corrects 3D MRI bias field More...

#include <itkMRIBiasFieldCorrectionFilter.h>

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

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

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

Public Member Functions
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
void	CorrectImage (BiasFieldType &bias, InputImageRegionType region)
void	CorrectInterSliceIntensityInhomogeneity (InputImageRegionType region)
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
virtual void	DebugOff () const
virtual void	DebugOn () const
virtual void	Delete ()
virtual void	EnlargeOutputRequestedRegion (DataObject *)
BiasFieldType	EstimateBiasField (InputImageRegionType region, unsigned int degree, int maximumIteration)
virtual const bool &	GetAbortGenerateData ()
virtual int	GetBiasFieldDegree () const
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
BiasFieldType::CoefficientArrayType	GetEstimatedBiasFieldCoefficients ()
virtual const bool &	GetGeneratingOutput ()
const InputImageType *	GetInput (void)
const InputImageType *	GetInput (unsigned int idx)
virtual ImageMaskType *	GetInputMask ()
DataObjectPointerArray &	GetInputs ()
virtual int	GetInterSliceCorrectionMaximumIteration () const
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual unsigned long	GetMTime () const
MultiThreader *	GetMultiThreader ()
virtual const char *	GetNameOfClass () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
virtual unsigned int	GetNumberOfLevels () const
DataObjectPointerArraySizeType	GetNumberOfOutputs () const
virtual const int &	GetNumberOfThreads ()
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
virtual double	GetOptimizerGrowthFactor () const
double	GetOptimizerInitialRadius ()
virtual double	GetOptimizerShrinkFactor () const
OutputImageType *	GetOutput (void)
OutputImageType *	GetOutput (unsigned int idx)
virtual ImageMaskType *	GetOutputMask ()
DataObjectPointerArray &	GetOutputs ()
virtual const float &	GetProgress ()
virtual int	GetReferenceCount () const
virtual const bool &	GetReleaseDataBeforeUpdateFlag ()
virtual bool	GetReleaseDataFlag () const
virtual const ScheduleType &	GetSchedule ()
virtual const InputImagePixelType &	GetSlabBackgroundMinimumThreshold ()
virtual const unsigned int &	GetSlabNumberOfSamples ()
virtual const double &	GetSlabTolerance ()
const unsigned int *	GetStartingShrinkFactors () const
virtual const bool &	GetUsingBiasFieldCorrection ()
virtual const bool &	GetUsingInterSliceIntensityCorrection ()
virtual const bool &	GetUsingSlabIdentification ()
virtual int	GetVolumeCorrectionMaximumIteration () const
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
virtual void	GraftOutput (DataObject *output)
bool	HasObserver (const EventObject &event) const
void	Initialize () throw (ExceptionObject)
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
void	IsBiasFieldMultiplicative (bool flag)
bool	IsBiasFieldMultiplicative ()
virtual DataObjectPointer	MakeOutput (unsigned int idx)
virtual void	Modified () const
virtual void	PopBackInput ()
virtual void	PopFrontInput ()
virtual void	PrepareOutputs ()
void	Print (std::ostream &os, Indent indent=0) const
virtual void	PropagateRequestedRegion (DataObject *output)
virtual void	PushBackInput (const InputImageType *image)
virtual void	PushFrontInput (const InputImageType *image)
virtual void	Register () const
virtual void	ReleaseDataBeforeUpdateFlagOff ()
virtual void	ReleaseDataBeforeUpdateFlagOn ()
void	ReleaseDataFlagOff ()
void	ReleaseDataFlagOn ()
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
virtual void	SetBiasFieldDegree (int _arg)
void	SetDebug (bool debugFlag) const
virtual void	SetGeneratingOutput (bool _arg)
void	SetInitialBiasFieldCoefficients (const BiasFieldType::CoefficientArrayType &coefficients)
virtual void	SetInput (const InputImageType *image)
virtual void	SetInput (unsigned int, const TInputImage *image)
void	SetInputMask (ImageMaskType *inputMask)
virtual void	SetInterSliceCorrectionMaximumIteration (int _arg)
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
void	SetNumberOfLevels (unsigned int num)
virtual void	SetNumberOfThreads (int _arg)
virtual void	SetOptimizerGrowthFactor (double _arg)
void	SetOptimizerInitialRadius (double initRadius)
virtual void	SetOptimizerShrinkFactor (double _arg)
void	SetOutputMask (ImageMaskType *outputMask)
virtual void	SetProgress (float _arg)
virtual void	SetReferenceCount (int)
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)
virtual void	SetReleaseDataFlag (bool flag)
void	SetSchedule (const ScheduleType &schedule)
virtual void	SetSlabBackgroundMinimumThreshold (InputImagePixelType _arg)
virtual void	SetSlabNumberOfSamples (unsigned int _arg)
virtual void	SetSlabTolerance (double _arg)
virtual void	SetSlicingDirection (int _arg)
void	SetStartingShrinkFactors (unsigned int factor)
void	SetStartingShrinkFactors (unsigned int *factors)
void	SetTissueClassStatistics (const Array< double > &means, const Array< double > &sigmas) throw (ExceptionObject)
virtual void	SetUsingBiasFieldCorrection (bool _arg)
virtual void	SetUsingInterSliceIntensityCorrection (bool _arg)
virtual void	SetUsingSlabIdentification (bool _arg)
virtual void	SetVolumeCorrectionMaximumIteration (int _arg)
virtual void	UnRegister () const
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float amount)

Static Public Member Functions
static void	BreakOnError ()
static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static bool	IsScheduleDownwardDivisible (const ScheduleType &schedule)
static Pointer	New ()
static void	SetGlobalWarningDisplay (bool flag)

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

Protected Types
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension)>	InputToOutputRegionCopierType
typedef int	InternalReferenceCountType
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension)>	OutputToInputRegionCopierType

Protected Member Functions
	MRIBiasFieldCorrectionFilter ()
virtual	~MRIBiasFieldCorrectionFilter ()
virtual void	AddInput (DataObject *input)
virtual void	AddOutput (DataObject *output)
void	AdjustSlabRegions (SlabRegionVectorType &slabs, OutputImageRegionType requestedRegion)
virtual void	AfterThreadedGenerateData ()
virtual void	AllocateOutputs ()
virtual void	BeforeThreadedGenerateData ()
virtual void	CacheInputReleaseDataFlags ()
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
bool	CheckMaskImage (ImageMaskType *mask)
template<class TSource , class TTarget >
void	CopyAndConvertImage (const TSource source, TTarget target, typename TTarget::RegionType requestedRegion)
void	ExpImage (InternalImageType source, InternalImageType target)
void	GenerateData ()
virtual void	GenerateInputRequestedRegion ()
virtual void	GenerateOutputInformation ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
void	GetBiasFieldSize (InputImageRegionType region, BiasFieldType::DomainSizeType &domainSize)
const DataObject *	GetInput (unsigned int idx) const
virtual const unsigned int &	GetNumberOfRequiredInputs ()
virtual const unsigned int &	GetNumberOfRequiredOutputs ()
const DataObject *	GetOutput (unsigned int idx) const
void	Log1PImage (InternalImageType source, InternalImageType target)
virtual void	PrintHeader (std::ostream &os, Indent indent) const
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
virtual void	PropagateResetPipeline ()
void	PushBackInput (const DataObject *input)
void	PushFrontInput (const DataObject *input)
virtual void	ReleaseInputs ()
virtual void	RemoveInput (DataObject *input)
virtual void	RemoveOutput (DataObject *output)
virtual void	RestoreInputReleaseDataFlags ()
virtual void	SetNthInput (unsigned int num, DataObject *input)
virtual void	SetNthOutput (unsigned int num, DataObject *output)
void	SetNumberOfInputs (unsigned int num)
void	SetNumberOfOutputs (unsigned int num)
virtual void	SetNumberOfRequiredInputs (unsigned int _arg)
virtual void	SetNumberOfRequiredOutputs (unsigned int _arg)
virtual int	SplitRequestedRegion (int i, int num, OutputImageRegionType &splitRegion)
virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, int threadId)

Static Protected Member Functions
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)

Protected Attributes
TimeStamp	m_OutputInformationMTime
InternalReferenceCountType	m_ReferenceCount
SimpleFastMutexLock	m_ReferenceCountLock
bool	m_Updating

Private Member Functions
	MRIBiasFieldCorrectionFilter (const Self &)
void	operator= (const Self &)

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

Detailed Description

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

corrects 3D MRI bias field

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

In MRI images, intensity inhomogenieties which are caused by magnetic settings, patients' postion, 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 paramters of a Legendre polynomial (bias field estimate) which minimizes the total energy value of each image after bias field is eleminated. The default Legendre polynomial degree is 3.

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

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

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

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

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

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

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

Definition at line 226 of file itkMRIBiasFieldCorrectionFilter.h.

Member Typedef Documentation

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Bias field object type defintion.

Definition at line 280 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

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

Definition at line 234 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TOutputImage>

typedef DataObject::Pointer itk::ImageSource< TOutputImage >::DataObjectPointer

inherited

Smart Pointer type to a DataObject.

Reimplemented from itk::ProcessObject.

Definition at line 62 of file itkImageSource.h.

typedef std::vector<DataObjectPointer> itk::ProcessObject::DataObjectPointerArray

inherited

STL Array of SmartPointers to DataObjects

Definition at line 103 of file itkProcessObject.h.

typedef DataObjectPointerArray::size_type itk::ProcessObject::DataObjectPointerArraySizeType

inherited

Size type of an std::vector

Definition at line 112 of file itkProcessObject.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 286 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Energy function type defintion.

Definition at line 285 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 263 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 264 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Mask image related type definitions.

Definition at line 262 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage>

typedef InputImageType::ConstPointer itk::ImageToImageFilter< TInputImage, TOutputImage >::InputImageConstPointer

inherited

Definition at line 84 of file itkImageToImageFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 256 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

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

Definition at line 257 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

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

Definition at line 255 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

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

Definition at line 259 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 258 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Some convenient typedefs.

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

Definition at line 254 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage>

typedef ImageToImageFilterDetail::ImageRegionCopier<itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension)> itk::ImageToImageFilter< TInputImage, TOutputImage >::InputToOutputRegionCopierType

protectedinherited

Typedef for the region copier function object that converts an input region to an output region.

