itk::MRASlabIdentifier< TInputImage > Class Template Reference

#include <itkMRASlabIdentifier.h>

Inheritance diagram for itk::MRASlabIdentifier< TInputImage >:

Collaboration diagram for itk::MRASlabIdentifier< TInputImage >:

Detailed Description

template<class TInputImage>
class itk::MRASlabIdentifier< TInputImage >

identifies slab in MR images comparing minimum intensity averages

This class is templated over the type of image. In many cases, a 3D MR image is constructed by merging smaller 3D blocks (slabs) which were acquired with different settings such as magnetic settings and patient positions. Therefore, stripe like patterns with slabs can be present in the resulting image. Such artifacts are called "slab boundary" artifacts or "venetian blind" artifacts.

With the slab boundary artifacts in an image, even a same tissue class's intensity values might vary significantly along the borders of slabs. Such rough value changes are not appropriate for some image processing methods. For example, MRIBiasFieldCorrectionFilter assumes a smooth bias field. However, with the slab boundary artifacts, the bias field estimation scheme that MRIBiasFieldCorrectionFilter uses might not adopt well. So, the MRIBiasFieldCorrectionFilter creates regions for slabs using the MRASlabIdentifier and then apply its bias correction scheme to each slab.

For this identifier, a slice means 2D image data which is extracted from the input image along one of three axes (x, y, z). Users can specify the slicing axis using the SetSlicingDirection(int dimension) member. (0 - x, 1 - y, 2 - z).

The identification scheme used here is very simple. 1) Users should specify how many pixels per slice the identifier will sample. 2) For each slice, the identifier searches the specified number of pixels of which intensity values are greater than 0 and less than those of the other pixels in the slice 3) The identifier calculates the average for each slice and the overall average using the search results. 4) For each slice, it subtracts the overall average from the slice average. If the sign of the subtraction result changes, then it assumes that a slab ends and another slab begins.

Definition at line 65 of file itkMRASlabIdentifier.h.

Public Types
typedef SmartPointer< const Self >	ConstPointer
typedef TInputImage::ConstPointer	ImageConstPointer
typedef TInputImage::IndexType	ImageIndexType
typedef TInputImage::PixelType	ImagePixelType
typedef TInputImage::Pointer	ImagePointer
typedef TInputImage::RegionType	ImageRegionType
typedef TInputImage::SizeType	ImageSizeType
typedef TInputImage	ImageType
typedef SmartPointer< Self >	Pointer
typedef MRASlabIdentifier	Self
typedef std::vector < ImageRegionType >	SlabRegionVectorType
typedef Object	Superclass
Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef Object	Self
typedef LightObject	Superclass
Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
void	GenerateSlabRegions (void)
virtual const char *	GetNameOfClass () const
SlabRegionVectorType	GetSlabRegionVector (void)
virtual void	SetImage (const ImageType *_arg)
virtual const ImageType *	GetImage ()
virtual void	SetNumberOfSamples (unsigned int _arg)
virtual const unsigned int &	GetNumberOfSamples ()
virtual void	SetBackgroundMinimumThreshold (ImagePixelType _arg)
virtual const ImagePixelType &	GetBackgroundMinimumThreshold ()
virtual void	SetTolerance (double _arg)
virtual const double &	GetTolerance ()
virtual void	SetSlicingDirection (int _arg)
virtual const int &	GetSlicingDirection ()
Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
virtual void	DebugOff () const
virtual void	DebugOn () const
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual ModifiedTimeType	GetMTime () const
virtual const TimeStamp &	GetTimeStamp () const
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
virtual void	Modified () const
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int)
virtual void	UnRegister () const
Public Member Functions inherited from itk::LightObject
virtual void	Delete ()
virtual int	GetReferenceCount () const
	itkCloneMacro (Self)
void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()
Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static Pointer	New ()
static void	SetGlobalWarningDisplay (bool flag)
Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()
static Pointer	New ()

