#include <itkMultiLabelSTAPLEImageFilter.h>

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 probability 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 119 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

Public Types
using	ConfusionMatrixType = Array2D< WeightsType >

using	ConstPointer = SmartPointer< const Self >

using	InputConstIteratorType = ImageRegionConstIterator< TInputImage >

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageType = TInputImage

using	InputPixelType = typename TInputImage::PixelType

using	OutputImagePointer = typename OutputImageType::Pointer

using	OutputImageType = TOutputImage

using	OutputIteratorType = ImageRegionIterator< TOutputImage >

using	OutputPixelType = typename TOutputImage::PixelType

using	Pointer = SmartPointer< Self >

using	PriorProbabilitiesType = Array< WeightsType >

using	Self = MultiLabelSTAPLEImageFilter

using	Superclass = ImageToImageFilter< TInputImage, TOutputImage >

using	WeightsType = TWeights

Public Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
using	ConstPointer = SmartPointer< const Self >

using	InputImageConstPointer = typename InputImageType::ConstPointer

using	InputImagePixelType = typename InputImageType::PixelType

using	InputImagePointer = typename InputImageType::Pointer

using	InputImageRegionType = typename InputImageType::RegionType

using	InputImageType = TInputImage

using	Pointer = SmartPointer< Self >

using	Self = ImageToImageFilter

using	Superclass = ImageSource< TOutputImage >

Public Types inherited from itk::ImageSource< TOutputImage >
using	ConstPointer = SmartPointer< const Self >

using	DataObjectIdentifierType = Superclass::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArraySizeType = Superclass::DataObjectPointerArraySizeType

using	OutputImagePixelType = typename OutputImageType::PixelType

using	OutputImagePointer = typename OutputImageType::Pointer

using	OutputImageRegionType = typename OutputImageType::RegionType

using	OutputImageType = TOutputImage

using	Pointer = SmartPointer< Self >

using	Self = ImageSource

using	Superclass = ProcessObject

Public Types inherited from itk::ProcessObject
using	ConstPointer = SmartPointer< const Self >

using	DataObjectIdentifierType = DataObject::DataObjectIdentifierType

using	DataObjectPointer = DataObject::Pointer

using	DataObjectPointerArray = std::vector< DataObjectPointer >

using	DataObjectPointerArraySizeType = DataObjectPointerArray::size_type

using	MultiThreaderType = MultiThreaderBase

using	NameArray = std::vector< DataObjectIdentifierType >

using	Pointer = SmartPointer< Self >

using	Self = ProcessObject

using	Superclass = Object

Public Types inherited from itk::Object
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = Object

using	Superclass = LightObject

Public Types inherited from itk::LightObject
using	ConstPointer = SmartPointer< const Self >

using	Pointer = SmartPointer< Self >

using	Self = LightObject

Public Member Functions
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 ()

const char *	GetNameOfClass () const override

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

void	PopBackInput () override

void	PopFrontInput () override

virtual void	PushBackInput (const InputImageType *input)

virtual void	PushFrontInput (const InputImageType *input)

virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)

virtual void	SetInput (const InputImageType *input)

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

virtual void	SetCoordinateTolerance (double _arg)

virtual double	GetCoordinateTolerance () const

virtual void	SetDirectionTolerance (double _arg)

virtual double	GetDirectionTolerance () const

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

OutputImageType *	GetOutput ()

const OutputImageType *	GetOutput () const

virtual void	GraftOutput (DataObject *graft)

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

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

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

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

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

virtual 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 float	GetProgress () const

NameArray	GetRequiredInputNames () const

bool	HasInput (const DataObjectIdentifierType &key) const

bool	HasOutput (const DataObjectIdentifierType &key) const

void	IncrementProgress (float increment)

virtual void	PrepareOutputs ()

virtual void	PropagateRequestedRegion (DataObject *output)

virtual void	ResetPipeline ()

virtual void	SetAbortGenerateData (bool _arg)

void	SetMultiThreader (MultiThreaderType *threader)

virtual void	Update ()

virtual void	UpdateLargestPossibleRegion ()

virtual void	UpdateOutputData (DataObject *output)

virtual void	UpdateOutputInformation ()

void	UpdateProgress (float progress)

virtual void	SetReleaseDataFlag (bool val)

virtual bool	GetReleaseDataFlag () const

void	ReleaseDataFlagOn ()

void	ReleaseDataFlagOff ()

virtual void	SetReleaseDataBeforeUpdateFlag (bool _arg)

virtual const bool &	GetReleaseDataBeforeUpdateFlag () const

virtual void	ReleaseDataBeforeUpdateFlagOn ()

virtual void	SetNumberOfWorkUnits (ThreadIdType _arg)

virtual const ThreadIdType &	GetNumberOfWorkUnits () const

Public Member Functions inherited from itk::Object
unsigned long	AddObserver (const EventObject &event, Command *)