Definition at line 161 of file itkImageToImageFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 269 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 270 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 271 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Internal (temporary) image related type definitions.

Definition at line 268 of file itkMRIBiasFieldCorrectionFilter.h.

typedef int itk::LightObject::InternalReferenceCountType

protectedinherited

Define the type of the reference count according to the target. This allows the use of atomic operations

Definition at line 137 of file itkLightObject.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Regions of the MRI slab identifier return.

Definition at line 274 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Normal variate Generator Type

Definition at line 289 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Optimizer type definition.

Definition at line 292 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 249 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

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

Definition at line 250 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 248 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Superclass typedefs.

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

Definition at line 252 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 251 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Input and output image related type definitions.

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 247 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage>

typedef ImageToImageFilterDetail::ImageRegionCopier<itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension)> itk::ImageToImageFilter< TInputImage, TOutputImage >::OutputToInputRegionCopierType

protectedinherited

Typedef for the region copier function object that converts an output region to an input region.

Definition at line 166 of file itkImageToImageFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

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

Definition at line 233 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

ScheduleType typedef support.

Definition at line 295 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Standard class typedefs.

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

Definition at line 231 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 277 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

Definition at line 276 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

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

Definition at line 232 of file itkMRIBiasFieldCorrectionFilter.h.

Constructor & Destructor Documentation

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protected

Definition at line 215 of file itkMRIBiasFieldCorrectionFilter.txx.

References NULL.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protectedvirtual

Definition at line 435 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Member Function Documentation

virtual void itk::ProcessObject::AbortGenerateDataOff ( )

virtualinherited

virtual void itk::ProcessObject::AbortGenerateDataOn ( )

virtualinherited

Turn on and off the AbortGenerateData flag.

void itk::ProcessObject::AddInput ( DataObject * input )

protectedvirtualinherited

Adds an input to the first null position in the input list. Expands the list memory if necessary

Reimplemented in otb::ObjectDetectionClassifier< TInputImage, TOutputVectorData, TLabel, TFunctionPrecision, TCoordRep >, otb::DescriptorsListSampleGenerator< TInputImage, TVectorData, TListSample, TLabelListSample, TOutputPrecision, TCoordRep >, otb::PersistentDescriptorsListSampleGenerator< TInputImage, TVectorData, TFunctionType, TListSample, TLabelListSample >, and otb::PersistentObjectDetectionClassifier< TInputImage, TOutputVectorData, TLabel, TFunctionType >.

Definition at line 144 of file itkProcessObject.cxx.

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *	cmd
	)

inherited

Allow people to add/remove/invoke observers (callbacks) to any ITK object. This is an implementation of the subject/observer design pattern. An observer is added by specifying an event to respond to and an itk::Command to execute. It returns an unsigned long tag which can be used later to remove the event or retrieve the command. The memory for the Command becomes the responsibility of this object, so don't pass the same instance of a command to two different objects

Definition at line 389 of file itkObject.cxx.

References itk::SubjectImplementation::AddObserver().

Referenced by otb::StreamingImageVirtualWriter< TInputImage >::GenerateData(), itk::ProgressAccumulator::RegisterInternalFilter(), otb::ImageFileWriter< TInputImage >::Update(), and otb::WriterWatcherBase::WriterWatcherBase().

unsigned long itk::Object::AddObserver	(	const EventObject &	event,
		Command *	cmd
	)		const

inherited

Definition at line 401 of file itkObject.cxx.

References itk::SubjectImplementation::AddObserver().

void itk::ProcessObject::AddOutput ( DataObject * output )

protectedvirtualinherited

Adds an output to the first null position in the output list. Expands the list memory if necessary

Definition at line 390 of file itkProcessObject.cxx.

References itk::DataObject::ConnectSource().

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protected

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

Definition at line 1124 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TOutputImage>

virtual void itk::ImageSource< TOutputImage >::AfterThreadedGenerateData ( void )

inlineprotectedvirtualinherited

If an imaging filter needs to perform processing after all processing threads have completed, the filter can can provide an implementation for AfterThreadedGenerateData(). The execution flow in the default GenerateData() method will be: 1) Allocate the output buffer 2) Call BeforeThreadedGenerateData() 3) Spawn threads, calling ThreadedGenerateData() in each thread. 4) Call AfterThreadedGenerateData() Note that this flow of control is only available if a filter provides a ThreadedGenerateData() method and NOT a GenerateData() method.

Definition at line 264 of file itkImageSource.h.

template<class TOutputImage >

void itk::ImageSource< TOutputImage >::AllocateOutputs ( )

protectedvirtualinherited

The GenerateData method normally allocates the buffers for all of the outputs of a filter. Some filters may want to override this default behavior. For example, a filter may have multiple outputs with varying resolution. Or a filter may want to process data in place by grafting its input to its output.

Definition at line 197 of file itkImageSource.txx.

References itk::ProcessObject::GetOutput(), and itk::ImageBase< VImageDimension >::SetBufferedRegion().

template<class TOutputImage>

virtual void itk::ImageSource< TOutputImage >::BeforeThreadedGenerateData ( void )

inlineprotectedvirtualinherited

If an imaging filter needs to perform processing after the buffer has been allocated but before threads are spawned, the filter can can provide an implementation for BeforeThreadedGenerateData(). The execution flow in the default GenerateData() method will be: 1) Allocate the output buffer 2) Call BeforeThreadedGenerateData() 3) Spawn threads, calling ThreadedGenerateData() in each thread. 4) Call AfterThreadedGenerateData() Note that this flow of control is only available if a filter provides a ThreadedGenerateData() method and NOT a GenerateData() method.

Definition at line 252 of file itkImageSource.h.

Referenced by otb::RenderingImageFilter< TInputImage, TOutputImage >::BeforeThreadedGenerateData().

void itk::LightObject::BreakOnError ( )

staticinherited

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

Definition at line 149 of file itkLightObject.cxx.

void itk::ProcessObject::CacheInputReleaseDataFlags ( )

protectedvirtualinherited

Cache the state of any ReleaseDataFlag's on the inputs. While the filter is executing, we need to set the ReleaseDataFlag's on the inputs to false in case the current filter is implemented using a mini-pipeline (which will try to release the inputs). After the filter finishes, we restore the state of the ReleaseDataFlag's before the call to ReleaseInputs().

Definition at line 1050 of file itkProcessObject.cxx.

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::CallCopyInputRegionToOutputRegion	(	OutputImageRegionType &	destRegion,
		const InputImageRegionType &	srcRegion
	)

protectedvirtualinherited

This function calls the actual region copier to do the mapping from input image space to output image space. It uses a Function object used for dispatching to various routines to copy an input region (start index and size) to an output region. For most filters, this is a trivial copy because most filters require the input dimension to match the output dimension. However, some filters like itk::UnaryFunctorImageFilter can support output images of a higher dimension that the input.

This function object is used by the default implementation of GenerateOutputInformation(). It can also be used in routines like ThreadedGenerateData() where a filter may need to map an input region to an output region.

The default copier uses a "dispatch pattern" to call one of three overloaded functions depending on whether the input and output images are the same dimension, the input is a higher dimension that the output, or the input is of a lower dimension than the output. The use of an overloaded function is required for proper compilation of the various cases.

For the latter two cases, trivial implementations are used. If the input image is a higher dimension than the output, the first portion of the input region is copied to the output region. If the input region is a lower dimension than the output, the input region information is copied into the first portion of the output region and the rest of the output region is set to zero.

If a filter needs a different default behavior, it can override this method.

Reimplemented in otb::WaveletFilterBank< TInputImage, TOutputImage, TWaveletOperator, Wavelet::INVERSE >, otb::WaveletFilterBank< TInputImage, TOutputImage, TWaveletOperator, Wavelet::FORWARD >, otb::SubsampleImageFilter< TInputImage, TOutputImage, TDirectionOfTransformation >, and otb::DecimateImageFilter< TInputImage, TOutputImage >.

Definition at line 165 of file itkImageToImageFilter.txx.

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::CallCopyOutputRegionToInputRegion	(	InputImageRegionType &	destRegion,
		const OutputImageRegionType &	srcRegion
	)

protectedvirtualinherited

This function calls the actual region copier to do the mapping from output image space to input image space. It uses a Function object used for dispatching to various routines to copy an output region (start index and size) to an input region. For most filters, this is a trivial copy because most filters require the input dimension to match the output dimension. However, some filters like itk::ExtractImageFilter can support output images of a lower dimension that the input.

This function object can be used by GenerateOutputInformation() to copy the input LargestPossibleRegion to the output LargestPossibleRegion and can also be used in GenerateData or ThreadedGenerateData() where a filter may need to map an output region to an input region.

The default copier uses a "dispatch pattern" to call one of three overloaded functions depending on whether the input and output images are the same dimension, the input is a higher dimension that the output, or the input is of a lower dimension than the output. The use of an overloaded function is required for proper compilation of the various cases.

For the latter two cases, trivial implementations are used. If the input image is a higher dimension than the output, the output region information is copied into the first portion of the input region and the rest of the input region is set to zero. If the input region is a lower dimension than the output, the first portion of the output region is copied to the input region.

If a filter needs a different default behavior, it can override this method. The ExtractImageFilter overrides this function object so that if the input image is a higher dimension than the output image, the filter can control "where" in the input image the output subimage is extracted (as opposed to mapping to first few dimensions of the input).

Reimplemented in otb::WaveletFilterBank< TInputImage, TOutputImage, TWaveletOperator, Wavelet::INVERSE >, otb::WaveletFilterBank< TInputImage, TOutputImage, TWaveletOperator, Wavelet::FORWARD >, otb::SubsampleImageFilter< TInputImage, TOutputImage, TDirectionOfTransformation >, and otb::DecimateImageFilter< TInputImage, TOutputImage >.

Definition at line 154 of file itkImageToImageFilter.txx.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protected

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

Definition at line 1018 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage, class TOutputImage, class TMaskImage>

template<class TSource , class TTarget >

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

inlineprotected

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

Definition at line 493 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Definition at line 765 of file itkMRIBiasFieldCorrectionFilter.txx.

References itk::ImageRegionIterator< TImage >::Begin(), itk::ImageConstIterator< TImage >::Get(), itk::ImageRegionConstIterator< TImage >::GoToBegin(), and itk::ImageConstIterator< TImage >::IsAtEnd().

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Definition at line 818 of file itkMRIBiasFieldCorrectionFilter.txx.

