#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 118 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 MultiThreader	MultiThreaderType

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 () const

const ConfusionMatrixType &	GetConfusionMatrix (const unsigned int i) const

virtual unsigned int	GetElapsedNumberOfIterations () const

virtual bool	GetHasLabelForUndecidedPixels ()

virtual bool	GetHasMaximumNumberOfIterations () const

virtual bool	GetHasPriorProbabilities ()

virtual OutputPixelType	GetLabelForUndecidedPixels ()

virtual const char *	GetNameOfClass () const

virtual const PriorProbabilitiesType &	GetPriorProbabilities () const


void	SetMaximumNumberOfIterations (const unsigned int mit)

virtual unsigned int	GetMaximumNumberOfIterations () const


void	UnsetMaximumNumberOfIterations ()


virtual void	SetTerminationUpdateThreshold (TWeights _arg)

virtual TWeights	GetTerminationUpdateThreshold () const


void	SetLabelForUndecidedPixels (const OutputPixelType l)


void	UnsetLabelForUndecidedPixels ()


void	SetPriorProbabilities (const PriorProbabilitiesType &ppa)


void	UnsetPriorProbabilities ()

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

const InputImageType *	GetInput (unsigned int idx) const

virtual void	PopBackInput () override

virtual void	PopFrontInput () override

virtual void	PushBackInput (const InputImageType *image)

virtual void	PushFrontInput (const InputImageType *image)

virtual void	SetInput (const InputImageType *image)

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

virtual void	SetCoordinateTolerance (double _arg)

virtual double	GetCoordinateTolerance () const

virtual void	SetDirectionTolerance (double _arg)

virtual double	GetDirectionTolerance () const

Public Member Functions inherited from itk::ImageSource< TOutputImage >
OutputImageType *	GetOutput (unsigned int idx)

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

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

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *output)

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

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

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

virtual void	AbortGenerateDataOn ()

virtual const bool &	GetAbortGenerateData () const

DataObjectPointerArray	GetIndexedInputs ()

DataObjectPointerArray	GetIndexedOutputs ()

NameArray	GetInputNames () const

DataObjectPointerArray	GetInputs ()

MultiThreaderType *	GetMultiThreader () const

DataObjectPointerArraySizeType	GetNumberOfIndexedInputs () const

DataObjectPointerArraySizeType	GetNumberOfIndexedOutputs () const

DataObjectPointerArraySizeType	GetNumberOfInputs () const

DataObjectPointerArraySizeType	GetNumberOfOutputs () const

virtual DataObjectPointerArraySizeType	GetNumberOfValidRequiredInputs () const

NameArray	GetOutputNames () const

DataObjectPointerArray	GetOutputs ()

virtual const float &	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (float progress)

void	SetProgress (float progress)

virtual void	SetReleaseDataFlag (bool flag)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	ReleaseDataBeforeUpdateFlagOff ()

virtual void	SetNumberOfThreads (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfThreads () const

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 ()

const MetaDataDictionary &	GetMetaDataDictionary () const

virtual ModifiedTimeType	GetMTime () const

virtual const TimeStamp &	GetTimeStamp () const

bool	HasObserver (const EventObject &event) const

void	InvokeEvent (const EventObject &)

void	InvokeEvent (const EventObject &) const

virtual void	Modified () const

virtual void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

virtual void	SetReferenceCount (int) override

virtual void	UnRegister () const noexceptoverride

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () 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 Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()

static void	GlobalWarningDisplayOff ()

static void	GlobalWarningDisplayOn ()

static Pointer	New ()

static void	SetGlobalWarningDisplay (bool flag)

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

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 *) override

void	GenerateData () override

void	GenerateInputRequestedRegion () override

	MultiLabelSTAPLEImageFilter ()

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

virtual	~MultiLabelSTAPLEImageFilter () override

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)

	ImageToImageFilter ()

virtual void	VerifyInputInformation () override

	~ImageToImageFilter () override

void	PushBackInput (const DataObject *input) override

void	PushFrontInput (const DataObject *input) override

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

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

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

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

virtual	~ImageSource () override

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

void	AddOptionalInputName (const DataObjectIdentifierType &)

void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	AddOutput (DataObject *output)

