itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage > Class Template Reference

#include <itkMRIBiasFieldCorrectionFilter.h>

Inheritance diagram for itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >:

Collaboration diagram for itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >:

List of all members.

Public Types
typedef MultivariateLegendrePolynomial	BiasFieldType
typedef SmartPointer< const Self >	ConstPointer
typedef EnergyFunctionType::Pointer	EnergyFunctionPointer
typedef MRIBiasEnergyFunction < InternalImageType, ImageMaskType, BiasFieldType >	EnergyFunctionType
typedef ImageMaskType::Pointer	ImageMaskPointer
typedef ImageMaskType::RegionType	ImageMaskRegionType
typedef TMaskImage	ImageMaskType
typedef TInputImage::IndexType	InputImageIndexType
typedef TInputImage::PixelType	InputImagePixelType
typedef TInputImage::Pointer	InputImagePointer
typedef TInputImage::RegionType	InputImageRegionType
typedef TInputImage::SizeType	InputImageSizeType
typedef TInputImage	InputImageType
typedef MRASlabIdentifier < InputImageType >	MRASlabIdentifierType
typedef Statistics::NormalVariateGenerator	NormalVariateGeneratorType
typedef OnePlusOneEvolutionaryOptimizer	OptimizerType
typedef TOutputImage::IndexType	OutputImageIndexType
typedef TOutputImage::PixelType	OutputImagePixelType
typedef TOutputImage::Pointer	OutputImagePointer
typedef TOutputImage::RegionType	OutputImageRegionType
typedef TOutputImage::SizeType	OutputImageSizeType
typedef TOutputImage	OutputImageType
typedef SmartPointer< Self >	Pointer
typedef Array2D< unsigned int >	ScheduleType
typedef MRIBiasFieldCorrectionFilter	Self
typedef SlabRegionVectorType::iterator	SlabRegionVectorIteratorType
typedef MRASlabIdentifierType::SlabRegionVectorType	SlabRegionVectorType
typedef ImageToImageFilter < TInputImage, TOutputImage >	Superclass
typedef Image< float, itkGetStaticConstMacro(ImageDimension) >	InternalImageType
typedef InternalImageType::PixelType	InternalImagePixelType
typedef InternalImageType::Pointer	InternalImagePointer
typedef InternalImageType::RegionType	InternalImageRegionType
Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef InputImageType::ConstPointer	InputImageConstPointer
Public Types inherited from itk::ImageSource< TOutputImage >
typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType
typedef DataObject::Pointer	DataObjectPointer
typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType
Public Types inherited from itk::ProcessObject
typedef std::vector < DataObjectPointer >	DataObjectPointerArray
typedef std::vector < DataObjectIdentifierType >	NameArray
Public Types inherited from itk::Object
Public Types inherited from itk::LightObject