References itk::MultivariateLegendrePolynomial::GetCoefficients().

template<class TInputImage, class TOutputImage, class TMaskImage>

virtual::itk::LightObject::Pointer itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::CreateAnother ( void ) const

virtual

Create an object from an instance, potentially deferring to a factory. This method allows you to create an instance of an object that is exactly the same type as the referring object. This is useful in cases where an object has been cast back to a base class.

Reimplemented from itk::Object.

void itk::Object::DebugOff ( ) const

virtualinherited

Turn debugging output off.

Definition at line 253 of file itkObject.cxx.

void itk::Object::DebugOn ( ) const

virtualinherited

Turn debugging output on.

Definition at line 242 of file itkObject.cxx.

void itk::LightObject::Delete ( )

virtualinherited

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

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

Definition at line 88 of file itkLightObject.cxx.

virtual void itk::ProcessObject::EnlargeOutputRequestedRegion ( DataObject * )

inlinevirtualinherited

Give the process object a chance to indictate that it will produce more output than it was requested to produce. For example, many imaging filters must compute the entire output at once or can only produce output in complete slices. Such filters cannot handle smaller requested regions. These filters must provide an implementation of this method, setting the output requested region to the size they will produce. By default, a process object does not modify the size of the output requested region.

Definition at line 224 of file itkProcessObject.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, 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.

Definition at line 634 of file itkMRIBiasFieldCorrectionFilter.txx.

References itk::Array< TValueType >::Fill(), itk::MultivariateLegendrePolynomial::SetCoefficients(), and itk::ExceptionObject::what().

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protected

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

Definition at line 1065 of file itkMRIBiasFieldCorrectionFilter.txx.

References itk::ImageConstIterator< TImage >::Get(), itk::ImageBase< VImageDimension >::GetLargestPossibleRegion(), itk::ImageRegionConstIterator< TImage >::GoToBegin(), itk::ImageConstIterator< TImage >::IsAtEnd(), and itk::ImageRegionIterator< TImage >::Set().

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protectedvirtual

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

See also:: ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 852 of file itkMRIBiasFieldCorrectionFilter.txx.

References itk::MultivariateLegendrePolynomial::GetNumberOfCoefficients(), and itk::MRASlabIdentifier< TInputImage >::New().

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::GenerateInputRequestedRegion ( void )

protectedvirtualinherited

What is the input requested region that is required to produce the output requested region? The base assumption for image processing filters is that the input requested region can be set to match the output requested region. If a filter requires more input (for instance a filter that uses neighborhoods needs more input than output to avoid introducing artificial boundary conditions) or less input (for instance a magnify filter) will have to override this method. In doing so, it should call its superclass' implementation as its first step. Note that imaging filters operate differently than the classes to this point in the class hierachy. Up till now, the base assumption has been that the largest possible region will be requested of the input.

This implementation of GenerateInputRequestedRegion() only processes the inputs that are a subclass of the ImageBase<InputImageDimension>. If an input is another type of DataObject (including an Image of a different dimension), they are skipped by this method. The subclasses of ImageToImageFilter are responsible for providing an implementation of GenerateInputRequestedRegion() when there are multiple inputs of different types.

See also:: ProcessObject::GenerateInputRequestedRegion(), ImageSource::GenerateInputRequestedRegion()

Reimplemented from itk::ProcessObject.

Definition at line 110 of file itkImageToImageFilter.txx.

References itk::ProcessObject::GetInput().

void itk::ProcessObject::GenerateOutputInformation ( void )

protectedvirtualinherited

Generate the information decribing the output data. The default implementation of this method will copy information from the input to the output. A filter may override this method if its output will have different information than its input. For instance, a filter that shrinks an image will need to provide an implementation for this method that changes the spacing of the pixels. Such filters should call their superclass' implementation of this method prior to changing the information values they need (i.e. GenerateOutputInformation() should call Superclass::GenerateOutputInformation() prior to changing the information.

Default implementation - copy information from first input to all outputs

Examples:: Fusion/BayesianFusionImageFilter.cxx.

Definition at line 1095 of file itkProcessObject.cxx.

Referenced by main().

void itk::ProcessObject::GenerateOutputRequestedRegion ( DataObject * output )

protectedvirtualinherited

Given one output whose requested region has been set, how should the requested regions for the remaining outputs of the process object be set? By default, all the outputs are set to the same requested region. If a filter needs to produce different requested regions for each output, for instance an image processing filter producing several outputs at different resolutions, then that filter may override this method and set the requested regions appropriatedly.

Note that a filter producing multiple outputs of different types is required to override this method. The default implementation can only correctly handle multiple outputs of the same type.

By default we set all the output requested regions to be the same.

Reimplemented in itk::watershed::Segmenter< TInputImage >, itk::watershed::Segmenter< InputImageType >, itk::watershed::SegmentTreeGenerator< TScalarType >, itk::watershed::SegmentTreeGenerator< ScalarType >, itk::MultiResolutionPyramidImageFilter< TInputImage, TOutputImage >, itk::watershed::Relabeler< TScalarType, TImageDimension >, itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>, itk::watershed::BoundaryResolver< TPixelType, TDimension >, itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >, and itk::RecursiveMultiResolutionPyramidImageFilter< TInputImage, TOutputImage >.

Definition at line 846 of file itkProcessObject.cxx.

virtual const bool& itk::ProcessObject::GetAbortGenerateData ( )

virtualinherited

Get the AbortGenerateData flag for the process object. Process objects may handle premature termination of execution in different ways.

Referenced by itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::IterateThreaderCallback().

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protected

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

Definition at line 1093 of file itkMRIBiasFieldCorrectionFilter.txx.

Command * itk::Object::GetCommand ( unsigned long tag )

inherited

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

Definition at line 414 of file itkObject.cxx.

References itk::Object::GetCommand(), and NULL.

Referenced by itk::Object::GetCommand().

bool itk::Object::GetDebug ( ) const

inherited

Get the value of the debug flag.

Definition at line 264 of file itkObject.cxx.

Referenced by otb::ogr::ImageReference< double >::GetDebug().

template<class TInputImage, class TOutputImage, class TMaskImage>

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

inline

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

Definition at line 375 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

bool itk::Object::GetGlobalWarningDisplay ( )

staticinherited

Get the value of the global debug output control flag.

Definition at line 381 of file itkObject.cxx.

template<class TInputImage , class TOutputImage >

const ImageToImageFilter< TInputImage, TOutputImage >::InputImageType * itk::ImageToImageFilter< TInputImage, TOutputImage >::GetInput ( void )

inherited

Reimplemented in otb::ImageAndVectorImageOperationFilter< TInputImage, TVectorInputImage, TOutputImage >, otb::RasterizeVectorDataFilter< TVectorData, TInputImage, TOutputImage >, otb::ImageToLabelMapWithAttributesFilter< TInputImage, TLabeledImage, TLabel, TLabelObject >, otb::ModulusAndDirectionImageToImageFilter< TInputImage, TInputImageDirection, TOutputImage >, and otb::ModulusAndDirectionImageToImageFilter< TInputModulus, TInputDirection, TOutputImage >.

Definition at line 82 of file itkImageToImageFilter.txx.

References itk::ProcessObject::GetInput().

Referenced by otb::RenderingImageFilter< TInputImage, TOutputImage >::BeforeThreadedGenerateData(), and otb::ROIdataConversion< TInputImage, TInputROIImage >::GetInputImage().

template<class TInputImage , class TOutputImage >

const ImageToImageFilter< TInputImage, TOutputImage >::InputImageType * itk::ImageToImageFilter< TInputImage, TOutputImage >::GetInput ( unsigned int idx )

inherited

Method used internally for getting an input.

Reimplemented from itk::ProcessObject.

Reimplemented in otb::RasterizeVectorDataFilter< TVectorData, TInputImage, TOutputImage >.

Definition at line 99 of file itkImageToImageFilter.txx.

References itk::ProcessObject::GetInput().

const DataObject * itk::ProcessObject::GetInput ( unsigned int idx ) const

protectedinherited

Reimplemented in otb::AngularProjectionSetImageFilter< TInputImage, TOutputImage, TAngleList, TPrecision >, otb::SparseUnmixingImageFilter< TInputImage, TOutputImage, VNbInputImage, TPrecision, TMotherWaveletOperator >, otb::AngularProjectionImageFilter< TInputImage, TOutputImage, TAngleArray, TPrecision >, otb::LabeledSampleLocalizationGenerator< TVectorData >, otb::ConcatenateVectorDataFilter< TVectorData >, itk::MeshToMeshFilter< TInputMesh, TOutputMesh >, and itk::MeshToMeshFilter< TInput, TOutput >.

Definition at line 482 of file itkProcessObject.cxx.

References NULL.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

DataObjectPointerArray& itk::ProcessObject::GetInputs ( )

inlineinherited

Return an array with all the inputs of this process object. This is useful for tracing back in the pipeline to construct graphs etc.

Definition at line 108 of file itkProcessObject.h.

Referenced by otb::PipelineMemoryPrintCalculator::EvaluateProcessObjectPrintRecursive().

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

MetaDataDictionary & itk::Object::GetMetaDataDictionary ( void )

inherited

Returns:: A reference to this objects MetaDataDictionary.

Warning:: This reference may be changed.

Reimplemented in otb::ImageMetadataInterfaceBase.

Definition at line 532 of file itkObject.cxx.

References NULL.

const MetaDataDictionary & itk::Object::GetMetaDataDictionary ( void ) const

inherited

Returns:: A constant reference to this objects MetaDataDictionary.

Reimplemented in otb::ImageMetadataInterfaceBase.

Definition at line 543 of file itkObject.cxx.

References NULL.

unsigned long itk::Object::GetMTime ( void ) const

virtualinherited

Return this objects modified time.

Return the modification for this object.

Definition at line 286 of file itkObject.cxx.

