
using | MovingImageMaskPointer = typename MovingImageMaskType::Pointer |
using | MovingImageMaskType = ImageMaskSpatialObject<Self::MovingPointSetDimension> |
using | MovingPointSetConstPointer = typename MovingPointSetType::ConstPointer |
using | MovingPointSetPixelType = typename MovingPointSetType::PixelType |
using | MovingPointSetType = TMovingPointSet |
using | NonZeroJacobianIndicesType = typename TransformType::NonZeroJacobianIndicesType |
using | OutputPointType = typename TransformType::OutputPointType |
using | PointDataIterator = typename FixedPointSetType::PointDataContainer::ConstIterator |
using | Pointer = SmartPointer<Self> |
using | PointIterator = typename FixedPointSetType::PointsContainer::ConstIterator |
using | Self = SingleValuedPointSetToPointSetMetric |
using | Superclass = SingleValuedCostFunction |
using | TransformJacobianType = typename TransformType::JacobianType |
using | TransformParametersType = typename TransformType::ParametersType |
using | TransformPointer = typename TransformType::Pointer |
using | TransformType |
Public Types inherited from elastix::MetricBase< TElastix > | |
using | AdvancedMetricType = itk::AdvancedImageToImageMetric<FixedImageType, MovingImageType> |
using | CoordinateRepresentationType = typename ITKBaseType::ParametersValueType |
using | ElastixType |
using | FixedImageType = typename ElastixType::FixedImageType |
using | FixedPointSetType |
using | FixedPointType = typename FixedImageType::PointType |
using | FixedPointValueType = typename FixedPointType::ValueType |
using | ImageSamplerBaseType = typename AdvancedMetricType::ImageSamplerType |
using | ITKBaseType = itk::SingleValuedCostFunction |
using | MeasureType = typename ITKBaseType::MeasureType |
using | MovingImageDerivativeScalesType = typename AdvancedMetricType::MovingImageDerivativeScalesType |
using | MovingImageType = typename ElastixType::MovingImageType |
using | MovingPointSetType |
using | MovingPointType = typename MovingImageType::PointType |
using | MovingPointValueType = typename MovingPointType::ValueType |
using | RegistrationType |
using | Self = MetricBase |
using | Superclass = BaseComponentSE<TElastix> |
Public Types inherited from elastix::BaseComponentSE< TElastix > | |
using | ElastixType = TElastix |
using | RegistrationType = typename ElastixType::RegistrationBaseType |
using | Self = BaseComponentSE |
using | Superclass = BaseComponent |
Public Member Functions | |
void | BeforeEachResolution () override |
void | BeforeRegistration () override |
elxClassNameMacro ("StatisticalShapePenalty") | |
virtual const char * | GetClassName () const |
void | Initialize () override |
ITK_DISALLOW_COPY_AND_MOVE (StatisticalShapePenalty) | |
itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension) | |
itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension) | |
unsigned int | ReadLandmarks (const std::string &landmarkFileName, typename PointSetType::Pointer &pointSet, const typename ImageType::ConstPointer image) |
unsigned int | ReadShape (const std::string &ShapeFileName, typename PointSetType::Pointer &pointSet) |
void | SelectNewSamples () override |
Public Member Functions inherited from itk::StatisticalShapePointPenalty< TFixedPointSet, TMovingPointSet > | |
virtual void | BaseVarianceNeedsUpdateOff () |
virtual void | BaseVarianceNeedsUpdateOn () |
virtual MeasureType | GetBaseVariance () const |
virtual MeasureType | GetCentroidXVariance () const |
virtual MeasureType | GetCentroidYVariance () const |
virtual MeasureType | GetCentroidZVariance () const |
virtual MeasureType | GetCutOffSharpness () const |
