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

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 >:

List of all members.

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 MRASlabIdentifier
< InputImageType > MRASlabIdentifierType

typedef
Statistics::NormalVariateGenerator NormalVariateGeneratorType

typedef
OnePlusOneEvolutionaryOptimizer OptimizerType

typedef TOutputImage::IndexType OutputImageIndexType

typedef TOutputImage::PixelType OutputImagePixelType

typedef TOutputImage::Pointer OutputImagePointer

typedef TOutputImage::RegionType OutputImageRegionType

typedef TOutputImage::SizeType OutputImageSizeType

typedef TOutputImage OutputImageType

typedef SmartPointer< Self > Pointer

typedef Array2D< unsigned int > ScheduleType

typedef
MRIBiasFieldCorrectionFilter Self

typedef
SlabRegionVectorType::iterator SlabRegionVectorIteratorType

typedef
MRASlabIdentifierType::SlabRegionVectorType SlabRegionVectorType

typedef ImageToImageFilter
< TInputImage, TOutputImage > Superclass

typedef
InternalImageType::PixelType InternalImagePixelType

typedef InternalImageType::Pointer InternalImagePointer

typedef
InternalImageType::RegionType InternalImageRegionType

typedef Image< float,
itkGetStaticConstMacro(ImageDimension) > InternalImageType

Public Member Functions

virtual void AbortGenerateDataOff ()

virtual void AbortGenerateDataOn ()

void CorrectImage (BiasFieldType &bias, InputImageRegionType region)

void CorrectInterSliceIntensityInhomogeneity (InputImageRegionType region)

virtual LightObject::Pointer CreateAnother () 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 ()

Command * GetCommand (unsigned long tag)

bool GetDebug () const

BiasFieldType::CoefficientArrayType GetEstimatedBiasFieldCoefficients ()

DataObjectPointerArray & GetInputs ()

const MetaDataDictionary & GetMetaDataDictionary (void) const

MetaDataDictionary & GetMetaDataDictionary (void)

virtual unsigned long GetMTime () const

MultiThreader * GetMultiThreader ()

virtual const char * GetNameOfClass () const

DataObjectPointerArraySizeType GetNumberOfInputs () const

virtual unsigned int GetNumberOfLevels () const

virtual
DataObjectPointerArraySizeType GetNumberOfValidRequiredInputs () const

virtual double GetOptimizerShrinkFactor () const

virtual ImageMaskType * GetOutputMask ()

virtual const float & GetProgress ()

virtual int GetReferenceCount () const

virtual const ScheduleType & GetSchedule ()

virtual const InputImagePixelType & GetSlabBackgroundMinimumThreshold ()

virtual const unsigned int & GetSlabNumberOfSamples ()

virtual const double & GetSlabTolerance ()

const unsigned int * GetStartingShrinkFactors () 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 &) const

void InvokeEvent (const EventObject &)

bool IsBiasFieldMultiplicative ()

void IsBiasFieldMultiplicative (bool flag)

itkStaticConstMacro (ImageDimension, unsigned int, TOutputImage::ImageDimension)

virtual DataObjectPointer MakeOutput (unsigned int idx)

virtual void Modified () const

virtual void PrepareOutputs ()

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

virtual void PropagateRequestedRegion (DataObject *output)

virtual void Register () const

void RemoveAllObservers ()

void RemoveObserver (unsigned long tag)

virtual void ResetPipeline ()

virtual void SetAbortGenerateData (bool _arg)

void SetDebug (bool debugFlag) const

void SetInitialBiasFieldCoefficients (const BiasFieldType::CoefficientArrayType &coefficients)

void SetMetaDataDictionary (const MetaDataDictionary &rhs)

void SetNumberOfLevels (unsigned int num)

virtual void SetOptimizerShrinkFactor (double _arg)

void SetOutputMask (ImageMaskType *outputMask)

virtual void SetProgress (float _arg)

virtual void SetReferenceCount (int)

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

virtual void UnRegister () const

virtual void Update ()

virtual void UpdateLargestPossibleRegion ()

virtual void UpdateOutputData (DataObject *output)

virtual void UpdateOutputInformation ()

void UpdateProgress (float amount)

unsigned long AddObserver (const EventObject &event, Command *) const

unsigned long AddObserver (const EventObject &event, Command *)

virtual int GetBiasFieldDegree () const

virtual void SetBiasFieldDegree (int _arg)

virtual const bool & GetGeneratingOutput ()

virtual void SetGeneratingOutput (bool _arg)

const InputImageType * GetInput (unsigned int idx)

const InputImageType * GetInput (void)

virtual void SetInput (unsigned int, const TInputImage *image)

virtual void SetInput (const InputImageType *image)

virtual ImageMaskType * GetInputMask ()

void SetInputMask (ImageMaskType *inputMask)

virtual int GetInterSliceCorrectionMaximumIteration () const

virtual int GetVolumeCorrectionMaximumIteration () const

virtual void SetInterSliceCorrectionMaximumIteration (int _arg)

virtual void SetVolumeCorrectionMaximumIteration (int _arg)