Referenced by itk::DeformationFieldSource< TOutputImage >::GetMTime(), itk::BoundingBox< TPointIdentifier, VPointDimension, TCoordRep, TPointsContainer >::GetMTime(), itk::InverseDeformationFieldImageFilter< TInputImage, TOutputImage >::GetMTime(), itk::TransformToDeformationFieldSource< TOutputImage, TTransformPrecisionType >::GetMTime(), itk::VectorResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >::GetMTime(), itk::SpatialObject< TDimension >::GetMTime(), itk::ResampleImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType >::GetMTime(), itk::SpatialObject< ::itk::GetMeshDimension< TMesh >::PointDimension >::GetObjectMTime(), otb::Function::NoStretchRenderingFunction< TPixel, TRGBPixel, TPixelRepresentationFunction, TTransferFunction >::Initialize(), otb::Function::StandardRenderingFunction< TPixel, TRGBPixel, TPixelRepresentationFunction, TTransferFunction >::Initialize(), itk::VTKImageExportBase::PipelineModifiedCallback(), and itk::ProcessObject::UpdateOutputInformation().

MultiThreader* itk::ProcessObject::GetMultiThreader ( )

inlineinherited

Return the multithreader used by this class.

Definition at line 280 of file itkProcessObject.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Run-time type information (and related methods)

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

DataObjectPointerArraySizeType itk::ProcessObject::GetNumberOfInputs ( ) const

inlineinherited

Get the size of the input vector. This is merely the size of the input vector, not the number of inputs that have valid DataObject's assigned. Use GetNumberOfValidRequiredInputs() to determine how many inputs are non-null.

Definition at line 118 of file itkProcessObject.h.

Referenced by otb::PipelineMemoryPrintCalculator::EvaluateProcessObjectPrintRecursive().

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Get the number of multi-resolution levels.

DataObjectPointerArraySizeType itk::ProcessObject::GetNumberOfOutputs ( ) const

inlineinherited

Reimplemented in otb::ImageSeriesFileReaderBase< TImage, TInternalImage >, otb::ImageSeriesFileReaderBase< VectorImage< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >, otb::ImageSeriesFileReaderBase< Image< TPixel, 2 >, Image< TInternalPixel, 2 > >, and otb::ImageSeriesFileReaderBase< Image< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >.

Definition at line 135 of file itkProcessObject.h.

Referenced by otb::PipelineMemoryPrintCalculator::EvaluateProcessObjectPrintRecursive().

virtual const unsigned int& itk::ProcessObject::GetNumberOfRequiredInputs ( )

protectedvirtualinherited

virtual const unsigned int& itk::ProcessObject::GetNumberOfRequiredOutputs ( )

protectedvirtualinherited

virtual const int& itk::ProcessObject::GetNumberOfThreads ( )

virtualinherited

Referenced by itk::BSplineScatteredDataPointSetToImageFilter< TInputPointSet, TOutputImage >::SplitRequestedRegion().

ProcessObject::DataObjectPointerArraySizeType itk::ProcessObject::GetNumberOfValidRequiredInputs ( ) const

virtualinherited

Get the number of valid inputs. This is the number of non-null entries in the input vector in the first NumberOfRequiredInputs slots. This method is used to determine whether the necessary required inputs have been set. Subclasses of ProcessObject may override this implementation if the required inputs are not the first slots in input vector.

Get the number of specified inputs

Reimplemented in itk::MultiResolutionPDEDeformableRegistration< TFixedImage, TMovingImage, TDeformationField, TRealType >, and itk::PDEDeformableRegistrationFilter< TFixedImage, TMovingImage, TDeformationField >.

Definition at line 112 of file itkProcessObject.cxx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

inline

Definition at line 394 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TOutputImage >

ImageSource< TOutputImage >::OutputImageType * itk::ImageSource< TOutputImage >::GetOutput ( void )

inherited

Get the output data of this process object. The output of this function is not valid until an appropriate Update() method has been called, either explicitly or implicitly. Both the filter itself and the data object have Update() methods, and both methods update the data. Here are three ways to use GetOutput() and make sure the data is valid. In these examples, image is a pointer to some Image object, and the particular ProcessObjects involved are filters. The same examples apply to non-image (e.g. Mesh) data as well.

anotherFilter->SetInput( someFilter->GetOutput() );

anotherFilter->Update();

In this situation, someFilter and anotherFilter are said to constitute a pipeline.

image = someFilter->GetOutput();

image->Update();

someFilter->Update();

image = someFilter->GetOutput();

(In the above example, the two lines of code can be in either order.)

Note that Update() is not called automatically except within a pipeline as in the first example. When streaming (using a StreamingImageFilter) is activated, it may be more efficient to use a pipeline than to call Update() once for each filter in turn.

For an image, the data generated is for the requested Region, which can be set using ImageBase::SetRequestedRegion(). By default, the largest possible region is requested.

For Filters which have multiple outputs of different types, the GetOutput() method assumes the output is of OutputImageType. For the GetOutput(unsigned int) method, a dynamic_cast is performed incase the filter has outputs of different types or image types. Derived classes should have names get methods for these outputs.

Reimplemented in otb::ImageToLabelMapWithAttributesFilter< TInputImage, TLabeledImage, TLabel, TLabelObject >, otb::ImageToModulusAndDirectionImageFilter< TInputImage, TOutputImage, TOutputImageDirection >, otb::ImageToModulusAndDirectionImageFilter< TInputImage, TOutputModulus, TOutputDirection >, otb::ImageToModulusAndDirectionImageFilter< TInputImage, TOutputImage, TOutputImageDirection >, otb::ImageToModulusAndDirectionImageFilter< TInputImage, TOutputModulus, TOutputDirection >, and otb::ImageListToSingleImageFilter< TInputImageType >.

Definition at line 66 of file itkImageSource.txx.

References itk::ProcessObject::GetOutput().

Referenced by itk::LaplacianSegmentationLevelSetFunction< TImageType, TFeatureImageType >::CalculateSpeedImage(), itk::ImageSeriesReader< TOutputImage >::ComputeMovingDimensionIndex(), otb::ImageSeriesFileReader< Image< TPixel, 2 >, Image< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< Image< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< VectorImage< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), and main().

template<class TOutputImage >

ImageSource< TOutputImage >::OutputImageType * itk::ImageSource< TOutputImage >::GetOutput ( unsigned int idx )

inherited

Method used internally for getting an output.

Reimplemented from itk::ProcessObject.

Definition at line 85 of file itkImageSource.txx.

References itk::ProcessObject::GetOutput(), and NULL.

const DataObject * itk::ProcessObject::GetOutput ( unsigned int idx ) const

protectedinherited

Definition at line 454 of file itkProcessObject.cxx.

References NULL.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Gets the output mask image pointer.

DataObjectPointerArray& itk::ProcessObject::GetOutputs ( )

inlineinherited

Return an array with all the outputs of this process object. This is useful for tracing forward in the pipeline to contruct graphs etc.

Definition at line 133 of file itkProcessObject.h.

Referenced by otb::PipelineMemoryPrintCalculator::EvaluateProcessObjectPrintRecursive().

virtual const float& itk::ProcessObject::GetProgress ( )

virtualinherited

Get the execution progress of a process object. The progress is a floating number in [0,1] with 0 meaning no progress and 1 meaning the filter has completed execution.

Referenced by itk::WatershedMiniPipelineProgressCommand::Execute(), otb::StreamingImageVirtualWriter< TInputImage >::ObserveSourceFilterProgress(), otb::ImageFileWriter< TInputImage >::ObserveSourceFilterProgress(), itk::LaplacianRecursiveGaussianImageFilter< TInputImage, TOutputImage >::ReportProgress(), and itk::XMLFilterWatcher::ShowProgress().

virtual int itk::LightObject::GetReferenceCount ( ) const

inlinevirtualinherited

Gets the reference count on this object.

Definition at line 105 of file itkLightObject.h.

virtual const bool& itk::ProcessObject::GetReleaseDataBeforeUpdateFlag ( )

virtualinherited

bool itk::ProcessObject::GetReleaseDataFlag ( ) const

virtualinherited

Definition at line 512 of file itkProcessObject.cxx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Get the multi-resolution schedule.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Get the starting shrink factors

Definition at line 351 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

static void itk::Object::GlobalWarningDisplayOff ( )

inlinestaticinherited

Definition at line 100 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

Referenced by itk::OutputWindow::DisplayText(), itk::Win32OutputWindow::PromptText(), and itk::Win32OutputWindow::WndProc().

static void itk::Object::GlobalWarningDisplayOn ( )

inlinestaticinherited

Definition at line 98 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

template<class TOutputImage >

void itk::ImageSource< TOutputImage >::GraftNthOutput	(	unsigned int	idx,
		DataObject *	output
	)

virtualinherited

Graft the specified data object onto this ProcessObject's idx'th output. This is similar to the GraftOutput method except it allows you to specify which output is affected. The specified index must be a valid output number (less than ProcessObject::GetNumberOfOutputs()). See the GraftOutput for general usage information.

Definition at line 113 of file itkImageSource.txx.

References itk::ProcessObject::GetOutput(), and itk::DataObject::Graft().

template<class TOutputImage >

void itk::ImageSource< TOutputImage >::GraftOutput ( DataObject * output )

virtualinherited

Graft the specified DataObject onto this ProcessObject's output. This method grabs a handle to the specified DataObject's bulk data to used as its output's own bulk data. It also copies the region ivars (RequestedRegion, BufferedRegion, LargestPossibleRegion) and meta-data (Spacing, Origin) from the specified data object into this filter's output data object. Most importantly, however, it leaves the Source ivar untouched so the original pipeline routing is intact. This method is used when a process object is implemented using a mini-pipeline which is defined in its GenerateData() method. The usage is:

        // setup the mini-pipeline to process the input to this filter
        firstFilterInMiniPipeline->SetInput( this->GetInput() );
   
        // setup the mini-pipeline to calculate the correct regions
        // and write to the appropriate bulk data block
        lastFilterInMiniPipeline->GraftOutput( this->GetOutput() );
    
        // execute the mini-pipeline
        lastFilterInMiniPipeline->Update();
    
        // graft the mini-pipeline output back onto this filter's output.
        // this is needed to get the appropriate regions passed back.
        this->GraftOutput( lastFilterInMiniPipeline->GetOutput() );

For proper pipeline execution, a filter using a mini-pipeline must implement the GenerateInputRequestedRegion(), GenerateOutputRequestedRegion(), GenerateOutputInformation() and EnlargeOutputRequestedRegion() methods as necessary to reflect how the mini-pipeline will execute (in other words, the outer filter's pipeline mechanism must be consistent with what the mini-pipeline will do).

Definition at line 101 of file itkImageSource.txx.

