itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights > Class Template Reference

#include <itkMultiLabelSTAPLEImageFilter.h>

Inheritance diagram for itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >:

Collaboration diagram for itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >:

Detailed Description

template<typename TInputImage, typename TOutputImage = TInputImage, typename TWeights = float>
class itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >

This filter performs a pixelwise combination of an arbitrary number of input images, where each of them represents a segmentation of the same scene (i.e., image).

The labelings in the images are weighted relative to each other based on their "performance" as estimated by an expectation-maximization algorithm. In the process, a ground truth segmentation is estimated, and the estimated performances of the individual segmentations are relative to this estimated ground truth.

The algorithm is based on the binary STAPLE algorithm by Warfield et al. as published originally in

S. Warfield, K. Zou, W. Wells, "Validation of image segmentation and expert quality with an expectation-maximization algorithm" in MICCAI 2002: Fifth International Conference on Medical Image Computing and Computer-Assisted Intervention, Springer-Verlag, Heidelberg, Germany, 2002, pp. 298-306

The multi-label algorithm implemented here is described in detail in

T. Rohlfing, D. B. Russakoff, and C. R. Maurer, Jr., "Performance-based classifier combination in atlas-based image segmentation using expectation-maximization parameter estimation," IEEE Transactions on Medical Imaging, vol. 23, pp. 983-994, Aug. 2004.

INPUTS

All input volumes to this filter must be segmentations of an image, that is, they must have discrete pixel values where each value represents a different segmented object.

Input volumes must all contain the same size RequestedRegions. Not all input images must contain all possible labels, but all label values must have the same meaning in all images.

The filter can optionally be provided with estimates for the a priori class probabilities through the SetPriorProbabilities function. If no estimate is provided, one is automatically generated by analyzing the relative frequencies of the labels in the input images.

OUTPUTS

The filter produces a single output volume. Each output pixel contains the label that has the highest probability of being the correct label, based on the performance models of the individual segmentations. If the maximum probaility is not unique, i.e., if more than one label have a maximum probability, then an "undecided" label is assigned to that output pixel.

By default, the label used for undecided pixels is the maximum label value used in the input images plus one. Since it is possible for an image with 8 bit pixel values to use all 256 possible label values, it is permissible to combine 8 bit (i.e., byte) images into a 16 bit (i.e., short) output image.

In addition to the combined image, the estimated confusion matrices for each of the input segmentations can be obtained through the GetConfusionMatrix member function.

PARAMETERS

The label used for "undecided" labels can be set using SetLabelForUndecidedPixels. This functionality can be unset by calling UnsetLabelForUndecidedPixels.

A termination threshold for the EM iteration can be defined by calling SetTerminationUpdateThreshold. The iteration terminates once no single parameter of any confusion matrix changes by less than this threshold. Alternatively, a maximum number of iterations can be specified by calling SetMaximumNumberOfIterations. The algorithm may still terminate after a smaller number of iterations if the termination threshold criterion is satisfied.

EVENTS

This filter invokes IterationEvent() at each iteration of the E-M algorithm. Setting the AbortGenerateData() flag will cause the algorithm to halt after the current iteration and produce results just as if it had converged. The algorithm makes no attempt to report its progress since the number of iterations needed cannot be known in advance.

Author

Torsten Rohlfing, SRI International, Neuroscience Program

Definition at line 117 of file itkMultiLabelSTAPLEImageFilter.h.