virtual MeasureType | GetCutOffValue () const |
void | GetDerivative (const TransformParametersType ¶meters, DerivativeType &Derivative) const override |
virtual const bool & | GetNormalizedShapeModel () |
virtual const int & | GetShapeModelCalculation () |
virtual MeasureType | GetShrinkageIntensity () const |
virtual MeasureType | GetSizeVariance () const |
MeasureType | GetValue (const TransformParametersType ¶meters) const override |
void | GetValueAndDerivative (const TransformParametersType ¶meters, MeasureType &Value, DerivativeType &Derivative) const override |
void | Initialize () override |
ITK_DISALLOW_COPY_AND_MOVE (StatisticalShapePointPenalty) | |
virtual void | NormalizedShapeModelOff () |
virtual void | NormalizedShapeModelOn () |
virtual void | SetBaseVariance (MeasureType _arg) |
virtual void | SetBaseVarianceNeedsUpdate (bool _arg) |
virtual void | SetCentroidXVariance (MeasureType _arg) |
virtual void | SetCentroidYVariance (MeasureType _arg) |
virtual void | SetCentroidZVariance (MeasureType _arg) |
virtual void | SetCovarianceMatrix (const vnl_matrix< double > *_arg) |
virtual void | SetCutOffSharpness (MeasureType _arg) |
virtual void | SetCutOffValue (MeasureType _arg) |
virtual void | SetEigenValues (const vnl_vector< double > *_arg) |
virtual void | SetEigenVectors (const vnl_matrix< double > *_arg) |
virtual void | SetMeanVector (const vnl_vector< double > *_arg) |
virtual void | SetNormalizedShapeModel (bool _arg) |
virtual void | SetShapeModelCalculation (int _arg) |
virtual void | SetShrinkageIntensity (MeasureType _arg) |
virtual void | SetShrinkageIntensityNeedsUpdate (bool _arg) |
virtual void | SetSizeVariance (MeasureType _arg) |
virtual void | SetVariancesNeedsUpdate (bool _arg) |
virtual void | ShrinkageIntensityNeedsUpdateOff () |
virtual void | ShrinkageIntensityNeedsUpdateOn () |
virtual void | VariancesNeedsUpdateOff () |
virtual void | VariancesNeedsUpdateOn () |
Public Member Functions inherited from itk::SingleValuedPointSetToPointSetMetric< TFixedPointSet, TMovingPointSet > | |
virtual void | BeforeThreadedGetValueAndDerivative (const TransformParametersType ¶meters) const |
virtual const FixedImageMaskType * | GetFixedImageMask () |
virtual const FixedPointSetType * | GetFixedPointSet () |
virtual const MovingImageMaskType * | GetMovingImageMask () |
virtual const MovingPointSetType * | GetMovingPointSet () |
unsigned int | GetNumberOfParameters () const override |
virtual const TransformType * | GetTransform () |
virtual const bool & | GetUseMetricSingleThreaded () |
ITK_DISALLOW_COPY_AND_MOVE (SingleValuedPointSetToPointSetMetric) | |
itkStaticConstMacro (FixedPointSetDimension, unsigned int, TFixedPointSet::PointDimension) | |
itkStaticConstMacro (MovingPointSetDimension, unsigned int, TMovingPointSet::PointDimension) | |
virtual void | SetFixedImageMask (const FixedImageMaskType *_arg) |
virtual void | SetFixedPointSet (const FixedPointSetType *_arg) |
virtual void | SetMovingImageMask (const MovingImageMaskType *_arg) |
virtual void | SetMovingPointSet (const MovingPointSetType *_arg) |
virtual void | SetTransform (TransformType *_arg) |
void | SetTransformParameters (const ParametersType ¶meters) const |
virtual void | SetUseMetricSingleThreaded (bool _arg) |
virtual void | UseMetricSingleThreadedOff () |
virtual void | UseMetricSingleThreadedOn () |
Public Member Functions inherited from elastix::MetricBase< TElastix > | |
void | AfterEachIterationBase () override |
void | BeforeEachResolutionBase () override |
virtual ImageSamplerBaseType * | GetAdvancedMetricImageSampler () const |
virtual bool | GetAdvancedMetricUseImageSampler () const |
