itk::CorrectGMUsingNeighbourhoodFilter< TImageType > Class Template Reference

Implements section 2.3 in Acosta et al. doi:10.1016/j.media.2009.07.003. More...

Inheritance diagram for itk::CorrectGMUsingNeighbourhoodFilter< TImageType >:

Collaboration diagram for itk::CorrectGMUsingNeighbourhoodFilter< TImageType >:

Public Types
typedef CorrectGMUsingNeighbourhoodFilter	Self
typedef BaseCTESegmentationFilter < TImageType >	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef Superclass::InputImageType	InputImageType
typedef Superclass::InputPixelType	InputPixelType
typedef Superclass::InputIndexType	InputIndexType
typedef Superclass::InputImagePointer	InputImagePointer
typedef Superclass::InputImageConstPointer	InputImageConstPointer
typedef Superclass::OutputPixelType	OutputPixelType
typedef Superclass::OutputImageType	OutputImageType
typedef OutputImageType::RegionType	OutputImageRegionType
typedef OutputImageType::IndexType	OutputImageIndexType
typedef OutputImageType::SizeType	OutputImageSizeType
typedef Superclass::OutputImagePointer	OutputImagePointer
typedef Superclass::OutputImageConstPointer	OutputImageConstPointer
Public Types inherited from itk::BaseCTESegmentationFilter< TImageType >
typedef BaseCTESegmentationFilter	Self
typedef BaseCTEFilter< TImageType >	Superclass
typedef SmartPointer< Self >	Pointer
typedef SmartPointer< const Self >	ConstPointer
typedef Superclass::InputImageType	InputImageType
typedef Superclass::InputPixelType	InputPixelType
typedef Superclass::InputIndexType	InputIndexType
typedef Superclass::InputSizeType	InputSizeType
typedef Superclass::InputImagePointer	InputImagePointer
typedef Superclass::InputImageConstPointer	InputImageConstPointer
typedef Superclass::OutputPixelType	OutputPixelType
typedef Superclass::OutputImageType	OutputImageType
typedef Superclass::OutputImagePointer	OutputImagePointer
typedef Superclass::OutputImageConstPointer	OutputImageConstPointer
typedef Superclass::OutputSizeType	OutputSizeType
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 InputImageType *image)
const std::vector < InputIndexType > &	GetListOfGreyMatterPixelsBeforeCorrection () const
const std::vector < InputIndexType > &	GetListOfGreyMatterPixelsAfterCorrection () const
virtual unsigned long int	GetNumberReclassified ()
virtual void	SetUseFullNeighbourHood (bool _arg)
virtual bool	GetUseFullNeighbourHood ()
Public Member Functions inherited from itk::BaseCTESegmentationFilter< TImageType >
virtual void	SetTrustPVMaps (bool _arg)
virtual bool	GetTrustPVMaps ()
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 ()

Protected Member Functions
	CorrectGMUsingNeighbourhoodFilter ()
virtual	~CorrectGMUsingNeighbourhoodFilter ()
virtual void	PrintSelf (std::ostream &, Indent) const
virtual void	GenerateData ()
Protected Member Functions inherited from itk::BaseCTESegmentationFilter< TImageType >
	BaseCTESegmentationFilter ()
virtual	~BaseCTESegmentationFilter ()
virtual void	CheckOrAssignLabels ()
virtual void	CheckPVMap (std::string name, const InputImageType *image)
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::BaseCTEFilter< TImageType >
InputPixelType	m_GreyMatterLabel
InputPixelType	m_WhiteMatterLabel
InputPixelType	m_ExtraCerebralMatterLabel
bool	m_UserHasSetTheLabelThresholds

Detailed Description

template<class TImageType>
class itk::CorrectGMUsingNeighbourhoodFilter< TImageType >

Implements section 2.3 in Acosta et al. doi:10.1016/j.media.2009.07.003.

