Implements section 2.3.2 in Bourgeat et. al. ISBI 2008. More...

Inheritance diagram for itk::LagrangianInitializedRelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >:

Collaboration diagram for itk::LagrangianInitializedRelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >:

Public Types
typedef LagrangianInitializedRelaxStreamlinesFilter	Self

typedef RelaxStreamlinesFilter < TImageType, TScalarType, NDimensions >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::InputVectorImagePixelType	InputVectorImagePixelType

typedef Superclass::InputVectorImageType	InputVectorImageType

typedef Superclass::InputVectorImagePointer	InputVectorImagePointer

typedef Superclass::InputVectorImageConstPointer	InputVectorImageConstPointer

typedef Superclass::InputVectorImageIndexType	InputVectorImageIndexType

typedef Superclass::InputScalarImagePixelType	InputScalarImagePixelType

typedef Superclass::InputScalarImageType	InputScalarImageType

typedef Superclass::InputScalarImageSpacingType	InputScalarImageSpacingType

typedef Superclass::InputScalarImagePointType	InputScalarImagePointType

typedef Superclass::InputScalarImagePointer	InputScalarImagePointer

typedef Superclass::InputScalarImageIndexType	InputScalarImageIndexType

typedef Superclass::InputScalarImageConstPointer	InputScalarImageConstPointer

typedef Superclass::InputScalarImageRegionType	InputScalarImageRegionType

typedef Superclass::OutputImageType	OutputImageType

typedef Superclass::OutputImagePixelType	OutputImagePixelType

typedef Superclass::OutputImagePointer	OutputImagePointer

typedef Superclass::OutputImageConstPointer	OutputImageConstPointer

typedef Superclass::OutputImageIndexType	OutputImageIndexType

typedef Superclass::OutputImageSpacingType	OutputImageSpacingType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef Superclass::OutputImageSizeType	OutputImageSizeType

typedef Superclass::VectorInterpolatorType	VectorInterpolatorType

typedef Superclass::VectorInterpolatorPointer	VectorInterpolatorPointer

typedef Superclass::VectorInterpolatorPointType	VectorInterpolatorPointType

typedef Superclass::ScalarInterpolatorType	ScalarInterpolatorType

typedef Superclass::ScalarInterpolatorPointer	ScalarInterpolatorPointer

typedef Superclass::ScalarInterpolatorPointType	ScalarInterpolatorPointType

typedef ContinuousIndex < TScalarType, NDimensions >	ContinuousIndexType

Public Types inherited from itk::RelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >
typedef RelaxStreamlinesFilter	Self

typedef BaseCTEStreamlinesFilter < TImageType, TScalarType, NDimensions >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef Vector< TScalarType, NDimensions >	InputVectorImagePixelType

typedef Image < InputVectorImagePixelType, NDimensions >	InputVectorImageType

typedef InputVectorImageType::Pointer	InputVectorImagePointer

typedef InputVectorImageType::ConstPointer	InputVectorImageConstPointer

typedef InputVectorImageType::IndexType	InputVectorImageIndexType

typedef TScalarType	InputScalarImagePixelType

typedef Image < InputScalarImagePixelType, NDimensions >	InputScalarImageType

typedef Point< TScalarType, NDimensions >	InputScalarImagePointType

typedef InputScalarImageType::SpacingType	InputScalarImageSpacingType

typedef InputScalarImageType::Pointer	InputScalarImagePointer

typedef InputScalarImageType::IndexType	InputScalarImageIndexType

typedef InputScalarImageType::ConstPointer	InputScalarImageConstPointer

typedef InputScalarImageType::RegionType	InputScalarImageRegionType

typedef InputScalarImageType	OutputImageType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::ConstPointer	OutputImageConstPointer

typedef OutputImageType::IndexType	OutputImageIndexType

typedef OutputImageType::SpacingType	OutputImageSpacingType

typedef OutputImageType::RegionType	OutputImageRegionType

typedef OutputImageType::SizeType	OutputImageSizeType

typedef VectorInterpolateImageFunction < InputVectorImageType,TScalarType >	VectorInterpolatorType

typedef VectorInterpolatorType::Pointer	VectorInterpolatorPointer

typedef VectorInterpolatorType::PointType	VectorInterpolatorPointType

typedef InterpolateImageFunction < InputScalarImageType,TScalarType >	ScalarInterpolatorType

typedef ScalarInterpolatorType::Pointer	ScalarInterpolatorPointer

typedef ScalarInterpolatorType::PointType	ScalarInterpolatorPointType

Public Types inherited from itk::BaseCTEStreamlinesFilter< TImageType, TScalarType, NDimensions >
typedef BaseCTEStreamlinesFilter	Self

typedef BaseCTEFilter< TImageType >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef Vector< TScalarType, NDimensions >	InputVectorImagePixelType

