itk::MRASlabIdentifier< TInputImage > Class Template Reference

#include <itkMRASlabIdentifier.h>

Inheritance diagram for itk::MRASlabIdentifier< TInputImage >:

[legend]Collaboration diagram for itk::MRASlabIdentifier< TInputImage >:

[legend]List of all members.

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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 Member Functions
virtual LightObject::Pointer	CreateAnother () const
virtual void	DebugOff () const
virtual void	DebugOn () const
virtual void	Delete ()
void	GenerateSlabRegions (void)
virtual const ImagePixelType &	GetBackgroundMinimumThreshold ()
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
virtual const ImageType *	GetImage ()
const MetaDataDictionary &	GetMetaDataDictionary (void) const
MetaDataDictionary &	GetMetaDataDictionary (void)
virtual unsigned long	GetMTime () const
virtual const char *	GetNameOfClass () const
virtual const unsigned int &	GetNumberOfSamples ()
virtual int	GetReferenceCount () const
SlabRegionVectorType	GetSlabRegionVector (void)
virtual const int &	GetSlicingDirection ()
virtual const double &	GetTolerance ()
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &) const
void	InvokeEvent (const EventObject &)
virtual void	Modified () const
void	Print (std::ostream &os, Indent indent=0) const
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
Set Get the minimum threshold value for the background pixels *virtual void	SetBackgroundMinimumThreshold (ImagePixelType _arg)
void	SetDebug (bool debugFlag) const
Set Get the input image *virtual void	SetImage (const ImageType *_arg)
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
Set Get the number of minimum intensity pixels per slice *virtual void	SetNumberOfSamples (unsigned int _arg)
virtual void	SetReferenceCount (int)
Set Get the direction of slicing *x y z axis *virtual void	SetSlicingDirection (int _arg)
Set Get the tolerance value *virtual void	SetTolerance (double _arg)
virtual void	UnRegister () const
Static Public Member Functions
static void	BreakOnError ()
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static Pointer	New ()
This is a global flag that controls whether any warning *or error messages are displayed *static void	SetGlobalWarningDisplay (bool flag)
Public Attributes
Allow people to add remove invoke observers(callbacks) to any ITK *object.This is an implementation of the subject/observer design *pattern.An observer is added by specifying an event to respond to *and an itk unsigned lon	AddObserver )(const EventObject &event, Command *) const
Set Get the direction of slicing *x y	axis
Set Get the direction of slicing *x	axis
This is a global flag that controls whether any	debug
Protected Member Functions
	MRASlabIdentifier ()
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
virtual	~MRASlabIdentifier ()
Protected Attributes
int	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock
Methods invoked by virtual 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.*/virtual void PrintSelf(std voi	PrintHeader )(std::ostream &os, Indent indent) const

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Member Typedef Documentation

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

Reimplemented from itk::Object. 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

Reimplemented from itk::Object. Definition at line 71 of file itkMRASlabIdentifier.h.

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

Standard class typedefs. Reimplemented from itk::Object. 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

Reimplemented from itk::Object. Definition at line 70 of file itkMRASlabIdentifier.h.

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Constructor & Destructor Documentation

template<class TInputImage> itk::MRASlabIdentifier< TInputImage >::MRASlabIdentifier (   )  [protected]

template<class TInputImage> virtual itk::MRASlabIdentifier< TInputImage >::~MRASlabIdentifier (   )  [inline, protected, virtual]

Definition at line 131 of file itkMRASlabIdentifier.h.

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Member Function Documentation

static void itk::LightObject::BreakOnError (   )  [static, inherited]

This method is called when itkExceptionMacro executes. It allows the debugger to break on error.

virtual LightObject::Pointer itk::Object::CreateAnother (   )  const [virtual, inherited]

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::LightObject.

virtual void itk::Object::DebugOff (   )  const [virtual, inherited]

Turn debugging output off.

virtual void itk::Object::DebugOn (   )  const [virtual, inherited]

Turn debugging output on.

virtual void itk::LightObject::Delete (   )  [virtual, inherited]

Delete an itk object. This method should always be used to delete an object when the new operator was used to create it. Using the C delete method will not work with reference counting.