Public Types
typedef Array2D< WeightsType >	ConfusionMatrixType
typedef SmartPointer< const Self >	ConstPointer
typedef ImageRegionConstIterator < TInputImage >	InputConstIteratorType
typedef InputImageType::Pointer	InputImagePointer
typedef TInputImage	InputImageType
typedef TInputImage::PixelType	InputPixelType
typedef OutputImageType::Pointer	OutputImagePointer
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef TOutputImage	OutputImageType
typedef ImageRegionIterator < TOutputImage >	OutputIteratorType
typedef TOutputImage::PixelType	OutputPixelType
typedef SmartPointer< Self >	Pointer
typedef Array< WeightsType >	PriorProbabilitiesType
typedef MultiLabelSTAPLEImageFilter	Self
typedef ImageToImageFilter < TInputImage, TOutputImage >	Superclass
typedef TWeights	WeightsType
Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef SmartPointer< const Self >	ConstPointer
typedef InputImageType::ConstPointer	InputImageConstPointer
typedef InputImageType::PixelType	InputImagePixelType
typedef InputImageType::Pointer	InputImagePointer
typedef InputImageType::RegionType	InputImageRegionType
typedef TInputImage	InputImageType
typedef Superclass::OutputImagePixelType	OutputImagePixelType
typedef Superclass::OutputImageRegionType	OutputImageRegionType
typedef SmartPointer< Self >	Pointer
typedef ImageToImageFilter	Self
typedef ImageSource< TOutputImage >	Superclass
Public Types inherited from itk::ImageSource< TOutputImage >
typedef SmartPointer< const Self >	ConstPointer
typedef Superclass::DataObjectIdentifierType	DataObjectIdentifierType
typedef DataObject::Pointer	DataObjectPointer
typedef Superclass::DataObjectPointerArraySizeType	DataObjectPointerArraySizeType
typedef OutputImageType::PixelType	OutputImagePixelType
typedef OutputImageType::Pointer	OutputImagePointer
typedef OutputImageType::RegionType	OutputImageRegionType
typedef TOutputImage	OutputImageType
typedef SmartPointer< Self >	Pointer
typedef ImageSource	Self
typedef ProcessObject	Superclass
Public Types inherited from itk::ProcessObject
typedef SmartPointer< const Self >	ConstPointer
typedef DataObject::DataObjectIdentifierType	DataObjectIdentifierType
typedef DataObject::Pointer	DataObjectPointer
typedef std::vector < DataObjectPointer >	DataObjectPointerArray
typedef DataObjectPointerArray::size_type	DataObjectPointerArraySizeType
typedef std::vector < DataObjectIdentifierType >	NameArray
typedef SmartPointer< Self >	Pointer
typedef ProcessObject	Self
typedef Object	Superclass
Public Types inherited from itk::Object
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef Object	Self
typedef LightObject	Superclass
Public Types inherited from itk::LightObject
typedef SmartPointer< const Self >	ConstPointer
typedef SmartPointer< Self >	Pointer
typedef LightObject	Self

Public Member Functions
virtual ::itk::LightObject::Pointer	CreateAnother (void) const
ConfusionMatrixType	GetConfusionMatrix (const unsigned int i)
OutputPixelType	GetLabelForUndecidedPixels () const
virtual const char *	GetNameOfClass () const
PriorProbabilitiesType	GetPriorProbabilities () const
void	SetMaximumNumberOfIterations (const unsigned int mit)
void	UnsetMaximumNumberOfIterations ()
void	SetTerminationUpdateThreshold (const TWeights thresh)
void	SetLabelForUndecidedPixels (const OutputPixelType l)
void	UnsetLabelForUndecidedPixels ()
void	SetPriorProbabilities (const PriorProbabilitiesType &ppa)
void	UnsetPriorProbabilities ()
Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual double	GetCoordinateTolerance ()
const InputImageType *	GetInput (void) const
const InputImageType *	GetInput (unsigned int idx) const
virtual void	PopBackInput ()
virtual void	PopFrontInput ()
virtual void	PushBackInput (const InputImageType *image)
virtual void	PushFrontInput (const InputImageType *image)
virtual void	SetCoordinateTolerance (double _arg)
virtual void	SetInput (const InputImageType *image)
virtual void	SetInput (unsigned int, const TInputImage *image)
virtual void	SetDirectionTolerance (double _arg)
virtual double	GetDirectionTolerance ()
Public Member Functions inherited from itk::ImageSource< TOutputImage >
OutputImageType *	GetOutput (unsigned int idx)
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
virtual void	GraftOutput (DataObject *output)
virtual void	GraftOutput (const DataObjectIdentifierType &key, DataObject *output)
OutputImageType *	GetOutput (void)
const OutputImageType *	GetOutput (void) const
virtual ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx)
Public Member Functions inherited from itk::ProcessObject
virtual void	AbortGenerateDataOff ()
virtual void	AbortGenerateDataOn ()
virtual const bool &	GetAbortGenerateData ()
NameArray	GetInputNames () const
MultiThreader *	GetMultiThreader () const
DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const
DataObjectPointerArraySizeType	GetNumberOfInputs () const
DataObjectPointerArraySizeType	GetNumberOfOutputs () const
virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const
NameArray	GetOutputNames () const
virtual const float &	GetProgress ()
NameArray	GetRequiredInputNames () const
bool	HasInput (const DataObjectIdentifierType &key) const
bool	HasOutput (const DataObjectIdentifierType &key) const
virtual DataObjectPointer	MakeOutput (const DataObjectIdentifierType &)
virtual void	PrepareOutputs ()
virtual void	PropagateRequestedRegion (DataObject *output)
virtual void	ResetPipeline ()
virtual void	SetAbortGenerateData (bool _arg)
virtual void	SetProgress (float _arg)
virtual void	Update ()
virtual void	UpdateLargestPossibleRegion ()
virtual void	UpdateOutputData (DataObject *output)
virtual void	UpdateOutputInformation ()
void	UpdateProgress (float amount)
DataObjectPointerArray	GetInputs ()
DataObjectPointerArray	GetOutputs ()
DataObjectPointerArray	GetIndexedInputs ()
DataObjectPointerArray	GetIndexedOutputs ()
DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const
virtual void	SetReleaseDataFlag (bool flag)
virtual bool	GetReleaseDataFlag () const
void	ReleaseDataFlagOn ()
void	ReleaseDataFlagOff ()
virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)
virtual const bool &	GetReleaseDataBeforeUpdateFlag ()
virtual void	ReleaseDataBeforeUpdateFlagOn ()
virtual void	ReleaseDataBeforeUpdateFlagOff ()
virtual void	SetNumberOfThreads (ThreadIdType _arg)
virtual const ThreadIdType &	GetNumberOfThreads ()
Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)
unsigned long	AddObserver (const EventObject &event, Command *) const
virtual void	DebugOff () const
virtual void	DebugOn () const
Command *	GetCommand (unsigned long tag)
bool	GetDebug () const
MetaDataDictionary &	GetMetaDataDictionary (void)
const MetaDataDictionary &	GetMetaDataDictionary (void) const
virtual ModifiedTimeType	GetMTime () const
virtual const TimeStamp &	GetTimeStamp () const
bool	HasObserver (const EventObject &event) const
void	InvokeEvent (const EventObject &)
void	InvokeEvent (const EventObject &) const
virtual void	Modified () const
virtual void	Register () const
void	RemoveAllObservers ()
void	RemoveObserver (unsigned long tag)
void	SetDebug (bool debugFlag) const
void	SetMetaDataDictionary (const MetaDataDictionary &rhs)
virtual void	SetReferenceCount (int)
virtual void	UnRegister () const
Public Member Functions inherited from itk::LightObject
virtual void	Delete ()
virtual int	GetReferenceCount () const
	itkCloneMacro (Self)
void	Print (std::ostream &os, Indent indent=0) const

