#include <itkMRIBiasFieldCorrectionFilter.h>

Detailed Description

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

Corrects 3D MRI bias field.

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

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

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

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

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

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

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

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

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

Definition at line 235 of file itkMRIBiasFieldCorrectionFilter.h.

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

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

Public Types
using	BiasFieldType = MultivariateLegendrePolynomial

using	ConstPointer = SmartPointer< const Self >

using	EnergyFunctionPointer = typename EnergyFunctionType::Pointer

using	EnergyFunctionType = MRIBiasEnergyFunction< InternalImageType, ImageMaskType, BiasFieldType >

using	ImageMaskPointer = typename ImageMaskType::Pointer

using	ImageMaskRegionType = typename ImageMaskType::RegionType

using	ImageMaskType = TMaskImage

using	InputImageIndexType = typename TInputImage::IndexType

using	InputImagePixelType = typename TInputImage::PixelType

using	InputImagePointer = typename TInputImage::Pointer

using	InputImageRegionType = typename TInputImage::RegionType

using	InputImageSizeType = typename TInputImage::SizeType

using	InputImageType = TInputImage

using	InternalImagePixelType = typename InternalImageType::PixelType

using	InternalImagePointer = typename InternalImageType::Pointer

using	InternalImageRegionType = typename InternalImageType::RegionType

using	InternalImageType = Image< float, Self::ImageDimension >

using	MRASlabIdentifierType = MRASlabIdentifier< InputImageType >

using	NormalVariateGeneratorType = Statistics::NormalVariateGenerator

using	OptimizerType = OnePlusOneEvolutionaryOptimizer

using	OutputImageIndexType = typename TOutputImage::IndexType

using	OutputImagePixelType = typename TOutputImage::PixelType

using	OutputImagePointer = typename TOutputImage::Pointer

using	OutputImageRegionType = typename TOutputImage::RegionType

using	OutputImageSizeType = typename TOutputImage::SizeType

using	OutputImageType = TOutputImage

using	Pointer = SmartPointer< Self >

using	ScheduleType = Array2D< unsigned int >

using	Self = MRIBiasFieldCorrectionFilter

using	SlabRegionVectorIteratorType = typename SlabRegionVectorType::iterator

using	SlabRegionVectorType = typename MRASlabIdentifierType::SlabRegionVectorType

using	Superclass = ImageToImageFilter< TInputImage, TOutputImage >

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	CorrectImage (BiasFieldType &bias, InputImageRegionType region)

void	CorrectInterSliceIntensityInhomogeneity (InputImageRegionType region)

BiasFieldType	EstimateBiasField (InputImageRegionType region, unsigned int degree, int maximumIteration)

BiasFieldType::CoefficientArrayType	GetEstimatedBiasFieldCoefficients ()

const char *	GetNameOfClass () const override

virtual unsigned int	GetNumberOfLevels () const

virtual double	GetOptimizerShrinkFactor () const

virtual const ScheduleType &	GetSchedule () const

virtual const InputImagePixelType &	GetSlabBackgroundMinimumThreshold () const

virtual const unsigned int &	GetSlabNumberOfSamples () const

virtual const double &	GetSlabTolerance () const

const unsigned int *	GetStartingShrinkFactors () const

void	Initialize ()

bool	IsBiasFieldMultiplicative ()

void	IsBiasFieldMultiplicative (bool flag)

void	SetNumberOfLevels (unsigned int num)

virtual void	SetOptimizerShrinkFactor (double _arg)

void	SetSchedule (const ScheduleType &schedule)

virtual void	SetSlabBackgroundMinimumThreshold (InputImagePixelType _arg)

virtual void	SetSlabNumberOfSamples (unsigned int _arg)

virtual void	SetSlabTolerance (double _arg)

void	SetStartingShrinkFactors (const unsigned int *factors)

void	SetStartingShrinkFactors (unsigned int factor)

void	SetTissueClassStatistics (const Array< double > &means, const Array< double > &sigmas)


void	SetInputMask (ImageMaskType *inputMask)

virtual ImageMaskType *	GetModifiableInputMask ()


void	SetOutputMask (ImageMaskType *outputMask)

virtual ImageMaskType *	GetModifiableOutputMask ()


virtual void	SetBiasFieldMultiplicative (bool _arg)