DataObjectPointerArraySizeType GetNumberOfOutputs () const

DataObjectPointerArray & GetOutputs ()

virtual const int & GetNumberOfThreads ()

virtual void SetNumberOfThreads (int _arg)

virtual double GetOptimizerGrowthFactor () const

virtual void SetOptimizerGrowthFactor (double _arg)

double GetOptimizerInitialRadius ()

void SetOptimizerInitialRadius (double initRadius)

OutputImageType * GetOutput (unsigned int idx)

OutputImageType * GetOutput (void)

virtual const bool & GetReleaseDataBeforeUpdateFlag ()

virtual void ReleaseDataBeforeUpdateFlagOff ()

virtual void ReleaseDataBeforeUpdateFlagOn ()

virtual void SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual bool GetReleaseDataFlag () const

void ReleaseDataFlagOff ()

void ReleaseDataFlagOn ()

virtual void SetReleaseDataFlag (bool flag)

virtual const bool & GetUsingBiasFieldCorrection ()

virtual void SetUsingBiasFieldCorrection (bool _arg)

virtual const bool & GetUsingInterSliceIntensityCorrection ()

virtual void SetUsingInterSliceIntensityCorrection (bool _arg)

virtual const bool & GetUsingSlabIdentification ()

virtual void SetUsingSlabIdentification (bool _arg)

itkStaticConstMacro (OutputImageDimension, unsigned int, TOutputImage::ImageDimension)

itkStaticConstMacro (InputImageDimension, unsigned int, TInputImage::ImageDimension)

virtual void PopBackInput ()

virtual void PopFrontInput ()

virtual void PushBackInput (const InputImageType *image)

virtual void PushFrontInput (const InputImageType *image)

void SetStartingShrinkFactors (unsigned int *factors)

void SetStartingShrinkFactors (unsigned int factor)

Static Public Member Functions

static void BreakOnError ()

static bool IsScheduleDownwardDivisible (const ScheduleType &schedule)

static Pointer New ()

static bool GetGlobalWarningDisplay ()

static void GlobalWarningDisplayOff ()

static void GlobalWarningDisplayOn ()

static void SetGlobalWarningDisplay (bool flag)

Protected Types

typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(OutputImageDimension),
itkGetStaticConstMacro(InputImageDimension)> InputToOutputRegionCopierType

typedef
ImageToImageFilterDetail::ImageRegionCopier
< itkGetStaticConstMacro(InputImageDimension),
itkGetStaticConstMacro(OutputImageDimension)> OutputToInputRegionCopierType

typedef int InternalReferenceCountType

Protected Member Functions

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)

void Log1PImage (InternalImageType *source, InternalImageType *target)

MRIBiasFieldCorrectionFilter ()

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

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

virtual void PropagateResetPipeline ()

virtual void ReleaseInputs ()

virtual void RestoreInputReleaseDataFlags ()

void SetNumberOfInputs (unsigned int num)

void SetNumberOfOutputs (unsigned int num)

virtual int SplitRequestedRegion (int i, int num, OutputImageRegionType &splitRegion)

virtual void ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, int threadId) ITK_NO_RETURN

virtual ~MRIBiasFieldCorrectionFilter ()

virtual void AddInput (DataObject *input)

virtual const unsigned int & GetNumberOfRequiredInputs ()

virtual void RemoveInput (DataObject *input)

virtual void SetNthInput (unsigned int num, DataObject *input)

virtual void SetNumberOfRequiredInputs (unsigned int _arg)

virtual void AddOutput (DataObject *output)

virtual const unsigned int & GetNumberOfRequiredOutputs ()

virtual void RemoveOutput (DataObject *output)

virtual void SetNthOutput (unsigned int num, DataObject *output)

virtual void SetNumberOfRequiredOutputs (unsigned int _arg)

const DataObject * GetInput (unsigned int idx) const

const DataObject * GetOutput (unsigned int idx) const

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

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

void PushBackInput (const DataObject *input)

void PushFrontInput (const DataObject *input)

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

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 227 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 282 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 235 of file itkMRIBiasFieldCorrectionFilter.h.

typedef DataObject::Pointer itk::ImageSource< TOutputImage >::DataObjectPointer [inherited]

Smart Pointer type to a DataObject.

Reimplemented from itk::ProcessObject.

Reimplemented in itk::SignedDanielssonDistanceMapImageFilter< TInputImage, TOutputImage >, itk::StreamingImageFilter< TInputImage, TOutputImage >, and itk::MultiScaleHessianBasedMeasureImageFilter< TInputImage, THessianImage, TOutputImage >.

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 288 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 287 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Definition at line 264 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Definition at line 265 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 263 of file itkMRIBiasFieldCorrectionFilter.h.

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 257 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 258 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 256 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 260 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Definition at line 259 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 255 of file itkMRIBiasFieldCorrectionFilter.h.