Referenced by otb::ImageSeriesFileReader< Image< TPixel, 2 >, Image< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< Image< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< VectorImage< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), and itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::IterateThreaderCallback().

bool itk::Object::HasObserver ( const EventObject & event ) const

inherited

Return true if an observer is registered for this event.

Definition at line 467 of file itkObject.cxx.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Definition at line 578 of file itkMRIBiasFieldCorrectionFilter.txx.

void itk::Object::InvokeEvent ( const EventObject & event )

inherited

Call Execute on all the Commands observing this event id.

Definition at line 446 of file itkObject.cxx.

Referenced by otb::Wrapper::Application::AddProcess(), itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::IterateThreaderCallback(), and itk::VTKImageExportBase::UpdateDataCallback().

void itk::Object::InvokeEvent ( const EventObject & event ) const

inherited

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

Definition at line 457 of file itkObject.cxx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

inline

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

Definition at line 313 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

inline

If the bias field is multiplicative, it returns true.

Definition at line 317 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

static

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

Definition at line 410 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protected

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

Definition at line 1036 of file itkMRIBiasFieldCorrectionFilter.txx.

References itk::ImageConstIterator< TImage >::Get(), itk::ImageBase< VImageDimension >::GetRequestedRegion(), itk::ImageRegionConstIterator< TImage >::GoToBegin(), itk::ImageConstIterator< TImage >::IsAtEnd(), and itk::ImageRegionIterator< TImage >::Set().

template<class TOutputImage >

ImageSource< TOutputImage >::DataObjectPointer itk::ImageSource< TOutputImage >::MakeOutput ( unsigned int idx )

virtualinherited

Make a DataObject of the correct type to used as the specified output. Every ProcessObject subclass must be able to create a DataObject that can be used as a specified output. This method is automatically called when DataObject::DisconnectPipeline() is called. DataObject::DisconnectPipeline, disconnects a data object from being an output of its current source. When the data object is disconnected, the ProcessObject needs to construct a replacement output data object so that the ProcessObject is in a valid state. So DataObject::DisconnectPipeline eventually calls ProcessObject::MakeOutput. Note that MakeOutput always returns a SmartPointer to a DataObject. If a subclass of ImageSource has multiple outputs of different types, then that class must provide an implementation of MakeOutput().

Reimplemented from itk::ProcessObject.

Definition at line 55 of file itkImageSource.txx.

void itk::Object::Modified ( void ) const

virtualinherited

Update the modification time for this object. Many filters rely on the modification time to determine if they need to recompute their data.

Make sure this object's modified time is greater than all others.

Definition at line 297 of file itkObject.cxx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

static

Method for creation through the object factory.

Reimplemented from itk::Object.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::PopBackInput ( )

virtualinherited

Model a stack on the input list by providing a pop back

Reimplemented from itk::ProcessObject.

Definition at line 193 of file itkImageToImageFilter.txx.

References itk::ProcessObject::PopBackInput().

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::PopFrontInput ( )

virtualinherited

Reimplemented from itk::ProcessObject.

Definition at line 211 of file itkImageToImageFilter.txx.

References itk::ProcessObject::PopFrontInput().

void itk::ProcessObject::PrepareOutputs ( )

virtualinherited

An opportunity to deallocate a ProcessObject's bulk data storage. Some filters may wish to reuse existing bulk data storage to avoid unnecessary deallocation/allocation sequences. The default implementation calls Initialize() on each output. DataObject::Initialize() frees its bulk data by default.

Reimplemented in itk::WatershedImageFilter< TInputImage >, and otb::GeometriesSource.

Definition at line 864 of file itkProcessObject.cxx.

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

inherited

Cause the object to print itself out.

Avoid DLL boundary problems. This function will be common to all itk objects. It just calls the header/self/trailer virtual print methods, which can be overriden by subclasses (any itk object).

Definition at line 135 of file itkLightObject.cxx.

References itk::Indent::GetNextIndent().

Referenced by itk::operator<<().

void itk::LightObject::PrintHeader	(	std::ostream &	os,
		Indent	indent
	)		const

protectedvirtualinherited

Define a default print header for all objects.

Definition at line 320 of file itkLightObject.cxx.

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

protectedinherited

Definition at line 478 of file itkObject.cxx.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

protectedvirtual

Methods invoked by Print() to print information about the object including superclasses. Typically not called by the user (use Print() instead) but used in the hierarchical print process to combine the output of several classes.

Chaining method to print an object's instance variables, as well as its superclasses.

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

Definition at line 442 of file itkMRIBiasFieldCorrectionFilter.txx.

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

protectedvirtualinherited

Define a default print trailer for all objects.

Definition at line 331 of file itkLightObject.cxx.

void itk::ProcessObject::PropagateRequestedRegion ( DataObject * output )

virtualinherited

Send the requested region information back up the pipeline (to the filters that preceed this one).

 check flag to avoid executing forever if there is a loop

 Give the subclass a chance to indicate that it will provide
 more data then required for the output. This can happen, for
 example, when a source can only produce the whole output.
 Although this is being called for a specific output, the source
 may need to enlarge all outputs.

 Give the subclass a chance to define how to set the requested
 regions for each of its outputs, given this output's requested
 region.  The default implementation is to make all the output
 requested regions the same.  A subclass may need to override this
 method if each output is a different resolution.

 Give the subclass a chance to request a larger requested region on 
 the inputs. This is necessary when, for example, a filter
 requires more data at the "internal" boundaries to 
 produce the boundary values - such as an image filter that
 derives a new pixel value by applying some operation to a 
 neighborhood of surrounding original values.

 Now that we know the input requested region, propagate this
 through all the inputs.

Reimplemented in itk::VTKImageImport< TOutputImage >, and itk::StreamingImageFilter< TInputImage, TOutputImage >.

Definition at line 766 of file itkProcessObject.cxx.

void itk::ProcessObject::PropagateResetPipeline ( )

protectedvirtualinherited

Called to allocate the input array. Copies old inputs. Propagate a call to ResetPipeline() up the pipeline. Called only from DataObject.

Propagate the ResetPipeline call

Definition at line 631 of file itkProcessObject.cxx.

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::PushBackInput ( const InputImageType * image )

virtualinherited

Push/Pop the input of this process object. These methods allow a filter to model its input vector as a queue or stack. These routines may not be appropriate for all filters, especially filters with different types of inputs. These routines follow the semantics of STL.

The routines are useful for applications that need to process "rolling" sets of images. For instance, if an application has 10 images and they need to run a filter on images 1, 2, 3, 4, then run the filter on images 2, 3, 4, 5, then run the filter on images 3, 4, 5, 6, the application can accomplish this by popping an input off the front of the input list and push a new image onto the back of input list. Again, this only makes sense for filters that single type of input.

Other uses are also possible. For a single input filter, pushing and popping inputs allow the application to temporarily replace an input to a filter.

Definition at line 184 of file itkImageToImageFilter.txx.

References itk::ProcessObject::PushBackInput().

template<class TInputImage, class TOutputImage>

void itk::ImageToImageFilter< TInputImage, TOutputImage >::PushBackInput ( const DataObject * input )

inlineprotectedvirtualinherited

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

Reimplemented from itk::ProcessObject.

Definition at line 248 of file itkImageToImageFilter.h.

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::PushFrontInput ( const InputImageType * image )

virtualinherited

Definition at line 202 of file itkImageToImageFilter.txx.

References itk::ProcessObject::PushFrontInput().

template<class TInputImage, class TOutputImage>

void itk::ImageToImageFilter< TInputImage, TOutputImage >::PushFrontInput ( const DataObject * input )

inlineprotectedvirtualinherited

Reimplemented from itk::ProcessObject.

Definition at line 250 of file itkImageToImageFilter.h.

void itk::Object::Register ( ) const

virtualinherited

Increase the reference count (mark as used by another object).

Reimplemented from itk::LightObject.

Definition at line 309 of file itkObject.cxx.

Referenced by itk::ObjectFactoryBase::RegisterFactory().

virtual void itk::ProcessObject::ReleaseDataBeforeUpdateFlagOff ( )

virtualinherited

virtual void itk::ProcessObject::ReleaseDataBeforeUpdateFlagOn ( )

virtualinherited

void itk::ProcessObject::ReleaseDataFlagOff ( )

inlineinherited

Definition at line 256 of file itkProcessObject.h.

void itk::ProcessObject::ReleaseDataFlagOn ( )

inlineinherited

Definition at line 255 of file itkProcessObject.h.

void itk::ProcessObject::ReleaseInputs ( )

protectedvirtualinherited

A filter may need to release its input's bulk data after it has finished calculating a new output. The filter may need to release the inputs because the user has turned on the ReleaseDataFlag or it may need to release the inputs because the filter is an "in place" filter and it has overwritten its input with its output data. The implementation here simply checks the ReleaseDataFlag of the inputs. InPlaceImageFilter overrides this method so release the input it has overwritten.

See also:: InPlaceImageFilter::ReleaseInputs()

Definition at line 886 of file itkProcessObject.cxx.

Referenced by itk::InPlaceImageFilter< TInputImage, TOutputImage >::ReleaseInputs(), and itk::InPlaceLabelMapFilter< TInputImage >::ReleaseInputs().

void itk::Object::RemoveAllObservers ( )

inherited

Remove all observers .

Definition at line 435 of file itkObject.cxx.

void itk::ProcessObject::RemoveInput ( DataObject * input )

protectedvirtualinherited

Remove an input.

Removes the first occurence of the given OutputObject from the inputs to this ProcessObject. If it's the last object on the list, shortens the list.

Definition at line 173 of file itkProcessObject.cxx.

void itk::Object::RemoveObserver ( unsigned long tag )

inherited

Remove the observer with this tag value.

Definition at line 425 of file itkObject.cxx.

Referenced by otb::StreamingImageVirtualWriter< TInputImage >::GenerateData(), and otb::ImageFileWriter< TInputImage >::Update().

void itk::ProcessObject::RemoveOutput ( DataObject * output )

protectedvirtualinherited

Definition at line 294 of file itkProcessObject.cxx.

void itk::ProcessObject::ResetPipeline ( )

virtualinherited

Reset the pipeline. If an exception is thrown during an Update(), the pipeline may be in an inconsistent state. This method clears the internal state of the pipeline so Update() can be called.

Definition at line 621 of file itkProcessObject.cxx.