virtual bool	GetBiasFieldMultiplicative () const

virtual void	BiasFieldMultiplicativeOn ()


virtual void	SetUsingInterSliceIntensityCorrection (bool _arg)

virtual bool	GetUsingInterSliceIntensityCorrection () const

virtual void	UsingInterSliceIntensityCorrectionOn ()


virtual void	SetUsingSlabIdentification (bool _arg)

virtual bool	GetUsingSlabIdentification () const

virtual void	UsingSlabIdentificationOn ()


virtual void	SetUsingBiasFieldCorrection (bool _arg)

virtual bool	GetUsingBiasFieldCorrection () const

virtual void	UsingBiasFieldCorrectionOn ()


virtual void	SetGeneratingOutput (bool _arg)

virtual bool	GetGeneratingOutput () const

virtual void	GeneratingOutputOn ()


virtual void	SetSlicingDirection (int _arg)

virtual int	GetSlicingDirection () const


virtual void	SetBiasFieldDegree (int _arg)

virtual int	GetBiasFieldDegree () const


void	SetInitialBiasFieldCoefficients (const BiasFieldType::CoefficientArrayType &coefficients)


virtual void	SetVolumeCorrectionMaximumIteration (int _arg)

virtual int	GetVolumeCorrectionMaximumIteration () const


virtual void	SetInterSliceCorrectionMaximumIteration (int _arg)

virtual int	GetInterSliceCorrectionMaximumIteration () const


virtual void	SetOptimizerInitialRadius (double _arg)

virtual double	GetOptimizerInitialRadius () const


virtual void	SetOptimizerGrowthFactor (double _arg)

virtual double	GetOptimizerGrowthFactor () const

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

const InputImageType *	GetInput (unsigned int idx) const

const char *	GetNameOfClass () const override

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 >
const char *	GetNameOfClass () const override

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 void	EnlargeOutputRequestedRegion (DataObject *)

virtual const bool &	GetAbortGenerateData () const

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

NameArray	GetInputNames () const

DataObjectPointerArray	GetInputs ()

MultiThreaderType *	GetMultiThreader () const

const char *	GetNameOfClass () const override

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 DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)

virtual DataObjectPointer	MakeOutput (DataObjectPointerArraySizeType idx)

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

const char *	GetNameOfClass () const override

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 Pointer	CreateAnother () const

virtual void	Delete ()

virtual const char *	GetNameOfClass () const

virtual int	GetReferenceCount () const

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

virtual void	Register () const

virtual void	SetReferenceCount (int)

virtual void	UnRegister () const noexcept

Static Public Member Functions
static bool	IsScheduleDownwardDivisible (const ScheduleType &schedule)

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 = TOutputImage::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	AdjustSlabRegions (SlabRegionVectorType &slabs, OutputImageRegionType requestedRegion)

bool	CheckMaskImage (ImageMaskType *mask)

template<typename TSource , typename TTarget >
void	CopyAndConvertImage (const TSource source, TTarget target, typename TTarget::RegionType requestedRegion)

void	ExpImage (InternalImageType source, InternalImageType target)

void	GenerateData () override

void	GetBiasFieldSize (InputImageRegionType region, BiasFieldType::DomainSizeType &biasSize)

void	Log1PImage (InternalImageType source, InternalImageType target)

	MRIBiasFieldCorrectionFilter ()

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

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

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)

void	GenerateData () override

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

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

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	GenerateData ()

virtual void	GenerateInputRequestedRegion ()

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

virtual void	PopBackInput ()

virtual void	PopFrontInput ()

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

	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	VerifyInputInformation () const

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

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

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

virtual void	PrintTrailer (std::ostream &os, Indent indent) const

virtual	~LightObject ()

Private Attributes
BiasFieldType::CoefficientArrayType	m_BiasFieldCoefficients {}