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

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

Definition at line 164 of file itkImageToImageFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Internal (temporary) image related type definitions.

Definition at line 270 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Internal (temporary) image related type definitions.

Definition at line 271 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Internal (temporary) image related type definitions.

Definition at line 272 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 269 of file itkMRIBiasFieldCorrectionFilter.h.

typedef int itk::LightObject::InternalReferenceCountType [protected, inherited]

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

Definition at line 139 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 276 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 291 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 294 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Definition at line 250 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 251 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 249 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 253 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Definition at line 252 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 248 of file itkMRIBiasFieldCorrectionFilter.h.

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

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

Definition at line 169 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 234 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 297 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 232 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Definition at line 279 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Definition at line 278 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 233 of file itkMRIBiasFieldCorrectionFilter.h.

Constructor & Destructor Documentation

template<class TInputImage , class TOutputImage , class TMaskImage >

itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::MRIBiasFieldCorrectionFilter ( ) [protected]

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Member Function Documentation

virtual void itk::ProcessObject::AbortGenerateDataOff ( ) [virtual, inherited]

virtual void itk::ProcessObject::AbortGenerateDataOn ( ) [virtual, inherited]

Turn on and off the AbortGenerateData flag.

virtual void itk::ProcessObject::AddInput ( DataObject * input ) [protected, virtual, inherited]

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

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

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

virtual void itk::ProcessObject::AddOutput ( DataObject * output ) [protected, virtual, inherited]

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

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.

virtual void itk::ImageSource< TOutputImage >::AfterThreadedGenerateData ( void ) [inline, protected, virtual, inherited]

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 265 of file itkImageSource.h.

virtual void itk::ImageSource< TOutputImage >::AllocateOutputs ( ) [protected, virtual, inherited]

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.

Reimplemented in itk::InPlaceImageFilter< TInputImage, TOutputImage >, itk::MaskedMovingHistogramImageFilter< TInputImage, TMaskImage, TOutputImage, TKernel, THistogram >, itk::InPlaceImageFilter< TInputImage, TOutputImage >, itk::InPlaceImageFilter< TLabelImage,TOutputImage >, itk::InPlaceImageFilter< TInputImage1,TOutputImage >, itk::InPlaceImageFilter< TInputImage,TOutputImage >, itk::InPlaceImageFilter< TFeatureImage, TOutputImage >, itk::InPlaceImageFilter< TInputImage1, TOutputImage >, and itk::MaskedMovingHistogramImageFilter< TInputImage, TMaskImage, TOutputImage, TKernel, MaskedRankHistogram< TInputImage::PixelType > >.

virtual void itk::ImageSource< TOutputImage >::BeforeThreadedGenerateData ( void ) [inline, protected, virtual, inherited]

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 253 of file itkImageSource.h.

static void itk::LightObject::BreakOnError ( ) [static, inherited]

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

virtual void itk::ProcessObject::CacheInputReleaseDataFlags ( ) [protected, virtual, inherited]

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().

virtual void itk::ImageToImageFilter< TInputImage , TOutputImage >::CallCopyInputRegionToOutputRegion	(	OutputImageRegionType &	destRegion,
		const InputImageRegionType &	srcRegion
	)			`[protected, virtual, inherited]`

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.

virtual void itk::ImageToImageFilter< TInputImage , TOutputImage >::CallCopyOutputRegionToInputRegion	(	InputImageRegionType &	destRegion,
		const OutputImageRegionType &	srcRegion
	)			`[protected, virtual, inherited]`

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).

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

template<class TSource , class TTarget >

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

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

Definition at line 505 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

virtual LightObject::Pointer itk::Object::CreateAnother ( ) const [virtual, inherited]

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::LightObject.

virtual void itk::Object::DebugOff ( ) const [virtual, inherited]

Turn debugging output off.

virtual void itk::Object::DebugOn ( ) const [virtual, inherited]

Turn debugging output on.

virtual void itk::LightObject::Delete ( ) [virtual, inherited]

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.

virtual void itk::ProcessObject::EnlargeOutputRequestedRegion ( DataObject * ) [inline, virtual, inherited]

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 225 of file itkProcessObject.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

void itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::GenerateData ( void ) [protected, virtual]

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 >.

virtual void itk::ImageToImageFilter< TInputImage , TOutputImage >::GenerateInputRequestedRegion ( void ) [protected, virtual, inherited]

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.

virtual void itk::ProcessObject::GenerateOutputInformation ( ) [protected, virtual, inherited]

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.

virtual void itk::ProcessObject::GenerateOutputRequestedRegion ( DataObject * output ) [protected, virtual, inherited]

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.

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

virtual const bool& itk::ProcessObject::GetAbortGenerateData ( ) [virtual, inherited]

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

Set/Get the degree of the bias field estimate.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

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.

bool itk::Object::GetDebug ( ) const [inherited]

Get the value of the debug flag.