Public Member Functions
void	CorrectImage (BiasFieldType &bias, InputImageRegionType region)
void	CorrectInterSliceIntensityInhomogeneity (InputImageRegionType region)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
BiasFieldType	EstimateBiasField (InputImageRegionType region, unsigned int degree, int maximumIteration)
BiasFieldType::CoefficientArrayType	GetEstimatedBiasFieldCoefficients ()
virtual ImageMaskType *	GetInputMask ()
virtual const char *	GetNameOfClass () const
virtual unsigned int	GetNumberOfLevels () const
virtual double	GetOptimizerShrinkFactor () const
virtual ImageMaskType *	GetOutputMask ()
virtual const ScheduleType &	GetSchedule ()
virtual const InputImagePixelType &	GetSlabBackgroundMinimumThreshold ()
virtual const unsigned int &	GetSlabNumberOfSamples ()
virtual const double &	GetSlabTolerance ()
const unsigned int *	GetStartingShrinkFactors () const
void	Initialize () throw ( ExceptionObject )
void	IsBiasFieldMultiplicative (bool flag)
bool	IsBiasFieldMultiplicative ()
void	SetInitialBiasFieldCoefficients (const BiasFieldType::CoefficientArrayType &coefficients)
void	SetInputMask (ImageMaskType *inputMask)
void	SetNumberOfLevels (unsigned int num)
virtual void	SetOptimizerShrinkFactor (double _arg)
void	SetOutputMask (ImageMaskType *outputMask)
void	SetSchedule (const ScheduleType &schedule)
virtual void	SetSlabBackgroundMinimumThreshold (InputImagePixelType _arg)
virtual void	SetSlabNumberOfSamples (unsigned int _arg)
virtual void	SetSlabTolerance (double _arg)
virtual void	SetSlicingDirection (int _arg)
void	SetStartingShrinkFactors (unsigned int factor)
void	SetStartingShrinkFactors (unsigned int *factors)
void	SetTissueClassStatistics (const Array< double > &means, const Array< double > &sigmas) throw ( ExceptionObject )
virtual void	SetUsingInterSliceIntensityCorrection (bool _arg)
virtual const bool &	GetUsingInterSliceIntensityCorrection ()
virtual void	SetUsingSlabIdentification (bool _arg)
virtual const bool &	GetUsingSlabIdentification ()
virtual void	SetUsingBiasFieldCorrection (bool _arg)
virtual const bool &	GetUsingBiasFieldCorrection ()
virtual void	SetGeneratingOutput (bool _arg)
virtual const bool &	GetGeneratingOutput ()
virtual void	SetBiasFieldDegree (int _arg)
virtual int	GetBiasFieldDegree () const
virtual void	SetVolumeCorrectionMaximumIteration (int _arg)
virtual int	GetVolumeCorrectionMaximumIteration () const
virtual void	SetInterSliceCorrectionMaximumIteration (int _arg)
virtual int	GetInterSliceCorrectionMaximumIteration () const
void	SetOptimizerInitialRadius (double initRadius)
double	GetOptimizerInitialRadius ()
virtual void	SetOptimizerGrowthFactor (double _arg)
virtual double	GetOptimizerGrowthFactor () const
Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
const InputImageType *	GetInput (void) const
const InputImageType *	GetInput (unsigned int idx) const
virtual void	PopBackInput ()
virtual void	PopFrontInput ()
virtual void	PushBackInput (const InputImageType *image)
virtual void	PushFrontInput (const InputImageType *image)
virtual void	SetInput (const InputImageType *image)
virtual void	SetInput (unsigned int, const TInputImage *image)
Public Member Functions inherited from itk::ImageSource< TOutputImage >
OutputImageType *	GetOutput (unsigned int idx)
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
virtual void	GraftOutput (DataObject *output)
virtual void	GraftOutput (const DataObjectIdentifierType &key, DataObject *output)
OutputImageType *	GetOutput (void)
const OutputImageType *	GetOutput (void) const
virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx)
Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
virtual void	EnlargeOutputRequestedRegion (DataObject *)
virtual const bool &	GetAbortGenerateData ()
NameArray	GetInputNames () const
MultiThreader *	GetMultiThreader () const
DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
DataObjectPointerArraySizeType	GetNumberOfOutputs () const
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
NameArray	GetOutputNames () const
virtual const float &	GetProgress ()
NameArray	GetRequiredInputNames () const
bool	HasInput (const DataObjectIdentifierType &key) const
bool	HasOutput (const DataObjectIdentifierType &key) const
virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)
virtual void	PrepareOutputs ()
virtual void	PropagateRequestedRegion (DataObject *output)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
virtual void	SetProgress (float _arg)
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float amount)
DataObjectPointerArray	GetInputs ()
DataObjectPointerArray	GetOutputs ()
DataObjectPointerArray	GetIndexedInputs ()
DataObjectPointerArray	GetIndexedOutputs ()
DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const
virtual void	SetReleaseDataFlag (bool flag)
virtual bool	GetReleaseDataFlag () const
void	ReleaseDataFlagOn ()
void	ReleaseDataFlagOff ()
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)
virtual const bool &	GetReleaseDataBeforeUpdateFlag ()
virtual void	ReleaseDataBeforeUpdateFlagOn ()
virtual void	ReleaseDataBeforeUpdateFlagOff ()
virtual void	SetNumberOfThreads (ThreadIdType _arg)
virtual const ThreadIdType &	GetNumberOfThreads ()
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 unsigned long	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 bool	IsScheduleDownwardDivisible (const ScheduleType &schedule)
static Pointer	New ()