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

unsigned long	AddObserver (const EventObject &event, std::function< void(const EventObject &)> function) const

LightObject::Pointer	CreateAnother () const override

virtual void	DebugOff () const

virtual void	DebugOn () const

Command *	GetCommand (unsigned long tag)

bool	GetDebug () const

MetaDataDictionary &	GetMetaDataDictionary ()

const MetaDataDictionary &	GetMetaDataDictionary () const

virtual ModifiedTimeType	GetMTime () const

virtual const TimeStamp &	GetTimeStamp () const

bool	HasObserver (const EventObject &event) const

void	InvokeEvent (const EventObject &)

void	InvokeEvent (const EventObject &) const

virtual void	Modified () const

void	Register () const override

void	RemoveAllObservers ()

void	RemoveObserver (unsigned long tag)

void	SetDebug (bool debugFlag) const

void	SetReferenceCount (int) override

void	UnRegister () const noexcept override

void	SetMetaDataDictionary (const MetaDataDictionary &rhs)

void	SetMetaDataDictionary (MetaDataDictionary &&rrhs)

virtual void	SetObjectName (std::string _arg)

virtual const std::string &	GetObjectName () const

Public Member Functions inherited from itk::LightObject
Pointer	Clone () const

virtual void	Delete ()

virtual int	GetReferenceCount () const

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

Static Public Member Functions
static Pointer	New ()

Static Public Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
static double	GetGlobalDefaultCoordinateTolerance ()

static double	GetGlobalDefaultDirectionTolerance ()

static void	SetGlobalDefaultCoordinateTolerance (double)

static void	SetGlobalDefaultDirectionTolerance (double)

Static Public Member Functions inherited from itk::Object
static bool	GetGlobalWarningDisplay ()

static void	GlobalWarningDisplayOff ()

static void	GlobalWarningDisplayOn ()

static Pointer	New ()

static void	SetGlobalWarningDisplay (bool val)

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

static Pointer	New ()

Static Public Attributes
static constexpr unsigned int	ImageDimension = TOutputImage::ImageDimension

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

static constexpr unsigned int	OutputImageDimension = TOutputImage::ImageDimension

Static Public Attributes inherited from itk::ImageSource< TOutputImage >
static constexpr unsigned int	OutputImageDimension = TOutputImage::ImageDimension

Protected Member Functions
TInputImage::PixelType	ComputeMaximumInputValue ()

void	EnlargeOutputRequestedRegion (DataObject *) override

void	GenerateData () override

void	GenerateInputRequestedRegion () override

	MultiLabelSTAPLEImageFilter ()

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

	~MultiLabelSTAPLEImageFilter () override=default

Protected Member Functions inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
virtual void	CallCopyInputRegionToOutputRegion (OutputImageRegionType &destRegion, const InputImageRegionType &srcRegion)

virtual void	CallCopyOutputRegionToInputRegion (InputImageRegionType &destRegion, const OutputImageRegionType &srcRegion)

	ImageToImageFilter ()

void	VerifyInputInformation () ITKv5_CONST override

	~ImageToImageFilter () override=default

virtual void	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

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

virtual void	AllocateOutputs ()

virtual void	BeforeThreadedGenerateData ()

void	ClassicMultiThread (ThreadFunctionType callbackFunction)

virtual const ImageRegionSplitterBase *	GetImageRegionSplitter () const

	ImageSource ()

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

	~ImageSource () override=default

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

virtual void	DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread)

virtual bool	GetDynamicMultiThreading () const

virtual void	SetDynamicMultiThreading (bool _arg)

virtual void	DynamicMultiThreadingOn ()

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

void	AddOptionalInputName (const DataObjectIdentifierType &)

void	AddOptionalInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	AddOutput (DataObject *output)

bool	AddRequiredInputName (const DataObjectIdentifierType &)

bool	AddRequiredInputName (const DataObjectIdentifierType &, DataObjectPointerArraySizeType idx)

virtual void	CacheInputReleaseDataFlags ()

virtual void	GenerateOutputInformation ()

virtual void	GenerateOutputRequestedRegion (DataObject *output)