Referenced by itk::ParallelSparseFieldLevelSetImageFilter< TInputImage, TOutputImage >::IterateThreaderCallback().

void itk::ProcessObject::RestoreInputReleaseDataFlags ( )

protectedvirtualinherited

Restore the cached input ReleaseDataFlags.

Definition at line 1075 of file itkProcessObject.cxx.

virtual void itk::ProcessObject::SetAbortGenerateData ( bool _arg )

virtualinherited

Set the AbortGenerateData flag for the process object. Process objects may handle premature termination of execution in different ways.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Set/Get the degree of the bias field estimate.

void itk::Object::SetDebug ( bool debugFlag ) const

inherited

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

Definition at line 275 of file itkObject.cxx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

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

void itk::Object::SetGlobalWarningDisplay ( bool val )

staticinherited

This is a global flag that controls whether any debug, warning or error messages are displayed.

Set the value of the global debug output control flag.

Definition at line 370 of file itkObject.cxx.

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

template<class TInputImage, class TOutputImage, class TMaskImage>

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

inline

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

Definition at line 367 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::SetInput ( const InputImageType * image )

virtualinherited

Set/Get the image input of this process object.

Reimplemented in otb::ConvexOrConcaveClassificationFilter< TInputImage, TOutputImage >, itk::WatershedImageFilter< TInputImage >, otb::ImageAndVectorImageOperationFilter< TInputImage, TVectorInputImage, TOutputImage >, itk::VoronoiSegmentationRGBImageFilter< TInputImage, TOutputImage >, otb::GeodesicMorphologyLevelingFilter< TInputImage, TInputMaps, TOutputImage >, and otb::ModulusAndDirectionImageToImageFilter< TInputImage, TInputImageDirection, TOutputImage >.

Definition at line 55 of file itkImageToImageFilter.txx.

References itk::ProcessObject::SetNthInput().

Referenced by itk::LaplacianSegmentationLevelSetFunction< TImageType, TFeatureImageType >::CalculateSpeedImage(), otb::ImageSeriesFileReader< Image< TPixel, 2 >, Image< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< Image< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< VectorImage< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), and otb::ROIdataConversion< TInputImage, TInputROIImage >::SetInputImage().

template<class TInputImage, class TOutputImage >

void itk::ImageToImageFilter< TInputImage, TOutputImage >::SetInput	(	unsigned int	index,
		const TInputImage *	image
	)

virtualinherited

Connect one of the operands for pixel-wise addition

Reimplemented in itk::WatershedImageFilter< TInputImage >, itk::VoronoiSegmentationRGBImageFilter< TInputImage, TOutputImage >, and otb::AngularProjectionImageFilter< TInputImage, TOutputImage, TAngleArray, TPrecision >.

Definition at line 69 of file itkImageToImageFilter.txx.

References itk::ProcessObject::SetNthInput().

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Definition at line 540 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

void itk::Object::SetMetaDataDictionary ( const MetaDataDictionary & rhs )

inherited

Returns:: Set the MetaDataDictionary

Reimplemented in otb::ImageMetadataInterfaceBase.

Definition at line 554 of file itkObject.cxx.

References NULL.

Referenced by otb::VectorImage< TPixel, VImageDimension >::CopyInformation(), and otb::Image< TPixel, VImageDimension >::CopyInformation().

void itk::ProcessObject::SetNthInput	(	unsigned int	idx,
		DataObject *	input
	)

protectedvirtualinherited

Protected methods for setting inputs. Subclasses make use of them for setting input.

Set an Input of this filter. This method does Register()/UnRegister() manually to deal with the fact that smart pointers aren't around to do the reference counting.

Reimplemented in itk::ImageToVectorImageFilter< TInputImage >.

Definition at line 210 of file itkProcessObject.cxx.

void itk::ProcessObject::SetNthOutput	(	unsigned int	idx,
		DataObject *	output
	)

protectedvirtualinherited

Protected methods for setting outputs. Subclasses make use of them for getting output.

Set an output of this filter. This method specifically does not do a Register()/UnRegister() because of the desire to break the reference counting loop.

Definition at line 333 of file itkProcessObject.cxx.

References itk::DataObject::ConnectSource().

Referenced by itk::AutomaticTopologyMeshSource< TOutputMesh >::AutomaticTopologyMeshSource(), itk::BalloonForceFilter< TInputMesh, TOutputMesh >::BalloonForceFilter(), itk::watershed::BoundaryResolver< TPixelType, TDimension >::BoundaryResolver(), itk::CoreAtomImageToDistanceMatrixProcess< TSourceImage >::CoreAtomImageToDistanceMatrixProcess(), itk::CoreAtomImageToUnaryCorrespondenceMatrixProcess< TSourceImage >::CoreAtomImageToUnaryCorrespondenceMatrixProcess(), itk::SimplexMeshToTriangleMeshFilter< TInputMesh, TOutputMesh >::CreateTriangles(), itk::DeformableMesh3DFilter< TInputMesh, TOutputMesh >::DeformableMesh3DFilter(), itk::DeformableSimplexMesh3DFilter< TInputMesh, TOutputMesh >::DeformableSimplexMesh3DFilter(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::EquivalenceRelabeler(), itk::ExtensionVelocitiesImageFilter< TLevelSet, TAuxValue, VAuxDimension >::ExtensionVelocitiesImageFilter(), itk::FastMarchingExtensionImageFilter< TLevelSet, TAuxValue, VAuxDimension, TSpeedImage >::FastMarchingExtensionImageFilter(), otb::FillGapsFilter::FillGapsFilter(), itk::ImageRegistrationMethod< TFixedImage, TMovingImage >::ImageRegistrationMethod(), itk::ImageSource< TOutputImage >::ImageSource(), itk::Statistics::ImageToListGenerator< TImage, TMaskImage >::ImageToListGenerator(), itk::ImageToMeshFilter< TInputImage, TOutputMesh >::ImageToMeshFilter(), itk::ImageToSpatialObjectRegistrationMethod< TFixedImage, TMovingSpatialObject >::ImageToSpatialObjectRegistrationMethod(), itk::SimplexMeshAdaptTopologyFilter< TInputMesh, TOutputMesh >::InsertNewCells(), otb::Statistics::ListSampleToBalancedListSampleFilter< TInputSampleList, TLabelSampleList, TOutputSampleList >::ListSampleToBalancedListSampleFilter(), otb::MeanShiftSmoothingImageFilter< TInputImage, TOutputImage, TKernel, TOutputIterationImage >::MeanShiftSmoothingImageFilter(), itk::MedialNodePairCorrespondenceProcess< TSourceImage >::MedialNodePairCorrespondenceProcess(), itk::MedialNodeTripletCorrespondenceProcess< TSourceImage >::MedialNodeTripletCorrespondenceProcess(), itk::MeshSource< TOutputMesh >::MeshSource(), itk::MinimumMaximumImageFilter< TInputImage >::MinimumMaximumImageFilter(), otb::MinMaxAttributesLabelMapFilter< TInputImage >::MinMaxAttributesLabelMapFilter(), itk::MultiResolutionImageRegistrationMethod< TFixedImage, TMovingImage >::MultiResolutionImageRegistrationMethod(), itk::MultiScaleHessianBasedMeasureImageFilter< TInputImage, THessianImage, TOutputImage >::MultiScaleHessianBasedMeasureImageFilter(), itk::PathSource< TOutputPath >::PathSource(), otb::PersistentCompareImageFilter< TInputImage >::PersistentCompareImageFilter(), otb::PersistentDescriptorsListSampleGenerator< TInputImage, TVectorData, TFunctionType, TListSample, TLabelListSample >::PersistentDescriptorsListSampleGenerator(), otb::PersistentHistogramVectorImageFilter< TInputImage >::PersistentHistogramVectorImageFilter(), otb::PersistentInnerProductVectorImageFilter< TInputImage >::PersistentInnerProductVectorImageFilter(), otb::PersistentMatrixTransposeMatrixImageFilter< TInputImage, TInputImage2 >::PersistentMatrixTransposeMatrixImageFilter(), otb::PersistentMinMaxImageFilter< TInputImage >::PersistentMinMaxImageFilter(), otb::PersistentMinMaxVectorImageFilter< TInputImage >::PersistentMinMaxVectorImageFilter(), otb::PersistentObjectDetectionClassifier< TInputImage, TOutputVectorData, TLabel, TFunctionType >::PersistentObjectDetectionClassifier(), otb::PersistentStatisticsImageFilter< TInputImage >::PersistentStatisticsImageFilter(), otb::PersistentStreamingStatisticsMapFromLabelImageFilter< TInputVectorImage, TLabelImage >::PersistentStreamingStatisticsMapFromLabelImageFilter(), otb::PersistentStreamingStatisticsVectorImageFilter< TInputImage, TPrecision >::PersistentStreamingStatisticsVectorImageFilter(), otb::PersistentVectorImageToMatrixFilter< TInputImage >::PersistentVectorImageToMatrixFilter(), itk::PointSetToImageRegistrationMethod< TFixedPointSet, TMovingImage >::PointSetToImageRegistrationMethod(), itk::PointSetToPointSetRegistrationMethod< TFixedPointSet, TMovingPointSet >::PointSetToPointSetRegistrationMethod(), otb::ProspectModel::ProspectModel(), itk::RegularSphereMeshSource< TOutputMesh >::RegularSphereMeshSource(), itk::watershed::Relabeler< TScalarType, TImageDimension >::Relabeler(), otb::SailModel::SailModel(), itk::watershed::Segmenter< TInputImage >::Segmenter(), itk::watershed::SegmentTreeGenerator< TScalarType >::SegmentTreeGenerator(), itk::watershed::Segmenter< InputImageType >::SetBoundary(), itk::watershed::BoundaryResolver< TPixelType, TDimension >::SetEquivalencyTable(), itk::MeshSource< TOutputMesh >::SetOutput(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::SetOutputImage(), itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>::SetOutputImage(), itk::watershed::Segmenter< InputImageType >::SetOutputImage(), itk::watershed::Segmenter< InputImageType >::SetSegmentTable(), itk::SimplexMeshAdaptTopologyFilter< TInputMesh, TOutputMesh >::SimplexMeshAdaptTopologyFilter(), itk::SphereMeshSource< TOutputMesh >::SphereMeshSource(), itk::StatisticsImageFilter< TInputImage >::StatisticsImageFilter(), itk::TriangleMeshToSimplexMeshFilter< TInputMesh, TOutputMesh >::TriangleMeshToSimplexMeshFilter(), itk::TwoOutputExampleImageFilter< TImage >::TwoOutputExampleImageFilter(), itk::VTKPolyDataReader< TOutputMesh >::VTKPolyDataReader(), otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD, TCost >::WaveletPacketTransform(), otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE, FullyDecomposedWaveletPacketCost< TInputImage > >::WaveletPacketTransform(), otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD >::WaveletTransform(), and otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE >::WaveletTransform().

void itk::ProcessObject::SetNumberOfInputs ( unsigned int num )

protectedinherited

Called to allocate the input array. Copies old inputs.