Static Public Member Functions
static Pointer	New ()

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

Protected Member Functions
TInputImage::PixelType	ComputeMaximumInputValue ()
void	EnlargeOutputRequestedRegion (DataObject *)
void	GenerateData ()
void	GenerateInputRequestedRegion ()
	MultiLabelSTAPLEImageFilter ()
void	PrintSelf (std::ostream &, Indent) const
virtual	~MultiLabelSTAPLEImageFilter ()
Protected Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)
virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)
virtual void	VerifyInputInformation ()
void	PushBackInput (const DataObject *input)
void	PushFrontInput (const DataObject *input)
	ImageToImageFilter ()
	~ImageToImageFilter ()
Protected Member Functions inherited from itk::ImageSource< TOutputImage >
virtual void	AfterThreadedGenerateData ()
virtual void	AllocateOutputs ()
virtual void	BeforeThreadedGenerateData ()
	ImageSource ()
virtual unsigned int	SplitRequestedRegion (unsigned int i, unsigned int num, OutputImageRegionType &splitRegion)
virtual void	ThreadedGenerateData (const OutputImageRegionType &outputRegionForThread, ThreadIdType threadId)
virtual	~ImageSource ()
Protected Member Functions inherited from itk::ProcessObject
virtual void	AddInput (DataObject *input)
virtual void	AddOutput (DataObject *output)
bool	AddRequiredInputName (const DataObjectIdentifierType &)
virtual void	CacheInputReleaseDataFlags ()
virtual void	GenerateOutputInformation ()
virtual void	GenerateOutputRequestedRegion (DataObject *output)
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs ()
bool	IsIndexedInputName (const DataObjectIdentifierType &) const
bool	IsIndexedOutputName (const DataObjectIdentifierType &) const
bool	IsRequiredInputName (const DataObjectIdentifierType &) const
	itkLegacyMacro (virtual void RemoveInput(DataObject *input))
	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))
	itkLegacyMacro (void SetNumberOfInputs(DataObjectPointerArraySizeType num))
	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))
DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const
DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const
DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const
DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const
	ProcessObject ()
virtual void	PropagateResetPipeline ()
virtual void	ReleaseInputs ()
virtual void	RemoveInput (const DataObjectIdentifierType &key)
virtual void	RemoveInput (DataObjectPointerArraySizeType)
virtual void	RemoveOutput (const DataObjectIdentifierType &key)
virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)
bool	RemoveRequiredInputName (const DataObjectIdentifierType &)
virtual void	RestoreInputReleaseDataFlags ()
virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)
virtual void	SetNthInput (DataObjectPointerArraySizeType num, DataObject *input)
virtual void	SetNthOutput (DataObjectPointerArraySizeType num, DataObject *output)
void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)
void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)
virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)
virtual void	SetOutput (const DataObjectIdentifierType &key, DataObject *output)
virtual void	SetPrimaryInput (DataObject *input)
virtual void	SetPrimaryOutput (DataObject *output)
void	SetRequiredInputNames (const NameArray &)
virtual void	VerifyPreconditions ()
	~ProcessObject ()
DataObject *	GetInput (const DataObjectIdentifierType &key)
const DataObject *	GetInput (const DataObjectIdentifierType &key) const
DataObject *	GetInput (DataObjectPointerArraySizeType)
const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryInput ()
const DataObject *	GetPrimaryInput () const
virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)
virtual const char *	GetPrimaryInputName () const
DataObject *	GetOutput (const DataObjectIdentifierType &key)
const DataObject *	GetOutput (const DataObjectIdentifierType &key) const
virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)
virtual const char *	GetPrimaryOutputName () const
DataObject *	GetOutput (DataObjectPointerArraySizeType idx)
const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const
DataObject *	GetPrimaryOutput ()
const DataObject *	GetPrimaryOutput () const
virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)
virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs ()
Protected Member Functions inherited from itk::Object
	Object ()
bool	PrintObservers (std::ostream &os, Indent indent) const
virtual void	SetTimeStamp (const TimeStamp &time)
virtual	~Object ()
Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const
	LightObject ()
virtual void	PrintHeader (std::ostream &os, Indent indent) const
virtual void	PrintTrailer (std::ostream &os, Indent indent) const
virtual	~LightObject ()

