#include <itkN4BiasFieldCorrectionImageFilter.h>

Inheritance diagram for itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >:

Collaboration diagram for itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >:

Detailed Description

template<typename TInputImage, typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
class itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >

Implementation of the N4 bias field correction algorithm.

The nonparametric nonuniform intensity normalization (N3) algorithm, as introduced by Sled et al. in 1998 is a method for correcting nonuniformity associated with MR images. The algorithm assumes a simple parametric model (Gaussian) for the bias field and does not require tissue class segmentation. In addition, there are only a couple of parameters to tune with the default values performing quite well. N3 has been publicly available as a set of perl scripts (http://www.bic.mni.mcgill.ca/ServicesSoftwareAdvancedImageProcessingTools/HomePage)

The N4 algorithm, encapsulated with this class, is a variation of the original N3 algorithm with the additional benefits of an improved B-spline fitting routine which allows for multiple resolutions to be used during the correction process. We also modify the iterative update component of algorithm such that the residual bias field is continually updated

Notes for the user:

Since much of the image manipulation is done in the log space of the intensities, input images with negative and small values (< 1) can produce poor results.
The original authors recommend performing the bias field correction on a downsampled version of the original image.
A binary mask or a weighted image can be supplied. If a binary mask is specified, those voxels in the input image which correspond to the voxels in the mask image with a value equal to m_MaskLabel, are used to estimate the bias field. If a confidence image is specified, the input voxels are weighted in the b-spline fitting routine according to the confidence voxel values.
The filter returns the corrected image. If the bias field is wanted, one can reconstruct it using the class itkBSplineControlPointImageFilter. See the IJ article and the test file for an example.
The 'Z' parameter in Sled's 1998 paper is the square root of the class variable 'm_WienerFilterNoise'.

The basic algorithm iterates between sharpening the intensity histogram of the corrected input image and spatially smoothing those results with a B-spline scalar field estimate of the bias field.

Author: Nicholas J. Tustison

Contributed by Nicholas J. Tustison, James C. Gee in the Insight Journal paper: http://hdl.handle.net/10380/3053

REFERENCE

J.G. Sled, A.P. Zijdenbos and A.C. Evans. "A Nonparametric Method for Automatic Correction of Intensity Nonuniformity in Data" IEEE Transactions on Medical Imaging, Vol 17, No 1. Feb 1998.

N.J. Tustison, B.B. Avants, P.A. Cook, Y. Zheng, A. Egan, P.A. Yushkevich, and J.C. Gee. "N4ITK: Improved N3 Bias Correction" IEEE Transactions on Medical Imaging, 29(6):1310-1320, June 2010.

Definition at line 93 of file itkN4BiasFieldCorrectionImageFilter.h.

Public Types
typedef BSplineFilterType::ArrayType	ArrayType

typedef BSplineFilterType::PointDataImageType	BiasFieldControlPointLatticeType

typedef BSplineScatteredDataPointSetToImageFilter < PointSetType, ScalarImageType >	BSplineFilterType

typedef SmartPointer< const Self >	ConstPointer

typedef TInputImage	InputImageType

typedef TMaskImage	MaskImageType

typedef MaskImageType::PixelType	MaskPixelType

typedef TOutputImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef RealImageType::Pointer	RealImagePointer

typedef Image< RealType, ImageDimension >	RealImageType

typedef float	RealType

typedef N4BiasFieldCorrectionImageFilter	Self

typedef ImageToImageFilter < TInputImage, TOutputImage >	Superclass

typedef Array< unsigned int >	VariableSizeArrayType


typedef Vector< RealType, 1 >	ScalarType

typedef PointSet< ScalarType, itkGetStaticConstMacro(ImageDimension)>	PointSetType

typedef Image< ScalarType, itkGetStaticConstMacro(ImageDimension)>	ScalarImageType

typedef PointSetType::Pointer	PointSetPointer

typedef PointSetType::PointType	PointType

Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef SmartPointer< const Self >	ConstPointer