Usage:

filter->SetSegmentedImage(segmentedImage);

filter->Update();

The filter takes an image with 3 labels, (GM, WM, CSF). To quote paper, "We implemented an algorithm that checks whether in the 3 x 3 x 3 neighbourhood of each WM boundary voxel, there is any CSF voxel breaking the GM/WM continuity, in which case it is reclassified as GM.".

This exposes 2 lists of indexes, one for all GM pixels before the update, and one for all GM pixels after the update.

See also

niftkCTEBourgeat2008

Member Typedef Documentation

template<class TImageType >

typedef SmartPointer<const Self> itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::ConstPointer

template<class TImageType >

typedef Superclass::InputImageConstPointer itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::InputImageConstPointer

template<class TImageType >

typedef Superclass::InputImagePointer itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::InputImagePointer

template<class TImageType >

typedef Superclass::InputImageType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::InputImageType

Image typedef support.

template<class TImageType >

typedef Superclass::InputIndexType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::InputIndexType

template<class TImageType >

typedef Superclass::InputPixelType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::InputPixelType

template<class TImageType >

typedef Superclass::OutputImageConstPointer itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::OutputImageConstPointer

template<class TImageType >

typedef OutputImageType::IndexType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::OutputImageIndexType

template<class TImageType >

typedef Superclass::OutputImagePointer itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::OutputImagePointer

template<class TImageType >

typedef OutputImageType::RegionType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::OutputImageRegionType

template<class TImageType >

typedef OutputImageType::SizeType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::OutputImageSizeType

template<class TImageType >

typedef Superclass::OutputImageType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::OutputImageType

template<class TImageType >

typedef Superclass::OutputPixelType itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::OutputPixelType

template<class TImageType >

typedef SmartPointer<Self> itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::Pointer

template<class TImageType >

typedef CorrectGMUsingNeighbourhoodFilter itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::Self

Standard "Self" & Superclass typedef.

template<class TImageType >

typedef BaseCTESegmentationFilter<TImageType> itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::Superclass

Constructor & Destructor Documentation

template<class TImageType >

itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::CorrectGMUsingNeighbourhoodFilter ( )

protected

template<class TImageType >

virtual itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::~CorrectGMUsingNeighbourhoodFilter ( )

inlineprotectedvirtual

Member Function Documentation

template<class TImageType >

virtual void itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::GenerateData ( )

protectedvirtual

template<class TImageType >

virtual const char* itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::GetClassName ( ) const

virtual

Run-time type information (and related methods)

Reimplemented from itk::BaseCTESegmentationFilter< TImageType >.

template<class TImageType >

const std::vector<InputIndexType>& itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::GetListOfGreyMatterPixelsAfterCorrection

(

)

const

Once the filter has run, a list of GM voxles in corrected segmented volume.

template<class TImageType >

const std::vector<InputIndexType>& itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::GetListOfGreyMatterPixelsBeforeCorrection

(

)

const

Once the filter has run, a list of GM voxels in original segmented volume

template<class TImageType >

virtual unsigned long int itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::GetNumberReclassified ( )

virtual

So we can extract the number reclassified immediately after an update.

template<class TImageType >

virtual bool itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::GetUseFullNeighbourHood ( )

virtual

template<class TImageType >

static Pointer itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::New ( )

static

Method for creation through the object factory.

template<class TImageType >

virtual void itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::PrintSelf ( std::ostream &  , Indent    ) const

protectedvirtual

Standard Print Self.

Reimplemented from itk::BaseCTESegmentationFilter< TImageType >.

template<class TImageType >

void itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::SetSegmentedImage ( const InputImageType *  image )

inline

Sets the segmented image, at input 0.

template<class TImageType >

virtual void itk::CorrectGMUsingNeighbourhoodFilter< TImageType >::SetUseFullNeighbourHood ( bool  _arg )

virtual

Set/Get flag to determine if we examine the full 27 connected, or just the local 6 connected neighbourhood. Default true.

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The documentation for this class was generated from the following file:

• itkCorrectGMUsingNeighbourhoodFilter.h