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 383 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

static bool itk::Object::GetGlobalWarningDisplay ( ) [static, inherited]

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

const DataObject* itk::ProcessObject::GetInput ( unsigned int idx ) const [protected, inherited]

Method used internally for getting an input.

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

Set/Get the image input of this process object.

Reimplemented from itk::ProcessObject.

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

Set/Get the image input of this process object.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

DataObjectPointerArray& itk::ProcessObject::GetInputs ( ) [inline, inherited]

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.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Set/Get the maximum iteration termination condition parameter.

const MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) const [inherited]

Returns:: A constant reference to this objects MetaDataDictionary.

MetaDataDictionary& itk::Object::GetMetaDataDictionary ( void ) [inherited]

Returns:: A reference to this objects MetaDataDictionary.

Warning:: This reference may be changed.

virtual unsigned long itk::Object::GetMTime ( ) const [virtual, inherited]

Return this objects modified time.

Referenced by itk::SpatialObject< ::itk::GetMeshDimension< TMesh >::PointDimension >::GetObjectMTime().

MultiThreader* itk::ProcessObject::GetMultiThreader ( ) [inline, inherited]

Return the multithreader used by this class.

Definition at line 284 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 [inline, inherited]

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.

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 [inline, inherited]

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 135 of file itkProcessObject.h.

virtual const unsigned int& itk::ProcessObject::GetNumberOfRequiredInputs ( ) [protected, virtual, inherited]

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

virtual const unsigned int& itk::ProcessObject::GetNumberOfRequiredOutputs ( ) [protected, virtual, inherited]

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

virtual const int& itk::ProcessObject::GetNumberOfThreads ( ) [virtual, inherited]

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

virtual DataObjectPointerArraySizeType itk::ProcessObject::GetNumberOfValidRequiredInputs ( ) const [virtual, inherited]

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.

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Set/Get the search radius grow factor.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Set/Get the initial search radius.

Definition at line 403 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

const DataObject* itk::ProcessObject::GetOutput ( unsigned int idx ) const [protected, inherited]

Method used internally for getting an output.

OutputImageType* itk::ImageSource< TOutputImage >::GetOutput ( unsigned int idx ) [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 from itk::ProcessObject.

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.

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 ( ) [inline, inherited]

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.

virtual const float& itk::ProcessObject::GetProgress ( ) [virtual, inherited]

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::XMLFilterWatcher::ShowProgress().

virtual int itk::LightObject::GetReferenceCount ( ) const [inline, virtual, inherited]

Gets the reference count on this object.

Definition at line 106 of file itkLightObject.h.

virtual const bool& itk::ProcessObject::GetReleaseDataBeforeUpdateFlag ( ) [virtual, inherited]

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.

virtual bool itk::ProcessObject::GetReleaseDataFlag ( ) const [virtual, inherited]

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.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Get the multi-resolution schedule.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Get the starting shrink factors

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Set/Get the maximum iteration termination condition parameter.

static void itk::Object::GlobalWarningDisplayOff ( ) [inline, static, inherited]

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

Definition at line 100 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

static void itk::Object::GlobalWarningDisplayOn ( ) [inline, static, inherited]

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

Definition at line 98 of file itkObject.h.

References itk::Object::SetGlobalWarningDisplay().

virtual void itk::ImageSource< TOutputImage >::GraftNthOutput	(	unsigned int	idx,
		DataObject *	output
	)			`[virtual, inherited]`

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.

virtual void itk::ImageSource< TOutputImage >::GraftOutput ( DataObject * output ) [virtual, inherited]

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).

bool itk::Object::HasObserver ( const EventObject & event ) const [inherited]

Return true if an observer is registered for this event.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

void itk::Object::InvokeEvent ( const EventObject & ) const [inherited]

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

void itk::Object::InvokeEvent ( const EventObject & ) [inherited]

Call Execute on all the Commands observing this event id.

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 320 of file itkMRIBiasFieldCorrectionFilter.h.

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 316 of file itkMRIBiasFieldCorrectionFilter.h.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

itk::ImageToImageFilter< TInputImage , TOutputImage >::itkStaticConstMacro	(	OutputImageDimension	,
		unsigned	int,
		TOutputImage ::ImageDimension
	)			`[inherited]`

ImageDimension constants

Reimplemented from itk::ImageSource< TOutputImage >.

itk::ImageToImageFilter< TInputImage , TOutputImage >::itkStaticConstMacro	(	InputImageDimension	,
		unsigned	int,
		TInputImage ::ImageDimension
	)			`[inherited]`

ImageDimension constants

template<class TInputImage , class TOutputImage , class TMaskImage >

itk::MRIBiasFieldCorrectionFilter< TInputImage, TOutputImage, TMaskImage >::itkStaticConstMacro	(	ImageDimension	,
		unsigned	int,
		TOutputImage::ImageDimension
	)

The dimension of the image.

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.

virtual DataObjectPointer itk::ImageSource< TOutputImage >::MakeOutput ( unsigned int idx ) [virtual, inherited]

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.