Static Public Attributes
static const unsigned int	ImageDimension = TOutputImage::ImageDimension
Static Public Attributes inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
static const unsigned int	InputImageDimension = TInputImage::ImageDimension
static const unsigned int	OutputImageDimension = TOutputImage::ImageDimension
Static Public Attributes inherited from itk::ImageSource< TOutputImage >

Protected Member Functions
void	AdjustSlabRegions (SlabRegionVectorType &slabs, OutputImageRegionType requestedRegion)
bool	CheckMaskImage (ImageMaskType *mask)
template<class TSource , class TTarget >
void	CopyAndConvertImage (const TSource *source, TTarget *target, typename TTarget::RegionType requestedRegion)
void	ExpImage (InternalImageType *source, InternalImageType *target)
void	GenerateData ()
void	GetBiasFieldSize (InputImageRegionType region, BiasFieldType::DomainSizeType &domainSize)
void	Log1PImage (InternalImageType *source, InternalImageType *target)
	MRIBiasFieldCorrectionFilter ()
void	PrintSelf (std::ostream &os, Indent indent) const
virtual	~MRIBiasFieldCorrectionFilter ()
Protected Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
virtual void	GenerateInputRequestedRegion ()
	ImageToImageFilter ()
virtual void	VerifyInputInformation ()
	~ImageToImageFilter ()
void	PushBackInput (const DataObject *input)
void	PushFrontInput (const DataObject *input)
Protected Member Functions inherited from itk::ImageSource< TOutputImage >
virtual void	AfterThreadedGenerateData ()
virtual void	AllocateOutputs ()
virtual void	BeforeThreadedGenerateData ()
	ImageSource ()
virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)
virtual	~ImageSource ()
Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)
virtual void	AddOutput (DataObject *output)
bool	AddRequiredInputName (const DataObjectIdentifierType &)
virtual void	CacheInputReleaseDataFlags ()
virtual void	GenerateOutputInformation ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs ()
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs ()
bool	IsIndexedName (const DataObjectIdentifierType &) const
bool	IsRequiredInputName (const DataObjectIdentifierType &) const
	itkLegacyMacro (virtual void RemoveInput(DataObject *input))
	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))
	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))
	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))
DataObjectPointerArraySizeType	MakeIndexFromName (const DataObjectIdentifierType &) const
DataObjectIdentifierType	MakeNameFromIndex (DataObjectPointerArraySizeType) const
	ProcessObject ()
virtual void	PropagateResetPipeline ()
virtual void	ReleaseInputs ()
virtual void	RemoveInput (const DataObjectIdentifierType &key)
virtual void	RemoveInput (DataObjectPointerArraySizeType)
virtual void	RemoveOutput (const DataObjectIdentifierType &key)
virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)
bool	RemoveRequiredInputName (const DataObjectIdentifierType &)
virtual void	RestoreInputReleaseDataFlags ()
virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)
virtual void	SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)
virtual void	SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
virtual void	SetOutput (const DataObjectIdentifierType &key, DataObject *output)
virtual void	SetPrimaryInput (DataObject *input)
virtual void	SetPrimaryOutput (DataObject *output)
void	SetRequiredInputNames (const NameArray &)
virtual void	VerifyPreconditions ()
	~ProcessObject ()
DataObject *	GetInput (const DataObjectIdentifierType &key)
const DataObject *	GetInput (const DataObjectIdentifierType &key) const
DataObject *	GetInput (DataObjectPointerArraySizeType)
const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryInput ()
const DataObject *	GetPrimaryInput () const
DataObject *	GetOutput (const DataObjectIdentifierType &key)
const DataObject *	GetOutput (const DataObjectIdentifierType &key) const
DataObject *	GetOutput (DataObjectPointerArraySizeType idx)
const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryOutput ()
const DataObject *	GetPrimaryOutput () const
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
	MRIBiasFieldCorrectionFilter (const Self &)
void	operator= (const Self &)