Called by constructor to set up input array.

Definition at line 96 of file itkProcessObject.cxx.

Referenced by otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD, TCost >::WaveletPacketTransform(), otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE, FullyDecomposedWaveletPacketCost< TInputImage > >::WaveletPacketTransform(), otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD >::WaveletTransform(), and otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE >::WaveletTransform().

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Definition at line 260 of file itkMRIBiasFieldCorrectionFilter.txx.

References itk::Array2D< TValueType >::Fill().

void itk::ProcessObject::SetNumberOfOutputs ( unsigned int num )

protectedinherited

Called to allocate the output array. Copies old outputs.

Called by constructor to set up output array.

Definition at line 424 of file itkProcessObject.cxx.

Referenced by otb::MeanShiftSmoothingImageFilter< TInputImage, TOutputImage, TKernel, TOutputIterationImage >::MeanShiftSmoothingImageFilter(), otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD, TCost >::WaveletPacketTransform(), otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE, FullyDecomposedWaveletPacketCost< TInputImage > >::WaveletPacketTransform(), otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD >::WaveletTransform(), and otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE >::WaveletTransform().

virtual void itk::ProcessObject::SetNumberOfRequiredInputs ( unsigned int _arg )

protectedvirtualinherited

Referenced by itk::DeformableSimplexMesh3DFilter< TInputMesh, TOutputMesh >::DeformableSimplexMesh3DFilter(), itk::ExtensionVelocitiesImageFilter< TLevelSet, TAuxValue, VAuxDimension >::ExtensionVelocitiesImageFilter(), itk::FastMarchingImageFilter< TLevelSet, TSpeedImage >::FastMarchingImageFilter(), otb::FillGapsFilter::FillGapsFilter(), otb::ImageToLabelMapWithAttributesFilter< TInputImage, TLabeledImage, TLabel, TLabelObject >::ImageToLabelMapWithAttributesFilter(), itk::ImageToMeshFilter< TInputImage, TOutputMesh >::ImageToMeshFilter(), itk::PasteImageFilter< TInputImage, TSourceImage, TOutputImage >::PasteImageFilter(), otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD, TCost >::WaveletPacketTransform(), otb::WaveletPacketTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE, FullyDecomposedWaveletPacketCost< TInputImage > >::WaveletPacketTransform(), otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::FORWARD >::WaveletTransform(), and otb::WaveletTransform< TInputImage, TOutputImage, TFilter, Wavelet::INVERSE >::WaveletTransform().

virtual void itk::ProcessObject::SetNumberOfRequiredOutputs ( unsigned int _arg )

protectedvirtualinherited

Referenced by itk::AutomaticTopologyMeshSource< TOutputMesh >::AutomaticTopologyMeshSource(), itk::BalloonForceFilter< TInputMesh, TOutputMesh >::BalloonForceFilter(), itk::CoreAtomImageToDistanceMatrixProcess< TSourceImage >::CoreAtomImageToDistanceMatrixProcess(), itk::CoreAtomImageToUnaryCorrespondenceMatrixProcess< TSourceImage >::CoreAtomImageToUnaryCorrespondenceMatrixProcess(), itk::DeformableMesh3DFilter< TInputMesh, TOutputMesh >::DeformableMesh3DFilter(), itk::DeformableSimplexMesh3DFilter< TInputMesh, TOutputMesh >::DeformableSimplexMesh3DFilter(), itk::ExtensionVelocitiesImageFilter< TLevelSet, TAuxValue, VAuxDimension >::ExtensionVelocitiesImageFilter(), itk::FastMarchingExtensionImageFilter< TLevelSet, TAuxValue, VAuxDimension, TSpeedImage >::FastMarchingExtensionImageFilter(), otb::FillGapsFilter::FillGapsFilter(), otb::GeometriesSource::GeometriesSource(), itk::ImageSource< TOutputImage >::ImageSource(), itk::ImageToMeshFilter< TInputImage, TOutputMesh >::ImageToMeshFilter(), itk::MedialNodePairCorrespondenceProcess< TSourceImage >::MedialNodePairCorrespondenceProcess(), itk::MedialNodeTripletCorrespondenceProcess< TSourceImage >::MedialNodeTripletCorrespondenceProcess(), itk::MeshSource< TOutputMesh >::MeshSource(), itk::MultiScaleHessianBasedMeasureImageFilter< TInputImage, THessianImage, TOutputImage >::MultiScaleHessianBasedMeasureImageFilter(), otb::OSMDataToVectorDataGenerator::OSMDataToVectorDataGenerator(), itk::PathSource< TOutputPath >::PathSource(), itk::RegularSphereMeshSource< TOutputMesh >::RegularSphereMeshSource(), itk::watershed::Relabeler< TScalarType, TImageDimension >::Relabeler(), itk::SimplexMeshAdaptTopologyFilter< TInputMesh, TOutputMesh >::SimplexMeshAdaptTopologyFilter(), itk::SphereMeshSource< TOutputMesh >::SphereMeshSource(), itk::TriangleMeshToSimplexMeshFilter< TInputMesh, TOutputMesh >::TriangleMeshToSimplexMeshFilter(), itk::TwoOutputExampleImageFilter< TImage >::TwoOutputExampleImageFilter(), and itk::VTKPolyDataReader< TOutputMesh >::VTKPolyDataReader().

virtual void itk::ProcessObject::SetNumberOfThreads ( int _arg )

virtualinherited

Get/Set the number of threads to create when executing.

Referenced by itk::CannyEdgeDetectionImageFilter< TInputImage, TOutputImage >::Compute2ndDerivative(), itk::CannyEdgeDetectionImageFilter< TInputImage, TOutputImage >::Compute2ndDerivativePos(), and itk::FiniteDifferenceSparseImageFilter< TInputImageType, TSparseOutputImageType >::PrecalculateChange().

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Set/Get the search radius grow factor.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

inline

Set/Get the initial search radius.

Definition at line 392 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Set/Get the search radius shrink factor.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Definition at line 559 of file itkMRIBiasFieldCorrectionFilter.txx.

virtual void itk::ProcessObject::SetProgress ( float _arg )

virtualinherited

Set the execution progress of a process object. The progress is a floating number in [0,1] with 0 meaning no progress and 1 meaning the filter has completed execution. The ProgressEvent is NOT invoked.

void itk::Object::SetReferenceCount ( int ref )

virtualinherited

Sets the reference count (use with care)

If there is a delete method, invoke it.

Reimplemented from itk::LightObject.

Definition at line 347 of file itkObject.cxx.

virtual void itk::ProcessObject::SetReleaseDataBeforeUpdateFlag ( bool _arg )

virtualinherited

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released/reallocated during an Update(). In limited memory scenarios, a user may want to force the elements of a pipeline to release any bulk data that is going to be regenerated anyway during an Update() in order to control peak memory allocation. Note that this flag is different from the ReleaseDataFlag. ReleaseDataFlag manages the deallocation of a ProcessObject's bulk output data once that data has been consumed by a downstream ProcessObject. The ReleaseDataBeforeUpdateFlag manages the deallocation/reallocation of bulk data during a pipeline update to control peak memory utilization. Default value is on.

void itk::ProcessObject::SetReleaseDataFlag ( bool flag )

virtualinherited

Turn on/off the flags to control whether the bulk data belonging to the outputs of this ProcessObject are released after being used by a downstream ProcessObject. Default value is off. Another options for controlling memory utilization is the ReleaseDataBeforeUpdateFlag.

Definition at line 528 of file itkProcessObject.cxx.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Set the multi-resolution schedule

Definition at line 362 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Set the starting shrink factors

Definition at line 296 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Set the starting shrink factors

Definition at line 316 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

Definition at line 987 of file itkMRIBiasFieldCorrectionFilter.txx.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

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

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

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

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

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

template<class TInputImage, class TOutputImage, class TMaskImage>

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

virtual

Set/Get the maximum iteration termination condition parameter.

template<class TOutputImage >

int itk::ImageSource< TOutputImage >::SplitRequestedRegion	(	int	i,
		int	num,
		OutputImageRegionType &	splitRegion
	)

protectedvirtualinherited

Split the output's RequestedRegion into "num" pieces, returning region "i" as "splitRegion". This method is called "num" times. The regions must not overlap. The method returns the number of pieces that the routine is capable of splitting the output RequestedRegion, i.e. return value is less than or equal to "num".

Reimplemented in itk::SignedMaurerDistanceMapImageFilter< TInputImage, TOutputImage >.

Definition at line 138 of file itkImageSource.txx.

Referenced by itk::DenseFiniteDifferenceImageFilter< TInputImage, TOutputImage >::ApplyUpdateThreaderCallback(), itk::DenseFiniteDifferenceImageFilter< TInputImage, TOutputImage >::CalculateChangeThreaderCallback(), itk::CannyEdgeDetectionImageFilter< TInputImage, TOutputImage >::Compute2ndDerivativePosThreaderCallback(), and itk::CannyEdgeDetectionImageFilter< TInputImage, TOutputImage >::Compute2ndDerivativeThreaderCallback().

template<class TOutputImage >

void itk::ImageSource< TOutputImage >::ThreadedGenerateData	(	const OutputImageRegionType &	outputRegionForThread,
		int	threadId
	)

protectedvirtualinherited

If an imaging filter can be implemented as a multithreaded algorithm, the filter will provide an implementation of ThreadedGenerateData(). This superclass will automatically split the output image into a number of pieces, spawn multiple threads, and call ThreadedGenerateData() in each thread. Prior to spawning threads, the BeforeThreadedGenerateData() method is called. After all the threads have completed, the AfterThreadedGenerateData() method is called. If an image processing filter cannot support threading, that filter should provide an implementation of the GenerateData() method instead of providing an implementation of ThreadedGenerateData(). If a filter provides a GenerateData() method as its implementation, then the filter is responsible for allocating the output data. If a filter provides a ThreadedGenerateData() method as its implementation, then the output memory will allocated automatically by this superclass. The ThreadedGenerateData() method should only produce the output specified by "outputThreadRegion" parameter. ThreadedGenerateData() cannot write to any other portion of the output image (as this is responsibility of a different thread).