Reimplemented in itk::SignedDanielssonDistanceMapImageFilter< TInputImage, TOutputImage >, itk::MaskedMovingHistogramImageFilter< TInputImage, TMaskImage, TOutputImage, TKernel, THistogram >, itk::MultiScaleHessianBasedMeasureImageFilter< TInputImage, THessianImage, TOutputImage >, and itk::MaskedMovingHistogramImageFilter< TInputImage, TMaskImage, TOutputImage, TKernel, MaskedRankHistogram< TInputImage::PixelType > >.

virtual void itk::Object::Modified ( ) const [virtual, inherited]

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

Referenced by itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::InsertNarrowBandNode(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetCenter(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetMatrix(), itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::SetNarrowBand(), itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::SetNarrowBandInnerRadius(), itk::NarrowBandImageFilterBase< TInputImage, TOutputImage >::SetNarrowBandTotalRadius(), itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetOffset(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetRealThresholds(), itk::NonUniformBSpline< TDimension >::SetSplineOrder(), itk::ThresholdLabelerImageFilter< TInputImage, TOutputImage >::SetThresholds(), itk::Statistics::GoodnessOfFitFunctionBase< TInputHistogram >::SetTotalObservedScale(), and itk::MatrixOffsetTransformBase< TScalarType, 3, 3 >::SetTranslation().

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.

virtual void itk::ImageToImageFilter< TInputImage , TOutputImage >::PopBackInput ( ) [virtual, inherited]

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.

Reimplemented from itk::ProcessObject.

virtual void itk::ImageToImageFilter< TInputImage , TOutputImage >::PopFrontInput ( ) [virtual, inherited]

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.

Reimplemented from itk::ProcessObject.

virtual void itk::ProcessObject::PrepareOutputs ( ) [virtual, inherited]

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 >.

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

Cause the object to print itself out.

Referenced by itk::WeakPointer< ProcessObject >::Print().

virtual void itk::LightObject::PrintHeader	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

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.

bool itk::Object::PrintObservers	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, inherited]`

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

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

virtual void itk::LightObject::PrintTrailer	(	std::ostream &	os,
		Indent	indent
	)			const `[protected, virtual, inherited]`

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.

virtual void itk::ProcessObject::PropagateRequestedRegion ( DataObject * output ) [virtual, inherited]

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

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

virtual void itk::ProcessObject::PropagateResetPipeline ( ) [protected, virtual, inherited]

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

void itk::ImageToImageFilter< TInputImage , TOutputImage >::PushBackInput ( const DataObject * input ) [inline, protected, virtual, inherited]

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 251 of file itkImageToImageFilter.h.

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

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.

void itk::ImageToImageFilter< TInputImage , TOutputImage >::PushFrontInput ( const DataObject * input ) [inline, protected, virtual, inherited]

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 253 of file itkImageToImageFilter.h.

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

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.

virtual void itk::Object::Register ( ) const [virtual, inherited]

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

Reimplemented from itk::LightObject.

virtual void itk::ProcessObject::ReleaseDataBeforeUpdateFlagOff ( ) [virtual, inherited]

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.

virtual void itk::ProcessObject::ReleaseDataBeforeUpdateFlagOn ( ) [virtual, inherited]

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::ReleaseDataFlagOff ( ) [inline, inherited]

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 257 of file itkProcessObject.h.

void itk::ProcessObject::ReleaseDataFlagOn ( ) [inline, inherited]

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 256 of file itkProcessObject.h.

virtual void itk::ProcessObject::ReleaseInputs ( ) [protected, virtual, inherited]

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()

void itk::Object::RemoveAllObservers ( ) [inherited]

Remove all observers .

virtual void itk::ProcessObject::RemoveInput ( DataObject * input ) [protected, virtual, inherited]

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

void itk::Object::RemoveObserver ( unsigned long tag ) [inherited]

Remove the observer with this tag value.

virtual void itk::ProcessObject::RemoveOutput ( DataObject * output ) [protected, virtual, inherited]

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

virtual void itk::ProcessObject::ResetPipeline ( ) [virtual, inherited]

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.

virtual void itk::ProcessObject::RestoreInputReleaseDataFlags ( ) [protected, virtual, inherited]

Restore the cached input ReleaseDataFlags.

virtual void itk::ProcessObject::SetAbortGenerateData ( bool _arg ) [virtual, inherited]

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.

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

static void itk::Object::SetGlobalWarningDisplay ( bool flag ) [static, inherited]

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

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 375 of file itkMRIBiasFieldCorrectionFilter.h.

virtual void itk::ImageToImageFilter< TInputImage , TOutputImage >::SetInput	(	unsigned	int,
		const TInputImage *	image
	)			`[virtual, inherited]`

Set/Get the image input of this process object.