DataObject *	GetInput (const DataObjectIdentifierType &key)

const DataObject *	GetInput (const DataObjectIdentifierType &key) const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredInputs () const

virtual const DataObjectPointerArraySizeType &	GetNumberOfRequiredOutputs () const

bool	IsIndexedInputName (const DataObjectIdentifierType &) const

bool	IsIndexedOutputName (const DataObjectIdentifierType &) const

bool	IsRequiredInputName (const DataObjectIdentifierType &) const

DataObjectPointerArraySizeType	MakeIndexFromInputName (const DataObjectIdentifierType &name) const

DataObjectPointerArraySizeType	MakeIndexFromOutputName (const DataObjectIdentifierType &name) const

DataObjectIdentifierType	MakeNameFromInputIndex (DataObjectPointerArraySizeType idx) const

DataObjectIdentifierType	MakeNameFromOutputIndex (DataObjectPointerArraySizeType idx) const

	ProcessObject ()

virtual void	PropagateResetPipeline ()

virtual void	PushBackInput (const DataObject *input)

virtual void	PushFrontInput (const DataObject *input)

virtual void	ReleaseInputs ()

virtual void	RemoveInput (const DataObjectIdentifierType &key)

virtual void	RemoveInput (DataObjectPointerArraySizeType)

virtual void	RemoveOutput (const DataObjectIdentifierType &key)

virtual void	RemoveOutput (DataObjectPointerArraySizeType idx)

bool	RemoveRequiredInputName (const DataObjectIdentifierType &)

virtual void	RestoreInputReleaseDataFlags ()

virtual void	SetInput (const DataObjectIdentifierType &key, DataObject *input)

virtual void	SetNthInput (DataObjectPointerArraySizeType idx, DataObject *input)

virtual void	SetNthOutput (DataObjectPointerArraySizeType idx, DataObject *output)

void	SetNumberOfIndexedInputs (DataObjectPointerArraySizeType num)

void	SetNumberOfIndexedOutputs (DataObjectPointerArraySizeType num)

virtual void	SetNumberOfRequiredInputs (DataObjectPointerArraySizeType)

virtual void	SetNumberOfRequiredOutputs (DataObjectPointerArraySizeType _arg)

virtual void	SetOutput (const DataObjectIdentifierType &name, DataObject *output)

virtual void	SetPrimaryInput (DataObject *object)

virtual void	SetPrimaryOutput (DataObject *object)

void	SetRequiredInputNames (const NameArray &)

virtual void	VerifyPreconditions () ITKv5_CONST

	~ProcessObject () override

DataObject *	GetInput (DataObjectPointerArraySizeType idx)

const DataObject *	GetInput (DataObjectPointerArraySizeType idx) const

DataObject *	GetPrimaryInput ()

const DataObject *	GetPrimaryInput () const

virtual void	SetPrimaryInputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryInputName () const

DataObject *	GetOutput (const DataObjectIdentifierType &key)

const DataObject *	GetOutput (const DataObjectIdentifierType &key) const

virtual void	SetPrimaryOutputName (const DataObjectIdentifierType &key)

virtual const char *	GetPrimaryOutputName () const

DataObject *	GetOutput (DataObjectPointerArraySizeType i)

const DataObject *	GetOutput (DataObjectPointerArraySizeType i) const

DataObject *	GetPrimaryOutput ()

const DataObject *	GetPrimaryOutput () const

virtual bool	GetThreaderUpdateProgress () const

virtual void	ThreaderUpdateProgressOn ()

virtual void	SetThreaderUpdateProgress (bool arg)

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

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

virtual void	SetTimeStamp (const TimeStamp &timeStamp)

	~Object () override

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

	LightObject ()

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

virtual void	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 { 0u }

bool	m_HasLabelForUndecidedPixels { false }

bool	m_HasMaximumNumberOfIterations { false }

bool	m_HasPriorProbabilities { false }

OutputPixelType	m_LabelForUndecidedPixels {}

unsigned int	m_MaximumNumberOfIterations { 0 }

PriorProbabilitiesType	m_PriorProbabilities {}

TWeights	m_TerminationUpdateThreshold {}

vcl_size_t	m_TotalLabelCount { 0 }

std::vector< ConfusionMatrixType >	m_UpdatedConfusionMatrixArray {}

Additional Inherited Members
Protected Types inherited from itk::ImageToImageFilter< TInputImage, TOutputImage >
using	InputToOutputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::OutputImageDimension, Self::InputImageDimension >

using	OutputToInputRegionCopierType = ImageToImageFilterDetail::ImageRegionCopier< Self::InputImageDimension, Self::OutputImageDimension >