Private Member Functions
void	AllocateConfusionMatrixArray ()
void	InitializeConfusionMatrixArrayFromVoting ()
void	InitializePriorProbabilities ()
	MultiLabelSTAPLEImageFilter (const Self &)
void	operator= (const Self &)

Private Attributes
std::vector< ConfusionMatrixType >	m_ConfusionMatrixArray
bool	m_HasLabelForUndecidedPixels
bool	m_HasMaximumNumberOfIterations
bool	m_HasPriorProbabilities
OutputPixelType	m_LabelForUndecidedPixels
unsigned int	m_MaximumNumberOfIterations
PriorProbabilitiesType	m_PriorProbabilities
TWeights	m_TerminationUpdateThreshold
InputPixelType	m_TotalLabelCount
std::vector< ConfusionMatrixType >	m_UpdatedConfusionMatrixArray

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(OutputImageDimension), itkGetStaticConstMacro(InputImageDimension) >	InputToOutputRegionCopierType
typedef ImageToImageFilterDetail::ImageRegionCopier < itkGetStaticConstMacro(InputImageDimension), itkGetStaticConstMacro(OutputImageDimension) >	OutputToInputRegionCopierType
Static Protected Member Functions inherited from itk::ImageSource< TOutputImage >
static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)
Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime
bool	m_Updating

Member Typedef Documentation

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef Array2D<WeightsType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ConfusionMatrixType

Definition at line 158 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef SmartPointer< const Self > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ConstPointer

Definition at line 125 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef ImageRegionConstIterator< TInputImage > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputConstIteratorType

Iterator types.

Definition at line 153 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef InputImageType::Pointer itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputImagePointer

Definition at line 146 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef TInputImage itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputImageType

Image typedef support

Definition at line 144 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef TInputImage::PixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputPixelType

Definition at line 136 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef OutputImageType::Pointer itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImagePointer

Definition at line 147 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef Superclass::OutputImageRegionType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImageRegionType

Superclass typedefs.

Definition at line 150 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef TOutputImage itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImageType

Definition at line 145 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef ImageRegionIterator< TOutputImage > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputIteratorType

Definition at line 154 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef TOutputImage::PixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputPixelType

Extract some information from the image types. Dimensionality of the two images is assumed to be the same.

Definition at line 131 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef SmartPointer< Self > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Pointer

Definition at line 124 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef Array<WeightsType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::PriorProbabilitiesType

Definition at line 159 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef MultiLabelSTAPLEImageFilter itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Self

Standard class typedefs.

Definition at line 122 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef ImageToImageFilter< TInputImage, TOutputImage > itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Superclass

Definition at line 123 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

typedef TWeights itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::WeightsType

Confusion matrix typedefs.