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

Set/Get the image input of this process object.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Set/Get the maximum iteration termination condition parameter.

void itk::Object::SetMetaDataDictionary ( const MetaDataDictionary & rhs ) [inherited]

Returns:: Set the MetaDataDictionary

virtual void itk::ProcessObject::SetNthInput	(	unsigned int	num,
		DataObject *	input
	)			`[protected, virtual, inherited]`

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

Reimplemented in itk::ImageToVectorImageFilter< TInputImage >.

Referenced by itk::watershed::BoundaryResolver< TPixelType, TDimension >::SetBoundaryA(), itk::watershed::BoundaryResolver< TPixelType, TDimension >::SetBoundaryB(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::SetEquivalencyTable(), itk::SegmentationLevelSetImageFilter< TInputImage, TFeatureImage, TOutputPixelType >::SetFeatureImage(), itk::NarrowBandLevelSetImageFilter< TInputImage, TFeatureImage, TOutputPixelType, Image< TOutputPixelType,::itk::GetImageDimension< TInputImage >::ImageDimension > >::SetFeatureImage(), itk::WatershedImageFilter< TInputImage >::SetInput(), itk::watershed::SegmentTreeGenerator< ScalarType >::SetInputEquivalencyTable(), itk::watershed::Segmenter< InputImageType >::SetInputImage(), itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>::SetInputImage(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::SetInputImage(), itk::watershed::SegmentTreeGenerator< ScalarType >::SetInputSegmentTable(), itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>::SetInputSegmentTree(), itk::DiffusionTensor3DReconstructionImageFilter< TReferenceImagePixelType, TGradientImagePixelType, TTensorPixelType >::SetReferenceImage(), and itk::ChangeInformationImageFilter< TInputImage >::SetReferenceImage().

virtual void itk::ProcessObject::SetNthOutput	(	unsigned int	num,
		DataObject *	output
	)			`[protected, virtual, inherited]`

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

Referenced by itk::watershed::BoundaryResolver< TPixelType, TDimension >::BoundaryResolver(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::EquivalenceRelabeler(), itk::watershed::Segmenter< InputImageType >::SetBoundary(), itk::watershed::BoundaryResolver< TPixelType, TDimension >::SetEquivalencyTable(), itk::watershed::Segmenter< InputImageType >::SetOutputImage(), itk::watershed::Relabeler< ScalarType, itkGetStaticConstMacro(ImageDimension)>::SetOutputImage(), itk::watershed::EquivalenceRelabeler< TScalarType, TImageDimension >::SetOutputImage(), and itk::watershed::Segmenter< InputImageType >::SetSegmentTable().

void itk::ProcessObject::SetNumberOfInputs ( unsigned int num ) [protected, inherited]

Called to allocate the input array. Copies old inputs.

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.

void itk::ProcessObject::SetNumberOfOutputs ( unsigned int num ) [protected, inherited]

Called to allocate the output array. Copies old outputs.

virtual void itk::ProcessObject::SetNumberOfRequiredInputs ( unsigned int _arg ) [protected, virtual, inherited]

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

virtual void itk::ProcessObject::SetNumberOfRequiredOutputs ( unsigned int _arg ) [protected, virtual, inherited]

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

virtual void itk::ProcessObject::SetNumberOfThreads ( int _arg ) [virtual, inherited]

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

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 401 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.

virtual void itk::ProcessObject::SetProgress ( float _arg ) [virtual, inherited]

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.

virtual void itk::Object::SetReferenceCount ( int ) [virtual, inherited]

Sets the reference count (use with care)

Reimplemented from itk::LightObject.

virtual void itk::ProcessObject::SetReleaseDataBeforeUpdateFlag ( bool _arg ) [virtual, inherited]

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.

virtual void itk::ProcessObject::SetReleaseDataFlag ( bool flag ) [virtual, inherited]

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.

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

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

template<class TInputImage , class TOutputImage , class TMaskImage >

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

Set/Get the maximum iteration termination condition parameter.

virtual int itk::ImageSource< TOutputImage >::SplitRequestedRegion	(	int	i,
		int	num,
		OutputImageRegionType &	splitRegion
	)			`[protected, virtual, inherited]`

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 >.

virtual void itk::ImageSource< TOutputImage >::ThreadedGenerateData	(	const OutputImageRegionType &	outputRegionForThread,
		int	threadId
	)			`[protected, virtual, inherited]`

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()

static ITK_THREAD_RETURN_TYPE itk::ImageSource< TOutputImage >::ThreaderCallback ( void * arg ) [static, protected, inherited]

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().

virtual void itk::Object::UnRegister ( ) const [virtual, inherited]

Decrease the reference count (release by another object).

Reimplemented from itk::LightObject.

virtual void itk::ProcessObject::Update ( ) [virtual, inherited]

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.