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]

Command* itk::Object::GetCommand (  unsigned long  tag  )  [inherited]

Get the command associated with the given tag. NOTE: This returns a pointer to a Command, but it is safe to asign this to a Command::Pointer. Since Command inherits from LightObject, at this point in the code, only a pointer or a reference to the Command can be used.

bool itk::Object::GetDebug (   )  const [inherited]

Get the value of the debug flag.

static bool itk::Object::GetGlobalWarningDisplay (   )  [static, inherited]

template<class TInputImage> virtual const ImageType* itk::MRASlabIdentifier< TInputImage >::GetImage (   )  [virtual]

const MetaDataDictionary& itk::Object::GetMetaDataDictionary (  void   )  const [inherited]

Returns: A constant reference to this objects MetaDataDictionary.

MetaDataDictionary& itk::Object::GetMetaDataDictionary (  void   )  [inherited]

Returns: A reference to this objects MetaDataDictionary. Warning: This reference may be changed.

virtual unsigned long itk::Object::GetMTime (   )  const [virtual, inherited]

Return this objects modified time. Reimplemented in itk::ImageRegistrationMethod< TFixedImage, TMovingImage >, itk::DeformationFieldSource< TOutputImage >, itk::InverseDeformationFieldImageFilter< TInputImage, TOutputImage >, itk::ResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >, itk::VectorResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >, itk::BoundingBox< TPointIdentifier, VPointDimension, TCoordRep, TPointsContainer >, itk::SceneSpatialObject< SpaceDimension >, and itk::SceneSpatialObject< NDimensions >.

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]

virtual int itk::LightObject::GetReferenceCount (   )  const [inline, virtual, inherited]

Gets the reference count on this object. Definition at line 98 of file itkLightObject.h.

template<class TInputImage> SlabRegionVectorType itk::MRASlabIdentifier< TInputImage >::GetSlabRegionVector (  void   )

Get slab regions.

template<class TInputImage> virtual const int& itk::MRASlabIdentifier< TInputImage >::GetSlicingDirection (   )  [virtual]

template<class TInputImage> virtual const double& itk::MRASlabIdentifier< TInputImage >::GetTolerance (   )  [virtual]

static void itk::Object::GlobalWarningDisplayOff (   )  [inline, static, inherited]

Definition at line 100 of file itkObject.h. References itk::Object::SetGlobalWarningDisplay().

static void itk::Object::GlobalWarningDisplayOn (   )  [inline, static, inherited]

Definition at line 98 of file itkObject.h. References itk::Object::SetGlobalWarningDisplay().

bool itk::Object::HasObserver (  const EventObject &  event  )  const [inherited]

Return true if an observer is registered for this event.

void itk::Object::InvokeEvent (  const EventObject &   )  const [inherited]

Call Execute on all the Commands observing this event id. The actions triggered by this call doesn't modify this object.

void itk::Object::InvokeEvent (  const EventObject &   )  [inherited]

Call Execute on all the Commands observing this event id.

virtual void itk::Object::Modified (   )  const [virtual, inherited]

Update the modification time for this object. Many filters rely on the modification time to determine if they need to recompute their data. Referenced by itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetCenter(), itk::HistogramAlgorithmBase< TInputHistogram >::SetInputHistogram(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetMatrix(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetOffset(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetRealThresholds(), itk::CollidingFrontsImageFilter< TInputImage, TOutputImage >::SetSeedPoints1(), itk::CollidingFrontsImageFilter< TInputImage, TOutputImage >::SetSeedPoints2(), itk::NonUniformBSpline< TDimension >::SetSplineOrder(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetThresholds(), itk::Statistics::GoodnessOfFitFunctionBase< typename ComponentType::HistogramType >::SetTotalObservedScale(), and itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetTranslation().

template<class TInputImage> static Pointer itk::MRASlabIdentifier< TInputImage >::New (   )  [static]

Method for creation through the object factory. Reimplemented from itk::Object.