Static Protected Member Functions inherited from itk::ImageSource< TOutputImage >
static const ImageRegionSplitterBase *	GetGlobalDefaultSplitter ()

static ITK_THREAD_RETURN_FUNCTION_CALL_CONVENTION	ThreaderCallback (void *arg)

Static Protected Member Functions inherited from itk::ProcessObject
static constexpr float	progressFixedToFloat (uint32_t fixed)

static uint32_t	progressFloatToFixed (float f)

Protected Attributes inherited from itk::ImageSource< TOutputImage >
bool	m_DynamicMultiThreading {}

Protected Attributes inherited from itk::ProcessObject
TimeStamp	m_OutputInformationMTime {}

bool	m_Updating {}

Protected Attributes inherited from itk::LightObject
std::atomic< int >	m_ReferenceCount {}

Member Typedef Documentation

◆ ConfusionMatrixType

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

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

Definition at line 160 of file itkMultiLabelSTAPLEImageFilter.h.

◆ ConstPointer

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

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

Definition at line 128 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputConstIteratorType

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputConstIteratorType = ImageRegionConstIterator<TInputImage>

Iterator types.

Definition at line 155 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputImagePointer

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputImagePointer = typename InputImageType::Pointer

Definition at line 148 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputImageType

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputImageType = TInputImage

Image type alias support

Definition at line 146 of file itkMultiLabelSTAPLEImageFilter.h.

◆ InputPixelType

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::InputPixelType = typename TInputImage::PixelType

Definition at line 139 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputImagePointer

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImagePointer = typename OutputImageType::Pointer

Definition at line 149 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputImageType

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputImageType = TOutputImage

Definition at line 147 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputIteratorType

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputIteratorType = ImageRegionIterator<TOutputImage>

Definition at line 156 of file itkMultiLabelSTAPLEImageFilter.h.

◆ OutputPixelType

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::OutputPixelType = typename TOutputImage::PixelType

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

Definition at line 138 of file itkMultiLabelSTAPLEImageFilter.h.

◆ Pointer

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

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

Definition at line 127 of file itkMultiLabelSTAPLEImageFilter.h.

◆ PriorProbabilitiesType

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

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

Definition at line 161 of file itkMultiLabelSTAPLEImageFilter.h.

◆ Self

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Self = MultiLabelSTAPLEImageFilter

Standard class type aliases.

Definition at line 125 of file itkMultiLabelSTAPLEImageFilter.h.

◆ Superclass

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::Superclass = ImageToImageFilter<TInputImage, TOutputImage>

Definition at line 126 of file itkMultiLabelSTAPLEImageFilter.h.

◆ WeightsType

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

using itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::WeightsType = TWeights

Confusion matrix type alias.

Definition at line 159 of file itkMultiLabelSTAPLEImageFilter.h.

Constructor & Destructor Documentation

◆ MultiLabelSTAPLEImageFilter()

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

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

inlineprotected

Definition at line 285 of file itkMultiLabelSTAPLEImageFilter.h.

◆ ~MultiLabelSTAPLEImageFilter()

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

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

overrideprotecteddefault

Member Function Documentation

◆ AllocateConfusionMatrixArray()

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

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

private

◆ ComputeMaximumInputValue()

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

◆ EnlargeOutputRequestedRegion()

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 indicate 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.

◆ GenerateData()

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 DynamicThreadedGenerateData(). After all the threads have completed processing, the AfterThreadedGenerateData() method is called (if provided). If an image processing filter cannot be threaded, the filter should provide an implementation of GenerateData(). That implementation is responsible for allocating the output buffer. If a filter can be threaded, it should NOT provide a GenerateData() method but should provide a DynamicThreadedGenerateData() instead.

See also: ThreadedGenerateData()

Reimplemented from itk::ImageSource< TOutputImage >.

◆ GenerateInputRequestedRegion()

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 >.

◆ GetConfusionMatrix()

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 279 of file itkMultiLabelSTAPLEImageFilter.h.

◆ GetElapsedNumberOfIterations()

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.

◆ GetHasLabelForUndecidedPixels()

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.

◆ GetHasMaximumNumberOfIterations()

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.

◆ GetHasPriorProbabilities()

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.

◆ GetLabelForUndecidedPixels()

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.

◆ GetMaximumNumberOfIterations()

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.

◆ GetNameOfClass()

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

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

overridevirtual

See also: LightObject::GetNameOfClass()

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

◆ GetPriorProbabilities()

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.

◆ GetTerminationUpdateThreshold()

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.