Reimplemented in itk::CoreAtomImageToUnaryCorrespondenceMatrixProcess< TSourceImage >, itk::MedialNodePairCorrespondenceProcess< TSourceImage >, itk::MedialNodeTripletCorrespondenceProcess< TSourceImage >, itk::CoreAtomImageToDistanceMatrixProcess< TSourceImage >, itk::ImageFileWriter< TInputImage >, and itk::ImageSeriesWriter< TInputImage, TOutputImage >.

virtual void itk::ProcessObject::UpdateLargestPossibleRegion ( ) [virtual, inherited]

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().

virtual void itk::ProcessObject::UpdateOutputData ( DataObject * output ) [virtual, inherited]

Actually generate new output

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

virtual void itk::ProcessObject::UpdateOutputInformation ( ) [virtual, inherited]

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.

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

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.

Member Data Documentation

TimeStamp itk::ProcessObject::m_OutputInformationMTime [protected, inherited]

Time when GenerateOutputInformation was last called.

Definition at line 431 of file itkProcessObject.h.

InternalReferenceCountType itk::LightObject::m_ReferenceCount [mutable, protected, inherited]

Number of uses of this object by other objects.

Definition at line 144 of file itkLightObject.h.

SimpleFastMutexLock itk::LightObject::m_ReferenceCountLock [mutable, protected, inherited]

Mutex lock to protect modification to the reference count

Definition at line 147 of file itkLightObject.h.

bool itk::ProcessObject::m_Updating [protected, inherited]

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.

Definition at line 428 of file itkProcessObject.h.

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

itkMRIBiasFieldCorrectionFilter.h


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 MRASlabIdentifier < InputImageType >	MRASlabIdentifierType
typedef Statistics::NormalVariateGenerator	NormalVariateGeneratorType
typedef OnePlusOneEvolutionaryOptimizer	OptimizerType
typedef TOutputImage::IndexType	OutputImageIndexType
typedef TOutputImage::PixelType	OutputImagePixelType
typedef TOutputImage::Pointer	OutputImagePointer
typedef TOutputImage::RegionType	OutputImageRegionType
typedef TOutputImage::SizeType	OutputImageSizeType
typedef TOutputImage	OutputImageType
typedef SmartPointer< Self >	Pointer
typedef Array2D< unsigned int >	ScheduleType
typedef MRIBiasFieldCorrectionFilter	Self
typedef SlabRegionVectorType::iterator	SlabRegionVectorIteratorType
typedef MRASlabIdentifierType::SlabRegionVectorType	SlabRegionVectorType
typedef ImageToImageFilter < TInputImage, TOutputImage >	Superclass

typedef InternalImageType::PixelType	InternalImagePixelType
typedef InternalImageType::Pointer	InternalImagePointer
typedef InternalImageType::RegionType	InternalImageRegionType
typedef Image< float, itkGetStaticConstMacro(ImageDimension) >	InternalImageType
Public Member Functions
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
void	CorrectImage (BiasFieldType &bias, InputImageRegionType region)
void	CorrectInterSliceIntensityInhomogeneity (InputImageRegionType region)
virtual LightObject::Pointer	CreateAnother () 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 ()
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
BiasFieldType::CoefficientArrayType	GetEstimatedBiasFieldCoefficients ()
DataObjectPointerArray &	GetInputs ()
const MetaDataDictionary &	GetMetaDataDictionary (void) const
MetaDataDictionary &	GetMetaDataDictionary (void)
virtual unsigned long	GetMTime () const
MultiThreader *	GetMultiThreader ()
virtual const char *	GetNameOfClass () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
virtual unsigned int	GetNumberOfLevels () const
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
virtual double	GetOptimizerShrinkFactor () const
virtual ImageMaskType *	GetOutputMask ()
virtual const float &	GetProgress ()
virtual int	GetReferenceCount () const
virtual const ScheduleType &	GetSchedule ()
virtual const InputImagePixelType &	GetSlabBackgroundMinimumThreshold ()
virtual const unsigned int &	GetSlabNumberOfSamples ()
virtual const double &	GetSlabTolerance ()
const unsigned int *	GetStartingShrinkFactors () 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 &) const
void	InvokeEvent (const EventObject &)
bool	IsBiasFieldMultiplicative ()
void	IsBiasFieldMultiplicative (bool flag)
	itkStaticConstMacro (ImageDimension, unsigned int, TOutputImage::ImageDimension)
virtual DataObjectPointer	MakeOutput (unsigned int idx)
virtual void	Modified () const
virtual void	PrepareOutputs ()
void	Print (std::ostream &os, Indent indent=0) const
virtual void	PropagateRequestedRegion (DataObject *output)
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
void	SetDebug (bool debugFlag) const
void	SetInitialBiasFieldCoefficients (const BiasFieldType::CoefficientArrayType &coefficients)
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
void	SetNumberOfLevels (unsigned int num)
virtual void	SetOptimizerShrinkFactor (double _arg)
void	SetOutputMask (ImageMaskType *outputMask)
virtual void	SetProgress (float _arg)
virtual void	SetReferenceCount (int)
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	SetTissueClassStatistics (const Array< double > &means, const Array< double > &sigmas) throw (ExceptionObject)
virtual void	UnRegister () const
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float amount)