int	m_BiasFieldDegree { 3 }

bool	m_BiasFieldMultiplicative { true }

EnergyFunctionPointer	m_EnergyFunction {}

BiasFieldType::CoefficientArrayType	m_EstimatedBiasFieldCoefficients {}

bool	m_GeneratingOutput { true }

ImageMaskPointer	m_InputMask {}

InternalImagePointer	m_InternalInput {}

int	m_InterSliceCorrectionMaximumIteration { 4000 }

NormalVariateGeneratorType::Pointer	m_NormalVariateGenerator {}

unsigned int	m_NumberOfLevels { 0 }

double	m_OptimizerGrowthFactor { 1.05 }

double	m_OptimizerInitialRadius { 1.01 }

double	m_OptimizerShrinkFactor {}

ImageMaskPointer	m_OutputMask {}

ScheduleType	m_Schedule {}

InputImagePixelType	m_SlabBackgroundMinimumThreshold {}

unsigned int	m_SlabNumberOfSamples { 200 }

SlabRegionVectorType	m_Slabs {}

double	m_SlabTolerance { 0.0 }

int	m_SlicingDirection {}

Array< double >	m_TissueClassMeans {}

Array< double >	m_TissueClassSigmas {}

bool	m_UsingBiasFieldCorrection { true }

bool	m_UsingInterSliceIntensityCorrection {}

bool	m_UsingSlabIdentification { false }

int	m_VolumeCorrectionMaximumIteration { 2000 }

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

◆ BiasFieldType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::BiasFieldType = MultivariateLegendrePolynomial

Bias field object type definition.

Definition at line 288 of file itkMRIBiasFieldCorrectionFilter.h.

◆ ConstPointer

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Definition at line 245 of file itkMRIBiasFieldCorrectionFilter.h.

◆ EnergyFunctionPointer

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::EnergyFunctionPointer = typename EnergyFunctionType::Pointer

Definition at line 292 of file itkMRIBiasFieldCorrectionFilter.h.

◆ EnergyFunctionType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Energy function type definition.

Definition at line 291 of file itkMRIBiasFieldCorrectionFilter.h.

◆ ImageMaskPointer

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ImageMaskPointer = typename ImageMaskType::Pointer

Definition at line 273 of file itkMRIBiasFieldCorrectionFilter.h.

◆ ImageMaskRegionType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ImageMaskRegionType = typename ImageMaskType::RegionType

Definition at line 274 of file itkMRIBiasFieldCorrectionFilter.h.

◆ ImageMaskType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::ImageMaskType = TMaskImage

Mask image related type definitions.

Definition at line 272 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InputImageIndexType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImageIndexType = typename TInputImage::IndexType

Definition at line 266 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InputImagePixelType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImagePixelType = typename TInputImage::PixelType

Definition at line 267 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InputImagePointer

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImagePointer = typename TInputImage::Pointer

Definition at line 265 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InputImageRegionType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImageRegionType = typename TInputImage::RegionType

Definition at line 269 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InputImageSizeType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InputImageSizeType = typename TInputImage::SizeType

Definition at line 268 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InputImageType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Definition at line 264 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InternalImagePixelType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImagePixelType = typename InternalImageType::PixelType

Definition at line 278 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InternalImagePointer

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImagePointer = typename InternalImageType::Pointer

Definition at line 279 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InternalImageRegionType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImageRegionType = typename InternalImageType::RegionType

Definition at line 280 of file itkMRIBiasFieldCorrectionFilter.h.

◆ InternalImageType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::InternalImageType = Image<float, Self::ImageDimension>

Internal (temporary) image related type definitions.

Definition at line 277 of file itkMRIBiasFieldCorrectionFilter.h.

◆ MRASlabIdentifierType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Regions of the MRI slab identifier return.

Definition at line 283 of file itkMRIBiasFieldCorrectionFilter.h.

◆ NormalVariateGeneratorType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Normal variate Generator Type

Definition at line 295 of file itkMRIBiasFieldCorrectionFilter.h.

◆ OptimizerType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OptimizerType = OnePlusOneEvolutionaryOptimizer

Optimizer type definition.

Definition at line 298 of file itkMRIBiasFieldCorrectionFilter.h.

◆ OutputImageIndexType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImageIndexType = typename TOutputImage::IndexType

Definition at line 259 of file itkMRIBiasFieldCorrectionFilter.h.

◆ OutputImagePixelType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImagePixelType = typename TOutputImage::PixelType

Definition at line 260 of file itkMRIBiasFieldCorrectionFilter.h.

◆ OutputImagePointer

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImagePointer = typename TOutputImage::Pointer

Definition at line 258 of file itkMRIBiasFieldCorrectionFilter.h.

◆ OutputImageRegionType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImageRegionType = typename TOutputImage::RegionType

Definition at line 262 of file itkMRIBiasFieldCorrectionFilter.h.