Private Attributes
BiasFieldType::CoefficientArrayType	m_BiasFieldCoefficients
int	m_BiasFieldDegree
bool	m_BiasMultiplicative
EnergyFunctionPointer	m_EnergyFunction
BiasFieldType::CoefficientArrayType	m_EstimatedBiasFieldCoefficients
bool	m_GeneratingOutput
ImageMaskPointer	m_InputMask
InternalImagePointer	m_InternalInput
int	m_InterSliceCorrectionMaximumIteration
NormalVariateGeneratorType::Pointer	m_NormalVariateGenerator
unsigned int	m_NumberOfLevels
double	m_OptimizerGrowthFactor
double	m_OptimizerInitialRadius
double	m_OptimizerShrinkFactor
ImageMaskPointer	m_OutputMask
ScheduleType	m_Schedule
InputImagePixelType	m_SlabBackgroundMinimumThreshold
unsigned int	m_SlabNumberOfSamples
SlabRegionVectorType	m_Slabs
double	m_SlabTolerance
int	m_SlicingDirection
Array< double >	m_TissueClassMeans
Array< double >	m_TissueClassSigmas
bool	m_UsingBiasFieldCorrection
bool	m_UsingInterSliceIntensityCorrection
bool	m_UsingSlabIdentification
int	m_VolumeCorrectionMaximumIteration

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) >	InputToOutputRegionCopierType
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) >	OutputToInputRegionCopierType

---

Detailed Description

template<class TInputImage, class TOutputImage, class TMaskImage>
class itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >

corrects 3D MRI bias field

This class is templated over the type of the input image (TInputImage) and the type of the output image (TOutputImage).

In MRI images, intensity inhomogenieties which are caused by magnetic settings, patients' position, and other factors are not unusual. The main purpose of this filter is to reduce such bias field. To estimate the bias field, we use Legendre polynomials. The 1+1 evolutionary optimizer searches for the best parameters of a Legendre polynomial (bias field estimate) which minimizes the total energy value of each image after bias field is eliminated. The default Legendre polynomial degree is 3.

The correction performs by default a multiplicative bias field correction by first log-transforming the input image. This log transform only works on images with grayscale values bigger than 0. The log-transform can be disabled and the filter computes an additive bias field.

There are three major processes in the whole bias correction scheme: slab identification, inter-slice intensity correction, and actual bias correction process. Users can turn on and off each process within the whole bias correction scheme using SetUsingSlabIdentification(bool, false by default), SetUsingInterSliceIntensityCorrection(bool, true by default), and SetUsingBiasFieldCorrection(bool, true by default) member function.

Only the last process (the actual bias field correction) is implemented in a multiresolution framework (without smoothing). Default is a standard level 2 multiresolution schedule (2 2 2 1 1 1)

The bias field correction method was initially developed and implemented by Martin Styner, Univ. of North Carolina at Chapel Hill, and his colleagues.

The multiresolution pyramid implementation is based on itkMultiTesolutionPyramidImageFilter (without Gaussian smoothing)

For more details. refer to the following articles. "Parametric estimate of intensity inhomogeneities applied to MRI" Martin Styner, Guido Gerig, Christian Brechbuehler, Gabor Szekely, IEEE TRANSACTIONS ON MEDICAL IMAGING; 19(3), pp. 153-165, 2000, (http://www.cs.unc.edu/~styner/docs/tmi00.pdf)

"Evaluation of 2D/3D bias correction with 1+1ES-optimization" Martin Styner, Prof. Dr. G. Gerig (IKT, BIWI, ETH Zuerich), TR-197 (http://www.cs.unc.edu/~styner/docs/StynerTR97.pdf)

Definition at line 224 of file itkMRIBiasFieldCorrectionFilter.h.

---

Member Typedef Documentation

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef MultivariateLegendrePolynomial itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::BiasFieldType

Bias field object type definition.

Definition at line 277 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef SmartPointer< const Self > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ConstPointer

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 232 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef EnergyFunctionType::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::EnergyFunctionPointer

Definition at line 283 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef MRIBiasEnergyFunction< InternalImageType, ImageMaskType, BiasFieldType > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::EnergyFunctionType

Energy function type definition.