◆ InitializeConfusionMatrixArrayFromVoting()

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

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

private

◆ InitializePriorProbabilities()

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

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

private

◆ New()

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.

◆ PrintSelf()

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 >.

◆ SetLabelForUndecidedPixels()

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 203 of file itkMultiLabelSTAPLEImageFilter.h.

◆ SetMaximumNumberOfIterations()

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 169 of file itkMultiLabelSTAPLEImageFilter.h.

◆ SetPriorProbabilities()

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 243 of file itkMultiLabelSTAPLEImageFilter.h.

◆ SetTerminationUpdateThreshold()

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.

◆ UnsetLabelForUndecidedPixels()

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 226 of file itkMultiLabelSTAPLEImageFilter.h.

◆ UnsetMaximumNumberOfIterations()

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 184 of file itkMultiLabelSTAPLEImageFilter.h.

◆ UnsetPriorProbabilities()

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 266 of file itkMultiLabelSTAPLEImageFilter.h.

Member Data Documentation

◆ ImageDimension

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

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

staticconstexpr

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

Definition at line 143 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_ConfusionMatrixArray

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

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

private

Definition at line 321 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_ElapsedNumberOfIterations

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

unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_ElapsedNumberOfIterations { 0u }

private

Definition at line 331 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_HasLabelForUndecidedPixels

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

bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasLabelForUndecidedPixels { false }

private

Definition at line 313 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_HasMaximumNumberOfIterations

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

bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasMaximumNumberOfIterations { false }

private

Definition at line 329 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_HasPriorProbabilities

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

bool itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_HasPriorProbabilities { false }

private

Definition at line 315 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_LabelForUndecidedPixels

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

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

private

Definition at line 312 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_MaximumNumberOfIterations

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

unsigned int itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_MaximumNumberOfIterations { 0 }

private

Definition at line 330 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_PriorProbabilities

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

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

private

Definition at line 316 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_TerminationUpdateThreshold

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

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

private

Definition at line 333 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_TotalLabelCount

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

vcl_size_t itk::MultiLabelSTAPLEImageFilter< TInputImage, TOutputImage, TWeights >::m_TotalLabelCount { 0 }

private

Definition at line 310 of file itkMultiLabelSTAPLEImageFilter.h.

◆ m_UpdatedConfusionMatrixArray

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

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

private

Definition at line 322 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

◆ ConfusionMatrixType

◆ ConstPointer

◆ InputConstIteratorType

◆ InputImagePointer

◆ InputImageType

◆ InputPixelType

◆ OutputImagePointer

◆ OutputImageType

◆ OutputIteratorType

◆ OutputPixelType

◆ Pointer

◆ PriorProbabilitiesType

◆ Self

◆ Superclass

◆ WeightsType

Constructor & Destructor Documentation

◆ MultiLabelSTAPLEImageFilter()

◆ ~MultiLabelSTAPLEImageFilter()

Member Function Documentation

◆ AllocateConfusionMatrixArray()

◆ ComputeMaximumInputValue()

◆ EnlargeOutputRequestedRegion()

◆ GenerateData()

◆ GenerateInputRequestedRegion()

◆ GetConfusionMatrix()

◆ GetElapsedNumberOfIterations()

◆ GetHasLabelForUndecidedPixels()

◆ GetHasMaximumNumberOfIterations()

◆ GetHasPriorProbabilities()

◆ GetLabelForUndecidedPixels()

◆ GetMaximumNumberOfIterations()

◆ GetNameOfClass()

◆ GetPriorProbabilities()

◆ GetTerminationUpdateThreshold()

◆ InitializeConfusionMatrixArrayFromVoting()

◆ InitializePriorProbabilities()

◆ New()

◆ PrintSelf()

◆ SetLabelForUndecidedPixels()

◆ SetMaximumNumberOfIterations()

◆ SetPriorProbabilities()

◆ SetTerminationUpdateThreshold()

◆ UnsetLabelForUndecidedPixels()

◆ UnsetMaximumNumberOfIterations()

◆ UnsetPriorProbabilities()

Member Data Documentation

◆ ImageDimension

◆ m_ConfusionMatrixArray

◆ m_ElapsedNumberOfIterations

◆ m_HasLabelForUndecidedPixels

◆ m_HasMaximumNumberOfIterations

◆ m_HasPriorProbabilities

◆ m_LabelForUndecidedPixels

◆ m_MaximumNumberOfIterations

◆ m_PriorProbabilities

◆ m_TerminationUpdateThreshold

◆ m_TotalLabelCount

◆ m_UpdatedConfusionMatrixArray

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