typedef InputImageType::ConstPointer	InputImageConstPointer

typedef InputImageType::PixelType	InputImagePixelType

typedef InputImageType::Pointer	InputImagePointer

typedef InputImageType::RegionType	InputImageRegionType

typedef TInputImage	InputImageType

typedef Superclass::OutputImagePixelType	OutputImagePixelType

typedef Superclass::OutputImageRegionType	OutputImageRegionType

typedef SmartPointer< Self >	Pointer

typedef ImageToImageFilter	Self

typedef ImageSource< TOutputImage >	Superclass

Public Types inherited from itk::ImageSource< TOutputImage >
typedef SmartPointer< const Self >	ConstPointer

typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType

typedef OutputImageType::PixelType	OutputImagePixelType

typedef OutputImageType::Pointer	OutputImagePointer

typedef OutputImageType::RegionType	OutputImageRegionType

typedef TOutputImage	OutputImageType

typedef SmartPointer< Self >	Pointer

typedef ImageSource	Self

typedef ProcessObject	Superclass

Public Types inherited from itk::ProcessObject
typedef SmartPointer< const Self >	ConstPointer

typedef DataObject::DataObjectIdentifierType	DataObjectIdentifierType

typedef DataObject::Pointer	DataObjectPointer

typedef std::vector < DataObjectPointer >	DataObjectPointerArray

typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType

typedef std::vector < DataObjectIdentifierType >	NameArray

typedef SmartPointer< Self >	Pointer

typedef ProcessObject	Self

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 () const

virtual RealType	GetBiasFieldFullWidthAtHalfMaximum () const

const RealImageType *	GetConfidenceImage () const

virtual RealType	GetConvergenceThreshold () const

virtual RealType	GetCurrentConvergenceMeasurement () const

virtual unsigned int	GetCurrentLevel () const

virtual unsigned int	GetElapsedIterations () const

virtual BiasFieldControlPointLatticeType::Pointer	GetLogBiasFieldControlPointLattice () const

const MaskImageType *	GetMaskImage () const

virtual MaskPixelType	GetMaskLabel () const

virtual VariableSizeArrayType	GetMaximumNumberOfIterations () const

virtual const char *	GetNameOfClass () const

virtual ArrayType	GetNumberOfControlPoints () const

virtual ArrayType	GetNumberOfFittingLevels () const

virtual unsigned int	GetNumberOfHistogramBins () const

virtual unsigned int	GetSplineOrder () const

virtual RealType	GetWienerFilterNoise () const

virtual void	SetBiasFieldFullWidthAtHalfMaximum (RealType _arg)

virtual void	SetConvergenceThreshold (RealType _arg)

void	SetInput1 (const InputImageType *image)

virtual void	SetMaskLabel (MaskPixelType _arg)

virtual void	SetMaximumNumberOfIterations (VariableSizeArrayType _arg)

virtual void	SetNumberOfControlPoints (ArrayType _arg)

virtual void	SetNumberOfFittingLevels (ArrayType _arg)

void	SetNumberOfFittingLevels (unsigned int n)

virtual void	SetNumberOfHistogramBins (unsigned int _arg)

virtual void	SetSplineOrder (unsigned int _arg)

virtual void	SetWienerFilterNoise (RealType _arg)


void	SetMaskImage (const MaskImageType *mask)

void	SetInput2 (const MaskImageType *mask)


void	SetConfidenceImage (const RealImageType *image)

void	SetInput3 (const RealImageType *image)

Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
const InputImageType *	GetInput () const

const InputImageType *	GetInput (unsigned int idx) const

virtual void	PopBackInput () override

virtual void	PopFrontInput () override

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)

virtual void	SetCoordinateTolerance (double _arg)

virtual double	GetCoordinateTolerance () const

virtual void	SetDirectionTolerance (double _arg)

virtual double	GetDirectionTolerance () const

Public Member Functions inherited from itk::ImageSource< TOutputImage >
OutputImageType *	GetOutput (unsigned int idx)

virtual void	GraftNthOutput (unsigned int idx, DataObject *output)

virtual void	GraftOutput (const DataObjectIdentifierType &key, DataObject *output)

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *output)

virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override

virtual ProcessObject::DataObjectPointer	MakeOutput (const ProcessObject::DataObjectIdentifierType &) override

Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()

virtual void	AbortGenerateDataOn ()

virtual void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData () const

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

NameArray	GetInputNames () const

DataObjectPointerArray	GetInputs ()