Definition at line 282 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef ImageMaskType::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ImageMaskPointer

Definition at line 261 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef ImageMaskType::RegionType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ImageMaskRegionType

Definition at line 262 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TMaskImage itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ImageMaskType

Mask image related type definitions.

Definition at line 260 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TInputImage::IndexType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImageIndexType

Definition at line 254 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TInputImage::PixelType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImagePixelType

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 255 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TInputImage::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImagePointer

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 253 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TInputImage::RegionType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImageRegionType

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 257 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TInputImage::SizeType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImageSizeType

Definition at line 256 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TInputImage itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImageType

Some convenient typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 252 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef InternalImageType::PixelType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImagePixelType

Internal (temporary) image related type definitions.

Definition at line 266 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef InternalImageType::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImagePointer

Internal (temporary) image related type definitions.

Definition at line 267 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef InternalImageType::RegionType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImageRegionType

Internal (temporary) image related type definitions.

Definition at line 268 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef Image< float, itkGetStaticConstMacro(ImageDimension) > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImageType

Internal (temporary) image related type definitions.

Definition at line 265 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef MRASlabIdentifier< InputImageType > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::MRASlabIdentifierType

Regions of the MRI slab identifier return.

Definition at line 272 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef Statistics::NormalVariateGenerator itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::NormalVariateGeneratorType

Normal variate Generator Type

Definition at line 286 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef OnePlusOneEvolutionaryOptimizer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OptimizerType

Optimizer type definition.

Definition at line 289 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TOutputImage::IndexType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImageIndexType

Definition at line 247 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TOutputImage::PixelType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImagePixelType

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 248 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TOutputImage::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImagePointer

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 246 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TOutputImage::RegionType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImageRegionType

Superclass typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 250 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TOutputImage::SizeType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImageSizeType

Definition at line 249 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef TOutputImage itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImageType

Input and output image related type definitions.

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 245 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef SmartPointer< Self > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::Pointer

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 231 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef Array2D< unsigned int > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ScheduleType

ScheduleType typedef support.

Definition at line 292 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef MRIBiasFieldCorrectionFilter itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::Self

Standard class typedefs.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 229 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef SlabRegionVectorType::iterator itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SlabRegionVectorIteratorType

Definition at line 274 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef MRASlabIdentifierType::SlabRegionVectorType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SlabRegionVectorType

Definition at line 273 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

typedef ImageToImageFilter< TInputImage, TOutputImage > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::Superclass

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

Definition at line 230 of file itkMRIBiasFieldCorrectionFilter.h.

---

Constructor & Destructor Documentation

template<class TInputImage , class TOutputImage , class TMaskImage >

itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::MRIBiasFieldCorrectionFilter ( )

protected

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::~MRIBiasFieldCorrectionFilter ( )

protectedvirtual

template<class TInputImage , class TOutputImage , class TMaskImage >

itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::MRIBiasFieldCorrectionFilter ( const Self &  )

private

---

Member Function Documentation

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::AdjustSlabRegions ( SlabRegionVectorType &  slabs, OutputImageRegionType  requestedRegion  )

protected

Find overlapping regions between the slab regions and the output image's requested region. And then replace the original slab regions with the resulting overlapping regions.

template<class TInputImage , class TOutputImage , class TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::CheckMaskImage ( ImageMaskType *  mask )

protected

Checks if the mask image's dimensionality and size matches with those of the input image

template<class TInputImage , class TOutputImage , class TMaskImage >

template<class TSource , class TTarget >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::CopyAndConvertImage ( const TSource *  source, TTarget *  target, typename TTarget::RegionType  requestedRegion  )

inlineprotected

Converts pixel type, and copies image data from source to target.