unsigned long	AddObserver (const EventObject &event, Command *) const
unsigned long	AddObserver (const EventObject &event, Command *)

virtual int	GetBiasFieldDegree () const
virtual void	SetBiasFieldDegree (int _arg)

virtual const bool &	GetGeneratingOutput ()
virtual void	SetGeneratingOutput (bool _arg)

const InputImageType *	GetInput (unsigned int idx)
const InputImageType *	GetInput (void)
virtual void	SetInput (unsigned int, const TInputImage *image)
virtual void	SetInput (const InputImageType *image)

virtual ImageMaskType *	GetInputMask ()
void	SetInputMask (ImageMaskType *inputMask)

virtual int	GetInterSliceCorrectionMaximumIteration () const
virtual int	GetVolumeCorrectionMaximumIteration () const
virtual void	SetInterSliceCorrectionMaximumIteration (int _arg)
virtual void	SetVolumeCorrectionMaximumIteration (int _arg)

DataObjectPointerArraySizeType	GetNumberOfOutputs () const
DataObjectPointerArray &	GetOutputs ()

virtual const int &	GetNumberOfThreads ()
virtual void	SetNumberOfThreads (int _arg)

virtual double	GetOptimizerGrowthFactor () const
virtual void	SetOptimizerGrowthFactor (double _arg)

double	GetOptimizerInitialRadius ()
void	SetOptimizerInitialRadius (double initRadius)

OutputImageType *	GetOutput (unsigned int idx)
OutputImageType *	GetOutput (void)

virtual const bool &	GetReleaseDataBeforeUpdateFlag ()
virtual void	ReleaseDataBeforeUpdateFlagOff ()
virtual void	ReleaseDataBeforeUpdateFlagOn ()
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual bool	GetReleaseDataFlag () const
void	ReleaseDataFlagOff ()
void	ReleaseDataFlagOn ()
virtual void	SetReleaseDataFlag (bool flag)

virtual const bool &	GetUsingBiasFieldCorrection ()
virtual void	SetUsingBiasFieldCorrection (bool _arg)

virtual const bool &	GetUsingInterSliceIntensityCorrection ()
virtual void	SetUsingInterSliceIntensityCorrection (bool _arg)

virtual const bool &	GetUsingSlabIdentification ()
virtual void	SetUsingSlabIdentification (bool _arg)

	itkStaticConstMacro (OutputImageDimension, unsigned int, TOutputImage::ImageDimension)
	itkStaticConstMacro (InputImageDimension, unsigned int, TInputImage::ImageDimension)

virtual void	PopBackInput ()
virtual void	PopFrontInput ()
virtual void	PushBackInput (const InputImageType *image)
virtual void	PushFrontInput (const InputImageType *image)

void	SetStartingShrinkFactors (unsigned int *factors)
void	SetStartingShrinkFactors (unsigned int factor)
Static Public Member Functions
static void	BreakOnError ()
static bool	IsScheduleDownwardDivisible (const ScheduleType &schedule)
static Pointer	New ()

static bool	GetGlobalWarningDisplay ()
static void	GlobalWarningDisplayOff ()
static void	GlobalWarningDisplayOn ()
static void	SetGlobalWarningDisplay (bool flag)
Protected Types
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension)>	InputToOutputRegionCopierType
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension)>	OutputToInputRegionCopierType

typedef int	InternalReferenceCountType
Protected Member Functions
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)
void	Log1PImage (InternalImageType source, InternalImageType target)
	MRIBiasFieldCorrectionFilter ()
bool	PrintObservers (std::ostream &os, Indent indent) const
void	PrintSelf (std::ostream &os, Indent indent) const
virtual void	PropagateResetPipeline ()
virtual void	ReleaseInputs ()
virtual void	RestoreInputReleaseDataFlags ()
void	SetNumberOfInputs (unsigned int num)
void	SetNumberOfOutputs (unsigned int num)
virtual int	SplitRequestedRegion (int i, int num, OutputImageRegionType &splitRegion)
virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, int threadId) ITK_NO_RETURN
virtual	~MRIBiasFieldCorrectionFilter ()

virtual void	AddInput (DataObject *input)
virtual const unsigned int &	GetNumberOfRequiredInputs ()
virtual void	RemoveInput (DataObject *input)
virtual void	SetNthInput (unsigned int num, DataObject *input)
virtual void	SetNumberOfRequiredInputs (unsigned int _arg)

virtual void	AddOutput (DataObject *output)
virtual const unsigned int &	GetNumberOfRequiredOutputs ()
virtual void	RemoveOutput (DataObject *output)
virtual void	SetNthOutput (unsigned int num, DataObject *output)
virtual void	SetNumberOfRequiredOutputs (unsigned int _arg)

const DataObject *	GetInput (unsigned int idx) const

const DataObject *	GetOutput (unsigned int idx) const

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

void	PushBackInput (const DataObject *input)
void	PushFrontInput (const DataObject *input)
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

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

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected 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 >