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

	itkLegacyMacro (virtual void RemoveOutput(DataObject *output))

	itkLegacyMacro (void SetNumberOfOutputs(DataObjectPointerArraySizeType num))

	itkLegacyMacro (virtual void RemoveInput(DataObject *input))

	itkLegacyMacro (void SetNumberOfInputs(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	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

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 () override

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName (void) const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName (void) const

DataObject *	GetOutput (DataObjectPointerArraySizeType idx)

const DataObject *	GetOutput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

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

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

virtual void	SetTimeStamp (const TimeStamp &time)

virtual	~Object () override

Protected Member Functions inherited from itk::LightObject
virtual LightObject::Pointer	InternalClone () const

	LightObject ()

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

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

virtual	~LightObject ()

Private Member Functions
void	AllocateConfusionMatrixArray ()

void	InitializeConfusionMatrixArrayFromVoting ()

void	InitializePriorProbabilities ()

Private Attributes
std::vector< ConfusionMatrixType >	m_ConfusionMatrixArray

unsigned int	m_ElapsedNumberOfIterations

bool	m_HasLabelForUndecidedPixels

bool	m_HasMaximumNumberOfIterations

bool	m_HasPriorProbabilities

OutputPixelType	m_LabelForUndecidedPixels

unsigned int	m_MaximumNumberOfIterations

PriorProbabilitiesType	m_PriorProbabilities

TWeights	m_TerminationUpdateThreshold

vcl_size_t	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 const ImageRegionSplitterBase *	GetGlobalDefaultSplitter ()

static ITK_THREAD_RETURN_TYPE	ThreaderCallback (void *arg)

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime

bool	m_Updating

Protected Attributes inherited from itk::LightObject
AtomicInt< int >	m_ReferenceCount

Member Typedef Documentation

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

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

Definition at line 159 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 126 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 154 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 147 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 145 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 137 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 148 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 151 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

Definition at line 146 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 155 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 132 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 125 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 160 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 123 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 124 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 158 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 277 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

inlineoverrideprotectedvirtual

Definition at line 288 of file itkMultiLabelSTAPLEImageFilter.h.

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 ( ) 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 * )

overrideprotectedvirtual

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 ( )

overrideprotectedvirtual

A version of GenerateData() specific for image processing filters. This implementation will split the processing across multiple threads. The buffer is allocated by this method. Then the BeforeThreadedGenerateData() method is called (if provided). Then, a series of threads are spawned each calling 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 ( )

overrideprotectedvirtual

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>

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

inline

Get confusion matrix for the i-th input segmentation.

Definition at line 271 of file itkMultiLabelSTAPLEImageFilter.h.

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

virtual unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetElapsedNumberOfIterations ( ) const

virtual

Get the number of elapsed iterations of the iterative E-M algorithm.

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

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

virtual

True if LabelForUndecidedPixels has been manually set.

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

virtual bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetHasMaximumNumberOfIterations ( ) const

virtual

True if the MaximumNumberOfIterations has been manually set.

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

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

virtual

True if PriorProbabilities has been manually set.

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

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

virtual

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.

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

virtual unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::GetMaximumNumberOfIterations ( ) const

virtual

Set maximum number of iterations.

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>

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

virtual

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.

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

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

virtual

Set termination threshold based on confusion matrix parameter updates.

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

overrideprotectedvirtual

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

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

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 199 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 167 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 manual estimates for the a priori class probabilities.

 The size of the array must be greater than the value of the
 largest label. The index into the array corresponds to the label
 value in the segmented image for the class.

Definition at line 237 of file itkMultiLabelSTAPLEImageFilter.h.

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

virtual void itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::SetTerminationUpdateThreshold ( TWeights _arg )

virtual

Set termination threshold based on confusion matrix parameter updates.

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 221 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

inline

Unset the maximum number of iterations, and rely on the TerminationUpdateThreshold.

Definition at line 181 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 259 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 142 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 316 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

private

Definition at line 324 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 309 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 322 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 311 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 308 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 323 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 312 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 326 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

private

Definition at line 304 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 317 of file itkMultiLabelSTAPLEImageFilter.h.

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

itkMultiLabelSTAPLEImageFilter.h

Detailed Description

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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