Definition at line 499 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::CorrectImage	(	BiasFieldType &	bias,
		InputImageRegionType	region
	)

Correct the internal image using the bias field estimate created by EstimateBiasField() member function and the internal image data that are in the specified region.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::CorrectInterSliceIntensityInhomogeneity

(

InputImageRegionType

region

)

Internally calls EstimateBiasField() and CorrectImage() member functions for each slice to correct inter-slice intensity inhomogeneities.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual::itk::LightObject::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::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 , class TOutputImage , class TMaskImage >

BiasFieldType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::EstimateBiasField	(	InputImageRegionType	region,
		unsigned int	degree,
		int	maximumIteration
	)

Optimizes the bias field only using the image data that are in the specified region.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ExpImage ( InternalImageType *  source, InternalImageType *  target  )

protected

Converts image data from source to target applying vcl_exp(pixel) - 1 to all pixels.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GenerateData ( )

protectedvirtual

A version of GenerateData() specific for image processing filters. This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling ThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter an be threaded, it should NOT provide a GenerateData() method but should provide a ThreadedGenerateData() instead.

See also:

ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetBiasFieldDegree ( ) const

virtual

Set/Get the degree of the bias field estimate.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetBiasFieldSize ( InputImageRegionType  region, BiasFieldType::DomainSizeType &  domainSize  )

protected

Converts ImageRegion type (region) to DomainSize type (std::vector) NOTE: if the size of the last dimension of the image region is one, then the dimension of the resulting domain size will be one less than that of he image region

template<class TInputImage , class TOutputImage , class TMaskImage >

BiasFieldType::CoefficientArrayType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetEstimatedBiasFieldCoefficients ( )

inline

Get the result bias field coefficients after the bias field estimation (does not apply to the inter-slice intensity correction)

Definition at line 378 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const bool& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetGeneratingOutput ( )

virtual

Set/Gets the flag, If the flag is true, the output image (corrected image) will be created when this filter is updated. default - true

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual ImageMaskType* itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetInputMask ( )

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetInterSliceCorrectionMaximumIteration ( ) const

virtual

Set/Get the maximum iteration termination condition parameter.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const char* itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods)

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual unsigned int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetNumberOfLevels ( ) const

virtual

Get the number of multi-resolution levels.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetOptimizerGrowthFactor ( ) const

virtual

Set/Get the search radius grow factor.

template<class TInputImage , class TOutputImage , class TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetOptimizerInitialRadius ( )

inline

Set/Get the initial search radius.

Definition at line 398 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetOptimizerShrinkFactor ( ) const

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual ImageMaskType* itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetOutputMask ( )

virtual

Gets the output mask image pointer.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const ScheduleType& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetSchedule ( )

virtual

Get the multi-resolution schedule.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const InputImagePixelType& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetSlabBackgroundMinimumThreshold ( )

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const unsigned int& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetSlabNumberOfSamples ( )

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const double& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetSlabTolerance ( )

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

const unsigned int* itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetStartingShrinkFactors

(

)

const

Get the starting shrink factors

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const bool& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetUsingBiasFieldCorrection ( )

virtual

Set/Gets the bias correction flag. If the flag is true, bias field correction runs. This flag sounds odd. But if users want to use only the inter-slice intensity correction without actual bias correction, disabling bias field correction would be an useful option. default - true.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const bool& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetUsingInterSliceIntensityCorrection ( )

virtual

Set/Gets the intensity correction flag. if the flag is true, inter-slice intensity correction will be applied before bias field correction. default - true (3D input image), false (2D input image).

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual const bool& itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetUsingSlabIdentification ( )

virtual

Set/Gets the slab correction flag. If the flag is true, inter-slice intensity correction and bias field correction will be performed slab by slab which is identified by the slab identifier. default - false NOTE: if users want to slab identification, all the input image data should be buffered.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GetVolumeCorrectionMaximumIteration ( ) const

virtual

Set/Get the maximum iteration termination condition parameter.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::Initialize

(

)

throw ( ExceptionObject )

Initializes the energy function object and optimizer objects and creates the internal image object copying the input image data to it. Also, if the bias field is multiplicative, applies logarithm to pixel intensity values, tissue classes' statistics values and the optimizer's initial radius NOTE: If the tissue class statistics values (mean and sigma values) then it will throw exception.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::IsBiasFieldMultiplicative ( bool  flag )

inline

If you set this true, this filter assumes the bias field is multiplicative and internally uses log intensity values for every calculation.