See also:: GenerateData(), SplitRequestedRegion()

Definition at line 258 of file itkImageSource.txx.

template<class TOutputImage >

ITK_THREAD_RETURN_TYPE itk::ImageSource< TOutputImage >::ThreaderCallback ( void * arg )

staticprotectedinherited

Static function used as a "callback" by the MultiThreader. The threading library will call this routine for each thread, which will delegate the control to ThreadedGenerateData().

Definition at line 278 of file itkImageSource.txx.

References itk::ImageSource< TOutputImage >::ThreadStruct::Filter, and ITK_THREAD_RETURN_VALUE.

void itk::Object::UnRegister ( ) const

virtualinherited

Decrease the reference count (release by another object).

If there is a delete method, invoke it.

Reimplemented from itk::LightObject.

Definition at line 324 of file itkObject.cxx.

Referenced by itk::Object::New(), and itk::ObjectFactoryBase::UnRegisterFactory().

void itk::ProcessObject::Update ( void )

virtualinherited

Bring this filter up-to-date. Update() checks modified times against last execution times, and re-executes objects if necessary. A side effect of this method is that the whole pipeline may execute in order to bring this filter up-to-date. This method updates the currently prescribed requested region. If no requested region has been set on the output, then the requested region will be set to the largest possible region. Once the requested region is set, Update() will make sure the specified requested region is up-to-date. This is a confusing side effect to users who are just calling Update() on a filter. A first call to Update() will cause the largest possible region to be updated. A second call to Update() will update that same region. If a modification to the upstream pipeline cause a filter to have a different largest possible region, this second call to Update() will not cause the output requested region to be reset to the new largest possible region. Instead, the output requested region will be the same as the last time Update() was called. To have a filter always to produce its largest possible region, users should call UpdateLargestPossibleRegion() instead.

The following methods are used to coordinate the execution of the data processing pipeline.

Definition at line 611 of file itkProcessObject.cxx.

Referenced by otb::ImageSeriesFileReader< Image< TPixel, 2 >, Image< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< Image< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), otb::ImageSeriesFileReader< VectorImage< TPixel, 2 >, VectorImage< TInternalPixel, 2 > >::GenerateData(), itk::AutoCropLabelMapFilter< TInputImage >::GenerateOutputInformation(), itk::LabelMapMaskImageFilter< TInputImage, TOutputImage >::GenerateOutputInformation(), and itk::VoronoiSegmentationImageFilterBase< TInputImage, TOutputImage, TBinaryPriorImage >::RunSegmentOneStep().

void itk::ProcessObject::UpdateLargestPossibleRegion ( )

virtualinherited

Like Update(), but sets the output requested region to the largest possible region for the output. This is the method users should call if they want the entire dataset to be processed. If a user wants to update the same output region as a previous call to Update() or a previous call to UpdateLargestPossibleRegion(), then they should call the method Update().

Definition at line 1120 of file itkProcessObject.cxx.

void itk::ProcessObject::UpdateOutputData ( DataObject * output )

virtualinherited

Actually generate new output

 prevent chasing our tail

 Prepare all the outputs. This may deallocate previous bulk data.

 Propagate the update call - make sure everything we
 might rely on is up-to-date
 Must call PropagateRequestedRegion before UpdateOutputData if multiple 
 inputs since they may lead back to the same data object.

 Cache the state of any ReleaseDataFlag's on the inputs. While the
 filter is executing, we need to set the ReleaseDataFlag's on the
 inputs to false in case the current filter is implemented using a
 mini-pipeline (which will try to release the inputs).  After the
 filter finishes, we restore the state of the ReleaseDataFlag's
 before the call to ReleaseInputs().

 Tell all Observers that the filter is starting

 GenerateData this object - we have not aborted yet, and our progress
 before we start to execute is 0.0.

 Count the number of required inputs which have been assigned

 If we ended due to aborting, push the progress up to 1.0 (since
 it probably didn't end there)

 Notify end event observers

 Now we have to mark the data as up to date.

 Restore the state of any input ReleaseDataFlags

 Release any inputs if marked for release

Reimplemented in itk::StreamingImageFilter< TInputImage, TOutputImage >.

Definition at line 908 of file itkProcessObject.cxx.

void itk::ProcessObject::UpdateOutputInformation ( void )

virtualinherited

Update the information decribing the output data. This method transverses up the pipeline gathering modified time information. On the way back down the pipeline, this method calls GenerateOutputInformation() to set any necessary information about the output data objects. For instance, a filter that shrinks an image will need to provide an implementation for GenerateOutputInformation() that changes the spacing of the pixels. Such filters should call their superclass' implementation of GenerateOutputInformation prior to changing the information values they need (i.e. GenerateOutputInformation() should call Superclass::GenerateOutputInformation() prior to changing the information.

 Watch out for loops in the pipeline

   Since we are in a loop, we will want to update. But if
   we don't modify this filter, then we will not execute
   because our OutputInformationMTime will be more recent than
   the MTime of our output.

 We now wish to set the PipelineMTime of each output DataObject to
 the largest of this ProcessObject's MTime, all input DataObject's
 PipelineMTime, and all input's MTime.  We begin with the MTime of
 this ProcessObject.

 Loop through the inputs

     Propagate the UpdateOutputInformation call

     What is the PipelineMTime of this input? Compare this against
     our current computation to find the largest one.

     Pipeline MTime of the input does not include the MTime of the 
     data object itself. Factor these mtimes into the next PipelineMTime

 Call GenerateOutputInformation for subclass specific information.
 Since UpdateOutputInformation propagates all the way up the pipeline,
 we need to be careful here to call GenerateOutputInformation only if
 necessary. Otherwise, we may cause this source to be modified which
 will cause it to execute again on the next update.

   Keep track of the last time GenerateOutputInformation() was called

Reimplemented in itk::watershed::Segmenter< TInputImage >, itk::watershed::Segmenter< InputImageType >, and itk::VTKImageImport< TOutputImage >.

Definition at line 664 of file itkProcessObject.cxx.

References itk::Object::GetMTime(), itk::DataObject::GetPipelineMTime(), itk::DataObject::SetPipelineMTime(), and itk::DataObject::UpdateOutputInformation().

Referenced by itk::VTKImageExportBase::UpdateInformationCallback().

void itk::ProcessObject::UpdateProgress ( float amount )

inherited

Update the progress of the process object.

Sets the Progress ivar to amount and invokes any observers for the ProgressEvent. The parameter amount should be in [0,1] and is the cumulative (not incremental) progress.

Update the progress of the process object. If a ProgressMethod exists, execute it. Then set the Progress ivar to amount. The parameter amount should range between (0,1).

Definition at line 500 of file itkProcessObject.cxx.

Referenced by itk::WatershedMiniPipelineProgressCommand::Execute(), itk::ProgressReporter::ProgressReporter(), and itk::ProgressReporter::~ProgressReporter().

Member Data Documentation

template<class TInputImage, class TOutputImage, class TMaskImage>

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

static

The dimension of the image.

Definition at line 244 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage>

const unsigned int itk::ImageToImageFilter< TInputImage, TOutputImage >::InputImageDimension = TInputImage::ImageDimension

staticinherited

ImageDimension constants

Definition at line 90 of file itkImageToImageFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

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

Definition at line 576 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

The degree of the bias field estimate.

Definition at line 567 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

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

Definition at line 555 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Energy function object pointer.

Definition at line 534 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

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

Definition at line 580 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Definition at line 561 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Input mask image smart pointer.

Definition at line 540 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Internal image smart pointer.

Definition at line 546 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for the optimizer's maximum iteration number.

Definition at line 586 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Normal variate generator smart pointer

Definition at line 537 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

The number of levels for the multires schedule

Definition at line 570 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for the optimizer's search radius grow factor.

Definition at line 592 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for the optimizer's initial search radius.

Definition at line 589 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for the optimizer's search radius shrink factor.

Definition at line 595 of file itkMRIBiasFieldCorrectionFilter.h.

TimeStamp itk::ProcessObject::m_OutputInformationMTime

protectedinherited

Time when GenerateOutputInformation was last called.

Definition at line 421 of file itkProcessObject.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Output mask image smart pointer.

Definition at line 543 of file itkMRIBiasFieldCorrectionFilter.h.

InternalReferenceCountType itk::LightObject::m_ReferenceCount

mutableprotectedinherited

Number of uses of this object by other objects.

Definition at line 141 of file itkLightObject.h.

SimpleFastMutexLock itk::LightObject::m_ReferenceCountLock

mutableprotectedinherited

Mutex lock to protect modification to the reference count

Definition at line 144 of file itkLightObject.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

The multires schedule

Definition at line 572 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Definition at line 564 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Definition at line 563 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for the MRI slab identifier return.

Definition at line 549 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Definition at line 565 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

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

Definition at line 552 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for tissue classes' mean values.

Definition at line 598 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for tissue classes' variance values.

Definition at line 601 of file itkMRIBiasFieldCorrectionFilter.h.

bool itk::ProcessObject::m_Updating

protectedinherited

These ivars are made protected so filters like itkStreamingImageFilter can access them directly. This flag indicates when the pipeline is executing. It prevents infinite recursion when pipelines have loops.

Reimplemented in otb::ImageViewerBase< TPixel, TLabel >, and otb::HistogramAndTransferFunctionWidget< THistogram, TPixel >.

Definition at line 418 of file itkProcessObject.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Definition at line 560 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

operation selection flags.

Definition at line 558 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Definition at line 559 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage, class TMaskImage>

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

private

Storage for the optimizer's maximum iteration number.

Definition at line 583 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage, class TOutputImage>

const unsigned int itk::ImageToImageFilter< TInputImage, TOutputImage >::OutputImageDimension = TOutputImage::ImageDimension

staticinherited

ImageDimension constant

Reimplemented from itk::ImageSource< TOutputImage >.

Definition at line 92 of file itkImageToImageFilter.h.

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

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

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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