MultiThreader *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

DataObjectPointerArray	GetOutputs ()

virtual const float &	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (float progress)

void	SetProgress (float progress)

virtual void	SetReleaseDataFlag (bool flag)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	ReleaseDataBeforeUpdateFlagOff ()

virtual void	SetNumberOfThreads (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfThreads () const

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 ()

const MetaDataDictionary &	GetMetaDataDictionary () 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 override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) override

virtual void	UnRegister () const noexceptoverride

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () 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 ()

Static Public Attributes
static const unsigned int	ImageDimension = TInputImage::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 >
static const unsigned int	OutputImageDimension = TOutputImage::ImageDimension

Protected Member Functions
void	GenerateData () override

	N4BiasFieldCorrectionImageFilter ()

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

	~N4BiasFieldCorrectionImageFilter ()

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 () override

	ImageToImageFilter ()

virtual void	VerifyInputInformation () override

	~ImageToImageFilter ()

void	PushBackInput (const DataObject *input) override

void	PushFrontInput (const DataObject *input) override

Protected Member Functions inherited from itk::ImageSource< TOutputImage >
virtual void	AfterThreadedGenerateData ()

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int pieces, 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 &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) 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 (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName (void) const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName (void) 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
RealType	CalculateConvergenceMeasurement (const RealImageType , const RealImageType ) const

	N4BiasFieldCorrectionImageFilter (const Self &) ITK_DELETE_FUNCTION

void	operator= (const Self &) ITK_DELETE_FUNCTION

RealImagePointer	ReconstructBiasField (BiasFieldControlPointLatticeType *)

RealImagePointer	SharpenImage (const RealImageType *) const

RealImagePointer	UpdateBiasFieldEstimate (RealImageType *)

Private Attributes
RealType	m_BiasFieldFullWidthAtHalfMaximum

RealType	m_ConvergenceThreshold

RealType	m_CurrentConvergenceMeasurement

unsigned int	m_CurrentLevel

unsigned int	m_ElapsedIterations

BiasFieldControlPointLatticeType::Pointer	m_LogBiasFieldControlPointLattice

MaskPixelType	m_MaskLabel

VariableSizeArrayType	m_MaximumNumberOfIterations

ArrayType	m_NumberOfControlPoints

ArrayType	m_NumberOfFittingLevels

unsigned int	m_NumberOfHistogramBins

unsigned int	m_SplineOrder

RealType	m_WienerFilterNoise

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

Static Protected Member Functions inherited from itk::ImageSource< TOutputImage >
static const ImageRegionSplitterBase *	GetGlobalDefaultSplitter ()

static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount

Member Typedef Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef BSplineFilterType::ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ArrayType

Definition at line 136 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef BSplineFilterType::PointDataImageType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BiasFieldControlPointLatticeType

Definition at line 135 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef BSplineScatteredDataPointSetToImageFilter< PointSetType, ScalarImageType> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BSplineFilterType

B-sline filter typedefs

Definition at line 134 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef SmartPointer<const Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ConstPointer

Definition at line 101 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef TInputImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::InputImageType

Some convenient typedefs.

Definition at line 114 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef TMaskImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskImageType

Definition at line 116 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef MaskImageType::PixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskPixelType

Definition at line 117 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef TOutputImage itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::OutputImageType

Definition at line 115 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef SmartPointer<Self> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Pointer

Definition at line 100 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef PointSetType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetPointer

B-spline smoothing filter argument typedefs

Definition at line 128 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef PointSet<ScalarType, itkGetStaticConstMacro( ImageDimension )> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetType

B-spline smoothing filter argument typedefs

Definition at line 126 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef PointSetType::PointType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointType

B-spline smoothing filter argument typedefs

Definition at line 129 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef RealImageType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImagePointer

Definition at line 121 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Image<RealType, ImageDimension> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImageType

Definition at line 120 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef float itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealType

Definition at line 119 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Image<ScalarType, itkGetStaticConstMacro( ImageDimension )> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarImageType

B-spline smoothing filter argument typedefs

Definition at line 127 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Vector<RealType, 1> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarType

B-spline smoothing filter argument typedefs

Definition at line 125 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef N4BiasFieldCorrectionImageFilter itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Self

Standard class typedefs.