◆ OutputImageSizeType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::OutputImageSizeType = typename TOutputImage::SizeType

Definition at line 261 of file itkMRIBiasFieldCorrectionFilter.h.

◆ OutputImageType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Input and output image related type definitions.

Definition at line 257 of file itkMRIBiasFieldCorrectionFilter.h.

◆ Pointer

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Definition at line 244 of file itkMRIBiasFieldCorrectionFilter.h.

◆ ScheduleType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

ScheduleType type alias support

Definition at line 301 of file itkMRIBiasFieldCorrectionFilter.h.

◆ Self

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Standard class type aliases.

Definition at line 242 of file itkMRIBiasFieldCorrectionFilter.h.

◆ SlabRegionVectorIteratorType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SlabRegionVectorIteratorType = typename SlabRegionVectorType::iterator

Definition at line 285 of file itkMRIBiasFieldCorrectionFilter.h.

◆ SlabRegionVectorType

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

using itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SlabRegionVectorType = typename MRASlabIdentifierType::SlabRegionVectorType

Definition at line 284 of file itkMRIBiasFieldCorrectionFilter.h.

◆ Superclass

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Definition at line 243 of file itkMRIBiasFieldCorrectionFilter.h.

Constructor & Destructor Documentation

◆ MRIBiasFieldCorrectionFilter()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

protected

◆ ~MRIBiasFieldCorrectionFilter()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

overrideprotecteddefault

Member Function Documentation

◆ AdjustSlabRegions()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

protected

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

◆ BiasFieldMultiplicativeOn()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the multiplicative nature of the filter's bias field: if true, the filter assumes the bias field is multiplicative and internally uses log intensity values for every calculation.

◆ CheckMaskImage()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

protected

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

◆ CopyAndConvertImage()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

template<typename TSource , typename TTarget >

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

inlineprotected

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

Definition at line 550 of file itkMRIBiasFieldCorrectionFilter.h.

◆ CorrectImage()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

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

◆ CorrectInterSliceIntensityInhomogeneity()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::CorrectInterSliceIntensityInhomogeneity ( InputImageRegionType region )

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

◆ EstimateBiasField()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

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

◆ ExpImage()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

protected

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

◆ GenerateData()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

◆ GeneratingOutputOn()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ GetBiasFieldDegree()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the degree of the bias field estimate.

◆ GetBiasFieldMultiplicative()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the multiplicative nature of the filter's bias field: if true, the filter assumes the bias field is multiplicative and internally uses log intensity values for every calculation.

◆ GetBiasFieldSize()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

protected

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

◆ GetEstimatedBiasFieldCoefficients()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

inline

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

Definition at line 416 of file itkMRIBiasFieldCorrectionFilter.h.

◆ GetGeneratingOutput()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ GetInterSliceCorrectionMaximumIteration()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the maximum iteration termination condition parameter for the inter-slice intensity inhomogeneity correction.

◆ GetModifiableInputMask()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ GetModifiableOutputMask()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Get/Set the out mask image pointer. Without this mask, this filter corrects every pixel in the input image.

◆ GetNameOfClass()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

overridevirtual

See also: LightObject::GetNameOfClass()

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

◆ GetNumberOfLevels()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Get the number of multi-resolution levels.

◆ GetOptimizerGrowthFactor()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the search radius grow factor.

◆ GetOptimizerInitialRadius()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the initial search radius.

◆ GetOptimizerShrinkFactor()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

◆ GetSchedule()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Get the multi-resolution schedule.

◆ GetSlabBackgroundMinimumThreshold()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

◆ GetSlabNumberOfSamples()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

◆ GetSlabTolerance()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

◆ GetSlicingDirection()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ GetStartingShrinkFactors()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

Get the starting shrink factors.

◆ GetUsingBiasFieldCorrection()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ GetUsingInterSliceIntensityCorrection()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the intensity correction flag. If the flag is true, inter-slice intensity correction will be applied before bias field correction (default value is true for 3D input images, and false for 2D input images).

◆ GetUsingSlabIdentification()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ GetVolumeCorrectionMaximumIteration()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the maximum iteration termination condition parameter for the bias field correction.

◆ Initialize()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

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

◆ IsBiasFieldMultiplicative() [1/2]

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

inline

If the bias field is multiplicative, it returns true.