ITKBaseType * | GetAsITKBaseType () |
const ITKBaseType * | GetAsITKBaseType () const |
virtual MeasureType | GetCurrentExactMetricValue () const |
virtual bool | GetShowExactMetricValue () const |
ITK_DISALLOW_COPY_AND_MOVE (MetricBase) | |
itkStaticConstMacro (FixedImageDimension, unsigned int, FixedImageType::ImageDimension) | |
itkStaticConstMacro (MovingImageDimension, unsigned int, MovingImageType::ImageDimension) | |
virtual void | SetAdvancedMetricImageSampler (ImageSamplerBaseType *sampler) |
Public Member Functions inherited from elastix::BaseComponentSE< TElastix > | |
void | AddTargetCellToIterationInfo (const char *const name) |
const Configuration * | GetConfiguration () const |
ElastixType * | GetElastix () const |
auto & | GetIterationInfoAt (const char *const name) |
RegistrationType * | GetRegistration () const |
ITK_DISALLOW_COPY_AND_MOVE (BaseComponentSE) | |
void | RemoveTargetCellFromIterationInfo (const char *const name) |
void | SetConfiguration (const Configuration *_arg) |
void | SetElastix (ElastixType *_arg) |
Public Member Functions inherited from elastix::BaseComponent | |
virtual void | AfterEachIteration () |
virtual void | AfterEachResolution () |
virtual void | AfterEachResolutionBase () |
virtual void | AfterRegistration () |
virtual void | AfterRegistrationBase () |
virtual int | BeforeAll () |
virtual int | BeforeAllBase () |
virtual void | BeforeRegistrationBase () |
virtual const char * | elxGetClassName () const |
const char * | GetComponentLabel () const |
ITK_DISALLOW_COPY_AND_MOVE (BaseComponent) | |
itkTypeMacroNoParent (BaseComponent) | |
void | SetComponentLabel (const char *label, unsigned int idx) |
Static Public Member Functions | |
static Pointer | New () |
Static Public Member Functions inherited from itk::StatisticalShapePointPenalty< TFixedPointSet, TMovingPointSet > | |
static Pointer | New () |
Static Public Member Functions inherited from elastix::BaseComponent | |
template<typename TBaseComponent > | |
static auto | AsITKBaseType (TBaseComponent *const baseComponent) -> decltype(baseComponent->GetAsITKBaseType()) |
static void | InitializeElastixExecutable () |
static bool | IsElastixLibrary () |
Protected Member Functions | |
StatisticalShapePenalty ()=default | |
~StatisticalShapePenalty () override=default | |
Protected Member Functions inherited from itk::StatisticalShapePointPenalty< TFixedPointSet, TMovingPointSet > | |
void | PrintSelf (std::ostream &os, Indent indent) const override |
StatisticalShapePointPenalty () | |
~StatisticalShapePointPenalty () override | |
Protected Member Functions inherited from itk::SingleValuedPointSetToPointSetMetric< TFixedPointSet, TMovingPointSet > | |
void | PrintSelf (std::ostream &os, Indent indent) const override |
SingleValuedPointSetToPointSetMetric ()=default | |
~SingleValuedPointSetToPointSetMetric () override=default | |
Protected Member Functions inherited from elastix::MetricBase< TElastix > | |
virtual MeasureType | GetExactValue (const ParametersType ¶meters) |
MetricBase ()=default | |
~MetricBase () override=default | |
Protected Member Functions inherited from elastix::BaseComponentSE< TElastix > | |
BaseComponentSE ()=default | |
~BaseComponentSE () override=default | |
Protected Member Functions inherited from elastix::BaseComponent | |
BaseComponent ()=default | |
virtual | ~BaseComponent ()=default |
Private Attributes | |
elxOverrideGetSelfMacro | |
using elastix::StatisticalShapePenalty< TElastix >::CombinationTransformType = itk::AdvancedCombinationTransform<CoordRepType, Self::FixedImageDimension> |
Other typedef's.