Definition at line 157 of file itkMultiLabelSTAPLEImageFilter.h.

Constructor & Destructor Documentation

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::MultiLabelSTAPLEImageFilter ( )

inlineprotected

Definition at line 266 of file itkMultiLabelSTAPLEImageFilter.h.

References itk::Math::e.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

virtual itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::~MultiLabelSTAPLEImageFilter ( )

inlineprotectedvirtual

Definition at line 273 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::MultiLabelSTAPLEImageFilter ( const Self &  )

private

Member Function Documentation

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::AllocateConfusionMatrixArray ( )

private

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

TInputImage::PixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ComputeMaximumInputValue ( )

protected

Determine maximum value among all input images' pixels

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

virtual::itk::LightObject::Pointer itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::CreateAnother ( void  ) const

virtual

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

Reimplemented from itk::Object.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::EnlargeOutputRequestedRegion ( DataObject *  )

protectedvirtual

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.

Reimplemented from itk::ProcessObject.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GenerateData ( )

protectedvirtual

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

See Also

ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GenerateInputRequestedRegion ( )

protectedvirtual

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 hierarchy. 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::ImageToImageFilter< TInputImage, TOutputImage >.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

ConfusionMatrixType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetConfusionMatrix ( const unsigned int  i )

inline

Get confusion matrix for the i-th input segmentation.

Definition at line 260 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

OutputPixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetLabelForUndecidedPixels ( ) const

inline

Get label value used for undecided pixels. After updating the filter, this function returns the actual label value used for undecided pixels in the current output. Note that this value is overwritten when SetLabelForUndecidedPixels is called and the new value only becomes effective upon the next filter update.

Definition at line 208 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

virtual const char* itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetNameOfClass ( ) const

virtual

Run-time type information (and related methods)

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

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

PriorProbabilitiesType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetPriorProbabilities ( ) const

inline

Get prior class probabilities. After updating the filter, this function returns the actual prior class probabilities. If these were not previously set by a call to SetPriorProbabilities, then they are estimated from the input segmentations and the result is available through this function.

Definition at line 241 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InitializeConfusionMatrixArrayFromVoting ( )

private

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InitializePriorProbabilities ( )

private

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

static Pointer itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::New ( )

static

Method for creation through the object factory.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::operator= ( const Self &  )

private

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

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

protectedvirtual

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

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

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetLabelForUndecidedPixels ( const OutputPixelType  l )

inline

Set label value for undecided pixels.

Definition at line 194 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetMaximumNumberOfIterations ( const unsigned int  mit )

inline

Set maximum number of iterations.

Definition at line 163 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetPriorProbabilities ( const PriorProbabilitiesType &  ppa )

inline

Set label value for undecided pixels.

Definition at line 227 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetTerminationUpdateThreshold ( const TWeights  thresh )

inline

Set termination threshold based on confusion matrix parameter updates.

Definition at line 185 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::UnsetLabelForUndecidedPixels ( )

inline

Unset label value for undecided pixels and turn on automatic selection.

Definition at line 215 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::UnsetMaximumNumberOfIterations ( )

inline

Unset label value for undecided pixels and turn on automatic selection.

Definition at line 173 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::UnsetPriorProbabilities ( )

inline

Unset prior class probabilities and turn on automatic estimation.

Definition at line 248 of file itkMultiLabelSTAPLEImageFilter.h.

Member Data Documentation

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

const unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::ImageDimension = TOutputImage::ImageDimension

static

Extract some information from the image types. Dimensionality of the two images is assumed to be the same.

Definition at line 141 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

std::vector<ConfusionMatrixType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_ConfusionMatrixArray

private

Definition at line 302 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasLabelForUndecidedPixels

private

Definition at line 295 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasMaximumNumberOfIterations

private

Definition at line 308 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasPriorProbabilities

private

Definition at line 297 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

OutputPixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_LabelForUndecidedPixels

private

Definition at line 294 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_MaximumNumberOfIterations

private

Definition at line 309 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

PriorProbabilitiesType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_PriorProbabilities

private

Definition at line 298 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

TWeights itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_TerminationUpdateThreshold

private

Definition at line 311 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

InputPixelType itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_TotalLabelCount

private

Definition at line 292 of file itkMultiLabelSTAPLEImageFilter.h.

template<typename TInputImage , typename TOutputImage = TInputImage, typename TWeights = float>

std::vector<ConfusionMatrixType> itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_UpdatedConfusionMatrixArray

private

Definition at line 303 of file itkMultiLabelSTAPLEImageFilter.h.

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

• itkMultiLabelSTAPLEImageFilter.h