Definition at line 311 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::IsBiasFieldMultiplicative ( )

inline

If the bias field is multiplicative, it returns true.

Definition at line 315 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

static bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::IsScheduleDownwardDivisible ( const ScheduleType &  schedule )

static

Test if the schedule is downward divisible. This method returns true if at every level, the shrink factors are divisble by the shrink factors at the next level.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::Log1PImage ( InternalImageType *  source, InternalImageType *  target  )

protected

Converts image data from source to target applying vcl_log(pixel + 1) to all pixels. If the source pixel has negative value, it sets the value of the corresponding pixel in the targe image as zero.

template<class TInputImage , class TOutputImage , class TMaskImage >

static Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::New ( )

static

Method for creation through the object factory.

Reimplemented from itk::Object.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::operator= ( const Self &  )

private

PushBackInput(), PushFronInput() in the public section force the input to be the type expected by an ImageToImageFilter. However, these methods end of "hiding" the versions from the superclass (ProcessObject) whose arguments are DataObjects. Here, we re-expose the versions from ProcessObject to avoid warnings about hiding methods from the superclass.

Reimplemented from itk::ImageToImageFilter< TInputImage, TOutputImage >.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::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::ImageToImageFilter< TInputImage, TOutputImage >.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetBiasFieldDegree ( int  _arg )

virtual

Set/Get the degree of the bias field estimate.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetGeneratingOutput ( bool  _arg )

virtual

Set/Gets the flag, If the flag is true, the output image (corrected image) will be created when this filter is updated. default - true

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetInitialBiasFieldCoefficients ( const BiasFieldType::CoefficientArrayType &  coefficients )

inline

Sets the initial 3D bias field estimate coefficients that will be used for correcting each slab.

Definition at line 370 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetInputMask

(

ImageMaskType *

inputMask

)

Set/Get the input mask image pointer Without this mask, this filter calculates the energy value using all pixels in the input image.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetInterSliceCorrectionMaximumIteration ( int  _arg )

virtual

Set/Get the maximum iteration termination condition parameter.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetNumberOfLevels

(

unsigned int

num

)

Set the number of multi-resolution levels. The matrix containing the schedule will be resized accordingly. The schedule is populated with default values. At the coarset (0) level, the shrink factors are set 2^(nlevel - 1) for all dimension. These shrink factors are halved for subsequent levels. The number of levels is clamped to a minimum value of 1. All shrink factors are also clamped to a minimum value of 1.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetOptimizerGrowthFactor ( double  _arg )

virtual

Set/Get the search radius grow factor.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetOptimizerInitialRadius ( double  initRadius )

inline

Set/Get the initial search radius.

Definition at line 396 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetOptimizerShrinkFactor ( double  _arg )

virtual

Set/Get the search radius shrink factor.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetOutputMask

(

ImageMaskType *

outputMask

)

Sets the out mask image pointer. Without this mask, this filter corrects every pixel in the input image.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetSchedule

(

const ScheduleType &

schedule

)

Set a multi-resolution schedule. The input schedule must have only ImageDimension number of columns and NumberOfLevels number of rows. For each dimension, the shrink factor must be non-increasing with respect to subsequent levels. This function will clamp shrink factors to satisify this condition. All shrink factors less than one will also be clamped to the value of 1.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetSlabBackgroundMinimumThreshold ( InputImagePixelType  _arg )

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetSlabNumberOfSamples ( unsigned int  _arg )

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetSlabTolerance ( double  _arg )

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetSlicingDirection ( int  _arg )

virtual

Sets the direction of slicing. 0 - x axis, 1 - y axis, 2 - z axis

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetStartingShrinkFactors

(

unsigned int

factor

)

Set the starting shrink factor for the coarset (0) resolution level. The schedule is then populated with defaults values obtained by halving the factors at the previous level. All shrink factors are clamped to a minimum value of 1.

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetStartingShrinkFactors

(

unsigned int *

factors

)

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetTissueClassStatistics	(	const Array< double > &	means,
		const Array< double > &	sigmas
	)		throw ( ExceptionObject )

Set the tissue class statistics for energy function initialization If the numbers of elements in the means and the sigmas are not equal it will throw exception

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetUsingBiasFieldCorrection ( bool  _arg )

virtual

Set/Gets the bias correction flag. If the flag is true, bias field correction runs. This flag sounds odd. But if users want to use only the inter-slice intensity correction without actual bias correction, disabling bias field correction would be an useful option. default - true.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetUsingInterSliceIntensityCorrection ( bool  _arg )

virtual

Set/Gets the intensity correction flag. if the flag is true, inter-slice intensity correction will be applied before bias field correction. default - true (3D input image), false (2D input image).

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetUsingSlabIdentification ( bool  _arg )

virtual

Set/Gets the slab correction flag. If the flag is true, inter-slice intensity correction and bias field correction will be performed slab by slab which is identified by the slab identifier. default - false NOTE: if users want to slab identification, all the input image data should be buffered.

template<class TInputImage , class TOutputImage , class TMaskImage >

virtual void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetVolumeCorrectionMaximumIteration ( int  _arg )

virtual

Set/Get the maximum iteration termination condition parameter.

---

Member Data Documentation

template<class TInputImage , class TOutputImage , class TMaskImage >

const unsigned int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ImageDimension = TOutputImage::ImageDimension

static

The dimension of the image.

Definition at line 242 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

BiasFieldType::CoefficientArrayType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_BiasFieldCoefficients

private

Storage for the initial 3D bias field estimate coefficients that will be used for correcting each slab.

Definition at line 583 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_BiasFieldDegree

private

The degree of the bias field estimate.

Definition at line 573 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_BiasMultiplicative

private

Bias Field character if true, multiplicative. if false, additive.

Definition at line 561 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

EnergyFunctionPointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_EnergyFunction

private

Energy function object pointer.

Definition at line 540 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

BiasFieldType::CoefficientArrayType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_EstimatedBiasFieldCoefficients

private

Storage for the resulting 3D bias field estimate coefficients after optimization.

Definition at line 587 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_GeneratingOutput

private

Definition at line 567 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

ImageMaskPointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_InputMask

private

Input mask image smart pointer.

Definition at line 546 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

InternalImagePointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_InternalInput

private

Internal image smart pointer.

Definition at line 552 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_InterSliceCorrectionMaximumIteration

private

Storage for the optimizer's maximum iteration number.

Definition at line 593 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

NormalVariateGeneratorType::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_NormalVariateGenerator

private

Normal variate generator smart pointer

Definition at line 543 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

unsigned int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_NumberOfLevels

private

The number of levels for the multires schedule

Definition at line 576 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_OptimizerGrowthFactor

private

Storage for the optimizer's search radius grow factor.

Definition at line 599 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_OptimizerInitialRadius

private

Storage for the optimizer's initial search radius.

Definition at line 596 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_OptimizerShrinkFactor

private

Storage for the optimizer's search radius shrink factor.

Definition at line 602 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

ImageMaskPointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_OutputMask

private

Output mask image smart pointer.

Definition at line 549 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

ScheduleType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_Schedule

private

The multires schedule

Definition at line 579 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

InputImagePixelType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_SlabBackgroundMinimumThreshold

private

Definition at line 570 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

unsigned int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_SlabNumberOfSamples

private

Definition at line 569 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

SlabRegionVectorType itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_Slabs

private

Storage for the MRI slab identifier return.

Definition at line 555 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_SlabTolerance

private

Definition at line 571 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_SlicingDirection

private

[0 - x, 1 - y, 2 - z].

Definition at line 558 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

Array< double > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_TissueClassMeans

private

Storage for tissue classes' mean values.

Definition at line 605 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

Array< double > itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_TissueClassSigmas

private

Storage for tissue classes' variance values.

Definition at line 608 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_UsingBiasFieldCorrection

private

Definition at line 566 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_UsingInterSliceIntensityCorrection

private

operation selection flags.

Definition at line 564 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_UsingSlabIdentification

private

Definition at line 565 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_VolumeCorrectionMaximumIteration

private

Storage for the optimizer's maximum iteration number.

Definition at line 590 of file itkMRIBiasFieldCorrectionFilter.h.

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

• itkMRIBiasFieldCorrectionFilter.h