Definition at line 98 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef ImageToImageFilter<TInputImage, TOutputImage> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Superclass

Definition at line 99 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

typedef Array<unsigned int> itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::VariableSizeArrayType

Definition at line 122 of file itkN4BiasFieldCorrectionImageFilter.h.

Constructor & Destructor Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::N4BiasFieldCorrectionImageFilter ( )

protected

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::~N4BiasFieldCorrectionImageFilter ( )

inlineprotected

Definition at line 373 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::N4BiasFieldCorrectionImageFilter ( const Self & )

private

Member Function Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::CalculateConvergenceMeasurement	(	const RealImageType *	,
		const RealImageType *
	)		const

private

Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual::itk::LightObject::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::CreateAnother ( ) 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<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GenerateData ( )

overrideprotectedvirtual

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<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetBiasFieldFullWidthAtHalfMaximum ( ) const

virtual

Get the full width at half maximum parameter characterizing the width of the Gaussian deconvolution. Default = 0.15.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

const RealImageType* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetConfidenceImage ( ) const

inline

Get confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 193 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetConvergenceThreshold ( ) const

virtual

Get the convergence threshold. Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate. If this value is less than the specified threshold, the algorithm proceeds to the next fitting level or terminates if it is at the last level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetCurrentConvergenceMeasurement ( ) const

virtual

Get the current convergence measurement. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetCurrentLevel ( ) const

virtual

Get the current fitting level. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetElapsedIterations ( ) const

virtual

Get the number of elapsed iterations. This is a helper function for reporting observations.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual BiasFieldControlPointLatticeType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetLogBiasFieldControlPointLattice ( ) const

virtual

Typically, a reduced size image is used as input to the N4 filter using something like itkShrinkImageFilter. Since the output is a corrected version of the input, the user will probably want to apply the bias field correction to the full resolution image. This can be done by using the LogBiasFieldControlPointLattice to reconstruct the bias field at the full image resolution (using the class BSplineControlPointImageFilter).

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

const MaskImageType* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaskImage ( ) const

inline

Get mask image function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 161 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::GetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaskLabel ( ) const

virtual

Get mask label function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field. Default = 1.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual VariableSizeArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetMaximumNumberOfIterations ( ) const

virtual

Get the maximum number of iterations specified at each fitting level. Default = 50.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual const char* itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNameOfClass ( ) const

virtual

Runtime information support.

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

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfControlPoints ( ) const

virtual

Get the control point grid size defining the B-spline estimate of the scalar bias field. In each dimension, the B-spline mesh size is equal to the number of control points in that dimension minus the spline order. Default = 4 control points in each dimension for a mesh size of 1 in each dimension.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfFittingLevels ( ) const

virtual

Get the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetNumberOfHistogramBins ( ) const

virtual

Get number of bins defining the log input intensity histogram. Default = 200.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetSplineOrder ( ) const

virtual

Get the spline order defining the bias field estimate. Default = 3.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetWienerFilterNoise ( ) const

virtual

Get the noise estimate defining the Wiener filter. Default = 0.01.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

static Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::New ( )

static

Standard New method.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::operator= ( const Self & )

private

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PrintSelf	(	std::ostream &	os,
		Indent	indent
	)		const

overrideprotectedvirtual

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<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ReconstructBiasField ( BiasFieldControlPointLatticeType * )

private

Reconstruct bias field given the control point lattice.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetBiasFieldFullWidthAtHalfMaximum ( RealType _arg )

virtual

Set the full width at half maximum parameter characterizing the width of the Gaussian deconvolution. Default = 0.15.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConfidenceImage ( const RealImageType * image )

inline

Set confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 176 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::SetNthInput().

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput3().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConvergenceThreshold ( RealType _arg )

virtual

Set the convergence threshold. Convergence is determined by the coefficient of variation of the difference image between the current bias field estimate and the previous estimate. If this value is less than the specified threshold, the algorithm proceeds to the next fitting level or terminates if it is at the last level.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput1 ( const InputImageType * image )

inline

The image expected for input for bias correction.

