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 118 of file itkMultiLabelSTAPLEImageFilter.h.

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	OutputImageRegionType = typename Superclass::OutputImageRegionType
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	OutputImagePixelType = typename Superclass::OutputImagePixelType
using	OutputImageRegionType = typename Superclass::OutputImageRegionType
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
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
void	PopBackInput () override
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)
OutputImageType *	GetOutput ()
const OutputImageType *	GetOutput () const
virtual void	GraftOutput (DataObject *output)
virtual void	GraftOutput (const DataObjectIdentifierType &key, DataObject *output)
virtual void	GraftNthOutput (unsigned int idx, DataObject *output)
ProcessObject::DataObjectPointer	MakeOutput (ProcessObject::DataObjectPointerArraySizeType idx) override
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)
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 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	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
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 noexceptoverride
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
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 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
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 ()
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 &outputRegionForThread, ThreadIdType threadId)
virtual void	DynamicThreadedGenerateData (const OutputImageRegionType &outputRegionForThread)
virtual bool	GetDynamicMultiThreading () const
virtual void	SetDynamicMultiThreading (bool _arg)
virtual void	DynamicMultiThreadingOn ()
virtual void	DynamicMultiThreadingOff ()
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	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 () 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 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)
	~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)
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

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.

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.

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.

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.

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.

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.

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.

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

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

Superclass type alias.

Definition at line 152 of file itkMultiLabelSTAPLEImageFilter.h.

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.

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.

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.

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.

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.

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.

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.

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

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

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

inlineprotected

Definition at line 278 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

overrideprotecteddefault

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 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 >.

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 272 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 200 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 168 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 238 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 222 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 182 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 260 of file itkMultiLabelSTAPLEImageFilter.h.

Member Data Documentation

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

constexpr 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 143 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 309 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

private

Definition at line 317 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

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_HasMaximumNumberOfIterations {false}

private

Definition at line 315 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

private

Definition at line 304 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 301 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

private

Definition at line 316 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 305 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 319 of file itkMultiLabelSTAPLEImageFilter.h.

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

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

private

Definition at line 299 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 310 of file itkMultiLabelSTAPLEImageFilter.h.

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

• itkMultiLabelSTAPLEImageFilter.h