Protected Member Functions
	MRASlabIdentifier ()
void	PrintSelf (std::ostream &os, Indent indent) const
virtual	~MRASlabIdentifier ()
Protected Member Functions inherited from itk::Object
	Object ()
bool	PrintObservers (std::ostream &os, Indent indent) const
virtual void	SetTimeStamp (const TimeStamp &time)
virtual	~Object ()
Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const
	LightObject ()
virtual void	PrintHeader (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
virtual	~LightObject ()

Private Member Functions
	MRASlabIdentifier (const Self &)
void	operator= (const Self &)

Private Attributes
ImagePixelType	m_BackgroundMinimumThreshold
ImageConstPointer	m_Image
unsigned int	m_NumberOfSamples
SlabRegionVectorType	m_Slabs
int	m_SlicingDirection
double	m_Tolerance

Additional Inherited Members
Protected Types inherited from itk::LightObject
typedef int	InternalReferenceCountType
Protected Attributes inherited from itk::LightObject
InternalReferenceCountType	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock

Member Typedef Documentation

template<class TInputImage >

typedef SmartPointer< const Self > itk::MRASlabIdentifier< TInputImage >::ConstPointer

Definition at line 72 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef TInputImage::ConstPointer itk::MRASlabIdentifier< TInputImage >::ImageConstPointer

Const Pointer type for the image.

Definition at line 87 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef TInputImage::IndexType itk::MRASlabIdentifier< TInputImage >::ImageIndexType

Definition at line 91 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef TInputImage::PixelType itk::MRASlabIdentifier< TInputImage >::ImagePixelType

Type definition for the input image pixel type.

Definition at line 90 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef TInputImage::Pointer itk::MRASlabIdentifier< TInputImage >::ImagePointer

Pointer type for the image.

Definition at line 84 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef TInputImage::RegionType itk::MRASlabIdentifier< TInputImage >::ImageRegionType

Definition at line 93 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef TInputImage::SizeType itk::MRASlabIdentifier< TInputImage >::ImageSizeType

Definition at line 92 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef TInputImage itk::MRASlabIdentifier< TInputImage >::ImageType

Type definition for the input image.

Definition at line 78 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef SmartPointer< Self > itk::MRASlabIdentifier< TInputImage >::Pointer

Definition at line 71 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef MRASlabIdentifier itk::MRASlabIdentifier< TInputImage >::Self

Standard class typedefs.

Definition at line 69 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef std::vector< ImageRegionType > itk::MRASlabIdentifier< TInputImage >::SlabRegionVectorType

Definition at line 94 of file itkMRASlabIdentifier.h.

template<class TInputImage >

typedef Object itk::MRASlabIdentifier< TInputImage >::Superclass

Definition at line 70 of file itkMRASlabIdentifier.h.

Constructor & Destructor Documentation

template<class TInputImage >

itk::MRASlabIdentifier< TInputImage >::MRASlabIdentifier ( )

protected

template<class TInputImage >

virtual itk::MRASlabIdentifier< TInputImage >::~MRASlabIdentifier ( )

inlineprotectedvirtual

Definition at line 131 of file itkMRASlabIdentifier.h.

template<class TInputImage >

itk::MRASlabIdentifier< TInputImage >::MRASlabIdentifier ( const Self &  )

private

Member Function Documentation

template<class TInputImage >

virtual::itk::LightObject::Pointer itk::MRASlabIdentifier< TInputImage >::CreateAnother ( void  ) const

virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

template<class TInputImage >

void itk::MRASlabIdentifier< TInputImage >::GenerateSlabRegions

(

void

)

Compute the average values of miminum intensity pixels for each slice and compare the average values with overall averages.

template<class TInputImage >

virtual const ImagePixelType& itk::MRASlabIdentifier< TInputImage >::GetBackgroundMinimumThreshold ( )

virtual

Set/Get the minimum threshold value for the background pixels

template<class TInputImage >

virtual const ImageType* itk::MRASlabIdentifier< TInputImage >::GetImage ( )

virtual

Set/Get the input image.

template<class TInputImage >

virtual const char* itk::MRASlabIdentifier< TInputImage >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods).

Reimplemented from itk::Object.

template<class TInputImage >

virtual const unsigned int& itk::MRASlabIdentifier< TInputImage >::GetNumberOfSamples ( )

virtual

Set/Get the number of minimum intensity pixels per slice.

template<class TInputImage >

SlabRegionVectorType itk::MRASlabIdentifier< TInputImage >::GetSlabRegionVector

(

void

)

Get slab regions.

template<class TInputImage >

virtual const int& itk::MRASlabIdentifier< TInputImage >::GetSlicingDirection ( )

virtual

Set/Get the direction of slicing/ 0 - x axis, 1 - y axis, 2 - z axis

template<class TInputImage >

virtual const double& itk::MRASlabIdentifier< TInputImage >::GetTolerance ( )

virtual

Set/Get the tolerance value.

template<class TInputImage >

static Pointer itk::MRASlabIdentifier< TInputImage >::New ( )

static

Method for creation through the object factory.

template<class TInputImage >

void itk::MRASlabIdentifier< TInputImage >::operator= ( const Self &  )

private

template<class TInputImage >

void itk::MRASlabIdentifier< TInputImage >::PrintSelf ( std::ostream &  os, Indent  indent  ) const

protectedvirtual

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Reimplemented from itk::Object.

template<class TInputImage >

virtual void itk::MRASlabIdentifier< TInputImage >::SetBackgroundMinimumThreshold ( ImagePixelType  _arg )

virtual

Set/Get the minimum threshold value for the background pixels

template<class TInputImage >

virtual void itk::MRASlabIdentifier< TInputImage >::SetImage ( const ImageType *  _arg )

virtual

Set/Get the input image.

template<class TInputImage >

virtual void itk::MRASlabIdentifier< TInputImage >::SetNumberOfSamples ( unsigned int  _arg )

virtual

Set/Get the number of minimum intensity pixels per slice.

template<class TInputImage >

virtual void itk::MRASlabIdentifier< TInputImage >::SetSlicingDirection ( int  _arg )

virtual

Set/Get the direction of slicing/ 0 - x axis, 1 - y axis, 2 - z axis

template<class TInputImage >

virtual void itk::MRASlabIdentifier< TInputImage >::SetTolerance ( double  _arg )

virtual

Set/Get the tolerance value.

Member Data Documentation

template<class TInputImage >

ImagePixelType itk::MRASlabIdentifier< TInputImage >::m_BackgroundMinimumThreshold

private

Definition at line 146 of file itkMRASlabIdentifier.h.

template<class TInputImage >

ImageConstPointer itk::MRASlabIdentifier< TInputImage >::m_Image

private

Target image pointer that MRASlabIdentifier will use.

Definition at line 139 of file itkMRASlabIdentifier.h.

template<class TInputImage >

unsigned int itk::MRASlabIdentifier< TInputImage >::m_NumberOfSamples

private

The number of pixels per slice which will be included for average calculation. In a sense, it's sampling size per slice.

Definition at line 143 of file itkMRASlabIdentifier.h.

template<class TInputImage >

SlabRegionVectorType itk::MRASlabIdentifier< TInputImage >::m_Slabs

private

Definition at line 148 of file itkMRASlabIdentifier.h.

template<class TInputImage >

int itk::MRASlabIdentifier< TInputImage >::m_SlicingDirection

private

Definition at line 145 of file itkMRASlabIdentifier.h.

template<class TInputImage >

double itk::MRASlabIdentifier< TInputImage >::m_Tolerance

private

Definition at line 147 of file itkMRASlabIdentifier.h.

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

• itkMRASlabIdentifier.h