Definition at line 141 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ImageToImageFilter< TInputImage, TOutputImage >::SetInput().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput2 ( const MaskImageType * mask )

inline

Set mask image function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 153 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskImage().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput3 ( const RealImageType * image )

inline

Set confidence image function. If a confidence image is specified, estimation of the bias field weights the contribution of each voxel according the value of the corresponding voxel in the confidence image. For example, when estimating the bias field using brain , one can use a soft segmentation of the white matter as the confidence image instead of using a hard segmentation of the white matter as the mask image (as has been done in the literature) as an alternative strategy to estimating the bias field.

Definition at line 180 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetConfidenceImage().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskImage ( const MaskImageType * mask )

inline

Set mask image function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field.

Definition at line 149 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::ProcessObject::SetNthInput().

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetInput2().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaskLabel ( MaskPixelType _arg )

virtual

Set mask label function. If a binary mask image is specified, only those input image voxels corresponding with mask image values equal to m_MaskLabel are used in estimating the bias field. Default = 1.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetMaximumNumberOfIterations ( VariableSizeArrayType _arg )

virtual

Set the maximum number of iterations specified at each fitting level. Default = 50.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfControlPoints ( ArrayType _arg )

virtual

Set the control point grid size defining the B-spline estimate of the scalar bias field. In each dimension, the B-spline mesh size is equal to the number of control points in that dimension minus the spline order. Default = 4 control points in each dimension for a mesh size of 1 in each dimension.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels ( ArrayType _arg )

virtual

Set the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

Referenced by itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels ( unsigned int n )

inline

Set the number of fitting levels. One of the contributions of N4 is the introduction of a multi-scale approach to fitting. This allows one to specify a B-spline mesh size for initial fitting followed by a doubling of the mesh resolution for each subsequent fitting level. Default = 1 level.

Definition at line 295 of file itkN4BiasFieldCorrectionImageFilter.h.

References itk::FixedArray< TValue, VLength >::Fill(), and itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfFittingLevels().

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetNumberOfHistogramBins ( unsigned int _arg )

virtual

Set number of bins defining the log input intensity histogram. Default = 200.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetSplineOrder ( unsigned int _arg )

virtual

Set the spline order defining the bias field estimate. Default = 3.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetWienerFilterNoise ( RealType _arg )

virtual

Set the noise estimate defining the Wiener filter. Default = 0.01.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SharpenImage ( const RealImageType * ) const

private

Sharpen the intensity histogram of the current estimate of the corrected image and map those results to a new estimate of the unsmoothed corrected image.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealImagePointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::UpdateBiasFieldEstimate ( RealImageType * )

private

Given the unsmoothed estimate of the bias field, this function smooths the estimate and adds the resulting control point values to the total bias field estimate.

Member Data Documentation

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

const unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ImageDimension = TInputImage::ImageDimension

static

ImageDimension constants

Definition at line 111 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_BiasFieldFullWidthAtHalfMaximum

private

Definition at line 421 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ConvergenceThreshold

private

Definition at line 427 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentConvergenceMeasurement

private

Definition at line 428 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentLevel

private

Definition at line 429 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ElapsedIterations

private

Definition at line 426 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

BiasFieldControlPointLatticeType::Pointer itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_LogBiasFieldControlPointLattice

private

Definition at line 434 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

MaskPixelType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaskLabel

private

Definition at line 415 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

VariableSizeArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_MaximumNumberOfIterations

private

Definition at line 425 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfControlPoints

private

Definition at line 437 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

ArrayType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfFittingLevels

private

Definition at line 438 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfHistogramBins

private

Definition at line 419 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_SplineOrder

private

Definition at line 436 of file itkN4BiasFieldCorrectionImageFilter.h.

template<typename TInputImage , typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_WienerFilterNoise

private

Definition at line 420 of file itkN4BiasFieldCorrectionImageFilter.h.

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

itkN4BiasFieldCorrectionImageFilter.h

Detailed Description

template<typename TInputImage, typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage> class itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename TInputImage, typename TMaskImage = Image<unsigned char, TInputImage::ImageDimension>, class TOutputImage = TInputImage>
class itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >