#include <itkN4BiasFieldCorrectionImageFilter.h>

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 (https://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 are used to estimate the bias field. If a UseMaskLabel value is set to false (the default), all non-zero voxels in the MaskImage will be masked; otherwise only voxels in the MaskImage that match the MaskLabel will be used. 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: https://doi.org/10.54294/jculxw

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 96 of file itkN4BiasFieldCorrectionImageFilter.h.

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

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

Public Types
using	ArrayType = typename BSplineFilterType::ArrayType

using	BiasFieldControlPointLatticeType = typename BSplineFilterType::PointDataImageType

using	BSplineFilterType = BSplineScatteredDataPointSetToImageFilter< PointSetType, ScalarImageType >

using	ConstPointer = SmartPointer< const Self >

using	InputImageType = TInputImage

using	MaskImageType = TMaskImage

using	MaskPixelType = typename MaskImageType::PixelType

using	OutputImageType = TOutputImage

using	Pointer = SmartPointer< Self >

using	PointSetPointer = typename PointSetType::Pointer

using	PointSetType = PointSet< ScalarType, Self::ImageDimension >

using	PointType = typename PointSetType::PointType

using	RealImagePointer = typename RealImageType::Pointer

using	RealImageType = Image< RealType, ImageDimension >

using	RealType = float

using	ScalarImageType = Image< ScalarType, Self::ImageDimension >

using	ScalarType = Vector< RealType, 1 >

using	Self = N4BiasFieldCorrectionImageFilter

using	Superclass = ImageToImageFilter< TInputImage, TOutputImage >

using	VariableSizeArrayType = Array< unsigned int >

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

using	InputImageConstPointer = typename InputImageType::ConstPointer

using	InputImagePixelType = typename InputImageType::PixelType

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageRegionType = typename InputImageType::RegionType

using	InputImageType = TInputImage

using	Pointer = SmartPointer< Self >

using	Self = ImageToImageFilter

using	Superclass = ImageSource< TOutputImage >

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

using	DataObjectIdentifierType = Superclass::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArraySizeType = Superclass::DataObjectPointerArraySizeType

using	OutputImagePixelType = typename OutputImageType::PixelType

using	OutputImagePointer = typename OutputImageType::Pointer

using	OutputImageRegionType = typename OutputImageType::RegionType

using	OutputImageType = TOutputImage

using	Pointer = SmartPointer< Self >

using	Self = ImageSource

using	Superclass = ProcessObject

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

using	DataObjectIdentifierType = DataObject::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArray = std::vector< DataObjectPointer >

using	DataObjectPointerArraySizeType = DataObjectPointerArray::size_type

using	MultiThreaderType = MultiThreaderBase

using	NameArray = std::vector< DataObjectIdentifierType >

using	Pointer = SmartPointer< Self >

using	Self = ProcessObject

using	Superclass = Object

Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightObject

Public Member Functions
void	EnlargeOutputRequestedRegion (DataObject *) override

virtual RealType	GetBiasFieldFullWidthAtHalfMaximum () const

virtual const RealImageType *	GetConfidenceImage () const

virtual RealType	GetConvergenceThreshold () const

virtual RealType	GetCurrentConvergenceMeasurement () const

virtual unsigned int	GetCurrentLevel () const

virtual unsigned int	GetElapsedIterations () const

virtual const BiasFieldControlPointLatticeType *	GetLogBiasFieldControlPointLattice () const

virtual const MaskImageType *	GetMaskImage () const

virtual VariableSizeArrayType	GetMaximumNumberOfIterations () const

const char *	GetNameOfClass () const override

virtual ArrayType	GetNumberOfControlPoints () const

virtual ArrayType	GetNumberOfFittingLevels () const

virtual unsigned int	GetNumberOfHistogramBins () const

virtual unsigned int	GetSplineOrder () const

virtual RealType	GetWienerFilterNoise () const

RealImagePointer	ReconstructBiasField (const BiasFieldControlPointLatticeType *)

virtual void	SetBiasFieldFullWidthAtHalfMaximum (RealType _arg)

virtual void	SetConvergenceThreshold (RealType _arg)

void	SetInput1 (const InputImageType *image)

virtual void	SetMaximumNumberOfIterations (VariableSizeArrayType _arg)

virtual void	SetNumberOfControlPoints (ArrayType _arg)

virtual void	SetNumberOfFittingLevels (ArrayType _arg)

virtual void	SetNumberOfHistogramBins (unsigned int _arg)

virtual void	SetSplineOrder (unsigned int _arg)

virtual void	SetWienerFilterNoise (RealType _arg)


virtual void	SetMaskImage (const MaskImageType *input)

void	SetInput2 (const MaskImageType *mask)


virtual void	SetMaskLabel (MaskPixelType _arg)

virtual MaskPixelType	GetMaskLabel () const


virtual void	SetUseMaskLabel (bool _arg)

virtual bool	GetUseMaskLabel () const

virtual void	UseMaskLabelOn ()


virtual void	SetConfidenceImage (const RealImageType *input)

void	SetInput3 (const RealImageType *image)


void	SetNumberOfFittingLevels (unsigned int n)

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

const InputImageType *	GetInput (unsigned int idx) const

void	PopBackInput () override

void	PopFrontInput () override

virtual void	PushBackInput (const InputImageType *input)

virtual void	PushFrontInput (const InputImageType *input)

virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)

virtual void	SetInput (const InputImageType *input)

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)

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *graft)

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

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

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

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

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

virtual const bool &	GetAbortGenerateData () const

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

NameArray	GetInputNames () const

DataObjectPointerArray	GetInputs ()

MultiThreaderType *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

DataObjectPointerArray	GetOutputs ()

virtual float	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

void	IncrementProgress (float increment)

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

void	SetMultiThreader (MultiThreaderType *threader)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (float progress)

virtual void	SetReleaseDataFlag (bool val)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	SetNumberOfWorkUnits (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfWorkUnits () const

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *cmd) const

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

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

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag) const

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
Pointer	Clone () const

virtual void	Delete ()

virtual int	GetReferenceCount () const

void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
static double	GetGlobalDefaultCoordinateTolerance ()

static double	GetGlobalDefaultDirectionTolerance ()

static void	SetGlobalDefaultCoordinateTolerance (double)

static void	SetGlobalDefaultDirectionTolerance (double)

Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()

static void	GlobalWarningDisplayOff ()

static void	GlobalWarningDisplayOn ()

static Pointer	New ()

static void	SetGlobalWarningDisplay (bool val)

Static Public Member Functions inherited from itk::LightObject
static void	BreakOnError ()

static Pointer	New ()

Static Public Attributes
static constexpr unsigned int	ImageDimension = TInputImage::ImageDimension

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

static constexpr unsigned int	OutputImageDimension = TOutputImage::ImageDimension

Static Public Attributes inherited from itk::ImageSource< TOutputImage >
static constexpr unsigned int	OutputImageDimension = TOutputImage::ImageDimension

Protected Member Functions
void	GenerateData () override

	N4BiasFieldCorrectionImageFilter ()

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

	~N4BiasFieldCorrectionImageFilter () override=default

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)

void	GenerateInputRequestedRegion () override

	ImageToImageFilter ()

void	VerifyInputInformation () const override

	~ImageToImageFilter () override=default

virtual void	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

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

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

void	ClassicMultiThread (ThreadFunctionType callbackFunction)

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

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

	~ImageSource () override=default

virtual void	ThreadedGenerateData (const OutputImageRegionType &region, ThreadIdType threadId)

virtual void	DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread)

virtual bool	GetDynamicMultiThreading () const

virtual void	SetDynamicMultiThreading (bool _arg)

virtual void	DynamicMultiThreadingOn ()

Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)

void	AddOptionalInputName (const DataObjectIdentifierType &)

void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

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

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	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

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 idx, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType idx, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

virtual void	SetOutput (const DataObjectIdentifierType &name, DataObject *output)

virtual void	SetPrimaryInput (DataObject *object)

virtual void	SetPrimaryOutput (DataObject *object)

void	SetRequiredInputNames (const NameArray &)

virtual void	VerifyPreconditions () const

	~ProcessObject () override

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 () const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName () const

DataObject *	GetOutput (DataObjectPointerArraySizeType i)

const DataObject *	GetOutput (DataObjectPointerArraySizeType i) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

virtual bool	GetThreaderUpdateProgress () const

virtual void	ThreaderUpdateProgressOn ()

virtual void	SetThreaderUpdateProgress (bool arg)

Protected Member Functions inherited from itk::Object
	Object ()

bool	PrintObservers (std::ostream &os, Indent indent) const

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~Object () override

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

void	SharpenImage (const RealImageType unsharpenedImage, RealImageType sharpenedImage) const

RealImagePointer	UpdateBiasFieldEstimate (RealImageType *, vcl_size_t)

Private Attributes
RealType	m_BiasFieldFullWidthAtHalfMaximum { static_cast<RealType>(0.15) }

RealType	m_ConvergenceThreshold { static_cast<RealType>(0.001) }

RealType	m_CurrentConvergenceMeasurement {}

unsigned int	m_CurrentLevel { 0 }

unsigned int	m_ElapsedIterations { 0 }

BiasFieldControlPointLatticeType::Pointer	m_LogBiasFieldControlPointLattice {}

MaskPixelType	m_MaskLabel {}

VariableSizeArrayType	m_MaximumNumberOfIterations {}

ArrayType	m_NumberOfControlPoints {}

ArrayType	m_NumberOfFittingLevels {}

unsigned int	m_NumberOfHistogramBins { 200 }

unsigned int	m_SplineOrder { 3 }

bool	m_UseMaskLabel { false }

RealType	m_WienerFilterNoise { static_cast<RealType>(0.01) }

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
using	InputToOutputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::OutputImageDimension, Self::InputImageDimension >

using	OutputToInputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::InputImageDimension, Self::OutputImageDimension >

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

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreaderCallback (void *arg)

Static Protected Member Functions inherited from itk::ProcessObject
template<typename TSourceObject >
static void	MakeRequiredOutputs (TSourceObject &sourceObject, const DataObjectPointerArraySizeType numberOfRequiredOutputs)

static constexpr float	progressFixedToFloat (uint32_t fixed)

static uint32_t	progressFloatToFixed (float f)

Protected Attributes inherited from itk::ImageSource< TOutputImage >
bool	m_DynamicMultiThreading { true }

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime {}

bool	m_Updating {}

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

Member Typedef Documentation

◆ ArrayType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ArrayType = typename BSplineFilterType::ArrayType

Definition at line 137 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ BiasFieldControlPointLatticeType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::BiasFieldControlPointLatticeType = typename BSplineFilterType::PointDataImageType

Definition at line 136 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ BSplineFilterType

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

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

B-sline filter type alias

Definition at line 135 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ ConstPointer

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

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

Definition at line 105 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ InputImageType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::InputImageType = TInputImage

Some convenient type alias.

Definition at line 117 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ MaskImageType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskImageType = TMaskImage

Definition at line 119 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ MaskPixelType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::MaskPixelType = typename MaskImageType::PixelType

Definition at line 120 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ OutputImageType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::OutputImageType = TOutputImage

Definition at line 118 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ Pointer

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

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

Definition at line 104 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ PointSetPointer

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetPointer = typename PointSetType::Pointer

Definition at line 131 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ PointSetType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointSetType = PointSet<ScalarType, Self::ImageDimension>

Definition at line 129 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ PointType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::PointType = typename PointSetType::PointType

Definition at line 132 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ RealImagePointer

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealImagePointer = typename RealImageType::Pointer

Definition at line 124 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ RealImageType

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

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

Definition at line 123 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ RealType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::RealType = float

Definition at line 122 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ ScalarImageType

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::ScalarImageType = Image<ScalarType, Self::ImageDimension>

Definition at line 130 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ ScalarType

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

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

B-spline smoothing filter argument type alias

Definition at line 128 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ Self

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Self = N4BiasFieldCorrectionImageFilter

Standard class type aliases.

Definition at line 102 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ Superclass

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

using itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::Superclass = ImageToImageFilter<TInputImage, TOutputImage>

Definition at line 103 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ VariableSizeArrayType

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

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

Definition at line 125 of file itkN4BiasFieldCorrectionImageFilter.h.

Constructor & Destructor Documentation

◆ N4BiasFieldCorrectionImageFilter()

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

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

protected

◆ ~N4BiasFieldCorrectionImageFilter()

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

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

overrideprotecteddefault

Member Function Documentation

◆ CalculateConvergenceMeasurement()

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.

◆ EnlargeOutputRequestedRegion()

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

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::EnlargeOutputRequestedRegion ( DataObject * )

overridevirtual

Ensures that this filter can compute the entire output at once.

Reimplemented from itk::ProcessObject.

◆ GenerateData()

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 DynamicThreadedGenerateData(). 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 can be threaded, it should NOT provide a GenerateData() method but should provide a DynamicThreadedGenerateData() instead.

See also: ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

◆ GetBiasFieldFullWidthAtHalfMaximum()

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.

◆ GetConfidenceImage()

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

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

virtual

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.

◆ GetConvergenceThreshold()

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.

◆ GetCurrentConvergenceMeasurement()

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.

◆ GetCurrentLevel()

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.

◆ GetElapsedIterations()

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.

◆ GetLogBiasFieldControlPointLattice()

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

virtual const BiasFieldControlPointLatticeType* 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).

◆ GetMaskImage()

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

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

virtual

Get mask image function. If a binary mask image is specified, only those input image voxels inside the mask image values are used in estimating the bias field.

◆ GetMaskLabel()

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

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

virtual

Set/Get mask label value. If a binary mask image is specified and if UseMaskValue is true, only those input image voxels corresponding with mask image values equal to MaskLabel are used in estimating the bias field. If a MaskImage is specified and UseMaskLabel is false, all input image voxels corresponding to non-zero voxels in the MaskImage are used in estimating the bias field. Default = 1.

◆ GetMaximumNumberOfIterations()

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.

◆ GetNameOfClass()

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

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

overridevirtual

See also: LightObject::GetNameOfClass()

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

◆ GetNumberOfControlPoints()

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.

◆ GetNumberOfFittingLevels()

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.

◆ GetNumberOfHistogramBins()

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.

◆ GetSplineOrder()

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.

◆ GetUseMaskLabel()

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

virtual bool itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::GetUseMaskLabel ( ) const

virtual

Use a mask label for identifying mask functionality. See SetMaskLabel. Defaults to false.

◆ GetWienerFilterNoise()

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.

◆ New()

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.

◆ PrintSelf()

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 >.

◆ ReconstructBiasField()

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

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

Reconstruct bias field given the control point lattice.

◆ SetBiasFieldFullWidthAtHalfMaximum()

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.

◆ SetConfidenceImage()

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

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

virtual

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.

◆ SetConvergenceThreshold()

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.

◆ SetInput1()

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 147 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ SetInput2()

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 inside the mask image values are used in estimating the bias field.

Definition at line 159 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ SetInput3()

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 204 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ SetMaskImage()

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

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

virtual

Set mask image function. If a binary mask image is specified, only those input image voxels inside the mask image values are used in estimating the bias field.

◆ SetMaskLabel()

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/Get mask label value. If a binary mask image is specified and if UseMaskValue is true, only those input image voxels corresponding with mask image values equal to MaskLabel are used in estimating the bias field. If a MaskImage is specified and UseMaskLabel is false, all input image voxels corresponding to non-zero voxels in the MaskImage are used in estimating the bias field. Default = 1.

◆ SetMaximumNumberOfIterations()

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.

◆ SetNumberOfControlPoints()

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.

◆ SetNumberOfFittingLevels() [1/2]

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.

◆ SetNumberOfFittingLevels() [2/2]

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 306 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ SetNumberOfHistogramBins()

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.

◆ SetSplineOrder()

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.

◆ SetUseMaskLabel()

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

virtual void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SetUseMaskLabel ( bool _arg )

virtual

Use a mask label for identifying mask functionality. See SetMaskLabel. Defaults to false.

◆ SetWienerFilterNoise()

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.

◆ SharpenImage()

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

void itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::SharpenImage	(	const RealImageType *	unsharpenedImage,
		RealImageType *	sharpenedImage
	)		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.

◆ UpdateBiasFieldEstimate()

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

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

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.

◆ UseMaskLabelOn()

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

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

virtual

Use a mask label for identifying mask functionality. See SetMaskLabel. Defaults to false.

Member Data Documentation

◆ ImageDimension

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

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

staticconstexpr

ImageDimension constants

Definition at line 114 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_BiasFieldFullWidthAtHalfMaximum

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

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_BiasFieldFullWidthAtHalfMaximum { static_cast<RealType>(0.15) }

private

Definition at line 434 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_ConvergenceThreshold

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

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ConvergenceThreshold { static_cast<RealType>(0.001) }

private

Definition at line 440 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_CurrentConvergenceMeasurement

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 441 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_CurrentLevel

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

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_CurrentLevel { 0 }

private

Definition at line 442 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_ElapsedIterations

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

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_ElapsedIterations { 0 }

private

Definition at line 439 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_LogBiasFieldControlPointLattice

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 446 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_MaskLabel

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 427 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_MaximumNumberOfIterations

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 438 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_NumberOfControlPoints

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 449 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_NumberOfFittingLevels

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 450 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_NumberOfHistogramBins

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

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_NumberOfHistogramBins { 200 }

private

Definition at line 432 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_SplineOrder

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

unsigned int itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_SplineOrder { 3 }

private

Definition at line 448 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_UseMaskLabel

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

bool itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_UseMaskLabel { false }

private

Definition at line 428 of file itkN4BiasFieldCorrectionImageFilter.h.

◆ m_WienerFilterNoise

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

RealType itk::N4BiasFieldCorrectionImageFilter< TInputImage, TMaskImage, TOutputImage >::m_WienerFilterNoise { static_cast<RealType>(0.01) }

private

Definition at line 433 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

◆ ArrayType

◆ BiasFieldControlPointLatticeType

◆ BSplineFilterType

◆ ConstPointer

◆ InputImageType

◆ MaskImageType

◆ MaskPixelType

◆ OutputImageType

◆ Pointer

◆ PointSetPointer

◆ PointSetType

◆ PointType

◆ RealImagePointer

◆ RealImageType

◆ RealType

◆ ScalarImageType

◆ ScalarType

◆ Self

◆ Superclass

◆ VariableSizeArrayType

Constructor & Destructor Documentation

◆ N4BiasFieldCorrectionImageFilter()

◆ ~N4BiasFieldCorrectionImageFilter()

Member Function Documentation

◆ CalculateConvergenceMeasurement()

◆ EnlargeOutputRequestedRegion()

◆ GenerateData()

◆ GetBiasFieldFullWidthAtHalfMaximum()

◆ GetConfidenceImage()

◆ GetConvergenceThreshold()

◆ GetCurrentConvergenceMeasurement()

◆ GetCurrentLevel()

◆ GetElapsedIterations()

◆ GetLogBiasFieldControlPointLattice()

◆ GetMaskImage()

◆ GetMaskLabel()

◆ GetMaximumNumberOfIterations()

◆ GetNameOfClass()

◆ GetNumberOfControlPoints()

◆ GetNumberOfFittingLevels()

◆ GetNumberOfHistogramBins()

◆ GetSplineOrder()

◆ GetUseMaskLabel()

◆ GetWienerFilterNoise()

◆ New()

◆ PrintSelf()

◆ ReconstructBiasField()

◆ SetBiasFieldFullWidthAtHalfMaximum()

◆ SetConfidenceImage()

◆ SetConvergenceThreshold()

◆ SetInput1()

◆ SetInput2()

◆ SetInput3()

◆ SetMaskImage()

◆ SetMaskLabel()

◆ SetMaximumNumberOfIterations()

◆ SetNumberOfControlPoints()

◆ SetNumberOfFittingLevels() [1/2]

◆ SetNumberOfFittingLevels() [2/2]

◆ SetNumberOfHistogramBins()

◆ SetSplineOrder()

◆ SetUseMaskLabel()

◆ SetWienerFilterNoise()

◆ SharpenImage()

◆ UpdateBiasFieldEstimate()

◆ UseMaskLabelOn()

Member Data Documentation

◆ ImageDimension

◆ m_BiasFieldFullWidthAtHalfMaximum

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