typedef Image < InputVectorImagePixelType, NDimensions >	InputVectorImageType

typedef InputVectorImageType::Pointer	InputVectorImagePointer

typedef InputVectorImageType::ConstPointer	InputVectorImageConstPointer

typedef TScalarType	InputScalarImagePixelType

typedef Image < InputScalarImagePixelType, NDimensions >	InputScalarImageType

typedef InputScalarImageType::PointType	InputScalarImagePointType

typedef InputScalarImageType::Pointer	InputScalarImagePointer

typedef InputScalarImageType::IndexType	InputScalarImageIndexType

typedef InputScalarImageType::ConstPointer	InputScalarImageConstPointer

typedef InputScalarImageType::RegionType	InputScalarImageRegionType

typedef InputScalarImageType	OutputImageType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::ConstPointer	OutputImageConstPointer

typedef VectorInterpolateImageFunction < InputVectorImageType,TScalarType >	VectorInterpolatorType

typedef VectorInterpolatorType::Pointer	VectorInterpolatorPointer

typedef VectorInterpolatorType::PointType	VectorInterpolatorPointType

typedef InterpolateImageFunction < InputScalarImageType,TScalarType >	ScalarInterpolatorType

typedef ScalarInterpolatorType::Pointer	ScalarInterpolatorPointer

typedef ScalarInterpolatorType::PointType	ScalarInterpolatorPointType

Public Types inherited from itk::BaseCTEFilter< TImageType >
typedef BaseCTEFilter	Self

typedef ImageToImageFilter < TImageType, TImageType >	Superclass

typedef SmartPointer< Self >	Pointer

typedef SmartPointer< const Self >	ConstPointer

typedef TImageType	InputImageType

typedef InputImageType::PixelType	InputPixelType

typedef InputImageType::IndexType	InputIndexType

typedef InputImageType::SizeType	InputSizeType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputPixelType	OutputPixelType

typedef Image< OutputPixelType, TImageType::ImageDimension >	OutputImageType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::ConstPointer	OutputImageConstPointer

typedef OutputImageType::SizeType	OutputSizeType

Public Member Functions
virtual const char *	GetClassName () const

void	SetSegmentedImage (const InputScalarImageType *image)

void	SetGMPVMap (const InputScalarImageType *image)

virtual void	SetGreyMatterPVInterpolator (ScalarInterpolatorType *_arg)

virtual ScalarInterpolatorType *	GetGreyMatterPVInterpolator ()

virtual void	SetStepSizeThreshold (double _arg)

virtual double	GetStepSizeThreshold ()

virtual void	SetGreyMatterPercentage (double _arg)

virtual double	GetGreyMatterPercentage ()

virtual double	GetMaximumSearchDistance ()

void	SetMaximumSearchDistance (double d)

virtual void	SetDefaultMaximumSearchDistance (bool _arg)

virtual bool	GetDefaultMaximumSearchDistance ()

Public Member Functions inherited from itk::RelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >
	itkStaticConstMacro (Dimension, unsigned int, NDimensions)

void	SetScalarImage (const InputScalarImageType *image)

void	SetVectorImage (const InputVectorImageType *image)

void	SetSegmentedImage (const InputScalarImageType *image)

virtual void	SetEpsilonConvergenceThreshold (double _arg)

virtual double	GetEpsilonConvergenceThreshold ()

virtual void	SetMaximumNumberOfIterations (unsigned long int _arg)

virtual unsigned long int	GetMaximumNumberOfIterations ()

virtual void	SetMaximumLength (double _arg)

virtual double	GetMaximumLength ()

virtual void	SetInitializeBoundaries (bool _arg)

virtual bool	GetInitializeBoundaries ()

OutputImageType *	GetL0Image () const

OutputImageType *	GetL1Image () const

Public Member Functions inherited from itk::BaseCTEStreamlinesFilter< TImageType, TScalarType, NDimensions >
virtual void	SetLowVoltage (InputScalarImagePixelType _arg)

virtual InputScalarImagePixelType	GetLowVoltage ()

virtual void	SetHighVoltage (InputScalarImagePixelType _arg)

virtual InputScalarImagePixelType	GetHighVoltage ()

virtual void	SetVectorInterpolator (VectorInterpolatorType *_arg)

virtual const VectorInterpolatorType *	GetVectorInterpolator ()

virtual void	SetScalarInterpolator (ScalarInterpolatorType *_arg)

virtual const ScalarInterpolatorType *	GetScalarInterpolator ()

Public Member Functions inherited from itk::BaseCTEFilter< TImageType >
	itkStaticConstMacro (Dimension, unsigned int, TImageType::ImageDimension)

virtual InputPixelType	GetGreyMatterLabel ()

virtual InputPixelType	GetWhiteMatterLabel ()

virtual InputPixelType	GetExtraCerebralMatterLabel ()

void	SetLabelThresholds (InputPixelType greyMatterLabel, InputPixelType whiteMatterLabel, InputPixelType extraCerebralMatterLabel)

virtual bool	GetUserHasSetTheLabelThresholds ()

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::RelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >
static Pointer	New ()

Protected Member Functions
	LagrangianInitializedRelaxStreamlinesFilter ()

	~LagrangianInitializedRelaxStreamlinesFilter ()

void	PrintSelf (std::ostream &os, Indent indent) const

virtual void	InitializeBoundaries (std::vector< InputScalarImageIndexType > &completeListOfGreyMatterPixels, InputScalarImageType scalarImage, InputVectorImageType vectorImage, OutputImageType L0Image, OutputImageType L1Image, std::vector< InputScalarImageIndexType > &L0greyList, std::vector< InputScalarImageIndexType > &L1greyList)

OutputImagePixelType	LagrangianInitialisation (ContinuousIndexType &index, double &direction, double &defaultStepSize, double &minStepSize, InputVectorImageType vectorImage, InputScalarImageType greyMatterPVMap)

void	UpdateGMPVMap (std::vector< InputScalarImageIndexType > &listOfGreyMatterPixels, InputScalarImageType segmentedImage, InputVectorImageType vectorImage, InputScalarImageType gmPVMapImage, InputScalarImageType editedPVMap)

double	GetMaxStepSize (InputScalarImageType *image)

Protected Member Functions inherited from itk::RelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >
	RelaxStreamlinesFilter ()

	~RelaxStreamlinesFilter ()

void	PrintSelf (std::ostream &os, Indent indent) const

virtual void	GenerateData ()

virtual void	SolvePDE (bool isInnerBoundary, std::vector< InputScalarImageIndexType > &listOfGreyPixels, InputScalarImageType scalarImage, InputVectorImageType vectorImage, OutputImageType *outputImage)

Protected Member Functions inherited from itk::BaseCTEStreamlinesFilter< TImageType, TScalarType, NDimensions >
	BaseCTEStreamlinesFilter ()

	~BaseCTEStreamlinesFilter ()

Protected Member Functions inherited from itk::BaseCTEFilter< TImageType >
	BaseCTEFilter ()

virtual	~BaseCTEFilter ()

virtual void	GenerateInputRequestedRegion ()

virtual void	EnlargeOutputRequestedRegion (DataObject *itkNotUsed)

virtual void	CheckInputsAndOutputsSameSize ()

virtual bool	IsOnBoundary (const InputImageType *image, const InputIndexType &index, const InputPixelType boundaryValue, bool useFullyConnected)

virtual bool	IsOnCSFBoundary (const InputImageType *image, const InputIndexType &index, bool useFullyConnected)

virtual bool	IsOnWMBoundary (const InputImageType *image, const InputIndexType &index, bool useFullyConnected)

virtual bool	IsOnGMBoundary (const InputImageType *image, const InputIndexType &index, bool useFullyConnected)

Additional Inherited Members
Protected Attributes inherited from itk::RelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >
double	m_EpsilonConvergenceThreshold

unsigned long int	m_MaximumNumberOfIterations

double	m_MaximumLength

bool	m_InitializeBoundaries

Protected Attributes inherited from itk::BaseCTEStreamlinesFilter< TImageType, TScalarType, NDimensions >
VectorInterpolatorPointer	m_VectorInterpolator

ScalarInterpolatorPointer	m_ScalarInterpolator

InputScalarImagePixelType	m_LowVoltage

InputScalarImagePixelType	m_HighVoltage

Protected Attributes inherited from itk::BaseCTEFilter< TImageType >
InputPixelType	m_GreyMatterLabel

InputPixelType	m_WhiteMatterLabel

InputPixelType	m_ExtraCerebralMatterLabel

bool	m_UserHasSetTheLabelThresholds

Detailed Description

template<class TImageType, typename TScalarType, unsigned int NDimensions>
class itk::LagrangianInitializedRelaxStreamlinesFilter< TImageType, TScalarType, NDimensions >

Implements section 2.3.2 in Bourgeat et. al. ISBI 2008.

This class is implemented as a sub-class of RelaxStreamlinesFilter to make it clear that apart from initializing the boundaries, there is no difference in terms of PDE solving.

Usage: See the implementation of niftkCTEBourgeat2008.cxx

You can additionally set the interpolator, but it defaults to Linear which should be fine. The StepSize threshold is the minimum step size in the dichotomy search, which defaults to 0.001 as mentioned in the paper. This class assumes that at the boundary you are modelling two tissue types, so that when the paper says the stopping point for Lagrangian Initialization (i.e. ray casting) is "where the PV maps are equal", then in this implementation, we simply search for the threshold 0.5. So GreyMatterPercentage defaults to 0.5, but you can tweak it if you want to.

See also: RelaxStreamlinesFilter