Definition at line 118 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::ConstPointer = SmartPointer<const Self> |
Definition at line 72 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::CoordRepType = typename OutputPointType::CoordRepType |
Definition at line 109 of file elxStatisticalShapePenalty.h.
using elastix::MetricBase< TElastix >::FixedImageType |
Other typedef's.
Definition at line 89 of file elxMetricBase.h.
using elastix::StatisticalShapePenalty< TElastix >::ImageType = FixedImageType |
Definition at line 138 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::InitialTransformType = typename CombinationTransformType::InitialTransformType |
Definition at line 119 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::ITKBaseType = typename Superclass2::ITKBaseType |
Definition at line 124 of file elxStatisticalShapePenalty.h.
using elastix::MetricBase< TElastix >::MovingImageType |
Definition at line 92 of file elxMetricBase.h.
using elastix::StatisticalShapePenalty< TElastix >::Pointer = SmartPointer<Self> |
Definition at line 71 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::PointSetType = FixedPointSetType |
Assuming fixed and moving pointsets are of equal type, which implicitly assumes that the fixed and moving image are of the same type.
Definition at line 137 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::Self = StatisticalShapePenalty |
Standard ITK-stuff.
Definition at line 67 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::Superclass1 |
Definition at line 68 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::Superclass2 = MetricBase<TElastix> |
Definition at line 70 of file elxStatisticalShapePenalty.h.
using elastix::StatisticalShapePenalty< TElastix >::VnlVectorType = vnl_vector<CoordRepType> |
Definition at line 110 of file elxStatisticalShapePenalty.h.
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protecteddefault |
The constructor.
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overrideprotecteddefault |
The destructor.
|
overridevirtual |
Reimplemented from elastix::BaseComponent.
|
overridevirtual |
Do some things before registration:
Reimplemented from elastix::BaseComponent.
elastix::StatisticalShapePenalty< TElastix >::elxClassNameMacro | ( | "StatisticalShapePenalty< TElastix >" | ) |
Name of this class. Use this name in the parameter file to select this specific metric.
example: (Metric "StatisticalShapePenalty")
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virtual |
Run-time type information (and related methods).
Reimplemented from itk::StatisticalShapePointPenalty< TFixedPointSet, TMovingPointSet >.
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overridevirtual |
Sets up a timer to measure the initialization time and calls the Superclass' implementation.
Reimplemented from itk::SingleValuedPointSetToPointSetMetric< TFixedPointSet, TMovingPointSet >.
elastix::StatisticalShapePenalty< TElastix >::ITK_DISALLOW_COPY_AND_MOVE | ( | StatisticalShapePenalty< TElastix > | ) |
elastix::StatisticalShapePenalty< TElastix >::itkStaticConstMacro | ( | FixedImageDimension | , |
unsigned int | , | ||
FixedImageType::ImageDimension | ) |
The fixed image dimension.
elastix::StatisticalShapePenalty< TElastix >::itkStaticConstMacro | ( | MovingImageDimension | , |
unsigned int | , | ||
MovingImageType::ImageDimension | ) |
The moving image dimension.
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static |
Method for creation through the object factory.
unsigned int elastix::StatisticalShapePenalty< TElastix >::ReadLandmarks | ( | const std::string & | landmarkFileName, |
typename PointSetType::Pointer & | pointSet, | ||
const typename ImageType::ConstPointer | image ) |
Function to read the corresponding points.
unsigned int elastix::StatisticalShapePenalty< TElastix >::ReadShape | ( | const std::string & | ShapeFileName, |
typename PointSetType::Pointer & | pointSet ) |
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inlineoverridevirtual |
Overwrite to silence warning.
Reimplemented from elastix::MetricBase< TElastix >.
Definition at line 167 of file elxStatisticalShapePenalty.h.
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private |
Definition at line 177 of file elxStatisticalShapePenalty.h.
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