void itk::LightObject::Print (  std::ostream &  os, Indent  indent = 0 )  const [inherited]

Cause the object to print itself out.

bool itk::Object::PrintObservers (  std::ostream &  os, Indent  indent )  const [protected, inherited]

template<class TInputImage> void itk::MRASlabIdentifier< TInputImage >::PrintSelf (  std::ostream &  os, Indent  indent )  const [protected, virtual]

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.

virtual void itk::LightObject::PrintTrailer (  std::ostream &  os, Indent  indent )  const [protected, virtual, inherited]

virtual void itk::Object::Register (   )  const [virtual, inherited]

Increase the reference count (mark as used by another object). Reimplemented from itk::LightObject.

void itk::Object::RemoveAllObservers (   )  [inherited]

Remove all observers .

void itk::Object::RemoveObserver (  unsigned long  tag  )  [inherited]

Remove the observer with this tag value.

template<class TInputImage> Set Get the minimum threshold value for the background pixels* virtual void itk::MRASlabIdentifier< TInputImage >::SetBackgroundMinimumThreshold (  ImagePixelType  _arg  )  [virtual]

void itk::Object::SetDebug (  bool  debugFlag  )  const [inherited]

Set the value of the debug flag. A non-zero value turns debugging on.

This is a global flag that controls whether any warning* or error messages are displayed* static void itk::Object::SetGlobalWarningDisplay (  bool  flag  )  [static, inherited]

Referenced by itk::Object::GlobalWarningDisplayOff(), and itk::Object::GlobalWarningDisplayOn().

template<class TInputImage> Set Get the input image* virtual void itk::MRASlabIdentifier< TInputImage >::SetImage (  const ImageType *  _arg  )  [virtual]

void itk::Object::SetMetaDataDictionary (  const MetaDataDictionary &  rhs  )  [inherited]

Returns: Set the MetaDataDictionary

template<class TInputImage> Set Get the number of minimum intensity pixels per slice* virtual void itk::MRASlabIdentifier< TInputImage >::SetNumberOfSamples (  unsigned int  _arg  )  [virtual]

virtual void itk::Object::SetReferenceCount (  int   )  [virtual, inherited]

Sets the reference count (use with care) Reimplemented from itk::LightObject.

template<class TInputImage> Set Get the direction of slicing* x y z axis* virtual void itk::MRASlabIdentifier< TInputImage >::SetSlicingDirection (  int  _arg  )  [virtual]

template<class TInputImage> Set Get the tolerance value* virtual void itk::MRASlabIdentifier< TInputImage >::SetTolerance (  double  _arg  )  [virtual]

virtual void itk::Object::UnRegister (   )  const [virtual, inherited]

Decrease the reference count (release by another object). Reimplemented from itk::LightObject.

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Member Data Documentation

Allow people to add remove invoke observers (callbacks) to any ITK * object. This is an implementation of the subject/observer design * pattern. An observer is added by specifying an event to respond to * and an itk unsigned lon itk::Object::AddObserver)(const EventObject &event, Command *) const [inherited]

template<class TInputImage> Set Get the direction of slicing* x y itk::MRASlabIdentifier< TInputImage >::axis

Definition at line 113 of file itkMRASlabIdentifier.h.

template<class TInputImage> Set Get the direction of slicing* x itk::MRASlabIdentifier< TInputImage >::axis

Definition at line 113 of file itkMRASlabIdentifier.h.

This is a global flag that controls whether any itk::Object::debug [inherited]

Definition at line 94 of file itkObject.h.

int itk::LightObject::m_ReferenceCount [mutable, protected, inherited]

Number of uses of this object by other objects. Definition at line 119 of file itkLightObject.h.

SimpleFastMutexLock itk::LightObject::m_ReferenceCountLock [mutable, protected, inherited]

Mutex lock to protect modification to the reference count Definition at line 122 of file itkLightObject.h.

Methods invoked by virtual 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. */ virtual void PrintSelf(std voi itk::LightObject::PrintHeader)(std::ostream &os, Indent indent) const [protected, inherited]

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

• itkMRASlabIdentifier.h

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