Definition at line 340 of file itkMRIBiasFieldCorrectionFilter.h.

◆ IsBiasFieldMultiplicative() [2/2]

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

inline

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

Definition at line 323 of file itkMRIBiasFieldCorrectionFilter.h.

◆ IsScheduleDownwardDivisible()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

static

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

◆ Log1PImage()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

protected

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

◆ New()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

static

Method for creation through the object factory.

◆ PrintSelf()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

◆ SetBiasFieldDegree()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the degree of the bias field estimate.

◆ SetBiasFieldMultiplicative()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the multiplicative nature of the filter's bias field: if true, the filter assumes the bias field is multiplicative and internally uses log intensity values for every calculation.

◆ SetGeneratingOutput()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ SetInitialBiasFieldCoefficients()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

inline

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

Definition at line 405 of file itkMRIBiasFieldCorrectionFilter.h.

◆ SetInputMask()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetInputMask ( ImageMaskType * inputMask )

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

◆ SetInterSliceCorrectionMaximumIteration()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the maximum iteration termination condition parameter for the inter-slice intensity inhomogeneity correction.

◆ SetNumberOfLevels()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetNumberOfLevels ( unsigned int num )

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

◆ SetOptimizerGrowthFactor()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the search radius grow factor.

◆ SetOptimizerInitialRadius()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the initial search radius.

◆ SetOptimizerShrinkFactor()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the search radius shrink factor.

◆ SetOutputMask()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetOutputMask ( ImageMaskType * outputMask )

Get/Set the out mask image pointer. Without this mask, this filter corrects every pixel in the input image.

◆ SetSchedule()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetSchedule ( const ScheduleType & schedule )

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

◆ SetSlabBackgroundMinimumThreshold()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

◆ SetSlabNumberOfSamples()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

◆ SetSlabTolerance()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

◆ SetSlicingDirection()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ SetStartingShrinkFactors() [1/2]

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetStartingShrinkFactors ( const unsigned int * factors )

◆ SetStartingShrinkFactors() [2/2]

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::SetStartingShrinkFactors ( unsigned int factor )

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

◆ SetTissueClassStatistics()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

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

◆ SetUsingBiasFieldCorrection()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ SetUsingInterSliceIntensityCorrection()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the intensity correction flag. If the flag is true, inter-slice intensity correction will be applied before bias field correction (default value is true for 3D input images, and false for 2D input images).

◆ SetUsingSlabIdentification()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ SetVolumeCorrectionMaximumIteration()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the maximum iteration termination condition parameter for the bias field correction.

◆ UsingBiasFieldCorrectionOn()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

◆ UsingInterSliceIntensityCorrectionOn()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

Set/Get the intensity correction flag. If the flag is true, inter-slice intensity correction will be applied before bias field correction (default value is true for 3D input images, and false for 2D input images).

◆ UsingSlabIdentificationOn()

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

virtual

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

Member Data Documentation

◆ ImageDimension

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

staticconstexpr

The dimension of the image.

Definition at line 254 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_BiasFieldCoefficients

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

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

Definition at line 631 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_BiasFieldDegree

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_BiasFieldDegree { 3 }

private

The degree of the bias field estimate.

Definition at line 621 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_BiasFieldMultiplicative

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_BiasFieldMultiplicative { true }

private

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

Definition at line 608 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_EnergyFunction

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Energy function object pointer.

Definition at line 587 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_EstimatedBiasFieldCoefficients

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

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

Definition at line 635 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_GeneratingOutput

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_GeneratingOutput { true }

private

Definition at line 614 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_InputMask

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Input mask image smart pointer.

Definition at line 593 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_InternalInput

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Internal image smart pointer.

Definition at line 599 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_InterSliceCorrectionMaximumIteration

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_InterSliceCorrectionMaximumIteration { 4000 }

private

Definition at line 639 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_NormalVariateGenerator

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Normal variate generator smart pointer.

Definition at line 590 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_NumberOfLevels

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

unsigned int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_NumberOfLevels { 0 }

private

The number of levels for the multires schedule.

Definition at line 624 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_OptimizerGrowthFactor

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_OptimizerGrowthFactor { 1.05 }

private

Storage for the optimizer's search radius grow factor.

Definition at line 645 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_OptimizerInitialRadius

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_OptimizerInitialRadius { 1.01 }

private

Storage for the optimizer's initial search radius.

Definition at line 642 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_OptimizerShrinkFactor

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Storage for the optimizer's search radius shrink factor.

Definition at line 648 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_OutputMask

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Output mask image smart pointer.

Definition at line 596 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_Schedule

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

The multires schedule

Definition at line 627 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_SlabBackgroundMinimumThreshold

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Definition at line 617 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_SlabNumberOfSamples

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

unsigned int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_SlabNumberOfSamples { 200 }

private

Definition at line 616 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_Slabs

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Storage for the MRI slab identifier return.

Definition at line 602 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_SlabTolerance

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

double itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_SlabTolerance { 0.0 }

private

Definition at line 618 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_SlicingDirection

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

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

Definition at line 605 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_TissueClassMeans

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Storage for tissue classes' mean values.

Definition at line 651 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_TissueClassSigmas

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

Storage for tissue classes' variance values.

Definition at line 654 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_UsingBiasFieldCorrection

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_UsingBiasFieldCorrection { true }

private

Definition at line 613 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_UsingInterSliceIntensityCorrection

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

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

private

operation selection flags.

Definition at line 611 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_UsingSlabIdentification

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

bool itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_UsingSlabIdentification { false }

private

Definition at line 612 of file itkMRIBiasFieldCorrectionFilter.h.

◆ m_VolumeCorrectionMaximumIteration

template<typename TInputImage , typename TOutputImage , typename TMaskImage >

int itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::m_VolumeCorrectionMaximumIteration { 2000 }

private

Definition at line 637 of file itkMRIBiasFieldCorrectionFilter.h.

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

itkMRIBiasFieldCorrectionFilter.h

Detailed Description

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ BiasFieldType

◆ ConstPointer

◆ EnergyFunctionPointer

◆ EnergyFunctionType

◆ ImageMaskPointer

◆ ImageMaskRegionType

◆ ImageMaskType

◆ InputImageIndexType

◆ InputImagePixelType

◆ InputImagePointer

◆ InputImageRegionType

◆ InputImageSizeType

◆ InputImageType

◆ InternalImagePixelType

◆ InternalImagePointer

◆ InternalImageRegionType

◆ InternalImageType

◆ MRASlabIdentifierType

◆ NormalVariateGeneratorType

◆ OptimizerType

◆ OutputImageIndexType

◆ OutputImagePixelType

◆ OutputImagePointer

◆ OutputImageRegionType

◆ OutputImageSizeType

◆ OutputImageType

◆ Pointer

◆ ScheduleType

◆ Self

◆ SlabRegionVectorIteratorType

◆ SlabRegionVectorType

◆ Superclass

Constructor & Destructor Documentation

◆ MRIBiasFieldCorrectionFilter()

◆ ~MRIBiasFieldCorrectionFilter()

Member Function Documentation

◆ AdjustSlabRegions()

◆ BiasFieldMultiplicativeOn()

◆ CheckMaskImage()

◆ CopyAndConvertImage()

◆ CorrectImage()

◆ CorrectInterSliceIntensityInhomogeneity()

◆ EstimateBiasField()

◆ ExpImage()

◆ GenerateData()

◆ GeneratingOutputOn()

◆ GetBiasFieldDegree()

◆ GetBiasFieldMultiplicative()

◆ GetBiasFieldSize()

◆ GetEstimatedBiasFieldCoefficients()

◆ GetGeneratingOutput()

◆ GetInterSliceCorrectionMaximumIteration()

◆ GetModifiableInputMask()

◆ GetModifiableOutputMask()

◆ GetNameOfClass()

◆ GetNumberOfLevels()

◆ GetOptimizerGrowthFactor()

◆ GetOptimizerInitialRadius()

◆ GetOptimizerShrinkFactor()

◆ GetSchedule()

◆ GetSlabBackgroundMinimumThreshold()

◆ GetSlabNumberOfSamples()

◆ GetSlabTolerance()

◆ GetSlicingDirection()

◆ GetStartingShrinkFactors()

◆ GetUsingBiasFieldCorrection()

◆ GetUsingInterSliceIntensityCorrection()

◆ GetUsingSlabIdentification()

◆ GetVolumeCorrectionMaximumIteration()

◆ Initialize()

◆ IsBiasFieldMultiplicative() [1/2]